UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

 

Form 10-K

 

þ

ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 20142017

OR

¨

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from                      to

Commission File Number 001-36407

 

ALNYLAM PHARMACEUTICALS, INC.

(Exact Name of Registrant as Specified in Its Charter)

 

Delaware

Delaware

77-0602661

(State or Other Jurisdiction of

Incorporation or Organization)

(I.R.S. Employer

Identification No.)

300 Third Street, Cambridge, MA 02142

(Address of Principal Executive Offices) (Zip Code)

Registrant’s telephone number, including area code: (617) 551-8200

Securities registered pursuant to Section 12(b) of the Act:

 

Title of Each Class

Name of Each Exchange on Which Registered

Common Stock, $0.01 par value per share

The Nasdaq Global Select Market

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  þ    No  ¨

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ¨    No  þ

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  þ    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  þ    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.    þ

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer”filer,” “smaller reporting company,” and “smaller reporting“emerging growth company” in Rule 12b-2 of the Exchange Act. (Check one):

 

Large accelerated filerþ

Accelerated filer¨

Non-accelerated filer    ¨Smaller reporting company    ¨

(Do

Non-accelerated filer

  (Do not check if a smaller reporting company)

Smaller reporting company

Emerging growth company

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).    Yes  ¨    No   þ

The aggregate market value of the registrant’s common stock, $0.01 par value per share (“Common Stock”), held by non-affiliates of the registrant, based on the last sale price of the Common Stock at the close of business on June 30, 2014,2017, was $4,772,901,068.$7,243,192,478. For the purpose of the foregoing calculation only, all directors and executive officers of the registrant are assumed to be affiliates of the registrant.

At January 30, 2015,31, 2018, the registrant had 83,760,14399,867,820 shares of Common Stock outstanding.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the registrant’s definitive proxy statement for its 20152018 annual meeting of stockholders, which the registrant intends to file pursuant to Regulation 14A with the Securities and Exchange Commission not later than 120 days after the registrant’s fiscal year end of December 31, 2014,2017, are incorporated by reference into Part II, Item 5 and Part III of this Form 10-K.

 

 

 


ALNYLAM PHARMACEUTICALS, INC.

ANNUAL REPORT ON FORM 10-K

For the Year Ended December 31, 20142017

TABLE OF CONTENTS

 

PART I

ITEM 1.

BUSINESS

1

ITEM 1A.

RISK FACTORS

47

39

ITEM 1B.

UNRESOLVED STAFF COMMENTS

73

64

ITEM 2.

PROPERTIES

73

65

ITEM 3.

LEGAL PROCEEDINGS

73

65

ITEM 4.

MINE SAFETY DISCLOSURES

73

65

PART II

ITEM 5.

MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

74

66

ITEM 6.

SELECTED CONSOLIDATED FINANCIAL DATA

76

68

ITEM 7.

MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

77

69

ITEM 7A.

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

99

85

ITEM 8.

FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

100

86

ITEM 9.

CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

141

126

ITEM 9A.

CONTROLS AND PROCEDURES

141

126

ITEM 9B.

OTHER INFORMATION

141

126

PART III

ITEM 10.

DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

141

127

ITEM 11.

EXECUTIVE COMPENSATION

141

127

ITEM 12.

SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

142

127

ITEM 13.

CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

142

127

ITEM 14.

PRINCIPAL ACCOUNTANT FEES AND SERVICES

142

127

PART IV

ITEM 15.

EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

142

128

ITEM 16.

FORM 10-K SUMMARY

133

SIGNATURES

143

134

 

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This annual report on Form 10-K contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended, that involve risks and uncertainties. All statements other than statements relating to historical matters should be considered forward-looking statements. When used in this report, the words “believe,” “expect,” “plan,” “anticipate,” “estimate,” “predict,” “may,” “could,” “should,” “intend,” “will,” “target,” “goal” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these words. Our actual results could differ materially from those discussed in the forward-looking statements as a result of a number of important factors, including the factors discussed in this annual report on Form 10-K, including those discussed in Item 1A of this report under the heading “Risk Factors,” and the risks discussed in our other filings with the Securities and Exchange Commission. Readers are cautioned not to place undue reliance on these forward-looking statements, which reflect management’s analysis, judgment, belief or expectation only as of the date hereof. We explicitly disclaim any obligation to update these forward-looking statements to reflect events or circumstances that arise after the date hereof.

PART I

 

ITEM 1.

BUSINESS

Overview

We are a global biopharmaceutical company developing novel therapeutics based on RNA interference, or RNAi. RNAi is a naturally occurring biological pathway within cells for selectivelysequence-specific silencing and regulatingregulation of gene expression. We are harnessing the expressionRNAi pathway to develop a potential new class of specific genes. Since many diseasesinnovative medicines, known as RNAi therapeutics. RNAi therapeutics are causedcomprised of small interfering RNA, or siRNA, and function upstream of today’s medicines by the inappropriate activity of specific genes, the ability to silence genes selectively through RNAi could providepotently silencing messenger RNA, or mRNA, that encode for disease-causing proteins, thus preventing them from being made. This is a new way to treat a wide range of human diseases. We believe that drugs that work through RNAi haverevolutionary approach with the potential to become a broad new classtransform the care of drugs, like small molecule, proteinpatients with genetic and antibody drugs. Using our intellectual property and expertise, we are developing what we believe to be a reproducible and modular approach to develop RNAi therapeutics for a variety of humanother diseases.

Our research and development strategy is focused primarily on use of our proprietaryN-acetylgalactosamine, or GalNAc-conjugate strategy for delivery of small interfering RNAs, or “siRNAs” — the molecules that mediate RNAi — towardto target genetically validated liver-expressed genes involvedthat have been implicated in the cause or pathway of human diseases.disease. We are also focusedutilize a lipid nanoparticle, or LNP, or N-acetylgalactosamine, or GalNAc, conjugate approach to enable hepatic delivery of siRNAs. Our focus is on clinical indications where there areis a high unmet medical needs,need, early biomarkers for the assessment of clinical activity in Phase 1 clinical studies, and a definable path for drug development, regulatory approval, patient access and commercialization.

Specifically, our broad pipeline of investigational RNAi therapeutics is focused in three Strategic Therapeutic Areas, or “STArs:” Genetic Medicines, with a broad pipeline of RNAi therapeutics for the treatment of rare diseases;Medicines; Cardio-Metabolic Disease, with a pipeline of RNAi therapeutics toward genetically validated, liver-expressed disease targets for unmet needs in cardiovascular and metabolic diseases, such as dyslipidemia, hypertension, non-alcoholic steatohepatitis, or NASH, and type 2 diabetes;Diseases; and Hepatic Infectious Disease, with a pipeline of RNAi therapeutics designedDiseases. We are committed to address the major global health challenges of hepatic infectious diseases. In early 2015, we launched our “Alnylam 2020” guidance for the advancement and commercialization of RNAi therapeutics as a whole new class of innovative medicines. Specifically, by the end ofour Alnylam 2020 we expect strategy, which is to achieve a company profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs.

Based on our expertise in RNAi therapeutics and broad intellectual property estate we have formed alliances with leading pharmaceutical and life sciences companies, including Isis Pharmaceuticals, Inc., or Isis, Medtronic, Inc., or Medtronic, Novartis Pharma AG, or Novartis, F. Hoffmann-La Roche Ltd, or Roche (which assigned its rights and obligations to Arrowhead Research Corporation, or Arrowhead), Takeda Pharmaceutical Company Limited, or Takeda, Kyowa Hakko Kirin Co., Ltd., or Kyowa Hakko Kirin, Cubist Pharmaceuticals, Inc., or Cubist, Ascletis BioScience Co., Ltd., or Ascletis, Monsanto Company, or Monsanto, Genzyme Corporation, a Sanofi company, or Genzyme, and The Medicines Company, or MDCO. We also have established collaborations with and, in some instances, received funding from, major medical and disease associations. Finally, to further

1


enable the field and monetize our intellectual property rights, we also grant licenses to biotechnology companies for the development and commercialization of RNAi therapeutics for specified targets in which we have no direct strategic interest under our InterfeRx™ program, and to research companies that commercialize RNAi reagents or services under our research product licenses.

Recent Developments

Public Offering

In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $496.4 million. We intend to use these proceeds for general corporate purposes, focused on achieving our Alnylam 2020 profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs by the end of 2020. In December 2017, we filed our first new drug application, or NDA, and marketing authorisation application, or MAA, for patisiran. In January 2018, we announced that the European Medicines Agency, or EMA, has accepted the MAA and initiated its review. Patisiran was previously granted an accelerated assessment by the EMA.  In early February 2018, we announced that the United States Food and Drug Administration, or FDA, has accepted our NDA and granted our request for priority review, with an action date of August 11, 2018. If approved, we expect to launch patisiran and begin generating product revenues in 2018.

Finally, based on our expertise in RNAi therapeutics and broad intellectual property estate, we have formed alliances with leading pharmaceutical and life sciences companies to support our development and commercialization efforts, including Sanofi Genzyme, Stock Purchasesthe specialty care global business unit of Sanofi, The Medicines Company, or MDCO, and Vir Biotechnology, Inc.  

Key 2017 Highlights

Investigational Clinical Pipeline

Patisiran - Hereditary Transthyretin-Mediated (hATTR) Amyloidosis, or hATTR Amyloidosis

o

Reported positive, final results from APOLLO Phase 3 study

o

EMA granted accelerated assessment status

o

FDA granted Breakthrough Therapy Designation

o

FDA expanded Orphan Drug Designation, or ODD, to treatment of ATTR amyloidosis

o

Completed submission of NDA with FDA

o

Completed submission of MAA with EMA


Givosiran - Acute Hepatic Porphyrias

o

Aligned with FDA and other regulatory authorities on Phase 3 trial design, including, with the FDA, on an interim analysis based on reduction of urinary aminolevulinic acid, or ALA, as surrogate endpoint reasonably likely to predict clinical benefit

o

Initiated ENVISION Phase 3 clinical study with interim analysis data readout expected mid-2018 and potential for NDA filing at or around year-end 2018

Fitusiran - Hemophilia A and B, With and Without Inhibitors

o

Initiated ATLAS Phase 3 study

o

Suspended dosing due to a fatal thrombotic event reported in September

o

Aligned with FDA on clinical risk mitigation measures; clinical hold lifted by FDA in December

o

Resumed dosing in Phase 2 open-label extension, or OLE; expect to dose in ATLAS Phase 3 study in early 2018

Inclisiran - Hypercholesterolemia

o

Reported with MDCO positive data from the ORION-1 Phase 2 study

o

MDCO initiated comprehensive ORION Phase 3 program

Early to mid-stage programs

o

Reported positive preliminary results from Phase 1 study of ALN-TTRsc02 for the treatment of ATTR amyloidosis

o

Reported positive interim results from Phase 1/2 study for lumasiran (ALN-GO1) for treatment of primary hyperoxaluria type 1, or PH1

o

Initiated Phase 2 trial for cemdisiran (ALN-CC5) for treatment of atypical hemolytic-uremic syndrome, or aHUS

Corporate Highlights

Finance

o

Completed two successful public offerings raising $1.14 billion in net proceeds

o

Ended 2017 with $1.73 billion in cash, cash equivalents, fixed income marketable securities and restricted investments

Business

o

Formed strategic alliance with Vir Biotechnology to advance RNAi therapeutics for infectious diseases

Commercial/Medical Affairs

o

Enabled our supply chain, medical, quality, compliance and commercial organizations in the U.S. and Western Europe

o

Established or enhanced existing diagnostic screening and patient/physician education initiatives to detect disease and raise awareness


Commercial Readiness

In preparation for a potential global commercial launch of patisiran in 2018 and potentially subsequent global product launches in 2019 and beyond, we are:

Expanding the organization with approximately 250 new hires deployed in customer facing activities across the world, initially in the United States and major European countries, followed by Canada and Switzerland, with a phased approach to the Asia Pacific, Latin American and Middle Eastern regions, with broad experience in marketing, sales, patient access, patient services, distribution and product reimbursement, in particular for orphan diseases;

Expanding our commercial capabilities with incorporation of appropriate quality systems, compliance policies, systems and procedures, and implementation of internal systems and infrastructure in order to support global commercial sales and establish patient-focused programs; and

Planning to expand our global footprint in major European markets and beyond with the continued hiring of country general managers, medical experts, market access professionals and marketing and sales professionals.

Recent Developments

Sanofi Genzyme Restructuring

On January 2015,6, 2018, we and Sanofi Genzyme entered into an amendment to our 2014 collaboration, which is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of Genetic Medicines. In connection with our public offering described above, Genzyme exercised its right under our investor agreement with Genzyme to purchase directly from us, in concurrent private placements, 744,566 shares of common stock, at the public offering price of $95.00 per share, resulting in proceeds to us of approximately $70.7 million. The sales of common stock to Genzyme were not registered as part of the public offering, though they were consummatedand simultaneously with entering into the public offering.2018 amendment to the 2014 Sanofi Genzyme collaboration, we and Sanofi Genzyme also entered into an Exclusive License Agreement with respect to all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, referred to as the Exclusive TTR License, and the ALN-AT3 Global License Terms with respect to fitusiran and any back-up products, referred to as the AT3 License Terms.  

Under the investor agreement,2014 Sanofi Genzyme collaboration, Sanofi Genzyme has certain rights to our current and future Genetic Medicine programs that reach human proof-of-principal study completion, or Human POP, by the end of 2019, subject to extension to the end of 2021 in various circumstances.  Under the 2014 Sanofi Genzyme collaboration, we were leading development and commercialization of patisiran in the United States, Canada and Western Europe (Alnylam Territory), while Sanofi Genzyme had rights to develop and commercialize the product in the rest of the world (Sanofi Genzyme Territory). Sanofi Genzyme also hashad a right to opt in to co-develop and co-promote ALN-TTRsc02 in the Alnylam Territory along with its regional opt-in rights.  In addition, Sanofi Genzyme had opted in to co-develop and co-promote fitusiran in the Alnylam Territory, as well as develop and commercialize fitusiran in the Sanofi Genzyme Territory.

The 2018 amendment, together with the Exclusive TTR License and the AT3 License Terms, revise the terms and conditions of the 2014 collaboration to (i) provide us with the exclusive right to pursue the further global development and commercialization of all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, (ii) provide Sanofi Genzyme the exclusive right to pursue the further global development and commercialization of fitusiran and any back-up products and (iii) terminate the previous co-development and co-commercialization rights related to revusiran, ALN-TTRsc02 and fitusiran under the 2014 Sanofi Genzyme collaboration.

Sanofi Genzyme continues to have the right each January to purchaseopt into our other rare genetic disease programs for development and commercialization in territories outside of the Alnylam Territory as contemplated in the 2014 Sanofi Genzyme collaboration, as well as one right to a number of shares of our common stock based onglobal license.

The transaction is subject to customary closing conditions and clearances, including clearance under the number of shares we issuedHart-Scott-Rodino Antitrust Improvements Act.  We expect the transaction to close during the previous year for compensatory purposes.first quarter of 2018.

The 2014 Sanofi Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock oncollaboration, as amended in January 22, 2015 for approximately $18.3 million. The sale of these shares to Genzyme was consummated2018, as a private placement.

In each instance,well as the purchase by Genzyme described above allowed Genzyme to maintain its ownership level of our common stock of approximately 12%.

Isis Agreement

In January 2015, weExclusive TTR License and Isis entered into a second amended and restated strategic collaboration and license agreement. The 2015 Isis agreement provides for certain new exclusive target cross-licenses of intellectual property on four disease targets, providing each company with exclusive RNA therapeutic license rights for two programs, and extends the parties’ existing non-exclusive technology cross-license, which was originally entered into in 2004 and was amended and restated in 2009, through April 2019. The 2015 Isis agreement isAT3 License Terms, are described below under the heading “Strategic Alliances.”


RNA InterferenceUK Biobank Consortium

In December 2017, we entered into a 'pre-competitive' consortium together with Regeneron Pharmaceuticals, Inc., or Regeneron, AbbVie Inc., AstraZeneca PLC, Biogen Inc. and OpportunityPfizer Inc., to fund the generation of exome sequence data from the 500,000 volunteer participants who make up the UK Biobank health resource by the end of 2019. We and each of the other collaborators agreed to commit $10.0 million to enable an acceleration of sequencing timelines.  Regeneron will conduct the sequencing effort and the data will be paired with detailed, de-identified medical and health records within the UK Biobank resource, to create a comprehensive resource for linking human genetic variations to human biology and disease.  All consortium members will have a limited period of exclusive access to the sequencing data, before the data will be made available to other health researchers by UK Biobank. Consortium members have committed to make all significant research findings public. We believe that the broad and ongoing access to detailed health and full exome sequencing data for the 500,000 UK Biobank participants will greatly enhance our target identification and validation efforts, contributing to the sustainability of our RNAi therapeutics product engine.

RNAi Therapeutics – A Potential New Class of Innovative Medicines

RNAi is a natural biological pathwaycellular process that occurs within cells to selectively silence the activity of specific genes. The discovery of RNAi first occurred in plants and wormswas discovered in 1998 and twowas recognized with the award of the scientists who made this discovery,2006 Nobel Prize for Physiology and Medicine to Dr. Andrew Fire and Dr. Craig Mello, received the 2006 Nobel Prize for Physiology or Medicine.Mello.

RNAi therapeutics harness the natural RNAi pathway to silence disease-associated genes and knock down production of disease-causing proteins. RNAi therapeutics represent anproteins, representing the opportunity to create a wholepotential new class of innovative medicines. This potential new drug class is similar to the opportunity created with other major biological discoveries such as recombinant DNA and monoclonal antibodies. Specifically, RNAi therapeutics achieveexert their biological effects through a highly potent, catalytic mechanism.  Further, RNAi therapeuticsThis unique mechanism of action confers a number of attributes that we believe have the potential to silence any disease-associated gene, including so-called “undruggable” targets, where conventional therapeutic modalities (e.g., small molecule drugsprovide meaningful differentiation and biologics) have not been successful.

distinct value for our investigational RNAi therapeutics relative to other drug classes.

 

Key Features of Alnylam Investigational RNAi Therapeutics

Potential Attributes for Differentiation and Value

Potential to silence any disease-associated gene, including so-called “undruggable” targets, where conventional therapeutic modalities (e.g., small molecule drugs and biologics) have not been successful

Demonstrated potential in clinical trials to achieve robust clinical activity with up to 99 percent target gene knockdown in some cases

Clamped pharmacodynamic effect that has potential to provide improved and consistent efficacy compared with intermittent and transient effects often achieved with other drug classes

Demonstrated durability of effect in clinical trials that enables once-monthly, once-quarterly and, in some cases, possible bi-annual dose regimens

Ability to be administered via subcutaneous injection when using our proprietary GalNAc-conjugate delivery platform

Potential for room temperature stability, avoiding the inconveniences, costs and global challenges of a cold chain distribution

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We believe that the combination of these attributes represents a very promising profile for our investigational therapeutics, even in competitive markets, and in December 2017, we filed the first ever regulatory applications with the FDA and the EMA for approval of an RNAi therapeutics also have a distinct mechanism of action, acting “upstream” of today’s medicines. Finally, as a reproducible and modular approach for drug discovery and development, RNAi therapeutics represent a simplified and efficient approach for new medicines.

therapeutic.  We have reported on our advances in developing RNAi therapeutics as potential drugs in a large number of peer-reviewed publications and many scientific meetings, including publications by Alnylam scientists in the journalsNature, Nature Medicine, Nature Biotechnology, Cell, Proceedings of the National Academy of Sciences, theThe New England Journal of MedicineandThe Lancet.Lancet.


Our Product Platform

We believe that we have created a reproducible and modular platform for drug discovery, development and commercialization of innovative medicines.

Alnylam Reproducible and Modular Platform

Strategic Framework for Innovative Medicines

 1

Genetically validated, liver-expressed target gene

    High unmet need population 

    Opportunity for highly competitive profile

    Delivery with GalNAc-conjugate platform

 2

Biomarker for human proof-of-concept in Phase 1

    Blood- or urine-based

    Informative disease correlation

    Establish dose/regimen for late stage development

 3

Definable path to potential approval and market

    Clinical development plans with established endpoints

    Demonstrable value for payors

Delivery of RNAi Therapeutics

In the early years of developing RNAi therapeutics, a challenge to the promise of RNAi as a therapeutic modality was delivery, i.e., getting the siRNA into the right body organs and cells so that it could trigger the RNAi mechanism. In recent years, a tremendous amount of progress has been made in effectively delivering RNAi therapeutics to targeted organs and cells, and we believe Alnylam has been athe leader of this advancement. This delivery success is now enabling execution on our productAlnylam 2020 strategy.

Early efforts focused on delivery of RNAi therapeutics utilizing lipid nanoparticles, or LNPs, where siRNA molecules are encapsulated in specific lipid-based formulations. This technology enables systemic delivery with intravenous drug administration. Results with LNP-based investigational RNAi therapeutics demonstratedemonstrated potent, rapid and durable target gene silencing in pre-clinical and clinical studies. Further, LNP-based investigational RNAi therapeutics have been found to be generally well tolerated in clinical studies conducted to date.  Our lead product, patisiran, is formulated utilizing LNPs.

More recently, we began advancing proprietary technology that conjugates a sugar molecule called GalNAc to the siRNA molecule. This simpler delivery approach enables more convenient, subcutaneous administration of our drug candidates. Recent findingscandidates, a key aspect of our platform. Results from our Enhanced Stabilization Chemistry (ESC)-GalNAc-conjugate delivery platform demonstrated a substantial increase in potency over our earlier “standardstandard template chemistry”chemistry (STC)-GalNAc-conjugate approach in pre-clinical and clinical studies, and a durability of effect that we believe, based on our clinical results, supports once-monthly, oronce-quarterly, and in some cases, possibly even less frequentbi-annual subcutaneous dosingdose regimens. Due to this increased potency and durability, as well as a wide therapeutic index, this conjugate platform has become our primary approach for development of investigational RNAi therapeutics.

In early 2014,  During 2017, we continued to invest in the enhancement of this platform and extendedreported pre-clinical results from our commitmentESC Plus (ESC+) GalNAc-conjugates. ESC+ GalNAc-conjugates utilize advanced design features to further improve specificity, including a glycol nucleic acid, or GNA, modification in the antisense seed region of the siRNA, while maintaining potency and durability, further improving our already wide therapeutic index by six-fold.  The ESC+ design is now being applied to all of our pre-clinical programs and has shown successful translation of potency from rodents to non-human primates. We intend to employ our ESC+ GalNAc-conjugate platform in future development programs.

We have extensive human safety experience with our investigational RNAi therapeutics. Our data demonstrate that to date, RNAi therapeutics innovationhave been generally well tolerated with minimal platform-related safety findings. Based on data as of December 2016, in over 1,000 patients or volunteers dosed for over three years in more than ten clinical programs, the safety findings, set forth below, occur at a low incidence and are monitorable. They are also generally asymptomatic and reversible even with continued dosing.  As noted, as of December 2016, these findings include:  

Low incidence (2.2 percent) of generally mild, asymptomatic, reversible liver function test increases greater than three times the upper limit of normal

Low incidence (15.2 percent) of generally mild, transient injection site reactions, or ISRs

In our view, this is an acceptable tolerability profile in the high unmet need indications that we pursue. Continued review of data across our programs since December 2016 has not led to any meaningful change in human safety with respect to our RNAi platform.


In October 2016, we observed an apparent imbalance in mortality in the treatment arm of the ENDEAVOUR Phase 3 study for revusiran, our first generation, subcutaneously administered, investigational therapeutic for the treatment of cardiomyopathy due to hATTR amyloidosis, which utilized our STC-GalNAc-conjugate delivery throughplatform. With patient safety at the acquisitionforefront, the ENDEAVOUR study was discontinued and a comprehensive investigation into the causality of Sirna Therapeutics, Inc.,this imbalance was conducted.

The investigation revealed no overall baseline imbalance, although there was a greater number of older patients randomized to the revusiran arm. There was no clinical evidence for revusiran-mediated cardiotoxicity or Sirna, from Merck Sharp & Dohme Corp.,findings that would suggest that the mortality imbalance was the result of revusiran pharmacokinetic or Merck. This acquisition extended and complementedpharmacodynamic effects. While our progress and continued focus oninvestigation could not fully exclude a possible drug-related cause, there was some evidence for imbalance due to a lower-than-expected mortality rate in the placebo arm at the time of study discontinuation.

Due to lack of evidence of any broader platform issue, the decision to discontinue development of revusiran did not affect patisiran, which utilizes our LNP delivery platform, or any of our other investigational RNAi therapeutics. It also acceleratedtherapeutic programs in development, which utilize our overall efforts to develop and commercialize siRNAESC-GalNAc-conjugate or ESC+ GalNAc-conjugate delivery technologies, including GalNAc-siRNA conjugate technology.

Our Product Platformplatform.

We are leading the translation ofbelieve RNAi astherapeutics represent a simplified and efficient potential new class of innovative medicines, with a core focus onmedicines. We have achieved human proof of concept in multiple clinical trials of our investigational RNAi therapeutics toward genetically defined targetscandidates, providing strong support for the treatment of serious, life-threatening diseases with limited treatment options for patients and their caregivers. With RNAi therapeutics,our approach to drug development.  Moreover, we believe that we have created aour reproducible and modular approachplatform will support the achievement of our 2020 goals, such that by the end of 2020, we can grow into a multi-product commercial stage company with a deep and sustainable pipeline that can fuel continued growth for the development and commercialization of innovative medicines. The product candidates we are developing with this approach share several key characteristics, including:future.

the potential to have a major impact in a high unmet need population;

a genetically defined, liver-expressed target gene involved in disease and validated in human genetics;

the ability to leverage our Alnylam RNAi delivery platform;

the opportunity to monitor an early, blood-based biomarker with strong disease correlation in Phase 1 clinical trials for human proof of concept; and

the existence of clinically relevant endpoints for the filing of a new drug application, or NDA, or foreign regulatory equivalent, with a focused patient database and possible accelerated paths for regulatory approval and commercialization.

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In December 2014, we evolved our strategy with a focus on development and commercialization of investigational RNAi therapeutics in three STArs: Genetic Medicines; Cardio-Metabolic Diseases; and Hepatic Infectious Diseases.

Our Product Pipeline

Our broad pipeline of investigational RNAi therapeutics is focused in three STArs: Genetic Medicines, for the treatment of rare diseases;Medicines; Cardio-Metabolic Disease, focused on genetically validated, liver-expressed genes for unmet needs in dyslipidemia, hypertension, NASH and type 2 diabetes;Diseases; and Hepatic Infectious Disease, addressing major global health challenges, including but not limited to the hepatitis B virus, or HBV.Diseases. The followingchart below is a summary of our product development programs in each of our STArs as of January 31, 2015:2018. It identifies those programs in which we have achieved human proof-of-concept, or POC, by demonstrating target gene knockdown and/or additional evidence of activity in clinical studies, those programs for which we have received Breakthrough Therapy Designation from the FDA, the development stage of our programs, and our commercial rights to such programs:


We have spent substantial funds over the past three years to develop our product pipeline and expect to continue to do so in the future. We incurred research and development costsexpenses of $190.2$390.6 million in 2014, $113.02017, $382.4 million in 20132016 and $86.6$276.5 million in 2012.

Genetic Medicine STAr2015.

InThe investigational therapeutics described below are in various stages of clinical development and the scientific information included about these therapeutics is preliminary and investigative. None of our Genetic Medicine STAr, we are advancing a broad pipelineinvestigational therapeutics have been approved by the FDA, EMA or any other health authority and no conclusions can or should be drawn regarding the safety or efficacy of these investigational therapeutics.

Late Stage Clinical Development Programs

Patisiran —  Hereditary Transthyretin-Mediated (hATTR) Amyloidosis

Patisiran, our most advanced investigational RNAi therapeutics for rare diseases. Across our Genetic Medicine STAr, we plan on commercializing our products through direct marketing and sales in North America and Western Europe, while leveraging our 2014 alliance with Genzyme for commercializationtherapeutic, is currently under priority regulatory review in the rest ofUnited States and accelerated assessment in the world, subject to certain broader rights. Our Genetic Medicine development programs are described in more detail below.

TTR-Mediated Amyloidosis (ATTR)

Our most advanced Genetic Medicine product development program targets the transthyretin,European Union, or TTR, geneEU, for the treatment of TTR-mediatedhATTR amyloidosis. If approved, we expect to make patisiran commercially available to patients in the United States in mid-2018 and in the EU in late 2018.  We also plan to file for regulatory approval in Japan in mid-2018 and in one or more additional countries by the end of the year.

hATTR amyloidosis or ATTR. ATTR is an inherited,a rare, progressively debilitating and often fatal disease affecting approximately 50,000 patients worldwide. It is caused by deposition of wild-type and mutant transthyretin, or TTR, in peripheral tissues, such as the nerves, heart and gastrointestinal tract. Thus, polyneuropathy and cardiomyopathy are two cardinal manifestations of this disease, with most patients exhibiting a mutation in the TTR gene,spectrum of which over 100 mutations have been identified.both. TTR protein is produced primarily in the liver and is normally a carrier for retinol binding protein, used to transportof vitamin A around the body. We believe TTR is a suitable target for an RNAi therapeutic formulated to maximize

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delivery to liver cells, which are the primary source of TTR synthesis. Mutations in TTR result in the accumulation of damaging toxic deposits of the wild-type and mutant protein in several body organs and tissues, including the peripheral nervous system, heart and/or gastrointestinal tract, which leads to familial amyloidotic polyneuropathy, or FAP, and/or familial amyloidotic cardiomyopathy, or FAC. FAP is associated with severe pain and loss of autonomic nervous system function, whereas FAC is associated with heart failure. ALN-TTRA. Patisiran targets wild-type and all known mutant forms of TTR, including the V30M mutation, which isand V122I, the major mutation of ATTR, particularly in FAP,most common disease-causing mutations, and therefore isit represents a potential therapeutic approach for the treatment of all formshATTR amyloidosis.

hATTR amyloidosis is a progressive disease, with an overall survival of ATTR, including FAP and FAC.

ATTR represents a major unmet medical need with significant morbidity and mortality as an orphan, or rare, disease. Based on our analysis of the available patient and market data, we estimate that FAP affects approximately 10,000 people worldwide and FAC affects at least 40,000 people worldwide. ATTR patients with FAP have a mean life expectancy of fivetwo to 15 years from symptom onset, and thebut only treatment options for early stage disease aretwo to five years in patients presenting with cardiomyopathy. Orthotopic liver transplantationtransplant, or OLT, and TTR tetramer stabilizers, such as tafamidis (approved in Europe, Japan and certain countries in Latin America, specific indication varies by region), are the only approved treatment options. However, availability is limited and most patients continue to experience significant morbidity and mortality associated with disease progression.  Palliative therapies directed at specific symptoms such as pain, nausea, vomiting and diarrhea have been the mainstay of treatment despite their limited effectiveness. Other investigational drugs in development for the treatment of hATTR amyloidosis include the TTR-targeting antisense oligonucleotide, or ASO, inotersen, which showed statistically significant slowing of neuropathy progression and improvement in quality of life relative to placebo in a small molecule stabilizer of the TTR protein for early-stage FAP patients that has been approvedrandomized Phase 3 trial and is currently under regulatory review in the European Union, orUnited States and the EU, and diflunisal, a commercially available non-steroidal anti-inflammatory agent. The mean survival for FAC patients is approximately 2.5fibril-disrupting drug combination of doxycycline and tauroursodeoxycholic acid, which to five years following diagnosis, and there are no approved therapies. Senile systemic amyloidosis, or SSA, is a non-hereditary form of TTR cardiac amyloidosis caused by idiopathic deposition of wild-type TTR; its prevalence is generally unknown, but is associated with advanced age. Although limited treatment options are available,date has only been tested in small single-arm Phase 2 studies. Thus, there remains a significanthigh unmet medical need for novel therapeutics to treat patients with TTR amyloid polyneuropathy and/or cardiomyopathy.a safe and effective therapy that can benefit the broad hATTR amyloidosis population.

We are developing two investigational RNAi therapeutic candidates for ATTR: patisiran and revusiran.

Patisiran (ALN-TTR02).Patisiran is our most advanced product candidate in clinical development. In November 2013, we initiated our ongoing APOLLO Phase 3 clinical trial of patisiran. TheClinical Trial

Trial Design: Initiated in November 2013 and completed in September 2017, APOLLO Phase 3 clinical trial is athe largest pivotal study conducted to date in hATTR amyloidosis patients with polyneuropathy, with 225 patients enrolled, representing 39 TTR genotypes from across 19 countries. This randomized, double-blind, placebo-controlled, global study was designed to evaluate the efficacy and safety of patisiran in ATTRhATTR amyloidosis patients with FAP.polyneuropathy. The primary endpoint of the study iswas the difference in the change from baseline in the modified composite Neuropathy Impairment Score (NIS), termed “mNIS+neuropathy impairment score, or mNIS+7,” between patisiran and placebo at 18 months. The mNIS+7 score is an evaluation of muscle weakness, sensory and autonomic function, and nerve conductance across a 304-point scale, where neuropathy progression leads to an increased score over time. Secondary endpoints include:A key secondary endpoint was the Norfolk Quality of Life-DiabeticLife Diabetic Neuropathy, (QOL-DN) score; Neuropathy Impairment Score, or NIS-weakness;Norfolk QOL-DN, questionnaire, which is a validated instrument that measures clinical benefit. Additional secondary endpoints included: NIS-weakness, the subdomain of mNIS+7 assessing muscle strength; Rasch-built Overall Disability Scale, or R-ODS, a patient reported outcome measure of activities of daily living and disability; timed 10-meter walk test, assessing ambulatory ability and gait speed; modified body mass index, or mBMI; timed ten-meter walk;mBMI, assessing nutritional status; and COMPASS-31, a patient questionnaire assessing autonomic disease symptoms. Exploratory endpoints measured the COMPASS-31 autonomic symptom score. The trial is designed to enroll up to 200 FAP patients with a baseline NIS in the range of five to 130, which represents patients with Stage 1 or Stage 2 disease.effects on cardiac structure and function. Patients are beingwere randomized two-to-one,2:1, patisiran-to-placebo, with patisiran administered at 0.30 mg/kg once every three weeks for 18 months. Themonths by intravenous infusion. 99 percent of patients who completed the APOLLO study was designedrolled over into the Phase 3 OLE study, called the Global OLE.  


Trial Results:

Efficacy:Patisiran met the primary endpoint of mNIS+7 change from baseline at 18 months relative to placebo, and all secondary study endpoints. Specifically:

Patisiran treatment (N=148) resulted in a negative 6.0-point mean change (improvement) in mNIS+7 score from baseline at 18 months as compared to a 28.0-point mean increase (worsening) reported for the placebo group (N=77), resulting in a 34.0-point mean difference relative to placebo (p=9.26 x 10-24).

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Improvement in mNIS+7 from patisiran treatment was also consistently observed across all defined patient subgroups, including age, sex, race, geographic region, baseline neuropathy impairment, genotype, prior TTR stabilizer use, baseline Familial Amyloid Polyneuropathy, or FAP, stage, and inclusion in the pre-specified cardiac subpopulation.

Patisiran treatment resulted in a negative 6.7-point mean change (improvement) in Norfolk QoL-DN score from baseline at 18 months as compared to a 14.4-point mean increase (worsening) reported for the placebo group, resulting in a 21.1-point mean difference relative to placebo (p=1.10 x 10-10).

In a pre-specified binary analysis of neurological improvement, 56 percent (95 percent confidence interval, or CI: 48.1, 64.1) of patisiran patients had an improvement in mNIS+7 (less than 0-point change compared to baseline at 18 months), while 4 percent (95 percent CI: 0.0, 8.2) of placebo patients had an improvement (p=1.82 x 10-15).

Similarly, 51 percent (95 percent CI: 43.3, 59.4) of patisiran patients had an improvement in Norfolk QoL-DN (less than 0-point change compared to baseline at 18 months), versus 10 percent (95 percent CI: 3.6, 17.2) for placebo (p=1.95 x 10-10).

Patisiran also demonstrated statistically significant and clinically meaningful improvements over placebo in all other secondary endpoints at 18 months.

Cardiac Subpopulation Results: Favorable and significant changes in several exploratory cardiac measures, including N-terminal pro b-type natriuretic peptide, or NT-proBNP, and certain echocardiographic parameters, were reported in patisiran-treated patients with 90% power to conservatively detect as littlepre-defined cardiac involvement (baseline left ventricular (LV) wall thickness ≥ 1.3 cm with no history of hypertension or aortic valve disease). Specifically:

Patisiran treatment resulted in a median decrease (improvement) of 49.9 pg/ml in NT-proBNP levels as compared to a median increase (worsening) of 320 pg/ml reported for the placebo arm at 18 months (nominal p=7.74 x 10-8, based on analysis of log-transformed values).

Regarding echocardiographic measures, patisiran treatment resulted in a 37.5% differencemean 0.93 mm reduction (improvement) in change in mNIS+7 between treatment groups, with a two-sided alpha of 0.05. The placebo mNIS+7 progression rate was derived from an Alnylam analysis of natural history data from 283 FAP patients. We presented data from this natural history study during 2014. This cross-sectional analysis demonstrated a rapid progression in NISleft ventricular (LV) wall thickness (nominal p=0.0173) and a high correlation of this measurement with disease severity. These results give us confidence that our APOLLO Phase 3 trial of patisiran is robustly poweredmean absolute 1.37 percent improvement in longitudinal strain (nominal p=0.0154) relative to show the potential impact of TTR lowering on the mNIS+7 endpoint used in that study. All patients completing the APOLLO Phase 3 clinical trial will be eligible to enroll in a Phase 3 open-label extension, or OLE study.placebo.

We have completed a Phase 2 clinical trial of patisiran whichSafety and Tolerability: Patisiran showed that multiple doses of patisiran led to robust and statistically significant knockdown of serum TTR protein levels of up to 96%, with mean levels of TTR knockdown exceeding 85%. In addition, patisiran was found to be generally well tolerated in this Phase 2 study. Patients participating in the Phase 2 study were eligible to participate in a Phase 2 OLE study with patisiran; 27 patients rolled into the OLE. Patients in the Phase 2 OLE are receiving patisiran at a dose of 0.30 mg/kg every three weeks for up to two years. The primary objective of this study is to evaluate the long-terman encouraging safety and tolerability profile relative to placebo with up to 18 months of patisiran administration. In addition, the study is measuring a number of clinical endpoints every six months, including mNIS+7. A number of additional clinical endpoints are being assessed.

dosing. Specifically:

 

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In October 2014, weThe most commonly reported six-month clinical data from this ongoing Phase 2 OLE study. Specifically, results showed a mean 0.95 point decrease in mNIS+7 at six months in 19 patients. This decrease in neuropathy progression compares favorably with the seven to ten point increase in mNIS+7 at six months that can be estimated from published historical data sets in untreated FAP patients with similar baseline characteristics. In addition, patisiran treatment achieved a sustained mean serum TTR knockdown at the 80% target level for over nine months, with an up to 89.6% knockdown achieved between doses. In the ongoing Phase 2 OLE study, patisiran was found to be generally well tolerated in FAP patients (N=27), with minimal adverse events, reported for a period of upor AEs, that occurred more frequently in patisiran patients were peripheral edema (29.7 percent versus 22.1 percent in placebo) and infusion-related reactions, or IRRs (18.9 percent versus 9.1 percent in placebo). These were generally mild to one year. Infusion-related reactions were infrequent (14.8%), mildmoderate in severity and did not result in any discontinuations. All other reportedonly one patient discontinued due to an IRR (0.7 percent).

Compared to placebo, patisiran treatment was associated with fewer treatment discontinuations (4.7 versus 14.3 percent) and fewer study withdrawals (4.7 versus 11.7 percent) due to AEs.

The incidence of serious adverse events, or SAEs, across the patisiran (36.5 percent) and placebo (40.3 percent) groups was similar.

SAEs reported in 2 or more patients in the patisiran group included: diarrhea (5.4 percent), cardiac failure, congestive cardiac failure, orthostatic hypotension, pneumonia, and atrioventricular block complete (2 percent each). These were mildall considered unrelated to moderate,patisiran, except for one SAE of diarrhea. SAEs occurred with similar frequency in the placebo group, except for diarrhea (1.3 percent in placebo group).  

Deaths were recorded with a similar incidence across the patisiran (4.7 percent) and thereplacebo (7.8 percent) treatment groups.

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No deaths were considered related to study drug.

There were no clinically significant changes in liver function tests,safety signals with regard to hepatic or renal function, tests, or other laboratory or hematological parameters.evidence of thrombocytopenia, due to patisiran.


Regulatory Designations

The Committee for

Patisiran has been granted the following regulatory designations:

Orphan Medicinal Products, or COMP, of the European Medicines Agency, or EMA, has designated patisiran as an orphan medicinal product for the treatment of FAP. Product Designation (EMA)

Orphan Drug Designation or ODD, by the European Commission, or EC, provides regulatory and financial incentives for companies developing orphan drugs to develop and market therapies that treat a life-threatening or chronically debilitating condition affecting no more than five in 10,000 persons in the EU. In addition to a ten-year period of marketing exclusivity in the EU after product approval, ODD provides companies with protocol assistance from the EMA during the product development phase, direct access to centralized marketing authorization and reduced regulatory fees. In addition, the United States Food and Drug Administration, or FDA, provided ODD to patisiran as a therapeutic for the treatment of FAP. The FDA’s ODD program provides orphan status to drugs and biologics which are defined as those intended for the safe and effective treatment, diagnosis or prevention of rare diseases/disorders that affect fewer than 200,000 people in the United States.(FDA)

In November 2013, the FDA granted Fast Track designation to patisiran forDesignation (FDA)

Breakthrough Therapy Designation (FDA)

Orphan Drug Designation (Japanese Pharmaceuticals and Medical Devices Agency (PMDA))

Promising Innovative Medicine (PIM) Designation (UK Medicines and Healthcare Products Regulatory Agency (MHRA))

As a result of the treatment of FAP. According2018 amendment to the FDA, Fast Track is a process designed to facilitateSanofi Genzyme collaboration and the Exclusive TTR License, following the closing of the transaction, we will have global rights for the development and expedite the reviewcommercialization of drugs to treat serious conditionspatisiran, together with ALN-TTRsc02, discussed below, and to fill an unmet medical need.all back-up products. The purpose is to get important new drugs to the patient earlier.

Revusiran (ALN-TTRsc). In addition to patisiran, we are also advancing revusiran, which utilizes our proprietary STC-GalNAc-conjugate approach enabling subcutaneous dose administration, with a wide therapeutic index. Revusiran is currently2014 Sanofi Genzyme collaboration, as amended in a Phase 3 clinical trial.

In December 2014, we initiated our ENDEAVOUR Phase 3 clinical trial of revusiran in TTR-mediated FAC. The ENDEAVOUR trial is a randomized, double-blind, placebo-controlled, global study designed to evaluate the efficacy and safety of revusiran in patients with FAC. The co-primary endpoints of the study are the change compared to baseline in 6-minute walk distance, or 6-MWD, and the percent reduction in TTR plasma levels between placebo- and revusiran-treated patients at 18 months. Secondary endpoints include a composite endpoint of cardiovascular mortality and cardiovascular hospitalization, New York Heart Association (NYHA) class, Kansas City Cardiomyopathy Questionnaire (KCCQ), cardiovascular, or CV, mortality, CV hospitalization and all-cause mortality. The trial is designed to enroll up to 200 FAC patients with a documented TTR mutation, including V122I or other mutations, in addition to amyloid deposits as identified by biopsy. Patients will be randomized two-to-one, revusiran-to-placebo, with subcutaneous administration at 500 mg daily for five days then weekly for 18 months. The trial design was informed by results from a natural history study which showed a progressive decrease in 6-MWD in FAC patients over an 18-month period. The ENDEAVOUR study was designed with 90% power to detect as little as 39% difference in the 18-month change from baseline for 6-MWD between treatment groups, with a significance level of p < 0.05 (two-sided). An unblinded interim analysis for futility may be conducted when 50% of patients reach 18 months. All patients completing the ENDEAVOUR Phase 3 study will be eligible to enroll in a Phase 3 OLE study.

In November 2014, we announced positive initial results from our Phase 2 open-label, multi-dose clinical trial with revusiran in TTR cardiac amyloidosis patients. Initial results from the pilot Phase 2 study from 26 patients, including 14 with FAC and 12 with SSA, were based on a data cutoff date of October 3, 2014. Study results showed that revusiran was generally well tolerated in patients with significant disease burden. The most common adverse event was injection site reaction (23% of patients). One patient had an approximate four-fold

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elevation in liver transaminases that was deemed a serious adverse event that was graded mild in severity; this event resolved during continued dosing. There were no other clinically significant adverse events, discontinuations or other clinically significant laboratory abnormalities. In addition, data showed an up to 98.2% knockdown of both mutant and wild-type forms of TTR, the disease-causing protein, with a mean maximum knockdown of 87.2% +/- 9.1%. As would be expected with the short treatment duration of five weeks, there were no significant changes observed in exploratory clinical measurements. All patients that completed dosing in our Phase 2 clinical trial are eligible to be enrolled in our open-label, Phase 2 OLE study, which was initiated in November 2014 and is designed to evaluate the tolerability and clinical activity of revusiran with long-term dosing for up to two years. In addition to data on mortality, hospitalization, general tolerability and measurement of serum TTR levels, the Phase 2 OLE study will assess the same clinical measures, every six months, included in the pilot Phase 2 trial noted aboveJanuary 2018, as well as additional measures of amyloid burden including technetium imaging of the heart and quantitation of amyloid in abdominal fat pad aspirates.Exclusive TTR License, are described below under the heading “Strategic Alliances.”

During 2014, we also initiated our DISCOVERY trial, a screening study examining the prevalence of TTR mutations in patients suspected of having cardiac amyloidosis. With this study, we aim to identify and facilitate the diagnosis of FAC.Givosiran — Acute Hepatic Porphyrias

The COMP of the EMA has designated revusiran as an orphan medicinal product for the treatment of FAC.

ALN-AT3 — Hemophilia and Rare Bleeding Disorders (RBD)

ALN-AT3Givosiran is an investigational, RNAi therapeutic targeting antithrombin, or AT, a genetically defined target, for the treatment of hemophilia and RBD. Hemophilias are hereditary disorders caused by genetic deficiencies of various blood clotting factors, resulting in recurrent bleeds into joints, muscles and other major internal organs. Hemophilia A, or HA, is defined by loss-of-function mutations in Factor VIII, and there are greater than 40,000 registered people in the United States and EU with HA. Hemophilia B, or HB, defined by loss-of-function mutations in Factor IX, affects greater than 9,500 registered people in the United States and EU. Other RBD are defined by congenital deficiencies of other blood coagulation factors, including Factors II, V, VII, X and XI. Based on our analysis of the available patient and market data, we estimate that there are approximately 1,000 people with RBD worldwide with a severe bleeding phenotype. Standard treatment for people living with hemophilia involves replacement of the missing clotting factor either as prophylaxis or on-demand therapy. However, as many as one-third of people with severe HA will develop an antibody to their replacement factor, a very serious complication. People with ‘inhibitors’ become refractory to standard replacement therapy. There remains a significant need for novel therapeutics to treat people living with hemophilia and RBD.

There exists a small subset of people living with hemophilia who have co-inherited a prothrombotic mutation, such as Factor V Leiden, antithrombin deficiency, protein C deficiency and prothrombin G20210A. People who have co-inherited these prothrombotic mutations are characterized as having a later onset of disease, lower risk of bleeding, and reduced requirements for Factor VIII or Factor IX treatment as part of their disease management. ALN-AT3 is a novel therapeutic approach aimed at re-balancing the coagulation cascade and normalizing hemostasis in severe HA and HB patients, including patients with inhibitors against their replacement factor. The program aims to reproduce the human genetic findings of a milder clinical disease in people with hemophilia who have co-inherited prothrombotic mutations.

We are evaluating ALN-AT3 in an ongoing Phase 1 study. Part A of the Phase 1 study, which is complete, was a randomized, single-blind, placebo-controlled, single-dose, dose-escalation study (n=4 per cohort; three-to-one randomization of ALN-AT3-to-placebo) in healthy volunteer subjects. This part of the study was completed after the first dose cohort that received a single subcutaneous dose of ALN-AT3 at 30 micrograms/kilogram (mcg/kg). Part B of the study, which is ongoing, is an open-label, multi-dose, dose-escalation study enrolling up to 18 subjects with moderate or severe HA or HB. The primary objective of this part of the study is to evaluate the safety and tolerability of multiple doses of subcutaneously administered ALN-AT3 in hemophilia subjects. Secondary objectives include assessment of clinical activity as determined by knockdown of circulating AT levels and increase in thrombin generation at pharmacologic doses of ALN-AT3.

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In January 2015, we announced updated results from our ongoing Phase 1 study of ALN-AT3. Specifically, new data were presented from the second dose cohort of hemophilia subjects (n=3), where ALN-AT3 was administered subcutaneously once weekly for three weeks at a low dose of 45 mcg/kg; all preliminary results are as of a data cut-off date of January 6, 2015. ALN-AT3 administration resulted in an up to 70% knockdown of AT. Based on the most advanced subject in the cohort, the nadir effect appears to occur at approximately day 28, and AT knockdown effects were found to be highly durable, lasting about 60 days. In addition, initial evidence for the potential correction of the hemophilia phenotype was observed in the severe HA subjects. Specifically, ALN-AT3 administration was found to be associated with statistically significant increase in thrombin generation of up to 334%. This level of thrombin generation increase is consistent with thrombin generation levels observed in mild hemophilia. In addition, ALN-AT3 administration was associated with improvements in whole blood clotting. Finally, as of the current data cut-off date of January 6, 2015, the most advanced subject in the study — who has a self-reported Annualized Bleeding Rate (ABR) of 10-12 bleeds per year, was found to be free of bleeding for up to 47 days in association with AT knockdown of over 50%. As of the current data cut-off,ALN-AT3 continues to be generally well tolerated in all subjects receiving study drug in the study (n=9), including subjects enrolled in the second dose cohort (n=3). The most common adverse event observed in hemophilia subjects was the occurrence of mild to moderate bleeds unrelated to study drug and consistent with an underlying hemophilia condition. All bleeds were successfully managed with replacement factor administration.

The ALN-AT3 Phase 1 study continues to enroll hemophilia subjects in additional dose cohorts, including the potential to explore a once-monthly subcutaneous dose regimen following a protocol amendment.

ALN-CC5 — Complement-Mediated Diseases

ALN-CC5 is an investigational RNAi therapeutic targeting the C5 component of the complement pathway for the treatment of complement-mediated diseases. The complement system plays a central role in immunity as a protective mechanism for host defense, but its dysregulation results in life-threatening complications in a broad range of human diseases including paroxysmal nocturnal hemoglobinuria, or PNH, atypical hemolytic-uremic syndrome, or aHUS, myasthenia gravis, neuromyelitis optica and membranous nephropathy, amongst others. Complement component C5, which is predominantly expressed in liver cells, is a genetically and clinically validated target. Loss of function human mutations are associated with an attenuated immune response against certain infections. Intravenous anti-C5 monoclonal antibody therapy (eculizumab) has demonstrated clinical activity and tolerability in a number of complement-mediated diseases. Eculizumab is approved for the treatment PNH and aHUS in the United States, Europe and other countries. A subcutaneously administered RNAi therapeutic that silences C5 represents a novel approach to the treatment of complement-mediated diseases, with a potentially competitive profile compared with intravenously administered anti-C5 monoclonal antibody therapy.

ALN-CC5 utilizes Alnylam’s ESC-GalNAc conjugate technology, which enables subcutaneous dosing with increased potency and durability and a wide therapeutic index. Our clinical trial application, or CTA, which we filed in November 2014, was approved by the U.K. Medicines and Healthcare products Regulatory Agency, or MHRA and we initiated our Phase 1/2 clinical trial with ALN-CC5 in January 2015. The Phase 1/2 study is designed in three parts: Parts A and B will be single ascending dose and multiple ascending dose studies in normal healthy human volunteers; Part C will be a study in patients with PNH.

Preclinical data presented in December 2014 shows an up to 99.2% knockdown of serum C5 and up to 96.2% inhibition of serum hemolytic activity in non-human primates, or NHPs, with continued bi-weekly or monthly subcutaneous dosing for over seven months. In addition, data showed an up to 96.9% inhibition of complement alternative pathway (CAP) activity (mean 95.1 ± 0.93%), and up to 96.2% inhibition of hemolysis (mean 88.0 ± 6.1%) with twice-monthly dosing. This level of C5 knockdown and inhibition of hemolytic activity exceeds the 80% threshold established by existing therapy and is expected to be associated with clinical benefit.

ALN-AS1 — Hepatic Porphyrias

ALN-AS1 is a subcutaneously administered, investigational RNAi therapeutic targeting aminolevulinate synthase-1, or ALAS-1,ALAS1, for the treatment of hepatic porphyrias. Porphyrias are a family of rare metabolic disorders caused by a genetic mutation in one of the eight enzymes responsible for heme biosynthesis. Hepatic

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porphyrias constitute a subset where the enzyme deficiency occurs within the liver, and includes acute intermittent porphyria, or AIP, hereditary coproporphyria and variegate porphyria. The initial focus of theALN-AS1 program is on AIP, the most common acute hepatic porphyria, whichporphyrias, or AHPs. It is duedesigned to a mutation in porphobilinogen deaminase, or PBGD. Exposuretarget and silence the ALAS1 mRNA, blocking the production of AIP patients to certain drugs, dieting or hormonal changes can trigger strong induction of ALAS-1,ALAS1 protein, the first,liver-expressed rate-limiting enzyme in the pathway, which can lead toheme biosynthesis pathway. Lowering of ALAS1 may reduce the accumulation of neurotoxic heme intermediates, upstreamALA and porphobilinogen, or PBG, that cause the clinical manifestations of the deficient PBGD enzyme that precipitateAHPs, including acute debilitating neurovisceral attacks as well as chronic disabling disease symptoms. Patients with AIP can suffer from a range of symptoms that can include acute and/or recurrent life-threatening attacks with severe abdominal pain, peripheral and autonomic neuropathy, neuropsychiatric manifestations, and possibly death if untreated or if there are delays in treatment. It is estimated that approximately 5,000 patients in the United States and Europe suffer AIPsporadic AHP attacks annually, and approximately 5001,000 patients are afflicted with recurrent, debilitating attacks.  The only availableThere are no approved therapies for prevention of acute attacks. Intravenous, or IV, hemin is currently approved for the treatment for AIP is the use of hematin, which is a preparation of heme derived from human blood. Hematin requires administration through a central intravenous lineacute AHP attacks, and is associatedsometimes used prophylactically off-label by some porphyria specialists to prevent attacks, despite its unclear efficacy, short duration of action and association with a number of complications including thrombophlebitis and iron overload.significant side effects. There is a clear unmet need for new therapies for AIP that could be both safernovel therapeutics with an enhanced efficacy and more effectivesafety profile and convenient than available therapies.durable lowering of ALA and PBG, in order to prevent attacks, diminish chronic symptoms in between attacks, and improve patients’ quality of life.

ALN-AS1 utilizes our ESC-GalNAc conjugate technology, which enables subcutaneous dosing with increased potency and durability and a wide therapeutic index, andGivosiran has the potential to be a therapyutilized for the chronic treatment of acuteAHPs. In September 2017, we aligned with the FDA on a pivotal Phase 3 trial design that includes an interim analysis based on reduction of urinary ALA as a surrogate endpoint reasonably likely to predict clinical benefit. This will enable a potential NDA filing at or around year-end 2018, pending FDA review of the program at the time of interim analysis and assuming positive results. The ENVISION Phase 3 pivotal study for givosiran was initiated in November 2017 and we expect to report interim analysis data in mid-2018.

ENVISION Trial Design:

The ENVISION Phase 3 trial is a randomized, double-blind, placebo-controlled, global, multicenter study in more than 20 countries to evaluate the efficacy and safety of givosiran in approximately 75 patients with a documented diagnosis of AHPs. Patients will be randomized on a 1:1 basis to receive 2.5 mg/kg of givosiran or placebo subcutaneously administered monthly, over a six-month treatment period. The primary endpoint is the annualized rate of porphyria attacks requiring hospitalization, urgent healthcare visit or IV hemin administration at home over the six-month treatment period. The planned interim analysis will evaluate reduction of a urinary biomarker, ALA, in 30 patients after three months of dosing, as a surrogate endpoint reasonably likely to predict clinical benefit. The interim analysis is also designed to conduct a blinded assessment of the porphyria attack rate for the purpose of a study sample size adjustment from approximately 75 patients to up to approximately 94 patients. Key secondary and exploratory endpoints will evaluate reductions in the cardinal symptoms of AHPs, such as pain, nausea and fatigue, as well as a prophylactic approachimpact on quality of life. All patients completing the six-month treatment period will be eligible to continue on an OLE study in which they will receive treatment with givosiran for the prevention of recurrent attacks. In pre-clinical studies, multi-dose administration of a GalNAc-siRNA targeting ALAS-1 ledup to rapid, dose-dependent knockdown of the ALAS-1 mRNA in NHPs, with an ED50 of approximately 1.25 mg/kg. Further, in a rat model of AIP, ALN-AS1 administration at doses as low as 2.5 mg/kg resulted in a complete inhibition of phenobarbital-induced over-production of ALA and PBG, the toxic heme intermediates in AIP.30 months.

In December 2014, we filed a CTA with the Swedish Medical Products Agency, or MPA, to initiate a Phase 1 clinical trial with ALN-AS1. Per the filed CTA, theClinical Trial (Part C and OLE)

During 2017, we reported interim data from Part C of our Phase 1 clinical trial of ALN-AS1 will be performed firstgivosiran, which was conducted as a randomized, double-blind, placebo-controlled study in up to 24 patients with acute intermittent porphyria, or AIP, the most common AHP sub-type, who experienced recurrent porphyria attacks, along with data from the Phase 1 OLE study of givosiran.


As of the data transfer date of April 21, 2017, givosiran achieved potent silencing of the ALAS1 mRNA, which resulted in robust and durable lowering of ALA and PBG. Data from the OLE study demonstrated that longer-term treatment with givosiran was associated with consistent reductions in the annualized porphyria attack rate, with preliminary evidence suggesting the potential for further reductions in the attack rate with extended dosing. As of the data cutoff date, givosiran administration was generally well tolerated in recurrent attack AIP patients who are asymptomatic “high excreters,” or ASHE, patients with a mutation in the PBGD gene and elevated urinary ALA and PBG levels, but no recent symptomscohorts 1-3 in Part C of a porphyria attack. The Phase 1 clinical trial will then move to AIP patients who experience recurrent porphyria attacks. Following approval of the CTA, we expect to initiate the Phase 1 study and in mid-2015.

During 2014, we also initiatedcohorts 1 and 2 of the EXPLORE trialongoing OLE study, with our collaborators froma mean of 169 and 111 days on study, respectively, and up to 12 months on givosiran. As previously reported, one death occurred in a patient in cohort 3 in the American Porphyria Consortiumgivosiran arm due to hemorrhagic pancreatitis complicated by a pulmonary embolism and The European Porphyria Network,following a prospective observationalrecent hospitalization for bacteremia; the death was considered to be unlikely related to study of patients with hepatic porphyrias suffering from recurrent attacks. With this study, wedrug by the investigator and clinical investigators aim to learn more about the clinical course, management and disease burden of patients with hepatic porphyrias who suffer from recurrent attacks.

Additional Genetic Medicine Programsstudy's Safety Review Committee.

In addition toRegulatory Designations

Givosiran has been granted the programs described above, we are also advancing other early stage Genetic Medicine programs. These programs include: ALN-AAT, an investigational RNAi therapeutic targeting alpha-1 antitrypsin, or AAT,following regulatory designations for the treatment of AAT deficiency liver disease; ALN-GO1, an investigational RNAi therapeutic targeting glycolate oxidase, or GO, for the treatment of primary hyperoxaluria type 1, or PH1; ALN-TMP, an investigational RNAi therapeutic targeting transmembrane protease, serine 6, or TMPRSS6, for the treatment of beta-thalassemia and iron-overload disorders; and other yetAHPs:

Orphan Drug Designation (FDA)

Orphan Medicinal Product Designation (EMA)

PRIME Designation (EMA)

Breakthrough Therapy Designation (FDA)

During 2016, Sanofi Genzyme elected not to be disclosed programs. We intend to file an Investigational New Drug (IND) application, or IND equivalent, such as a CTA, for AAT in mid-2015 and to advance additional Genetic Medicine programs to support the filing of two or more INDs or IND equivalents in 2016.

Genzyme Alliance

In January 2014, we enteredopt into the 2014 Genzyme collaboration which is an exclusive relationship for the worldwide development and commercialization of RNAi therapeuticsgivosiran in the field of Genetic Medicines, which includes our current and future Genetic Medicine programs that reach human proof-of-principal study

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completion, or Human POP, by the end of 2019, subject to extension to the end of 2021 in various circumstances. We will retain product rights in North America and Western Europe, whileSanofi Genzyme will obtain exclusive rights to develop and commercialize collaboration products in the restTerritory, providing us with full global control of the world, referred to as the Genzyme Territory, together with certain broader co-development/co-promote or worldwide rightsprogram for certain products. Genzyme’s rights are structured as an opt-in that is triggered upon achievement of Human POP. We maintain development control for all programs prior to Genzyme’s opt-in and maintainfurther development and commercialization, control after Genzyme’s opt-in for all programs in our territory.

In addition to its regional rights for our current and future Genetic Medicine STAr programs in the Genzyme Territory, Genzyme has the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other RBD in our territory, with us maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme will exercise this selection right upon the completion of Human POP for both the ALN-AT3 and ALN-AS1 programs. Finally, Genzyme has the right for a global license to a single, future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. We will retain global rights to any RNAi therapeutic Genetic Medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions.

We are leading development and commercialization of patisiran in North America and Western Europe while Genzyme will develop and commercialize the product in the Genzyme Territory. In addition, we and Genzyme are co-developing and co-commercializing revusiran in North America and Western Europe, with Genzyme developing and commercializing the product in the Genzyme Territory.

if approved. The 2014 Sanofi Genzyme collaboration, as amended in January 2018, is described below under the heading “Strategic Alliances.”

Fitusiran — Hemophilia and Rare Bleeding Disorders

Fitusiran is a subcutaneously administered, investigational RNAi therapeutic targeting antithrombin, or AT, for the treatment of people with hemophilia A and B, with and without inhibitors.  Fitusiran also has the potential to be used for rare bleeding disorders, or RBD. Fitusiran is designed to lower levels of AT with the goal of promoting sufficient thrombin generation to prevent bleeding. AT acts by inactivating thrombin and other coagulation factors, and plays a key role in normal hemostasis by helping to limit the process of fibrin clot formation. Hemophilia is a hereditary bleeding disorder characterized by an underlying defect in the ability to generate adequate levels of thrombin needed for effective fibrin clot formation, thereby resulting in recurrent bleeds into joints, muscles, and major internal organs. Lowering AT in the hemophilia setting may promote the generation of sufficient levels of thrombin needed to form an effective fibrin clot and prevent bleeding. This rationale is supported by human genetic data suggesting that co-inheritance of thrombophilic mutations, including AT deficiency, may ameliorate bleeding in hemophilia. We believe this approach is a unique and innovative strategy for preventing bleeding in people with hemophilia.

There are approximately 200,000 people living with hemophilia A and hemophilia B worldwide. Standard treatment for people with hemophilia currently involves replacement of the deficient clotting factor either as prophylaxis or on-demand therapy, which can lead to a temporary restoration of thrombin generation capacity. However, with current factor replacement treatments people with hemophilia are at risk of developing neutralizing antibodies, or inhibitors, to their replacement factor, a very serious complication affecting as many as one third of people with severe hemophilia A and a smaller fraction of people with hemophilia B. People who develop inhibitors become refractory to replacement factor therapy and are twice as likely to be hospitalized for a bleeding episode.

During 2017, we initiated the ATLAS Phase 3 program to evaluate the safety and efficacy of fitusiran in people with hemophilia A and B, with and without inhibitors. Fitusiran is also currently being evaluated in an ongoing Phase 2 OLE study.  In September 2017, we reported a fatal thrombotic event in a patient with hemophilia A without inhibitors in the Phase 2 OLE study of fitusiran.  As a result, we elected to suspend dosing in all ongoing fitusiran studies pending review of the safety event and development of a risk mitigation strategy.  In early November 2017, we and the FDA reached alignment on clinical risk mitigation measures, including protocol-specified guidelines and additional investigator and patient education concerning reduced doses of replacement factor or bypassing agent to treat any breakthrough bleeds in fitusiran studies. Based on this, amended protocols were submitted to the regulatory authorities and in December 2017, the FDA lifted the clinical hold.  Dosing has resumed in the Phase 2 OLE study and we expect to begin dosing patients in the ATLAS Phase 3 program in early 2018.


Cardio-Metabolic Disease STArATLAS Phase 3 Clinical Program

Trial Design: ATLAS is a global, multicenter program designed to evaluate the safety and efficacy of fitusiran in three separate trials, including patients with hemophilia A and B with or without inhibitors.

ATLAS-INH, a nine-month, open-label, randomized, controlled trial designed to enroll approximately 50 patients with hemophilia A or B with inhibitors receiving prior on-demand therapy with bypassing agents. The study's primary endpoint is the annualized bleeding rate, or ABR, and secondary endpoints include the annualized spontaneous bleeding rate, annualized joint bleeding rate, and quality of life as measured by the Haem-A-QOL score.

ATLAS-A/B, a nine-month, open-label, randomized, controlled trial designed to enroll approximately 120 patients with hemophilia A or B without inhibitors receiving prior on-demand therapy with factor. The study's primary endpoint is the ABR, and secondary endpoints include the annualized spontaneous bleeding rate, annualized joint bleeding rate, and quality of life as measured by the Haem-A-QOL score.

ATLAS-PPX, an open-label, one-way crossover study designed to enroll approximately 30 patients with hemophilia A or B with inhibitors receiving prior prophylaxis therapy with bypassing agents. In this study, patients will receive standard of care bypassing agent prophylaxis therapy for six months and then transition to fitusiran treatment for seven months. The ABR will be prospectively measured in both periods. The study's primary endpoint is the ABR in the fitusiran period and in the bypassing agent prophylaxis period. Secondary endpoints include the annualized spontaneous bleeding rate, annualized joint bleeding rate, and quality of life as measured by the Haem-A-QOL score.

Phase 2 OLE Clinical Study

In our Cardio-Metabolic Disease STAr,July 2017, we are advancing our pipelinereported interim results from the ongoing fitusiran Phase 2 OLE study which includes patients with hemophilia A and B, and includes 14 patients with inhibitors, including one with hemophilia B. As of investigational RNAi therapeutics toward genetically validated, liver-expressed disease targets for unmet needsa June 15, 2017 data transfer date, once-monthly subcutaneous administration of fitusiran achieved lowering of AT, increases in dyslipidemias, hypertension, NASHthrombin generation, and, type 2 diabetes. We believe that new discoveriesin a post-hoc exploratory analysis, reductions in the human geneticsmedian estimated ABR in patients with and without inhibitors. With respect to safety, three SAEs were considered possibly related to study drug, including one fatal cerebral venous sinus thrombosis, as noted above, that occurred after the data cutoff date.  The majority of cardio-metabolic disease, together with innovative clinical development strategiesAEs were mild or moderate in morbid sub-populations, create opportunitiesseverity.

Regulatory Designations

Fitusiran has been granted the following regulatory designations for new, potentially transformative medicines. Further, we believe the emerging profiletreatment of our ESC-GalNAc conjugates with once-monthlyhemophilia A and possibly once-quarterly, low-volume, subcutaneous dose administrationB:

Orphan Drug Designation (FDA)

Orphan Medicinal Product Designation (EMA)

As a result of the January 2018 amendment to the Sanofi Genzyme collaboration and a wide therapeutic index supports advancementthe AT3 License Terms, following the closing of new medicinesthe transaction, Sanofi Genzyme will have global rights to develop and commercialize fitusiran.  We expect to substantially complete the transition of the fitusiran program to Sanofi Genzyme by mid-2018.  The 2014 Sanofi Genzyme collaboration, as amended in this disease area. We intend to seek strategic collaboration opportunities for programs in our Cardio-Metabolic Disease STAr, while retaining significant product commercialization rights inJanuary 2018, as well as the United States and EU.

Our Cardio-Metabolic Disease development programsAT3 License Terms, are described in more detail below.below under the heading “Strategic Alliances.”

ALN-PCSInclisiran   — Hypercholesterolemia

ALN-PCSscInclisiran is a subcutaneously administered, investigational RNAi therapeutic targeting proprotein convertase subtilisin/kexin type 9, or PCSK9, for the treatment of hypercholesterolemia. PCSK9 is a protein involved in the regulation of low-density lipoprotein receptor, or LDL receptor, levels on hepatocytes and the metabolism of LDL cholesterol, or LDL-C, which is commonly referred to as “bad” cholesterol. PCSK9 is produced by the liver and circulates in the bloodstream. Both intracellular and extracellular PCSK9 reduce the liver’s capacity to absorb LDL-C by decreasing LDL receptor levels. Published studies indicate that, if PCSK9 activity could be reduced, the liver’s uptake of LDL-C should increase and blood cholesterol levels should decrease. In fact, published case reports have shown individuals with loss-of-function genetic mutations

Despite advances in PCSK9 have decreased blood cholesterol levels. In turn, these individuals have been shown to have a dramatically reduced risk of coronary arterytreatment, cardiovascular disease, or CAD, including myocardial infarction or heart attack. In addition, studies have shown that PCSK9 levels are increased by statin therapy, limiting their effect, suggesting that the introduction of a PCSK9 inhibitor to statin therapy may result in even further reductions in LDL-C levels. HypercholesterolemiaCVD, is a condition characterized by very high levels of cholesterol in the blood which is known to increase the risk of coronary artery disease, the leading cause of death worldwide, resulting in over 17 million deaths annually. Eighty percent of all CVD deaths are due to coronary heart disease, or CHD, or strokes. Elevated LDL-C is a major risk factor for the United States. Some formsdevelopment of hypercholesterolemia canCVD and has recently been described as causative. Lowering LDL-C has been shown to reduce the risk of cardiovascular death or heart attack, and within the range of effects achieved so far, the clinical risk reduction is linearly-proportional to absolute LDL-C reduction.


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beApproximately 100 million people worldwide are treated through dietary restrictions, lifestyle modifications (e.g., exercisewith lipid lowering therapies, predominantly statins, to reduce LDL-C and smoking cessation)the associated risk of death, nonfatal myocardial infarction and medicines such as statins.nonfatal stroke or associated events. However, a large proportionresidual risk for cardiovascular events remains and statins are associated with well-known limitations. First, not all subjects reach LDL-C levels associated with optimal protection against clinical events. Second, not all subjects tolerate statins or are able to take statins at sufficiently-intensive doses. Third, observational studies have demonstrated that >50 percent of patients do not adhere to statin therapy for more than six months. Despite statins alone or in combination with hypercholesterolemia, including genetic other lipid lowering medications, current therapies for the management of elevated LDL-C remain insufficient in some subjects. This is particularly true in patients with pre-existing CHD and/or diabetes or a history of familial hypercholesterolemia, patients, acute coronary syndrome patients, high-risk patient populations (e.g., patients with CAD, diabetes, symptomatic carotid artery disease)or FH, who are at the highest risk and other patients that are statin intolerant, are not achieving target LDL-C goals with statin therapy. Severe forms of hypercholesterolemia are estimated to affect more than 500,000 patients worldwide, and as a result, thererequire the most intensive management. There is a significantan unmet need for novel therapeutics to treat patients with hypercholesterolemia whose disease is inadequately managed by existing therapies.

In December 2014, we initiated a Phase 1 clinical trial withALN-PCSsc. The Phase 1 trial is being conducted in the U.K. as a randomized,single-blind,placebo-controlled, singleascending- andmulti-dose study. The study is designed to enroll up to 76 volunteer subjects with elevated baseline LDL-C (³ 100 mg/dL), with subjects randomized three-to-one, drug-to-placebo. The study will be performed in two phases: a single ascending dose, or SAD, phase and a multiple dose, or MD, phase. In the MD phase, subjects will receive two subcutaneous doses of either ALN-PCSsc or placebo administered four weeks apart. The MD phase will also include subjects both on and off statin co-medication. The primary objectiveadditional treatment options beyond currently-available treatments for lowering of the Phase 1 study isLDL-C level to evaluate the safety and tolerability of ALN-PCSsc. Secondary objectives include assessment of clinical activity as determined by knockdown of plasma PCSK9 levels and serum LDL-C levels, as well as pharmacokinetics of ALN-PCSsc.reduce cardiovascular risk.

ALN-PCSsc utilizes our proprietary ESC-GalNAc-siRNA conjugate delivery platform. Pre-clinical data in NHPs demonstrates that monthly subcutaneous administration of ALN-PCSsc resulted in PCSK9 knockdown of up to 92% and LDL-C lowering, in the absence of statin co-administration, of up to 77%; mean maximum knockdown of PCSK9 was 83.2% +/- 7.2%, and mean maximum LDL-C reduction was 59.0% +/- 13.3%. As a PCSK9 synthesis inhibitor, ALN-PCSsc showed rapid, durable and clamped knockdown of PCSK9 and reduction of LDL-C, which contrasts with the cyclical variation in LDL-C observed with monthly dose regimens of anti-PCSK9 monoclonal antibodies. In aggregate, these pre-clinical data are supportive of a once-monthly, and possibly once-quarterly, dosing regimen for ALN-PCSsc, which we believe could represent a highly competitive target product profile.

In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9 for the treatment of hypercholesterolemia and other human diseases. Under the terms of the agreement, we will complete certain pre-clinical studiesMDCO assumed responsibility for the development and a Phase 1 clinical studycommercialization of ALN-PCSsc, and MDCO is responsible for leading and funding developmentinclisiran from Phase 2 forward as well as potential commercialization.forward. A description of our agreement with MDCO is included below under the heading “Strategic Alliances.”

In 2017, MDCO initiated the ORION Phase 3 program for inclisiran, a comprehensive set of clinical trials to assess LDL-C lowering and safety in a wide range of patients.  The Phase 3 program includes the four pivotal Phase 3 clinical trials described below and represents the largest clinical experience for an investigational RNAi therapeutic to date:

ORION-11 – a placebo-controlled, double-blind, randomized Phase 3 study of inclisiran versus placebo (1:1) in patients (N=1,500) with atherosclerotic cardiovascular disease, or ASCVD, or ASCVD-risk equivalents, and elevated LDL-C despite maximum tolerated doses of LDL-C lowering therapies, including statins. This pivotal trial was initiated in November 2017.  In January 2018, MDCO announced that this trial had exceeded its target enrollment of 1,500 patients.

ORION-10 – a placebo-controlled, double-blind, randomized Phase 3 study of inclisiran versus placebo (1:1) in ASCVD patients (N=1,500).  This pivotal trial was initiated in November 2017 and MDCO expects to complete enrollment during the first half of 2018.

ORION-9 – a placebo-controlled, double-blind, randomized Phase 3 study of inclisiran versus placebo (1:1) in patients (N=400) with heterozygous FH.  This pivotal trial was initiated in November 2017 and MDCO expects to complete enrollment during the first half of 2018.

ORION-5 – a placebo-controlled, double-blind, randomized Phase 3 study of inclisiran versus placebo (1:1) in patients (N=60) with homozygous FH, or HoFH.  MDCO expects to initiate this pivotal trial in 2018.

Additional Cardio-Metabolic Disease ProgramsORION-1 Phase 2 Clinical Trial

In additionDuring 2017, we and MDCO reported final results from ORION-1, a placebo-controlled, double-blind, randomized Phase 2 study of inclisiran in patients (N=501) with ASCVD or ASCVD-risk equivalents (e.g., diabetes and FH) and elevated LDL-C despite maximum tolerated doses of LDL-C lowering therapies.  The Phase 2 study, conducted by MDCO, compared the effect of different doses of inclisiran and evaluated the potential for an infrequent dosing regimen. The primary endpoint of the study was the percentage change in LDL-C from baseline at Day-180. Inclisiran demonstrated significant and sustained reductions in LDL-C of over 50 percent. For all dose groups, at all time points, differences in the primary (LDL-C) and secondary (PCSK9) endpoints between inclisiran and placebo were statistically significant (p < 0.0001). Inclisiran represents the largest safety experience for one of our investigational RNAi therapeutics to ALN-PCSsc, we are also advancing other early stage Cardio-Metabolic Disease programs. These programs include additional investigational programsdate.  Inclisiran was generally well tolerated and no material safety issue was observed, including no significant elevations of liver enzymes considered related to study medication and no neuropathy, change in renal function, thrombocytopenia or anti-drug antibodies.  

The results from the Phase 2 study of inclisiran were published in April 2017 in The New England Journal of Medicine.

Regulatory Designations

Inclisiran has been granted the following regulatory designation for the treatment of dyslipidemias, includingHoFH:

Orphan Drug Designation (FDA)


ALN-AC3Early Stage Clinical Development Programs

ALN-TTRsc02 —  TTR-Mediated (ATTR) Amyloidosis

ALN-TTRsc02 is a subcutaneously administered, investigational RNAi therapeutic targeting Apolipoprotein C3, or ApoC3,TTR for the treatment of hypertriglyceridemia and ALN-ANG targeting Angiopoetin-like 3, or ANGPTL3,ATTR amyloidosis, representing an extension of our program for ATTR amyloidosis, discussed in more detail above under the heading “Patisiran.”  We believe ALN-TTRsc02 has the potential to offer an attractive option for patients as a once-quarterly, low-volume, subcutaneously administered RNAi therapeutic for the treatment of hypertriglyceridemiaATTR amyloidosis.

We are evaluating ALN-TTRsc02 in a randomized, placebo-controlled, single ascending-dose Phase 1 study in healthy volunteers and mixed hyperlipidemia. In addition, we expect to advance ALN-TTRsc02 into a Phase 3 clinical trial in late 2018.

As a result of the 2018 amendment to the Sanofi Genzyme collaboration and the Exclusive TTR License, following the closing of the transaction, we will have global rights for the development and commercialization of patisiran, discussed above, together with ALN-TTRsc02 and all back-up products. The 2014 Sanofi Genzyme collaboration, as amended in January 2018, as well as the Exclusive TTR License, are developing ALN-AGT,described below under the heading “Strategic Alliances.”

Lumasiran (ALN-GO1) — Primary Hyperoxaluria 1

Lumasiran is an investigational RNAi therapeutic targeting angiotensinogen,glycolate oxidase, or AGT,GO, in development for the treatment of hypertensive disordersprimary hyperoxaluria type 1, or PH1.  PH1 is an autosomal recessive disorder of pregnancy including preeclampsia. Finally, weglyoxylate metabolism, resulting in excessive oxalate production. Excess oxalate in PH1 patients results in the deposition of calcium oxalate crystals in the kidneys and urinary tract and can lead to the formation of recurrent kidney stones or nephrocalcinosis. Renal damage is caused by a combination of tubular toxicity from oxalate, calcium oxalate deposition in the kidneys, and urinary obstruction by calcium oxalate stones. Compromised kidney function exacerbates the disease as the excess oxalate can no longer be effectively excreted, resulting in subsequent accumulation and crystallization in bones, eyes, skin, and heart, leading to severe illness and death. Lumasiran is designed to reduce the hepatic levels of the GO enzyme, thereby depleting the substrate necessary for oxalate production, which directly contributes to the pathophysiology of PH1. 

We are advancing a number of undisclosed pre-clinical programsevaluating lumasiran for the treatment of NASHpatients with PH1 in a randomized, single-blind, placebo-controlled Phase 1/2 clinical trial.

Sanofi Genzyme has the right to opt in to develop and type 2 diabetes. We intend to advance additional Cardio-Metabolic Disease programs to support the filing of at least one IND or IND equivalent in 2016.

Hepatic Infectious Disease STAr

In our Hepatic Infectious Disease STAr, we are advancing a pipeline of investigational RNAi therapeutics that address major global health challenges, including but not limited to HBV. We intend to seek strategic collaboration opportunities for programs in our Hepatic Infectious Disease STAr, while retaining significant product commercialization rightscommercialize lumasiran in the United StatesSanofi Genzyme Territory and EU.could elect to exercise its one right to a global license for lumasiran. The 2014 Sanofi Genzyme collaboration, as amended in January 2018, is described below under the heading “Strategic Alliances.”

Cemdisiran (ALN-CC5) —  Complement-Mediated Diseases

 

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Our Hepatic Infectious Disease development programs are described in more detail below.

ALN-HBV — Hepatitis B Virus (HBV)

HBVCemdisiran is the most common serious liver infection in the world. Worldwide, two billion people (one out of three people) have been infected with HBV and 400 million people have become chronically infected. An estimated one million people die each year from HBV and its complications worldwide; about 5,000 of those are in the United States. The clinical manifestations are severe. Worldwide, chronic infection with hepatitis causes 80% of all hepatocellular carcinoma, or HCC, and more than 500,000 people die each year from this form of cancer. About five percent of the population are chronic carriers of HBV, and nearly 25% of all carriers develop serious liver diseases such as chronic hepatitis, cirrhosis and HCC. Despite the use of nucleoside analog inhibitors of viral DNA synthesis and interferon therapies, the cure rate for chronic HBV infection is less than ten percent. Reduction in HBV surface antigen, or HBsAg, levels of over 0.5 log10 is the single best predictor of immunologic cure. We believe an RNAi therapeutic targeting the HBV genome could have the potential to achieve a “functional cure” by effectively decreasing expression of HBsAg, in addition to inhibiting all steps of the HBV life cycle.

During 2014, we identified a Development Candidate for our ALN-HBV program. The ALN-HBV Development Candidate is an ESC-GalNAc-siRNA targeting the HBV genome. In a rodent model of HBV, a single subcutaneous dose at 3 mg/kg resulted in an up to 3.9 log10 reduction in HBsAg levels (mean 1.8 log10 reduction). We expect to file an IND or IND equivalent for this program in late 2015.

Our ALN-HBV program derives from our 2014 acquisition of the RNAi assets of Merck, including Sirna.

Additional Hepatic Infectious Disease Programs

In addition to ALN-HBV, we are also advancing other early stage Hepatic Infectious Disease programs. These programs include: ALN-HDV, an investigational RNAi therapeutic targeting the hepatitis delta virus, or HDV,C5 component of the complement pathway in development for the treatment of HDV infection; ALN-PDL,complement-mediated diseases. The complement system plays a central role in immunity as a protective mechanism for host defense, but its dysregulation results in life-threatening complications in a broad range of human diseases including paroxysmal nocturnal hemoglobinuria, or PNH, and aHUS, amongst others. Complement component C5, which is predominantly expressed in liver cells, is a genetically and clinically validated target; loss-of-function human mutations are associated with an investigationalattenuated immune response against certain infections and intravenous anti-C5 monoclonal antibody, or mAb, therapy has demonstrated clinical activity and tolerability in a number of complement-mediated diseases. A subcutaneously administered RNAi therapeutic targeting hepatocyte-expressed programmed death ligand 1, or PD-L1, an immune checkpoint inhibitor,that silences C5 represents a novel approach for the potential treatment of complement-mediated diseases.

We are evaluating cemdisiran for the treatment of chronic liver infections;patients with aHUS in a Phase 2 clinical trial initiated in September 2017.

During 2016, Sanofi Genzyme elected not to opt into the development and commercialization of cemdisiran in the Sanofi Genzyme Territory, providing us with full global control of the program for further development and commercialization, if approved. The 2014 Sanofi Genzyme collaboration, as amended in January 2018, is described below under the heading “Strategic Alliances.”

Additional Early Stage and Pre-clinical Programs

In addition to the programs listed above, we are also advancing other yetearlier-stage clinical pipeline programs and expect multiple data read-outs throughout 2018. We also plan to be disclosed programs.file one or more new clinical trial applications, or CTAs, in 2018, and to advance our infectious disease collaboration with Vir Biotechnology.


Our Collaboration and Licensing Strategy

Our business strategy is to develop and commercialize a broad pipeline of RNAi therapeutic products directed towards our three STArs: Genetic Medicines; Cardio-Metabolic Diseases; and Hepatic Infectious Diseases. As part of this strategy, we have entered into, and expect to enter into additional, collaboration and licensing agreements as a means of obtaining resources, capabilities and funding to advance our investigational RNAi therapeutic programs.

Our collaboration strategy is to form alliances that create significant value for ourselves and our collaborators in the advancement of RNAi therapeutics as a potential new class of innovative medicines. Specifically, with respect to our Genetic Medicine pipeline, we formed a broad strategic alliance with Sanofi Genzyme in 2014 pursuant to which we retain development and commercial rights for our current and future Genetic Medicine products in North Americathe United States, Canada and Western Europe, and Sanofi Genzyme will develop and commercialize our current and future Genetic Medicine products principallyfor which it elects to opt-in, in territories outsidethe rest of North America and Western Europe,the world, subject to certain broader rights. In January 2018, we and Sanofi Genzyme amended our 2014 collaboration to provide that we would develop and commercialize patisiran globally and Sanofi Genzyme would develop and commercialize fitusiran globally. With respect to our Cardio-Metabolic and Hepatic Infectious Disease pipelines,pipeline, we intend to seek future strategic alliances for these programs, while retaining significantunder which we may retain certain product commercialization rights in the United States and EU. We currently have a global alliance with MDCO for the development and commercialization ofrights, or we may structure as global alliances, as we did in our ALN-PCSsc program.

We also seekcollaboration with MDCO to form or advance new ventures and opportunitiesinclisiran. With respect to our Hepatic Infectious Disease pipeline, in areas outside our primary focus on RNAi therapeutics. In 2007,October 2017, we and Isis formed Regulus to capitalize on our technology and intellectual property in the field of microRNA therapeutics. Currently, we own approximately 12% of Regulus’ outstanding common stock.

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To generate revenues from our intellectual property rights, we also grant licenses to biotechnology companies under our InterfeRx programannounced an exclusive licensing agreement with Vir Biotechnology for the development and commercialization of RNAi therapeutics for specified targets in which we have no direct strategic interest. infectious diseases, including chronic hepatitis B virus infection.

We also have entered into license key aspects of ouragreements to obtain rights to intellectual property to companies active in the research products and services market, which includes the manufacture and salefield of reagents. We expect our InterfeRx and research product licenses to generate modest revenues that we can re-invest in the development of our proprietary RNAi therapeutics pipeline. As of January 31, 2015, we had granted such licenses, on both an exclusive and non-exclusive basis, to approximately 20 companies.

SinceRNAi. In addition, because delivery of RNAi therapeutics has historically been an important objective of our research activities, we have also evaluated potentialentered into various collaboration and licensing arrangements with other companies and academic institutions to gain access to delivery technologies. For example, we entered into agreements with Tekmira Pharmaceuticals Corporation, or TPC, Protiva Biotherapeutics, Inc., a wholly owned subsidiary of TPC, and together with TPC, referred to as Tekmira, The University of British Columbia, or UBC, and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.), or Acuitas, among others, related totechnologies, including various LNP delivery technologies.

We have also entered into license agreements with Isis, Max Planck Innovation GmbH (formerly known as Garching Innovation GmbH), or Max Planck Innovation, Tekmira, Cancer Research Technology Limited, or CRT, and Whitehead Institute for Biomedical Research, or Whitehead, as well as a number of other entities, to obtain rights to intellectual property in the field of RNAi. Finally, we have sought, and may seek in the future, funding for the development of our proprietary RNAi therapeutics pipeline from the government and foundations.

Strategic Alliances

We have formed, and intend to continue to form, strategic alliances to gain access to the financial, technical, clinical and commercial resources necessary to develop and market RNAi therapeutics. We expect these alliances to provide us with financial support in the form of upfront cash payments, license fees, equity investments, research, development, and developmentsales and marketing funding, milestone payments and/or royalties or profit sharing based on sales of RNAi therapeutics. Below is a brief description of our key strategic alliance and license agreements.

Product Alliances.

Sanofi Genzyme.Genzyme.    In January 2014, we entered into a global, strategic collaboration with Sanofi Genzyme to discover, develop and commercialize RNAi therapeutics as Genetic Medicines to treat orphan diseases.  The 2014 Genzyme collaboration supersededOn January 6, 2018, we and replaced the previous collaboration between us andSanofi Genzyme entered into in October 2012an amendment to develop and commercialize RNAi therapeutics targeting TTR for the treatment of ATTR, including patisiran and revusiran, in Japan and the Asia-Pacific region.

The 2014 Sanofi Genzyme collaboration, which is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of Genetic Medicines, which includesMedicines. In connection and simultaneously with entering into the 2018 amendment to the 2014 Sanofi Genzyme collaboration, we and Sanofi Genzyme also entered into the Exclusive TTR License with respect to all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, and the AT3 License Terms with respect to fitusiran and any back-up products.  

Under the 2014 Sanofi Genzyme collaboration, Sanofi Genzyme has certain rights to our current and future Genetic Medicine programs that reach Human POP by the end of 2019, subject to extension to the end of 2021 in various circumstances.  We will retain product rights in North America and Western Europe, referred to asUnder the Alnylam Territory, while2014 Sanofi Genzyme will obtain exclusive rights to develop and commercialize collaboration, products in the Genzyme Territory, together with certain broader co-development/co-promote or worldwide rights for certain products. Genzyme’s rights, described in detail below, are structured as an opt-in that is triggered upon achievement of Human POP. We maintain development control for all programs prior to Genzyme’s opt-in and maintainwe were leading development and commercialization control after Genzyme’s opt-in for all programs in the Alnylam Territory.

Specifically, in addition to its regional rights for our current and future Genetic Medicine programs in the Genzyme Territory, Genzyme has the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other RBD in the Alnylam Territory, with us maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme may

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exercise this selection right upon the completion of Human POP for both the ALN-AT3 and ALN-AS1 programs. Finally, Genzyme has the right for a global license to a single, future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. We will retain global rights to any RNAi therapeutic Genetic Medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions. We retain full rights to all current and future RNAi therapeutic programs outside of the field of Genetic Medicines, including the right to form new collaborations.

Under the 2014 Genzyme collaboration, Genzyme’s specific license rights include the following:

Regional license terms — Upon opt-in, we will retain product rightspatisiran in the Alnylam Territory, while Sanofi Genzyme will obtain exclusivehad rights to develop and commercialize the product in the Sanofi Genzyme Territory. Sanofi Genzyme can elect this license for any of our currentalso had a right to opt in to co-develop and future Genetic Medicine programs that complete Human POP by the end of 2019, subject to limited extension. Development costs for products, once Genzyme exercises an option, will be shared between Genzyme and us, with Genzyme responsible for twenty percent of the global development costs. Upon the effective date of the 2014 Genzyme collaboration, Genzyme expanded the scope of its regional license and collaboration for patisiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial for the treatment of ATTR patients with FAP, which was originally established under the 2012 Genzyme agreement. Genzyme will be required to make payments totaling up to $50.0 million upon the achievement of certain patisiran development milestones. In addition, Genzyme will be required to make payments totaling up to $75.0 million per product other than patisiran, including up to $55.0 million in development milestones and $20.0 million in commercial milestones. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each regional product based on annual net sales, if any, of such regional product by Genzyme, its affiliates and sublicensees.

Co-development/co-promote license terms — Upon opt-in, we will retain product rightsALN-TTRsc02 in the Alnylam Territory whilealong with its regional opt-in rights.  In addition, Sanofi Genzyme will obtain exclusive rightshad opted in to co-develop and co-promote fitusiran in the Alnylam Territory, as well as develop and commercialize the productfitusiran in the Sanofi Genzyme Territory,Territory.

The 2018 amendment, together with the Exclusive TTR License and will co-promote the product inAT3 License Terms, revise the Alnylam Territory. Upon the effective dateterms and conditions of the 2014 Sanofi Genzyme collaboration to (i) provide us with the exclusive right to pursue the further global development and commercialization of all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, (ii) provide Sanofi Genzyme expanded its regionalthe exclusive right to pursue the further global development and commercialization of fitusiran and any back-up products and (iii) terminate the previous co-development and co-commercialization rights forrelated to revusiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial for the treatment of ATTR patients with TTR amyloid cardiomyopathy, which were originally grantedALN-TTRsc02 and fitusiran under the 20122014 Sanofi Genzyme agreement,collaboration.


Sanofi Genzyme continues to include a co-development/co-promote license and collaboration. Genzyme also hashave the right to elect a co-development/co-promote licenseopt into our other rare genetic disease programs for development and collaboration for ALN-AT3, if it does not elect a global license and collaboration for ALN-AS1. Development costs for co-development/co-promote products, once Genzyme exercises an option, will be shared between Genzyme and us, with Genzyme responsible for fifty percentcommercialization in territories outside of the global development costs. Genzyme will be required to make payments totaling up to $75.0 million in development milestones for each of revusiran and ALN-AT3, if selected. In December 2014, we earned a development milestone payment of $25.0 million based upon the initiation of the first global Phase 3 clinical trial for revusiran. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each co-development/co-promote product based on annual net sales, if any,Alnylam Territory as contemplated in the 2014 Sanofi Genzyme Territory for such co-development/co-promote product by Genzyme, its affiliates and sublicensees. The parties will share profits equally and we expect to book product sales in the Alnylam Territory.

Global license terms — Upon opt-in, Genzyme will obtain a worldwide license to develop and commercialize the product. Genzyme can elect a global license for ALN-AS1, if it does not elect a co-development/co-promote license for ALN-AT3. Genzyme will also havecollaboration, as well as one right to a global license through 2019,license.

The transaction is subject to limited extension, for a future Genetic Medicine program that was not onecustomary closing conditions and clearances, including clearance under the Hart-Scott-Rodino Antitrust Improvements Act.  We expect the transaction to close during the first quarter of our defined Genetic Medicine programs as of the effective date of2018.

For more information regarding the 2014 Sanofi Genzyme collaboration. Genzyme shall be responsible for one hundred percent of global development costs. Genzyme will be required to make payments totaling up to $200.0 million per global product, including up to $60.0 millioncollaboration, as amended in development milestones and $140.0 million in commercial milestones. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each global product based on annual net sales, if any, of each global product by Genzyme, its affiliates and sublicensees.

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Due toJanuary 2018, as well as the uncertainty of pharmaceutical developmentExclusive TTR License and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Genzyme under the 2014 Genzyme collaboration.

Under the master agreement, the parties will collaborate in the development of option products, with us leading development for all programs prior to Genzyme’s opt-in and also leading development and commercialization for all programs in the Alnylam Territory after Genzyme’s opt-in. If Genzyme does not exercise its option to license rights to a particular program, we will retain the exclusive right to develop and commercialize such program throughout the world,AT3 License Terms, including the rightongoing or expected financial and accounting impact on our business, please read Note 3, Significant Agreements, to sublicense to third parties.

The 2014 Genzyme collaboration is governed by an alliance joint steering committee that is comprised of an equal number of representatives from each party. There will also be additional committees to manage various aspects of each regional, co-developed/co-promotedour consolidated financial statements included in Part II, Item 8, “Financial Statements and global program. We and Genzyme intend to enter into supply agreements to provide for supply of collaboration products to Genzyme for clinical studies, and, at Genzyme’s request, commercial sales. Genzyme also has certain rights to manufacture collaboration products. Additionally, Genzyme has certain limited opt-out rights, as specified in the master agreement, upon which products revert fully back to us with no further obligations to Genzyme.

The master agreement (including the license terms appended thereto) contains certain termination provisions, including for material breach by the other party. Unless terminated earlier pursuant to its terms, the master agreement will terminate upon the last to expire of any of the option periods under the master agreement or the license terms appended thereto.

In consideration for the rights granted to Genzyme under the master agreement and pursuant to the terms of a stock purchase agreement dated January 11, 2014, upon the closing of the equity transaction in February 2014, we sold to Genzyme 8,766,338 shares of our common stock and Genzyme paid $700.0 million in aggregate cash consideration to us. As a condition to the closing of the equity transaction, Genzyme entered into an investor agreement with us. Under the investor agreement, until the earlier of the fifth anniversary of the expiration or earlier termination of the 2014 Genzyme collaboration and the date on which Genzyme and its affiliates cease to beneficially own at least 5% of our outstanding common stock, Genzyme and its affiliates are bound by certain “standstill” provisions. The standstill provisions include agreements not to acquire more than 30% of our outstanding common stock, call stockholder meetings, nominate directors other than those approved by our board of directors, subject to certain limited exceptions, or propose or support a proposal to acquire us. Further, Genzyme has agreed to vote, and cause its affiliates to vote, all shares of our voting securities they are entitled to vote, up to a maximum of 20% of our outstanding common stock, in a manner either as recommended by our board of directors or proportionally with the votes cast by our other stockholders, except with respect to certain change of control transactions or our liquidation or dissolution. Until Genzyme owns less than 7.5% of our outstanding common stock, subject to Genzyme’s limited right to maintain its ownership percentage as described below, if we issue common stock or securities convertible into or exercisable for common stock to a third party that holds at least 30% of our outstanding common stock or, in connection with a collaboration or license transaction, to a third party that will initially hold at least the percentage of our outstanding common stock represented by the shares purchased by Genzyme at the closing of the equity transaction, we will offer Genzyme an opportunity to amend the standstill and voting provisions in the investor agreement to be consistent with the terms provided to such third party.

Under the investor agreement, Genzyme has also agreed not to dispose of any shares of common stock beneficially owned by it immediately after the closing of the stock purchase until the earlier of (i) December 31, 2019 (subject to extension by up to two years if Genzyme’s option to select additional compounds under the master agreement is extended beyond December 31, 2019) and (ii) six months after the expiration or earlier valid termination of the collaboration, in each case subject to earlier termination in the event certain clinical activities under the collaboration fail to occur. Following the expirationSupplementary Data,” of this lock-up period, Genzyme will be permitted to sell such shares of common stock subject to certain limitations, including volume and manner of sale restrictions. Notwithstanding the foregoing, following the two-year anniversary of the closing of the stock purchase, in the event that the market price per share of our common stock is at least 100% higher than the

annual report on Form 10-K.

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market price per share of our common stock at closing of the stock purchase (in each case based upon a ten-day trailing average), Genzyme may sell up to 25% of its initial shares, subject to certain restrictions on post-lock-up period dispositions as described above.

Under the investor agreement, following the lock-up period, Genzyme will have three demand rights to require us to conduct a registered underwritten public offering with respect to the shares of common stock beneficially owned by Genzyme immediately after the closing of the stock purchase. In addition, following the lock-up period, subject to certain conditions, Genzyme will be entitled to participate in registered underwritten public offerings by us if other selling stockholders are included in the registration.

The investor agreement provides that, until Genzyme owns less than 7.5% of our outstanding common stock, subject to Genzyme’s limited right to maintain its ownership percentage as described herein, in connection with new issuances of common stock, subject to certain exceptions, Genzyme will be entitled to a right of first offer to participate proportionally to maintain its then-current ownership percentage of our common stock. If Genzyme is not entitled to a right of first offer with respect to a new issuance, Genzyme will have the opportunity, on a post-transaction basis, to purchase additional shares sufficient to maintain its pre-transaction ownership percentage of our common stock (subject to the same 7.5% ownership threshold).

In accordance with our investor agreement with Genzyme, as a result of our issuance of shares in connection with our acquisition of Sirna in March 2014, Genzyme exercised its right to purchase an additional 344,448 shares of our common stock for approximately $23.0 million. In addition, in January 2015, in connection with our public offering, Genzyme exercised its right to purchase directly from us, in concurrent private placements, 744,566 shares of common stock at the public offering price resulting in approximately $70.7 million in proceeds to us. The sales of common stock to Genzyme were not registered as part of the public offering, though they were consummated simultaneously with the public offering.

In addition, as part of these rights under the investor agreement, Genzyme has the right each January to purchase a number of shares of our common stock based on the number of shares we issued during the previous year for compensatory purposes. Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock on January 22, 2015 for approximately $18.3 million. The sale of these shares to Genzyme was consummated as a private placement.

In each instance, the purchase by Genzyme described above allowed Genzyme to maintain its ownership level of our common stock of approximately 12%.

Finally, in the event Genzyme and its affiliates acquire at least 20% or more of our outstanding common stock, Genzyme will be entitled to appoint one individual to our board of directors. Genzyme will also be entitled to certain information rights, including with respect to financial information in the event Genzyme or its affiliates require such information for its own financial reporting purposes. The rights and restrictions under the investor agreement are subject to termination upon the occurrence of certain events.

The Medicines Company.In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9 for the treatment of hypercholesterolemia and other human diseases.  MDCO paid us an upfront cash payment of $25.0 million. Upon the achievement of certain events, we will be entitled to receive milestone payments, up to an aggregate of $180.0 million, including up to $30.0 million in specified development milestones, $50.0 million in specified regulatory milestones and $100.0 million in specified commercialization milestones. In addition, we will be entitled to royalties ranging from the low- to high-teens, based on annual worldwide net sales, if any, of licensed products by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances. In December 2014, we earned a development milestone payment of $10.0 million based upon the initiation of our Phase 1 clinical trial for ALN-PCSsc. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from MDCO.

Under the MDCO agreement, we and MDCO will collaborate in the further development of ALN-PCSsc. We retainhad responsibility for the development of ALN-PCSscinclisiran until Phase 1 Completion, as defined in the MDCO

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agreement, at our cost, up to an agreed upon initial development cost cap.cost. In late 2015, MDCO will assume all otherassumed responsibility for theall development and commercialization of ALN-PCSsc,inclisiran, at its sole cost. The collaboration between uscost, and MDCO is governed byadvancing inclisiran in a joint steering committee comprised of an equal number of representatives from each party.

We are solely responsible for obtaining supply of finished product reasonably required for the conduct of our obligations under the initialcomprehensive Phase 3 development plan through Phase 1 Completion, and supplying MDCO with finished product reasonably required for the first Phase 2 clinical trial of ALN-PCSsc conducted by MDCO, at our expense, provided such costs do not exceed the development costs cap, subject to certain exceptions. After such time, MDCO will have the sole right and responsibility to manufacture and supply ALN-PCSsc for development and commercialization under the MDCO development plan, subject to the terms of the MDCO agreement. We and MDCO intend to enter into a supply and technical transfer agreement to provide for supply of ALN-PCSsc to MDCO within a specified time following the effective date of the MDCO agreement.

Unless terminated earlier in accordance with the terms of the agreement,program. For more information regarding the MDCO agreement, expiresincluding its ongoing financial and accounting impact on a licensed product-by-licensed productour business, please read Note 3, Significant Agreements, to our consolidated financial statements included in Part II, Item 8, “Financial Statements and country-by-country basis upon expirationSupplementary Data,” of the last royalty term for any licensed product in any country, where a royalty term is defined as the latest to occur of (1) the expiration of the last valid claim of patent rights covering a licensed product, (2) the expiration of the Regulatory Exclusivity, as defined in the MDCO agreement, and (3) the twelfth anniversary of the first commercial sale of the licensed product in such country. We estimate that our fundamental RNAi patents covering licensed products under the MDCO agreement will expire both in and outside of the United States generally between 2015 and 2028. We also estimate that our ALN-PCS product-specific patents covering licensed products under the MDCO agreement in the United States and elsewhere will expire at the end of 2033. These patent rights are subject to potential patent term extensions and/or supplemental protection certificates extending such terms in countries where such extensions may become available. In addition, more patent filings relating to the collaboration may be made in the future.this annual report on Form 10-K.

Either party may terminate the MDCO agreement in the event the other party fails to cure a material breach or upon patent-related challenges by the other party. In addition, MDCO has the right to terminate the agreement without cause at any time upon four months’ prior written notice.

During the term of the MDCO agreement, neither party will, alone or with an affiliate or third party, research, develop or commercialize, or grant a license to any third party to research, develop or commercialize, in any country, any product directed to the PCSK9 gene, other than a licensed product, without the prior written agreement of the other party, subject to the terms of the MDCO agreement.

Platform Alliances.

Monsanto Company.Monsanto.    In August 2012, we and Monsanto Company, or Monsanto, entered into a license and collaboration agreement, pursuant to which we granted to Monsanto a worldwide, exclusive, royalty bearing right and license, including the right to grant sublicenses, to our RNAi platform technology and intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. The Monsanto agreement also includesincluded the transfer of technology from us to Monsanto and initially included a collaborative research project. Under the Monsanto agreement, Monsanto will be our exclusive collaborator in the agriculture field for a ten-year period.

Monsanto paid us $29.2 million in upfront cash payments, and was also required to make near-term milestone payments to us upon the achievement of specified technology transfer and patent-related milestones. We were also entitled to receive additional funding for collaborative research efforts. In the aggregate, we had the ability to earn up to $5.0 million in milestone payments and research funding under the Monsanto alliance. We received a total of $4.0 million in milestone payments from Monsanto based upon the achievement of a specified patent-related event and the completion of technology transfer activities. In September 2014, we and Monsanto mutually determined not to pursue the discovery collaboration originally contemplated under the terms of the Monsanto agreement. Accordingly, Monsanto will not be required to pay us the final milestone of $1.0 million. There are no remaining milestones under the Monsanto agreement. Monsanto is required to pay to

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us a percentage of specified fees from certain sublicense agreements Monsanto may enter into that include access to our intellectual property, as well as low single-digit royalty payments on worldwide, net sales by Monsanto, its affiliates and sublicensees of certain licensed products, as defined in  For more information regarding the Monsanto agreement, if any. Dueincluding its ongoing financial and accounting impact on our business, please read Note 3, Significant Agreements, to the uncertaintyour consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of the application of RNAi technology in the field of agriculture, we may not receive any license fees or royalty payments from Monsanto.this annual report on Form 10-K.

The term of the Monsanto agreement generally ends upon the expiration of the last-to-expire patent licensed under the agreement. We estimate that our fundamental RNAi patents licensed under the Monsanto agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Monsanto may terminate the Monsanto agreement in its entirety upon 30-days’ prior written notice to us, provided, however, that Monsanto is required to continue to make royalty payments to us if any royalties were payable on net sales of a licensed product during the previous 24 months. The Monsanto agreement may also be terminated by either party in the event the other party fails to cure a material breach under the Monsanto agreement.

Under the terms of the Monsanto agreement, in the event that during the exclusivity period we cease to own or otherwise exclusively control certain licensed patent rights in the agriculture field, for any reason other than Monsanto’s breach of the Monsanto agreement or its negligence or willful misconduct, resulting in the loss of exclusivity with respect to Monsanto’s rights to such patent rights, and such loss of exclusivity has a material adverse effect on the licensed products, then we would be required to pay Monsanto up to $5.0 million as liquidated damages, and Monsanto’s royalty obligations to us under the Monsanto agreement would be reduced or, under certain circumstances, terminated. We have the right to cure any such loss of patent rights under the Monsanto agreement.

Takeda Pharmaceutical Company Limited.Takeda.    In May 2008, we entered into a license and collaboration agreement with Takeda Pharmaceutical Company Limited, or Takeda, to pursue the development and commercialization of RNAi therapeutics. Under the Takeda agreement, we granted to Takeda a non-exclusive, worldwide, royalty-bearing license to our intellectual property, including delivery-related intellectual property, controlled by us as of the date of the Takeda agreement or during the five years thereafter, to develop, manufacture, use and commercialize RNAi therapeutics, subject to our existing contractual obligations to third parties. The license initially is limited to the fields of oncology and metabolic disease and may be expanded at Takeda’s option to include other therapeutic areas, subject to specified conditions.

Takeda paid us an upfront payment of $100.0 million and an additional $50.0 million upon achievement of specified technology transfer milestones. In addition, for each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, we are entitled to receive specified development, regulatory and commercialization milestone payments, totaling up to $171.0 million per product, together with a double-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments per product include up to $26.0 million for the achievement of specified development milestones, up to $40.0 million for the achievement of specified regulatory milestones and up to $105.0 million for the achievement of specified commercialization milestones. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Takeda.

The collaboration is governed by a joint technology transfer committee, a joint research collaboration committee and a joint delivery collaboration committee, each of which is comprised of an equal number of representatives from each party. The term of  For more information regarding the Takeda agreement, generally ends upon the later of (i) the expiration ofincluding its ongoing financial and accounting impact on our last-to-expire patent covering a licensed product and (ii) the last-to-expire term of a profit sharing agreement in the event we elect to enter into such an agreement. We estimate that our fundamental RNAi patents covered under the Takeda agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. The Takeda agreement may be terminated by either party in the event the other party fails to cure a material breach under the agreement. In addition, Takeda may terminate the agreement on a licensed product-by-licensed product or country-by-country basis upon 180-days’ prior written notice to us, provided, however, that Takeda is required to continue to make royalty payments to us for the duration of the royalty term with respect to a licensed product.

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Roche/Arrowhead.    In July 2007, we and, for limited purposes, Alnylam Europe AG, or Alnylam Europe, entered into a license and collaboration agreement with Roche. Under the license and collaboration agreement, which became effective in August 2007, we granted Roche a non-exclusive licensebusiness, please read Note 3, Significant Agreements, to our intellectual property, including delivery-related intellectual property existing asconsolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of the date of the license and collaboration agreement, to develop and commercialize therapeutic products that function through RNAi, subject to our existing contractual obligations to third parties. In October 2011, Arrowhead acquired certain RNA therapeutics assets from Roche, including our license and collaboration agreement, and now owns all of the rights and obligations of Roche under the license and collaboration agreement. The license is initially limited to four therapeutic areas.this annual report on Form 10-K.

Roche paid us $273.5 million in upfront cash payments. In addition, for each RNAi therapeutic product developed by Arrowhead, its affiliates or sublicensees under the collaboration agreement, we are entitled to receive milestone payments upon achievement of specified development, regulatory and commercialization events, totaling up to an aggregate of $100.0 million per therapeutic target, together with a single-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments for each therapeutic target include up to $17.5 million for the achievement of specified development milestones, up to $62.5 million for the achievement of specified regulatory milestones and up to $20.0 million for the achievement of specified commercialization milestones. During 2014, we received a $1.0 million milestone payment from Arrowhead upon the achievement of a specified pre-clinical event for a licensed product. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Arrowhead.

The term of the license and collaboration agreement generally ends upon the later of ten years from the first commercial sale of a licensed product and the expiration of the last-to-expire patent covering a licensed product. We estimate that our fundamental RNAi patents covered under the license and collaboration agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Arrowhead may terminate the license and collaboration agreement, on a licensed product-by-licensed product, licensed patent-by-licensed patent, and country-by-country basis, upon 180-days’ prior written notice to us, but is required to continue to make milestone and royalty payments to us if any royalties were payable on net sales of a terminated licensed product during the previous 12 months. The license and collaboration agreement may also be terminated by either party in the event the other party fails to cure a material breach under the license and collaboration agreement.

Other Strategic License Agreements.

Ionis Pharmaceuticals, Inc. (formerly Isis Pharmaceuticals, Inc.).Isis.    In January 2015, we and IsisIonis Pharmaceuticals, Inc., or Ionis, entered into a second amended and restated strategic collaboration and license agreement.agreement, which we further amended in July 2015. The 2015 IsisIonis agreement provides for certain new exclusive target cross-licenses of intellectual property on foureight disease targets, providing each company with exclusive RNA therapeutic license rights for twofour programs, and extends the parties’ existing non-exclusive technology cross-license, which was originally entered into in 2004 and was amended and restated in 2009, through April 2019.

Pursuant to the 2015 Isis agreement, Isis granted to us an exclusive, low single-digit royalty-bearing license to its chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: antithrombin and aminolevulinic acid synthase-1. In exchange, we granted to Isis an exclusive, low single-digit royalty-bearing license to our chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: Factor XI and apolipoprotein (a).

In addition, under the 2015 Isis agreement, the parties agreed to extend the existing non-exclusive technology cross-license through April 2019. Specifically, Isis granted us a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for double-stranded RNAi therapeutics. In turn, we granted Isis a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for single-stranded antisense therapeutics. This broad, non-exclusive cross-license includes chemistry, motif and mechanism patents, but excludes patent claims on formulations, manufacturing and specific targets.

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Under the original 2004 agreement, IsisIonis licensed to us its patent estate related to antisense motifs and mechanisms and oligonucleotide chemistry for double-stranded RNAi products in exchange for a previously disclosed technology access fee, participation in fees for our partnering programs and future milestone and royalty payments from us for programs that incorporate Isis’ intellectual property. We have the right to use Isis’ intellectual property in our development programs or in collaborations and Isis agreed not to grant licenses under these patents to any other organization for the discovery, development and commercialization of double-stranded RNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which Isis plays an active role.

products.  In turn, under the original 2004 agreement, we non-exclusively licensed to IsisIonis our patent estate relating to antisense motifs and mechanisms and oligonucleotide chemistry to research, develop and commercialize single-stranded antisense therapeutics, single stranded RNAi therapeutics and to research double-stranded RNAi compounds. IsisIonis also received a license to develop and commercialize double-stranded RNAi drugs targeting a limited number of therapeutic targets on a non-exclusive basis. We granted these licenses for RNAi therapeutics in exchange for option fees, and future milestone and royalty payments from Isis for RNAi programs that incorporate certain of our intellectual property.

In August 2012, we and Isis amended the agreement to provide certain terms for the discovery, development and commercialization of double-stranded RNA products by us or our sublicensees in the field of agriculture.

As set forth inFor more information regarding the 2015 IsisIonis agreement, under the original 2004 agreement, we agreedincluding its ongoing financial and accounting impact on our business, please read Note 3, Significant Agreements, to pay Isis milestone payments, totaling up to approximately $3.4 million, upon the occurrenceour consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of specified development and regulatory events, and low single-digit royaltiesthis annual report on sales, if any, for each product that we or a collaborator develop using Isis intellectual property. In addition, we agreed to pay to Isis a percentage of specified fees from strategic collaborations we may enter into that include access to Isis’ intellectual property.

Isis has the right to elect up to ten non-exclusive target licenses under the agreement and has the right to purchase one additional non-exclusive target per year during the term of the collaboration. Isis agreed to pay us, per therapeutic target, a license fee of $0.5 million, milestone payments for double-stranded RNAi products totaling approximately $3.4 million, payable upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each double-stranded RNAi or single-stranded RNAi product developed by Isis or a collaborator that utilizes our intellectual property. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any milestone or royalty payments from Isis.

The term of 2015 Isis agreement generally ends upon the expiration of the last-to-expire patent licensed thereunder, whether such patent is a patent licensed by us to Isis, or vice versa. Either party may terminate the 2015 Isis agreement on 90 days’ prior written notice if the other party materially breaches the agreement and fails to cure the breach within the 90-day notice period and no substantial steps have otherwise been taken to cure the breach, provided, however, that neither party may terminate licenses granted to the other party to the extent necessary to develop or sell products that have at least reached investigational new drug-enabling studies (except for a party’s uncured failure of its payment obligations). Either party may also terminate the agreement in the event the other party undergoes specified bankruptcy events.

Novartis.    In the second half of 2005, we entered into a series of transactions with Novartis, which included a stock purchase agreement, an investor rights agreement and a research collaboration and license agreement. In October 2010, the research program under the collaboration and license agreement was substantially completed in accordance with the terms of such agreement, subject to certain surviving rights and obligations of the parties. Novartis made an upfront payment of $10.0 million to us in October 2005, partly to reimburse prior costs incurred by us to developin vivoRNAi technology. We also received research funding and development milestone payments from Novartis.Form 10-K.


In September 2010, Novartis exercised its right under the collaboration and license agreement to select 31 designated gene targets, for which Novartis has exclusive rights to discover, develop and commercialize RNAi therapeutic products using our intellectual property and technology, including delivery-related intellectual

20


property and related technology. Novartis’ right of first offer with respect to an exclusive license for additional targets has terminated. Under the terms of the collaboration and license agreement, for any RNAi therapeutic products Novartis develops against its selected targets, we are entitled to receive milestone payments upon achievement of certain specified development and annual net sales events, up to an aggregate of $75.0 million per therapeutic product, as well as royalties on annual net sales of any such product. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Novartis.

During 2014, Novartis publically indicated that they no longer intend to invest in the development of certain RNAi therapeutics and intend to divest certain of their RNAi assets. Novartis has the right to assign our collaboration and license agreement to athird-party that acquires substantially all of its assets relating to RNAi.

Intellectual Property Licenses

In December 2002, we entered into a co-exclusive license with Max Planck Innovation GmbH (formerly known as Garching Innovation GmbH), or Max Planck Innovation, for the worldwide rights to use and sublicense certain patented technology to develop and commercialize therapeutic products and related applications. We also obtained the rights to use, without the right to sublicense, the technology for all diagnostic uses other than for the purposes of therapeutic monitoring. We were also given the right to acquire the remaining 50%50 percent exclusive rights, which right we exercised upon our acquisition of Ribopharma AG in July 2003. In June 2005, we entered into an amendment to our agreement with Max Planck Innovation that secured our exclusivity to use and sublicense certain patented technology to develop and commercialize therapeutic products and related applications.

We are not obligated to pay any development or sales milestone payments to Max Planck Innovation, however, we will be required to pay Max Planck Innovation future single-digit royalties on net sales of all therapeutic and prophylactic products developed with the technology, if any.

Our agreements with Max Planck Innovation generally remain in effect until the expiration of the last-to-expire patent licensed thereunder. We estimate that the principal issued patents covered under the Max Planck Innovation agreements will expire both in and outside the United States during 2021, subject to any potential patent term extensions, restoration and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. We may terminate the agreements without cause with six months’ prior notice to Max Planck Innovation, and Max Planck Innovation may terminate the agreements in the event that we materially breach our obligations thereunder. Max Planck Innovation also has the right to terminate the agreements in the event that we, independently or through a third party, attack the validity of any of the licensed patents.

Delivery-Related License Agreements

Arbutus.Tekmira.    In November 2012, we, TPCArbutus Biopharma Corporation, or ABC (formerly Tekmira Pharmaceuticals Corporation), and Protiva Biotherapeutics, Inc., or Protiva, a wholly owned subsidiary of ABC, and together with ABC, referred to as Arbutus, agreed to restructure our existing contractual relationship. In connection with this restructuring, the parties entered into a cross-license agreement and agreed to terminate certainthat superseded the prior agreements, including: the May 2008 amended and restated license and collaboration between us and TPC, the May 2008 amended and restated cross-license agreement between us and Protiva, and the January 2009 manufacturing agreement between us and TPC.agreements among us.

Under the 2012 cross-license agreement, the parties consolidated certain intellectual property related to LNP technology for the systemic delivery of RNAi therapeutics. Specifically, certain patents and patent applications, including the MC3 lipid family used with patisiran, were assigned by us to TPC.ABC. We retain rights to use this intellectual property for the research, development and commercialization of RNAi therapeutic products, including the rights to sublicense this intellectual property on a product-by-product basis. TekmiraArbutus has also granted us a worldwide license to its LNP technology for the research, development and commercialization of LNP-based RNAi therapeutics, which license shall be exclusive for up to eight targets designated by us, and otherwise shall be non-exclusive. We have the right to sublicense on a product-by-product basis.

In addition, we elected to buy out our manufacturing obligations to TPCABC with respect to our LNP-based pipeline programs. Pursuant to the terms of the 2012 cross-license agreement, weWe made a one-time payment of

21


$30.0 $30.0 million to TPCABC for the termination of, and our release from, all of our obligations under the manufacturing agreement, including without limitation the obligations to obtain materials and/or services from TPC.agreement. We also have the right to manufacture and have manufactured our LNP-based RNAi therapeutics, which right may be sublicensed to our collaborators.

Further, as part of this restructuring, we elected to buy-down certain future potential milestone and royalty payments due to Tekmira for certain of our RNAi therapeutics, formulated using LNP technology. Specifically, pursuant to the 2012 cross-license agreement, we made a one-time payment of $35.0 million to TPC,ABC, which amount constitutedincluded a license termination payment, for the termination of the 2008 license agreements with TPC and Protiva and the parties’ rights and obligations thereunder, as well as the buy-down of certain milestone payments and the significant reduction of royalty rates for ALN-VSP, ALN-PCS02 and patisiran. As a result of this buy-down, future royalty rates for thesecertain LNP-based products, are now further reduced from the low single-digit royalties due on other products, as described below.including patisiran. In addition, we agreed to pay TPCABC an aggregate of $10.0 million in contingent milestone payments related to advancement of ALN-VSP and patisiran, which representrepresenting the only potential milestones due to Tekmiraremaining milestone obligations for ALN-VSP, ALN-PCS02 and patisiran.these products. In December 2013, we paid to TPCABC $5.0 million in connection with the initiation of our APOLLO Phase 3 clinical trial for patisiran, fulfilling one of these milestone obligations. With respect to the second $5.0 million milestone, in August 2013, we initiated binding arbitration proceedings to resolve a disagreement with TPCABC regarding the achievement by TPCABC of this milestone under our cross-license agreement relating to the manufacture of ALN-VSP clinical trial material for use in China. We currently expect that the Tekmira arbitration hearing will be heldprevailed in the second quarter of 2015.

Consistent with the prior license agreements, under the 2012 cross-license agreement, we are obligatedarbitration proceedings in March 2016 and were not required to pay TPC up to an aggregate of $16.0 million inthe second milestone payments for any future RNAi therapeutic formulated using Tekmira LNP technology, excluding ALN-VSP, ALN-PCS02 and patisiran, together with low single-digit royalty payments on annual product sales, if any.at that time.

Under the 2012 cross-license Agreement, Tekmira maintains the threeagreement, Arbutus has one exclusive and five non-exclusive licenses previously granted by us under the prior license agreements to research, develop and commercialize RNAi therapeutics directed to up to eightsix gene targets.  In addition, we granted Tekmira a non-exclusive license forAs of November 12, 2017, Arbutus’ right to select up to two additional geneexclusive targets on the same terms and conditions as the prior non-exclusive licenses. Tekmira also acquired from Acuitas its existing options for threeup to five additional non-exclusive licenses, which were included under the 2012 cross-license agreement. Tekmiratargets expired. Arbutus may sublicense theseits rights on a product-by-product basis. We waived our right under the prior license agreements to opt-in to the Tekmira research program directed to polo-like kinase 1, or PLK1. Under the 2012 cross-license agreement, we are eligible to receive from TekmiraArbutus up to an aggregate of $8.5 million in milestone payments for RNAi therapeutics directed to nineeach of four of the targets for which we have granted licenses to Tekmira,Arbutus, together with single-digit royalties on annual product sales, if any, of RNAi therapeutic products directed to all thirteensix of the targets for which we have granted licenses to Tekmira.Arbutus. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Tekmira.Arbutus.


The term of the 2012 cross-license agreement generally ends upon the expiration of the last-to-expire royalty term. Royalties are payable on a product-by-product and country-by-country basis commencing on the first commercial sale of a product in a country and continuing during any period in which (a) in the case of us, a valid claim within the TekmiraArbutus Royalty-Bearing Patents (as defined in the 2012 cross-license agreement) covers our applicable product in such country of sale, or (b) in the case of TekmiraArbutus products, a valid claim within our patents covers the applicable TekmiraArbutus product in such country of sale. We estimate that our fundamental RNAi patents covered under the 2012 cross-license agreement will expire both in and outside the United States generally between 2019 and 2021, and that the TekmiraArbutus LNP patents covered under the 2012 cross-license agreement will expire both in and outside the United States generally between 2020 and 2030, subject in each case to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Either party may terminate a license it granted to the other in the event that the other party fails to cure a material breach of its obligations relating to that license. Furthermore, either party may terminate the 2012 cross-license agreement in the event the other

22


party fails to cure a material breach of an obligation under the agreement. In addition, either party may terminate the 2012 cross-license agreement upon patent-related challenges by the other party.

UBC and Acuitas.In July 2009, we entered into a research agreement with The University of British Columbia, or UBC, and Acuitas Therapeutics Inc., or Acuitas (formerly AlCana Technologies, Inc.), that was focused on the discovery of novel lipids, such as the MC3 lipid, which is employed in patisiran. Pursuant to the terms of the research agreement, we funded collaborative research through July 2012, which was conducted by our scientists, together with scientists at UBC and Acuitas. Under the research agreement, UBC and Acuitas are eligible to receive up to an aggregate of $1.3 million in milestone payments from us for each licensed product (as defined in the research agreement) directed to a particular target (as defined in the research agreement), together with single-digit royalty payments on annual product sales, if any.

Concurrent with the execution of the research agreement, we also entered into a supplemental agreement with TPC,ABC, Protiva, UBC and Acuitas, which contains additional terms regarding the intellectual property rights arising out of the research agreement. In connection with 2012 cross-license agreement with TekmiraArbutus described above, we and TekmiraArbutus agreed to supersede the rights and obligations under the supplemental agreement as between ourselves, with the rights and obligations set forth in the 2012 cross-license agreement.

microRNA Therapeutics

Regulus.    In September 2007, we and Isis established Regulus, a company focused on the discovery, development and commercialization of microRNA therapeutics. Regulus leverages our and Isis’ technologies, know-how and intellectual property relating to microRNA therapeutics.

Regulus, which initially was established as a limited liability company, converted to a C corporation as of January 2, 2009 and changed its name to Regulus Therapeutics Inc. In consideration for our and Isis’ initial interests in Regulus, we and Isis each granted Regulus exclusive licenses to our intellectual property for certain microRNA therapeutics as well as certain patents in the microRNA field. Regulus operates as an independent company with a separate board of directors, scientific advisory board and management team. In October 2012, Regulus completed an underwritten initial public offering. Currently, we own approximately 12% of Regulus’ outstanding common stock.

Regulus is exploring therapeutic opportunities that arise from microRNA dysregulation. Since microRNAs are believed to regulate broad networks of genes and biological pathways, microRNA therapeutics define a new and potentially high-impact strategy to target multiple nodes on disease pathways. microRNAs are small non-coding RNAs that regulate the expression of other genes. More than 500 microRNAs have been identified to date in humans, each of which is believed to interact with a specific set of genes that control key aspects of cell biology. Since microRNAs may act as master regulators of the genome and are often found to be dysregulated in disease, microRNAs potentially represent an exciting new platform for drug discovery and development. Regulus is advancing microRNA therapeutics in several areas including oncology, fibrosis, hepatitis C virus and metabolic diseases.

Regulus has entered into a number of strategic alliances with leading pharmaceutical companies, including Sanofi, Biogen Idec and AstraZeneca PLC. Each of Alnylam and Isis is entitled to receive specified sublicense income in connection with certain collaborative agreements entered into by Regulus, as well as royalties on net sales, if any, of certain products developed by Regulus or its collaborators, in each case subject to the terms and conditions of the license and collaboration agreement among Regulus, Isis and Alnylam.

Patents and Proprietary Rights

We have devoted considerable effort and resources to establish what we believe to be a strong intellectual property position relevant to RNAi therapeutic products and delivery technologies. In this regard, we have amassed a portfolio of patents, patent applications and other intellectual property covering:

fundamental aspects of the structure and uses of siRNAs, including their use as therapeutics, and RNAi-related mechanisms;

chemical modifications to siRNAs that improve their suitability for therapeutic and other uses;

23


siRNAs directed to specific targets as treatments for particular diseases;

delivery technologies, such as in the fields of carbohydrate conjugates and cationic liposomes; and

all aspects of our specific development candidates.

We believe that no other company possesses a portfolio of such broad and exclusive rights to the patents and patent applications required for the commercialization of RNAi therapeutics. Our intellectual property estate for RNAi therapeutics includes over 2,0003,800 active cases and over 1,1001,700 granted or issued patents, of which over 400600 are issued or granted in the United States, the EU, including by the European Patent Office, or EPO, and Japan. Given the importance of our intellectual property portfolio to our business operations, we intend to vigorously enforce our rights and defend against challenges that have arisen or may arise in this area.

Intellectual Property Related to Fundamental Aspects and Uses of siRNA and RNAi-related Mechanisms

In this category, we include United States and certain foreign patents and patent applications that claim key aspects of siRNA architecture and RNAi-related mechanisms. Specifically included are patents and patent applications covering targeted cleavage of mRNA directed by RNA-like oligonucleotides and double-stranded RNAs of particular lengths and particular structural features, such as blunt and/or overhanging ends, as well as various types and patterns of chemical modifications. Our strategy has been to secure exclusive rights where possible and appropriate to key patents and patent applications that we believe cover fundamental aspects of RNAi.


The following table lists patents and/or patent applications to which we have secured rights that we regard as being fundamental for the use of siRNAs as therapeutics.

 

Patent

Licensor/Owner

Subject Matter

First

Priority Date

Inventors

Status

Expiration Date*

Alnylam Rights

Patent

Licensor/Owner

Subject Matter

First

Priority Date

Inventors

Status

Expiration Date*

Alnylam Rights

Isis

Inactivation

Carnegie

Institution of target mRNA

Washington

6/6/1996 (EP) and 6/6/1997 (U.S.)

Double-stranded RNAs to induce RNAi

S. Crooke

12/23/1997

A. Fire,

C. Mello

U.S. 5,898,031,6,506,559, U.S. 6,107,094,

7,560,438, U.S. 7,432,2507,538,095, U.S. 7,622,633, U.S. 8,580,754, U.S. 8,283,329 & U.S. 7,695,902

EP 09282909,102,939

 

Additional applications pending in the U.S. and several foreign jurisdictions

6/6/2016

 

12/18/2018

 

6/6/2017

Exclusive 

Non-exclusive
rights
for
therapeutic

purposes related
to siRNAs**

Carnegie

Institution of Washington

Double-stranded RNAs to induce RNAi12/23/1997

A. Fire,

C. Mello

U.S. 6,506,559, U.S. 7,560,438 &

U.S. 7,538,095

 

Additional applications pending in the U.S. and several foreign jurisdictions

12/18/2018

Non-exclusive
rights for
therapeutic
purposes

Medical

College of

Georgia Research

Institute, Inc.

Methods for inhibiting gene expression using double-stranded RNA

1/28/1999

Y. Li,

M. Farrell, M. Kirby

U.S. 7,888,325 & U.S. 8,148,345

AU 776150 (Australia)

 

Additional applications pending in the U.S., Europe and Canada

1/28/2020

Exclusive rights

Alnylam

Small double-stranded RNAs as therapeutic products

1/30/1999

R. Kreutzer, S. Limmer

U.S. 7,763,590, U.S. 7,829,697 & U.S. 7,994,309

EP 1798285, EP 2363479, EP 1144623, EP 1214945 (revoked/under appeal), EP 1550719 (revoked/under appeal), CA 2359180 (Canada), AU 778474 (Australia), ZA 2001/5909 (South Africa), DE 20023125 U1, DE 10066235 & DE 10080167 (Germany)

 

Additional applications pending in the U.S. and several foreign jurisdictions

1/29/2020

Owned

Alnylam

Medicament for inhibiting the expression of a target gene and medicament for treating a tumor disease

1/9/2001

R. Kreutzer,

S. Limmer,

H-P.Vornlocher,

P. Hadwiger,

A. Geick,

M. Ocker,

C. Herold,

D. Schuppan

U.S. 7,868,160 & U.S. 8,143,390

EP 1799270 & EP 1349927 (opposed and maintained in amended form)

1/9/2022

Owned

24


Patent

Licensor/Owner

Subject Matter

First

Priority Date

Inventors

Status

Expiration Date*

Alnylam Rights

Alnylam

Method for inhibiting the expression of a wide variety of oncology target genes with double-stranded RNA between 15-49 nucleotides

1/9/2001

R. Kreutzer,

S. Limmer,

P. Hadwiger

U.S. 8,273,870, U.S. 8,546,143 & U.S. 9,074,213

EP 1352061 (opposed, maintained with no further right to appeal)

1/9/2022

Owned

Alnylam

Alnylam

Composition and methods for inhibiting a target nucleic acid with double-stranded RNA of between 20-49 base pairs wherein at least one end is blunt

1/9/2001

R. Kreutzer,

St. Limmer,

Sy. Limmer,

P. Hadwiger

U.S. 9,587,240

1/9/2022

Owned

Alnylam

Composition and methods for inhibiting a target nucleic acid with double-stranded RNA

4/21/1999

C. Pachuk, C. Satishchandran

EP 1171586, AU 781598 (Australia)

 

Additional applications pending in the U.S. and several foreign jurisdictions

4/19/2020

Owned


Patent

Licensor/Owner

Subject Matter

First

Priority Date

Inventors

Status

Expiration Date*

Alnylam Rights

Cancer Research

Technology Limited

RNAi uses in mammalian oocytes, preimplantation embryos and somatic cells (EP only: wherein the RNAi compound is at least 25 base pairs)

11/19/1999

M. Zernicka- Goetz,

F. Wianny,

M.J. Evans, D.M. Glover

EP 1230375 (revoked/under appeal)successfully appealed and granted in amended form), SG 89569 (Singapore), AU 774285 (Australia)

 

Additional applications pending in the U.S. and several foreign jurisdictions

11/17/2020

Exclusive rights

for therapeutic

purposes

Massachusetts Institute of Technology,

Whitehead Institute for Biomedical Research, Max Planck

Gesellschaft,

University of Massachusetts ***

Mediation of RNAi by small RNAs 21-23 base pairs long with claims directed to compositions, methods of use and manufacture

3/30/2000

D.P. Bartel, P.A. Sharp, T. Tuschl, P.D. Zamore

U.S. 8,790,922, U.S. 8,742,092, U.S. 8,632,997, U.S. 8,552,171, U.S. 8,420,391,

U.S. 8,394,628, U.S. 8,957,157, U.S. 9,012,138, U.S. 9,012,621 & U.S. 8,394,6289,193,753

 

EP 1309726 (opposed and maintained in amended form/under appeal), EP 2028278 (opposed), EP 2345742, EP 2360253 (opposed) & EP 2361981 (opposed),

AU 2001249622 

(Australia), NZ 522045 (New Zealand), KR 08724437 & KR 10-0909681 (Korea)

 

Additional applications pending in the U.S. and several foreign jurisdictions

3/30/2021

Exclusive rights

for therapeutic

purposes***

Massachusetts Institute of Technology, Whitehead Institute, University of Massachusetts,

Max Planck

Gesellschaft (U.S.)****

 

Max Planck

Gesellschaft (ex-U.S.),

European Molecular Biology Laboratory (ex-U.S.)*****

Synthetic and chemically modified siRNAs as therapeutic products including patents with claims including those directed to double-stranded RNA of between 19 to 23 or 19 to 25 nucleotides, with and without a 3’ overhang; claims directed to double-stranded RNA of between 19 to 52 nucleotides with a 3’ overhang; claims directed to double-stranded RNA of 14 to 24 base pairs or up to 25 base pairs with at least one nucleotide analogue, along with methods of using and making such double-stranded RNA

12/1/2000 (EP),
4/24/2004 and
4/27/2004

T. Tuschl, S. Elbashir, W. Lendeckel,

M. Wilm#,

R. Lührmann#

 

#EMBL inventors

U.S. 7,056,704, U.S. 7,078,196, U.S. 8,329,463, U.S. 8,372,968, U.S. 8,362,231, U.S. 8,445,237, U.S. 8,765,930, U.S. 8,778,902, U.S. 8,796,016, U.S. 8,853,384, U.S. 8,895,721, U.S. 8,933,044, U.S. 8,895,718,  U.S. 8,993,745 & U.S. 8,445,237, U.S.8,765,930, U.S. 8,778,902,

U.S. 8,796,016, U.S.8,853,384, U.S. U.S.8,895,721 & U.S. 8,933,0449,567,582

 

EP 1407044 (opposed and maintained in amended form/under appeal), EP 1873259, EP 2348133, EP 2348134, & EP 2351852 (opposed), & EP 2813582 AU 2002235744 (Australia), ZA 2003/3929 (South Africa), SG 96891 (Singapore), NZ 52588 (New Zealand), JP 4 095 895 (Japan) (opposed and maintained), JP 4 494 392 (Japan), RU 2322500 (Russia), CN 1568373 (China)

 

Additional applications pending in the U.S. and several foreign jurisdictions

11/29/2021

Exclusive rights

for therapeutic

purposes****

25


Patent

Licensor/Owner


Patent

Licensor/Owner

Subject Matter

First

Priority Date

Inventors

Status

Expiration Date*

Alnylam Rights

Alnylam

Alnylam

Methods for inhibiting a target nucleic acid via the introduction of a vector encoding a double-stranded RNA

1/31/2001

T. Giordano, C. Pachuk, C. Satishchandran

U.S. 9,051,566

AU 785395 (Australia)

 

Additional applications pending in the U.S., Australia and Canada

1/31/2021

Owned

Stanford University

RNAi usesin vivoin mammalian liver

7/23/2001

M.A. Kay, A.P. McCaffrey

U.S. 9,018,179

EP 1409506, AU 2002326410 (Australia)

 

Additional applications pending in the U.S. and several foreign jurisdictions

7/23/2021

Exclusive
rights
for
therapeutic

purposes

Alnylam

Alnylam

Claims directed to carbohydrate conjugates linked to siRNA

4/17/2003

M. Manoharan

U.S. 7,723,509, U.S. 7,745,608, U.S. 7,851,615, U.S. 8,017,762, U.S. 8,507,661, U.S. 8,344,125, U.S. 8,796,436, U.S. 8,865,677 & U.S. 8,426,377

Additional applications pending in the U.S. and several foreign jurisdictions

9/21/2024

Owned

Alnylam

Claims directed to GalNAc-conjugated siRNA

12/13/4/2007

M. Manoharan

U.S. 8,106,022, U.S. 8,450,467, U.S. 8,828,956 & U.S. 8,828,9569,370,581

Additional applications pending in the U.S. and several foreign jurisdictions

2029

12/4/2028

Owned

Sirna******

Claims directed to highly chemically modified oligonucleotides with granted claims directed to double-stranded RNA of between 18 and 24 nucleotides with various combinations of chemical modifications

2/20/2002

J. McSwiggen

U.S. 7,923,547, U.S. 7,956,176, U.S. 7,989,612, U.S. 8, 232,383,8,232,383, U.S. 8,268,986, U.S. 8,236,944, U.S.8,272,979, U.S.8,273,866,U.S. 8,272,979, U.S. 8,273,866, U.S. 8,242,257, U.S. 8,618,277, U.S. 8,846,894, U.S. 8,648,185, U.S. 9,181,551, U.S. 9,732,344 & U.S. 8,648,1859,771,588

 

EP 1423406 (opposed and maintained), EP 2287306 (opposed)(opposed and maintained in amended form), EP2278004EP 2278004 (opposed, opposition withdrawn), EP1627061, EP1458741EP 1627061, EP 1458741 (opposed, opposition withdrawn) & EP 1931781,

AU 2003216324, AU 2006203725, CA 2526831 (Canada), JP 49481631 (Japan)

Additional cases pending in the US and EPEurope

2/20/2023-

2028

Owned

 

*

For applications filed after June 7, 1995, the patent term generally is 20 years from the earliest application filing date. However, under the Drug Price Competition and Patent Term Extension Act of 1984, known as the Hatch-Waxman Act, we may be able to apply for patent term extensions for our U.S. patents. We cannot predict whether or not any patent term extensions will be granted or the length of any patent term extension that might be granted.


**

We hold co-exclusive therapeutic rights with Isis. However, Isis has agreed not to license such rights to any third party, except in the context of a collaboration in which Isis plays an active role.

***

We hold exclusive rights to the interest owned by three co-owners. The University of Massachusetts, or UMass, licensed its interest separately to Sirna Therapeutics, Inc., or Sirna. In March 2014, we acquired Sirna from Merck Sharp & Dohme Corp, or Merck, thus we now hold exclusive rights.

****

We hold exclusive rights to the interest owned by all co-owners in the U.S. UMass had a right to sublicense the U.S. Tuschl II patent family to Merck but such right has been disclaimed by UMass.

*****

European Molecular Biology Laboratory, or EMBL, has a limited ownership interest in certain ex-US cases in this family with no rights to control or otherwise affect patent prosecution.

******

Sirna is our wholly-owned subsidiary.

We believe that we have a strong portfolio of broad rights to fundamental RNAi patents and patent applications. Many of these rights are exclusive, which we believe prevents potential competitors from commercializing products in the field of RNAi without taking a license from us. In securing these rights, we have focused on obtaining the strongest rights for those intellectual property assets we believe will be most important in providing competitive advantage with respect to RNAi therapeutic products.

We believe that the Crooke patent series, issued in several countries around the world, covers the use of modified oligonucleotides to achieve enzyme-mediated cleavage of a target mRNA. We have obtained rights to the Crooke patents for use with double-stranded RNA products, through a license agreement with Isis.Ionis. Under the terms of our agreement, IsisIonis agreed not to grant licenses under these patents to any other organization for double-stranded RNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which IsisIonis plays an active role. Our agreement with IsisIonis was amended and restated in January 2015 to, among other things, extend the license for an additional five years, through April 2019.

26


Through our acquisition of Ribopharma AG, now known as Alnylam Europe AG, we own the entire Kreutzer-Limmer patent portfolio, which includes pending applications in the United States and many countries worldwide.

The Glover patent series has resulted in several patent grants, including in Europe (EP 1230375). We have an exclusive license to the Glover patent for therapeutic uses from Cancer Research Technology Limited, or CRT.

The Tuschl patent applications filedowned by Whitehead Institute for Biomedical Research, or Whitehead, the Massachusetts Institute of Technology, or MIT, UMass and Max Planck Gesellschaft zur Foerderung der Wissenschaften e.V. on the invention by Dr. Tuschl and his colleagues, which we call the Tuschl I patent series, cover compositions and methods important for RNAi discovery. We are the exclusive licensee of the ownership interests of the Max Planck Gesellschaft zur Foerderung der Wissenschaften e.V., MIT and Whitehead in the Tuschl I patent series for RNAi therapeutics. The Tuschl patent applications filedowned by Max Planck Gesellschaft zur Foerderung der Wissenschaften e.V., Whitehead, MIT and UMass on the invention by Dr. Tuschl and his colleagues, which we call the Tuschl II patent series, cover what we believe are key structural features of siRNAs. Specifically, the Tuschl II patents and patent applications include claims directed to synthetic siRNAs and the use of chemical modifications to stabilize siRNAs. We have obtained an exclusive license to claims in the Tuschl II patent series uniquely covering the use of RNAi for therapeutic purposes. Collectively, the Tuschl I and II patent families cover a wide range of double-stranded RNA molecules between 19-52 nucleotides in length, including those unmodified and those comprising chemical modifications. Examples of those chemical modifications encompassed by the Tuschl claims include those modifications made in the ribose ring, e.g., at the 2’ position such as 2’-OMe, 2’-F or modifications such as those found in locked and unlocked (acyclic) nucleotides.

The Fire and Mello patent owned by the Carnegie Institution of Washington covers the use of double-stranded RNAs to induce RNAi. The Carnegie Institution has made this patent broadly available for licensing and we, like many companies, have taken a non-exclusive license to the patent for therapeutic purposes. We believe, however, that the claims of the Fire and Mello patent do not cover the structural features of double-stranded RNAs that are important for the biological activity of siRNAs in mammalian cells. We believe that these specific features are the subjects of the Crooke, Kreutzer-Limmer, Glover and Tuschl II patents and patent applications for which we have secured exclusive rights.

The other pending patent applications listed in the table above either provide further coverage for structural features of siRNAs or relate to the use of siRNAs in mammalian cells. For some of these, we have exclusive rights, and for others, we have non-exclusive rights. In addition, in December 2008, we acquired the intellectual property assets of Nucleonics, Inc., a privately held biotechnology company. This acquisition included over 100 active patent filings, including 15 patents that have been granted worldwide, of which five have been granted in the United States and Europe. With this acquisition, we obtained patents and patent applications with early priority dates, notably the “Li & Kirby,” “Pachuk I” and “Giordano” patent families, that cover broad structural features of RNAi therapeutics, thus extending the breadth of our fundamental intellectual property.


Intellectual Property Related to Chemical Modifications

Our amended and restated collaboration and license agreement with Isis providesIonis provided us with rights to practice the inventions covered by over 200 issued patents worldwide, as well as rights based on future chemistry patent applications through April 2014 for use with double-stranded RNA products. In January 2015, we entered into a second amended and restated agreement with IsisIonis to extend our rights to future chemistry applications through April 2019. These patents will expire both in and outside the United States generally between 2015 and 2035, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. These inventions cover chemical modifications we may wish to incorporate into double-stranded RNA therapeutic products designed to work through an RNAi mechanism. Under the terms of our agreement, IsisIonis agreed not to grant licenses under these patents to any other organization for double-stranded RNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which IsisIonis plays an active role.

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In addition to licensing these intellectual property rights from Isis,Ionis, we are also working to develop our own proprietary chemical modifications that may be incorporated into siRNAs to endow them with drug-like properties. We have filed a large number of patent applications relating to these novel and proprietary chemical modifications.

With the combination of the technology we have licensed from Isis,Ionis, various patents in the Tuschl II patent series and our own patent application filings, we possess issued claims that cover methods of making siRNAs that incorporate any of various chemical modifications, including the use of phosphorothioates, 2’-O-methyl and/or 2’-fluoro modifications and modifications such as those found in locked and unlocked (acyclic) nucleotides. These modifications are believed to be important for achieving “drug-like” properties for RNAi therapeutics. We hold exclusive worldwide rights to these claims for RNAi therapeutics.

In addition to the above, in March 2014, we acquired the RNAi assets from Merck, which included intellectual property developed at Sirna and Merck. The acquired patent portfolio includes the “McSwiggen” patent families with issued and pending claims covering highly chemically modified oligonucleotide compositions, both single- and double-stranded and independent of 5’ and 3’ architecture. A total of tenSeveral patents have granted in the United States with claims directed to various combinations of chemical modifications to double-stranded RNA of between 18 and 24 nucleotides. Notably, U.S. 8,273,866 was granted in September 2012 with significant patent term adjustment extending the expiration of this patent to mid-2028. EP423406 was granted in September 2010 with claims directed to double-stranded RNA of between 18 and 24 nucleotides with ten or more chemical modifications on the pyrimidine residues of the sense and/or antisense strand. As indicated in the chart above, four additional EP patents have granted with claims to various combinations of chemically modified compositions comprising double-stranded RNA of between 18 and 24 nucleotides and methods of making and using such combinations. In November 2015, U.S. 9,181,551 granted with claims directed to highly modified double-stranded RNA molecules comprising a ligand, with dependent claims wherein the ligand is chosen from a ligand for a cellular receptor, a protein localization sequence, an antibody, a nucleic acid aptamer, a vitamin, a co-factor, a phospholipid, a cholesterol, a polyamine, a galactose, a galactosamine, a folate, an N-acetyl-galactosamine (wherein the N-acetylgalactosamine is a mono-antennary, bi-antennary or a tri-antennary galactosamine). Additional dependent claims are directed to highly modified double-stranded RNA with modified nucleotides, including but not limited to unlocked (acyclic) and locked nucleotides. In addition, in August 2017 the United States Patent and Trademark Office, or USPTO, granted U.S. Patent No. 9,732,344 with claims directed to single-stranded antisense polynucleotide molecules of 18-20 nucleotides, comprising 10 or more phosphorothioates and 10 or more modified pyrimidine molecules.  

Intellectual Property Related to the Delivery of siRNAs to Cells

We also pursue internal research and collaborative approaches regarding the delivery of siRNAs to mammalian cells. These approaches include exploring technology that may allow delivery of siRNAs to cells through the use of cholesterol and carbohydrate conjugation, cationic lipids, peptide and antibody-based targeting, and polymer conjugations. Our collaborative efforts have included working with academic and corporate third parties to examine specific embodiments of these various approaches to delivery of siRNAs to appropriate cell tissue, and in-licensing and/or acquiring the most promising technology.

In September 2014, the United States Patent and Trademark Office, or USPTO granted U.S. Patent No. 8,828,956 with claims directed to compositions including those comprising a modified RNA agent linked to a biantennary or triantennary ligand. Specifically, the granted patent includes claims that broadly cover single-strandedsingle- or double-stranded, chemically modified RNA therapeuticstherapeutic molecules conjugated with a GalNAc ligand independent of length, sequence or disease target.


The acquisition of Sirna also accelerated our overall efforts to develop and commercialize siRNA delivery technologies, including GalNAc-siRNA and GalNAc-single stranded polynucleotide conjugate technology. As part of the Sirna acquisition, we obtained several patent families directed to various conjugate technologies including “tetra-GalNAc” compositions and methods. The tetra-GalNAc cases are pending worldwide and will expire May 1, 2033. Also included were patent families directed to novel lipid compositions and formulations that are pending worldwide and set to expire May 31, 2031.

In addition to the Sirna delivery technology, we have a license from UBC and TekmiraArbutus in the field of RNAi therapeutics to intellectual property covering cationic liposomes and their use to deliver nucleic acid to cells. The issued United States patents and foreign counterparts, including the Semple (U.S. Patent No 6,858,225) and Wheeler (U.S. Patent No. 6,815,432) patents, cover compositions, methods of making and methods of using cationic liposomes to deliver agents, such as nucleic acid molecules, to cells. These patents will expire both in and outside the United States on October 30, 2017 and June 7, 2015, respectively, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available.

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In addition, in April 2012, the USPTO granted U.S. Patent No. 8,158,601, covering composition of matter and formulations of the MC3 lipid, as well as methods of using these compositions and formulations. MC3 is being utilized in our patisiran development program. We assigned this patent, amongst other patents and patent applications relating to lipids and LNP technology, to TekmiraArbutus in connection with our November 2012 restructuring and cross-license agreement. We retain rights to use this intellectual property for the research, development and commercialization of RNAi therapeutic products, including the rights to sublicense this intellectual property on a product-by-product basis. A description of our 2012 restructuring and cross-license agreement with TekmiraArbutus is set forth above under “Strategic Alliances — Other Strategic License Agreements — Delivery-Related Licenses and CollaborationsLicense AgreementsTekmira.Arbutus.

Intellectual Property Related to siRNAs Directed to Specific Targets

We have filed a number of patent applications claiming specific siRNAs directed to various gene targets that correlate to specific diseases. While there may be a significant number of competing applications filed by other organizations claiming siRNAs to treat the same gene target, we were among the first companies to focus and file on RNAi therapeutics, and thus, we believe that a number of our patent applications may predate competing applications that others may have filed. Reflecting this, in August 2005, the EPO granted a broad patent, which we call the Kreutzer-Limmer II patent, with 103 allowed claims on therapeutic compositions, methods and uses comprising siRNAs that are complementary to mRNA sequences in over 125 disease target genes. In July 2009, the EPO ruled in our favor in an opposition proceeding related to the Kreutzer-Limmer II patent. The decision had been appealed by Sirna and was subsequently withdrawn upon our acquisition of Sirna. No further appeal before the EPO is available. The Kreutzer-Limmer II patent will expire on January 9, 2022, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Some of these claimed gene targets are being pursued by our development and pre-clinical programs, such as those expressed by viral pathogens including RSVrespiratory syncytial virus and influenza virus. In addition, the claimed targets include oncogenes, cytokines, cell adhesion receptors, angiogenesis targets, apoptosis and cell cycle targets, and additional viral disease targets, such as hepatitis C virus and HIV. The Kreutzer-Limmer II patent series is pending in the United States and many foreign countries. Granted U.S. patent 8,618,277 obtained in the Sirna acquisition and set to expire on February 20, 2023, contains claims directed to a highly chemically modified double-stranded siRNA of between 18-24 nucleotides specifically targeting the hepatitis B virus in a sequence independent manner. Moreover, a patent in the Tuschl II patent series, U.S. Patent No. 7,078,196, claims methods of preparing siRNAs that mediate cleavage of an mRNA in mammalian cells and, therefore, covers methods of making siRNAs directed toward any and all target genes. We hold exclusive worldwide rights to these claims for RNAi therapeutics.

In 2016, we were granted U.S. Patent Nos. 9,370,581, 9,370,582 and 9,352,048 containing claims that broadly cover single- or double-stranded RNA therapeutic molecules conjugated with any biantennary or triantennary ligand (including but not limited to GalNAc) independent of length, specifically inhibiting TTR, PCSK9 or hepatitis b virus, respectively, wherein the HBV-specific RNA molecule is fully chemically modified.

In August 2017, we were granted U.S. Patent No. 9,738,899 with claims directed to single-stranded antisense polynucleotide molecules, capable of inhibiting expression of the human transthyretin gene, of 18-20 nucleotides, comprising 10 or more phosphorothioates and 10 or more modified pyrimidine molecules, 2’-deoxy,-O-Methyl, -Fluoro, -methoxyethoxy (MOE), pyrimidines, LNA-pyrimidines or a combination, with or without conjugation to a galactosamine or cholesterol.

Intellectual Property Related to Our Development Candidates

As our development pipeline matures, we have made and plan to continue to make patent filings that claim all aspects of our development candidates, including dose, method of administration and manufacture.

Intellectual Property Challenges

As the field of RNAi therapeutics is maturing, patent applications are being fully processed by national patent offices around the world. There is uncertainty about which patents will issue, and, if they do, as to when, to whom and with what claims. It is likely that there will be significant litigation and other proceedings, such as interference, reexamination,inter partes review, post grantpost-grant review


and opposition proceedings, in various patent offices relating to patent rights in the RNAi field. On September 16, 2012, the America Invents Act went into effect and provided for expanded patent challenge, i.e.,inter partes review and post-grant review. These provide additional opportunities for third parties to challenge our patents. For example, as noted in the table above, various third parties have initiated oppositions to patents in our Kreutzer-Limmer and Tuschl II series in the EPO, as well as in other jurisdictions. We expect that additional oppositions will be filed in the EPO and elsewhere, and other challenges will be raised relating to other patents and patent applications in our portfolio. In many cases, the possibility of appeal exists for either us or our opponents, and it may be years before final,

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unappealable rulings are made with respect to these patents in certain jurisdictions. Given the importance of our intellectual property portfolio to our business operations, we intend to vigorously enforce our rights and defend against challenges that have arisen or may arise in this area. A description of ongoing legal matters relating to certain aspects of our intellectual property portfolio is set forth in Part I, Item 3, “Legal Proceedings,” of this annual report on Form 10-K.

Competition

The pharmaceutical marketplace is extremely competitive, with hundreds of companies competing to discover, develop and market new drugs. We face a broad spectrum of current and potential competitors, ranging from very large, global pharmaceutical companies with significant resources, to other biotechnology companies with resources and expertise comparable to our own, to smaller biotechnology companies with fewer resources and expertise than we have. We believe that for most or all of our drug development programs, there will be one or more competing programs under development at other companies. In many cases, the companies with competing programs will have access to greater resources and expertise than we do and may be more advanced in those programs.

Competition for Our Business in General

The competition we face can be grouped into three broad categories:

other companies working to develop RNAi and microRNA therapeutic products;

companies developing technology known as antisense, which, like RNAi, attempts to silence the activity of specific genes by targeting the mRNAs copied from them; and

marketed products and development programs for therapeutics that treat the same diseases for which we may also be developing treatments.

We are aware of several other companies that are working to develop RNAi therapeutic products. Some of these companies are seeking, as we are, to develop chemically synthesized siRNAs as drugs. Others are following a gene therapy approach, with the goal of treating patients not with synthetic siRNAs but with synthetic, exogenously-introduced genes designed to produce siRNA-like molecules within cells.

Companies working on chemically synthesized siRNAs include Takeda, Kyowa Hakko Kirin, Marina Biotech, Inc., or Marina, Arrowhead Pharmaceuticals, Inc., or Arrowhead, and its subsidiary, Calando Pharmaceuticals, Inc., or Calando, Quark Pharmaceuticals, Inc., or Quark, Silence Therapeutics plc, Tekmira,or Silence, Arbutus, Sylentis, S.A.U., or Sylentis, Dicerna Pharmaceuticals, Inc., or Dicerna, WAVE Life Sciences Ltd., or WAVE, and Arcturus Therapeutics.Therapeutics, Inc., or Arcturus. Many of these companies have licensed our intellectual property. Benitec Biopharma Ltd., or Benitec, is working on gene therapy approaches to RNAi therapeutics. Companies working on microRNA therapeutics include Regulus Therapeutics, Inc., or Regulus, Rosetta Genomics Ltd., F. Hoffmann-La Roche Ltd, or Roche, through its acquisition in 2014 of Santaris Pharma A/S, miRagen Therapeutics, Inc., Mirna Therapeutics, Inc. and Asuragen, Inc.

Antisense technology uses short, single-stranded, DNA-like molecules to block mRNAs encoding specific proteins. While we believe that RNAi drugs may potentially have significant advantages over antisense oligonucleotides, or ASOs, including greater potency and specificity, others are developing ASO drugs that are currently at a more advanced stage of development than RNAi drugs. For example, IsisIonis has developed theseveral ASO drugs fomivirsen, which was approved by the FDAthat have received regulatory approval. Ionis is also developing antisense drugs using ligand-conjugated GalNAc technology licensed from us, and these drugs have been shown to have increased potency at lower doses in 1998 for the treatment of cytomegalovirus retinitis, but is no longer available in the United States,clinical and mipomersen, which was approved by the FDA for the treatment of patientspre-clinical studies, compared with homozygous familial hypercholesterolemia, or HoFH.antisense drugs that do not use such licensed GalNAc technology.  In addition, a number of other companies have ASO-based product candidates in various stages of pre-clinical and clinical development, including Roche, Celgene Corporation, Akcea Therapeutics, Inc., or Akcea, Antisense Therapeutics, Ltd., WAVE and Sarepta Therapeutics, Inc. Because of their later stage of development, ASOs, rather than siRNAs, may become the preferred technology for drugs that target mRNAs in order to turn off the activity of specific genes.

The competitive landscape continues to expand and we expect that additional companies will initiate programs focused on the development of RNAi therapeutic products using the approaches described above as

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well as potentially new approaches that may result in the more rapid development of RNAi therapeutics or more effective technologies for RNAi drug development or delivery.


Competing Drugs for Our Investigational RNAi Therapeutics in Late Stage Clinical Development

Hereditary ATTR Amyloidosis.TTR-Mediated Amyloidosis (ATTR).    Until recently, organ transplantation was the only treatment option for patients with ATTR. Liver or combined heart/liver transplantations were the only available treatment options for FAP.hATTR amyloidosis. Only a subset of FAP patients with early stage disease qualify for this costly and invasive procedure, which carries significant morbidity and evenmortality. Even following liver transplantation, the disease continues to progress for many patients, presumably due to normalongoing deposition of wild-type TTR being deposited into preexisting fibrils. Moreover,protein. Currently there is a shortageonly one approved drug for ATTR amyloidosis, as well as several investigational drugs in varying stages of donors to provide healthy livers for transplantation. In November 2011, Pfizer received marketing approval fromclinical development. We believe that the EC for tafamidis for the treatment of transthyretin amyloidosis in adult patientsfollowing approved drugs and if approved, drug candidates, could compete with stage 1 symptomatic polyneuropathy to delay peripheral neurologic impairment. Tafamidis is intended to stabilize wild-type and variant TTR, to prevent dissociation of the TTR protein and thereby inhibit the formation of TTR oligomers and amyloid fibrils.patisiran:

Drug

Company

Drug Description

Phase

Administration/Dosing

Tafamidis

Pfizer

Small molecule drug to stabilize TTR protein

Approved in the EU, Japan and certain countries in Latin America (indication varies by region)

Daily oral capsule

Inotersen

Ionis

ASO to reduce production of TTR Protein

Registration

Subcutaneous (SC)

PRX004

Prothena Corporation plc

Monoclonal antibody to clear amyloid deposits

Preclinical

Unknown

Ionis-TTR-LRx

Ionis

ASO to reduce production of TTR Protein

Preclinical

SC

GSK 2398852 + 2315698

GlaxoSmith

Kline plc

Antibody combination to clear amyloid deposits

Phase 2

Intravenous (IV)

Diflunisal

N/A (generic)

Non-steroid anti-inflammatory agent

Approved

Daily oral capsule/doses

Tolcapone

SOM Biotech

Small molecule repurposed generic drug

Phase 1/2

Daily oral dose

AG10

Eidos Therapeutics

Small molecule drug to stabilize TTR protein

Phase 1

Daily oral dose

Acute Hepatic Porphyrias.The only currently availableapproved treatments for FACacute attacks are aimed at reliefpreparations of symptoms, such as diuretics, or water pills, to treat the swelling of the ankles, one of the symptoms of FAC. For patients with advanced cardiomyopathy (FAC and SSA) heart transplant is a therapeutic option. Again, the scarcity of organs for transplantation, and the mortality, morbidity and cost associated with this procedure render it a realistic option for only a very small number of patients. In December 2013, Pfizer initiated a Phase 3 clinical trial of tafamidis in patients with TTR amyloidosis cardiomyopathy. The study is expected to enroll up to 400 patients and study two dose levels, with a 30-month treatment duration for each patient.

Several drugs are in clinical development for the treatment of ATTR. Researchers at Boston University, in collaboration with the National Institute of Neurological Disorders and Stroke, conducted a Phase 2/3 clinical trial for diflunisal for the treatment of FAP. Diflunisal is a commercially available non-steroidal anti-inflammatory agent that has been found to stabilize TTRin vitro. This clinical trial concluded that the use of diflunisal compared with placebo for two years reduced the rate of progression of neurological impairment and preserved quality of life. As published, the discontinuation rate was high in this clinical trial in both treatment arms (approximately 50% overall) and the majority of patients continued to deteriorate, including patients on diflunisal. Furthermore, the safety profile of this drug and its known adverse effects, particularly on the kidney and heart, could likely limit the potential use of it in this disease.

In addition, Isis, together with its partner GlaxoSmithKline, is developing ISIS-TTRRx, an ASO designed to treat patients with FAP. Isis has completed a Phase 1 clinical trial evaluating the safety and activity of six subcutaneous doses of ISIS-TTRRx over four weeks in healthy volunteers. Isis reported that in this clinical trial, ISIS-TTRRx produced significant reductions of approximately 80% in TTR protein at the highest dose studied. This study reported that ISIS-TTRRx was generally well tolerated with no significant adverse events. The occurrence of injection site reactions and flu-like symptoms were reported in patients taking ISIS-TTRRx. Isis announced that ISIS-TTRRx was granted fast track designation by the FDA for the treatment of patients with FAP. Isis initiated a Phase 2/3 clinical trial in early 2013 that is expected to enroll up to 195 patients, with a treatment duration of 15 months for each patient.

Hemophilia.heme derived from human blood. The global market for treatments of hemophilia and bleeding disorders is valued at more than $9.0 billion. Products on the market include: Factor VIII replacement products marketed by Baxter Healthcare Corporation, Bayer Healthcare Pharmaceuticals, Pfizer and CSL Behring; Factor IX replacement products marketed by Pfizer (Wyeth), Baxter and CSL Behring; a Factor VIIa replacement product marketed by Novo Nordisk; and concentrated products for fibrinogen, FII, FX and FXI deficiencies. In 2014, long-acting factor VIII replacement and factor IX replacement products from Biogen Idec were approved by the FDA. Also in 2014, recombinant porcine Factor VIII was approved by the FDA for the treatment of acquired HA.

A number of products are currently in development for the treatment of hemophilia. Additional long-acting factor therapies will be on the market in the near future, and may extend the time between intravenous doses. For example, Novo Nordisk is developing two long-acting recombinant derivatives for the treatment of HB, both of which are in Phase 3 clinical trials. Baxter is also developing long-acting recombinant factor replacement

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products for the treatment of HB. Bayer is also developing a long-acting recombinant product and Pfizer is developing a recombinant Factor VIIa variant that is in a Phase 1 clinical trial in adults with HA or HB.

A particular segment of people with hemophilia develop neutralizing antibodies to the factors; these are called people with inhibitors. They cannot be given replacement factors VIII or IX since the inhibitor, an antibody, will lead to immediate clearance of any Factor VIII or Factor IX that is administered. Generally speaking, these individuals are monitored for signs of a bleed and then are given recombinant Factor VIIa or FEIBA. FEIBA is an anti-inhibitor coagulant complex from Baxter. It is approved in both the United States and the EU for the treatment of acute bleeds and for prophylactic treatment.

Molecules currently in development may offer new treatments for HA and HB subjects with and without inhibitors. Chugai and Roche are developing a bi-specific antibody (ACE-910) which binds to factors IXa and X and mimics the Factor VIII cofactor function in HA subjects. This product has completed a Phase 1 clinical trial and has been shown to reduce the incidence of bleeding events in people with hemophilia with and without inhibitors. Novo Nordisk is developing Anti-TFPI (NN7415), a monoclonal antibody against a tissue factor pathway inhibitor, for the treatment of HA and HB, currently in Phase 1 clinical trials. Baxter is developing a peptide which also targets a tissue factor pathway inhibitor for the treatment of HA and HB.

A number of companies are actively developing gene therapy products which use a virus to deliver a functional segment of a particular gene into the cells of the subject with hemophilia. In 2013, Biomarin licensed technology from University College London and St. Jude Children’s Research Hospital to develop gene therapy products for the treatment of HA. In 2014, Baxter acquired Chatham Therapeutics, which was developing a gene therapy product for the treatment of HB. In 2014, Bayer partnered with Dimension Therapeutics, or Dimension, to develop a gene therapy product for the treatment of HA. Dimension is also developing a gene therapy product for the treatment of HB.

Complement-Mediated Diseases.    The global market for drugs that specifically target complement-mediated diseases is significant. The only product in this market is eculizumab, a monoclonal antibody developed by Alexion Pharmaceuticals that inhibits the cleavage of the protein complement component 5 (C5) into its components C5a and C5b. In 2007, eculizumab was approved by the FDA and the EC to treat PNH, a hemolytic anemia caused by a deficiency of proteins on the red blood cell membrane that protect the cells from destruction by the complement system. In 2011, eculizumab was approved by the FDA and EC to treat aHUS, a systemic disease cause by chronic uncontrolled activation of the complement system. Eculizumab is also currently being studied in a number of other diseases that are believed to be complement-mediated including: neuromyelitis optica, myasthenia gravis, antibody-mediated rejection and delayed graft function.

A number of products are in development for the treatment of complement-mediated diseases. Swedish Orphan Biovitrium (SOBI) is developing SOBI002, an antibody to inhibit C5. In 2014, the Phase 1 trial for SOBI002 was placed on hold when adverse effects were observed in the study. Shire is conducting Phase 1 trials of a plasma-derived C1 esterase inhibitor for the treatment of PNH and acute neuromyelitis optica that is currently approved for the prevention of hereditary angioedema attacks. Apellis Pharmaceuticals is developing APL-2, a subcutaneously administered analogue of compstatin which inhibits Complement Component C3 (C3). A Phase 1 trial for APL-2 began in October 2014.

Hepatic Porphyrias.    The global market for hepatic porphyrias is less than $150.0 million. This marketAHP is made up of intravenous hemin in the United States and intravenous heme arginate in the EC.EU. Both products are currently manufactured by Recordati S.p.A. Both molecules are human-derived blood products which haveDespite the lack of randomized studies demonstrating clinical efficacy, heme has been shown in case studies to reducehasten recovery from attacks and has been marketed since 1999 in the duration of porphyria attacks.

Several other products are in developmentEU for the treatment of AIP. Theacute attacks of AIP, hereditary coproporphyria and variegate porphyria.

In addition to heme, the AIPGENE consortium, a European collaboration whichthat included industry sponsors UniQureuniQure and Digna Biotech, iswas developing AMT-021, a gene therapy product for the treatment of AIP. In 2014,AIP, but this development program is currently on hold.  We are aware of other companies that have pre-clinical development programs for the consortium released one-year follow-up data on thetreatment of AHPs.    

Hemophilia.AMT-021 which confirmed the safety   The global market for treatments of hemophilia and the successful transduction of the virus. No datableeding disorders is valued at more than $10.0 billion. Products on the observations relatedmarket include: Factor VIII replacement products; Factor IX replacement products; and more recently, factor replacement products with extended half-lives. For the treatment of persons with inhibitors, there is an approved Factor VIIa replacement product and an activated prothrombin complex concentrate.  In addition, new, innovative molecules are currently in development which may offer new treatments for people with hemophilia A and B, with and without inhibitors, including one such molecule that was recently approved for use in persons with hemophilia A with inhibitors in the United States. A number of companies are also actively developing gene therapy products that use virus-like particles to protein expression have been publically disclosed.deliver a functional section of a particular gene into the liver cells of a person with hemophilia.


We believe that the following approved drugs and, if approved, drug candidates, could compete with fitusiran, along with additional approved drugs and drug candidates:

 

Drug (Company)

Drug Description

Phase

Administration/

Dosing

Hemophilia A

Advate (Shire), Adynovate (Shire), Kogenate (Bayer), Kovaltry (Bayer), Novoeight (Novo Nordisk), Xyntha (Pfizer), Nuwiq (Octapharma), Eloctate (Bioverativ)

Recombinant FVIII factor products

Approved

IV

Valoctocogene roxaparvovec (BioMarin)

Gene therapy

Phase 3

IV - Single Administration

Emicizumab HemLibra, ACE-910 (Roche)

Bispecific antibody mimetic of FVIII

Phase 3 (Hemophilia A without inhibitors)

SC

Hemophilia B

Rixubis (Shire), Rebinyn (Novo Nordisk), BeneFIX (Pfizer), Alprolix (Bioverativ), Idelvion (CSL Behring)

Recombinant FIX factor products

Approved

IV

AMT-061, FIX (uniQure)

rAAV5 FIX gene therapy

Phase 2

IV - Single Administration

SPK-9001 (Spark Therapeutics)

Spark200 AAV FIX gene therapy

Phase 2

IV - Single Administration

Inhibitor Patients

Emicizumab HemLibra,

ACE-910 (Roche)

Bispecific antibody mimetic of FVIII

Approved

SC

Feiba (Shire)

Bypassing agent

Approved

IV

NovoSeven (Novo Nordisk)

Bypassing agent

Approved

IV

Hemophilia A and B

Concizumab, anti-TFPI (Novo Nordisk)

anti-TFPI antibody

Phase 2

IV - Single Administration

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Hypercholesterolemia.Hypercholesterolemia.     The current standard of care for patients with hypercholesterolemia includes the use of several agents.dietary changes, lifestyle modification and the use of pharmacologic therapy. Front line therapy consists of HMG CoAHMG-CoA reductase inhibitors, commonly known as statins, which block production of cholesterol by the liver and increase clearance of LDL-C from the bloodstream. These include atorvastatin, simvastatin, rosuvastatin and pravastatin. A different class of compounds, which includes ezetimibe and ezetimibe/simvastatin, function by blocking cholesterol uptake from the diet and are utilized on their own or in combination with statins. Aegerion Pharmaceuticals, Inc. is developing lomitapide, an microsomal triglyceride protein, or MTP, inhibitorSeveral anti-PCSK9 antibodies have also been approved for the treatment of dyslipidemia. In December 2012, the FDA approved lomitapide for use in patients with HoFH and in July 2013 lomitapide was approved for HoFHhypercholesterolemia in the EU.

In addition, mipomersen isUnited States and Europe. Other PCSK9-targeted approaches are in development at a lipid-lowering weekly injectable drug targeting apolipoprotein B-100 being developed by Isis in collaboration with Genzyme. In July 2011, Genzyme submitted a marketing authorization application for mipomersen in Europe. In December 2012, the CHMP recommended against approvalnumber of the drug in Europe for familial hypercholesterolemia. In January 2013, the FDA approved mipomersen for the treatment of patients with HoFH.

With regard to future therapies in clinical development, several anti-PCSK9 antibodies have advanced into clinical development, including alirocumab, which is being developed by Regeneron Pharmaceuticals, Inc., in collaboration with Sanofi. Data reported from a Phase 3 clinical trial evaluating alirocumab in 2,341 patients with heterozygous familial hypercholesterolemia or coronary heart disease demonstrated mean reductions in LDL-C from baseline of 61% and showed a statistically significant reduction in a post-hoc analysis of adjudicated major CV events. Numerous other Phase 3 clinical studies demonstrated similar results. In 2012, Regeneron announced the launch of ODYSSEY OUTCOMES, an 18,000 patient Phase 3 clinical trial designed to test the efficacy and safety of REGN727 added to maximal doses of statins in reducing cardiovascular morbidity and mortality in patients with recent acute coronary syndrome, a population at high risk of cardiovascular events despite best contemporary therapy. Regeneron filed an NDA for alirocumab with the FDA in 2014.

Amgen Inc. has also advanced evolocumab, an anti-PCSK9 antibody, through late-stage clinical development. Data reported from the 52-week Phase 3 DESCARTES trial in 905 patients showed that evolocumab reduced LDL-C by 57%. Numerous other phase 3 studies demonstrated similar results. In August 2014, Amgen filed an NDA with the FDA for evolocumab. In September 2014, Amgen filed a marketing application with the EC.companies.

We are also aware of ongoing programs at Pfizerbelieve that the following approved drugs and other companies to develop anti-PCSK9 molecules, and we are aware of several additional similar compounds in advanced pre-clinical development.if approved, drug candidates, could compete with inclisiran:

Drug

Company

Drug Description

Phase

Administration/Dosing

Repatha

Amgen

Anti-PSCK9 mAb

Marketed

SC

Praluent

Sanofi

Anti-PSCK9 mAb

Marketed

SC

Bempedoic Acid (ETC-1002)

Esperion

Oral fatty acid and cholesterol synthesis dual inhibitor

Phase 3

Oral

REGN1500 (evinacumab)

Regeneron

Anti-ANGPTL3 mAb for antihypercholesterolemia

Phase 2

SC

Volanesorsen

Akcea

ASO therapy to reduce levels of APOC3

Registration

SC

Akcea-ANGPTL3-LRx

Akcea

ASO therapy to reduce levels of ANGPTL3

Phase 2

SC


In addition, Esperion Therapeutics is developing bempedoic acid (ETC-1002), a small molecule drug which is both an ATP citrate lyase inhibitor and an activator of AMP kinase. In a Phase 2 trial in patients with hypercholesterolemia with or without statin intolerance, patients taking ETC-1002 had a 30% reduction inLDL-C compared with baseline. ETC-1002 is in Phase 2b clinical trials.Other Competition

Other Competition

Finally, for many of the diseases that are the subject of our RNAi therapeuticsearly stage clinical, pre-clinical development and discovery RNAi therapeutic programs, there are already drugs on the market or in development. For example, with respect toALN-HBV, oral nucleoside/nucleotide analogues have demonstrated the ability to potently inhibit HBV replication and suppress levels of HBV DNA in patients with HBV and are approved for the treatment of these patients in the United States, Europe and other countries. In addition, a large number of novel agents, including agents using chemically synthesized siRNA, are currently in development for the treatment of patients with HBV. However, notwithstanding the availability of existing drugs or drug candidates, we believe there currently exists sufficient unmet medical need to warrant the advancement of our investigational RNAi therapeutic programs.

Regulatory Matters

U.S. Regulatory Considerations

The research, testing, manufacture and marketing of drug products and their delivery systems are extensively regulated in the United States and the rest of the world. In the United States, drugs are subject to

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rigorous regulation by the FDA. The Federal Food, Drug, and Cosmetic Act, or FDCA, and other federal and state statutes and regulations govern, among other things, the research, development, testing, approval, manufacture, storage, record keeping, reporting, packaging, labeling, promotion and advertising, marketing and distribution of pharmaceuticaldrug products. Failure to comply with the applicable regulatory requirements may subject a company to a variety of administrative or judicially-imposed sanctions and the inability to obtain or maintain required approvals to test or market drug products. These sanctions could include, among other things, warning letters, product recalls, product seizures, total or partial suspension of production or distribution, clinical holds, injunctions, fines, civil penalties or criminal prosecution.

The steps ordinarily required before a new pharmaceuticaldrug product may be marketed in the United States include nonclinical laboratory tests, animal tests and formulation studies, the submission to the FDA of an investigational new drug, or IND, application, which must become effective prior to commencement of clinical testing, approval by an institutional review board, or IRB, at each clinical site before each trial may be initiated, completion of adequate and well-controlled clinical trials to establish that the drug product is safe and effective for the indication for which FDA approval is sought, submission to the FDA of an NDA review and recommendation by an advisory committee of independent experts (particularly for new chemical entities), satisfactory completion of an FDA inspection of the manufacturing facility or facilities at which the product is produced to assess compliance with current good manufacturing practice, or cGMP, requirements, satisfactory completion of an FDA inspection of the major investigational sites to ensure data integrity and assess compliance with good clinical practice, or GCP, requirements and FDA review and approval of the NDA. Satisfaction of FDA pre-market approval requirements typically takes several years, but may vary substantially depending upon the complexity of the product and the nature of the disease. Government regulation may delay or prevent marketing of potential products for a considerable period of time and impose costly procedures on a company’s activities. Success in early stage clinical trials does not necessarily assure success in later stage clinical trials. Data obtained from clinical activities, including but not limited to the data derived from our clinical trials for patisiran, revusiran, ALN-AT3fitusiran, givosiran and ALN-PCSsc, isinclisiran, are not always conclusive and may be subject to alternative interpretations that could delay, limit or even prevent regulatory approval. Even if a product receives regulatory approval, later discovery of previously unknown problems with a product, including new safety risks, may result in restrictions on the product or even complete withdrawal of the product from the market.

Nonclinical Tests and Clinical Trials.

Nonclinical tests include laboratory evaluation of product chemistry and formulation, as well as animal testing to assess the potential safety and efficacy of the product. The conduct of the nonclinical tests and formulation of compounds for testing must comply with federal regulations and requirements. The results of nonclinical testing are submitted to the FDA as part of an IND, together with chemistry, manufacturing and controls, or CMC, information, analytical and stability data, a proposed clinical trial protocol and other information.

A 30-day waiting period after the filing of  Clinical testing in humans may not commence until an IND is required priorin effect.

An IND becomes effective 30 days after receipt by the FDA unless the FDA notifies the sponsor that the proposed investigation(s) are subject to such application becoming effective and the commencement ofa clinical testing in humans.hold. If the FDA has not commented on, or questioned,imposes a clinical hold, the application during this 30-day waiting period, clinical trials may begin. If the FDA has comments or questions, theseFDA’s concerns must be resolved prior to the satisfaction of the FDA prior to commencement of clinical trials. The IND review process can result in substantial delay and expense. We, an IRB, or the FDA may, at any time, suspend, terminate or impose a clinical hold on ongoing clinical trials. For example, in October 2016, we decided to discontinue development of revusiran, an investigational RNAi therapeutic that was in development for the treatment of patients with cardiomyopathy due to hATTR amyloidosis, due to safety concerns. If the FDA imposes a clinical hold, clinical trials cannot commence or recommence without FDA authorization and then only under terms authorized by the FDA.  For example, in September 2017, we temporarily suspended dosing in all ongoing fitusiran studies pending further review of a fatal thrombotic SAE and agreement with regulatory authorities on a risk mitigation strategy. We have reached alignment with study investigators and the FDA on safety measures and a risk mitigation strategy to enable resumption of dosing in clinical studies with fitusiran, including our Phase 2 OLE study and the ATLAS Phase 3 program.


Clinical trials involve the administration of an investigational new drug to healthy volunteers or patients under the supervision of a qualified investigator. Clinical trials must be conducted in compliance with federal regulations and requirements, including GCP, which are ethical and scientific quality standards and FDA requirements for conducting, recording and reporting clinical trials to assure data integrity and protect the rights, safety and well-being of trial participants and include the requirement that all research subjects provide their informed consent for their participation in any clinical study. Clinical studies are conducted under protocols detailing, among other things, the objectives of the trial and the safety and effectiveness criteria to be evaluated. Each protocol involving testing on human subjects in the United States must be submitted to the FDA as part of the IND. In addition, clinical trials must be conducted in compliance with federal regulations and requirements, commonly referred to as good clinical practice, or GCP, to assure data integrity and protect the rights, safety and well-being of trial participants.  Among other things, GCP requires that all research subjects provide their informed consent prior to participating in any clinical study, and that an IRB at each institution participating in the clinical trial must review and approve the plan

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for any clinical trial before it commences at that institution and the IRB must conduct continuing review.review throughout the trial. The IRB must review and approve, among other things, the study protocol and informed consent information to be provided to study subjects. An IRB must operate in compliance with FDA regulations.

Clinical trials to support NDAs for marketing approval are typically conducted in three sequential phases, which may overlap or be combined.

In Phase 1, the initial introduction of the drug into healthy human subjects or patients, the drug is tested to primarily assess safety, tolerability, pharmacokinetics, pharmacological actions and metabolism associated with increasing doses.

Phase 2 usually involves trials in a limited patient population, to assess the optimum dosage and dose regimen, identify possible adverse effects and safety risks, and provide preliminary support for the efficacy of the drug in the indication being studied.

If Phase 2 clinical trials demonstrate that a drug may be effective and the risks are considered acceptable given the observed efficacy of the drug and the severity of the illness, Phase 3 clinical trials may be undertaken to further evaluate the drug’s clinical efficacy, side effects and safety in an expanded patient population, typically at geographically dispersed clinical trial sites, to establish the overall benefit-risk relationship of the drug and to provide adequate information for the labeling of the drug.

Phase 1, Phase 2 or Phase 3 testing of any drug candidates may not be completed successfully within any specified time period, if at all. The FDA closely monitors the progress of each of the three phases of clinical trials that are conducted in the United States. The FDA may, at its discretion, reevaluate, alter, suspend or terminate the testing based upon the data accumulated to that point and the FDA’s assessment of the risk/benefit ratio to the subject. The FDA, anAn IRB or a clinical trial sponsor also may suspend or terminate clinical trials at any time for various reasons, including a finding that the subjects or patients are being exposed to an unacceptable health risk. The FDA can also request that additional clinical trials be conducted as a condition to product approval. Finally, sponsors are required to publicly disseminate information about certain ongoing and completed clinical trials on a government website administered by the National Institutes of Health, or NIH, and are subject to civil monetary penalties and other civil and criminal sanctions for failing to meet these obligations. After successful completion of the required clinical testing, as well as nonclinical testing and manufacturing requirements, generally an NDA is prepared and submitted to the FDA.NIH.

New Drug Applications.

We believe that any RNAi product candidate we develop, whether for the treatment of ATTR amyloidosis, AHPs, hemophilia, and RBD, complement mediated diseases, hypercholesterolemia or the various indications targeted in our development or pre-clinicalnonclinical discovery programs, will be regulated as a non-biological new drug by the FDA. FDA approval of an NDA is required before marketingcommercial distribution of a non-biological new drug may begin in the United States. TheIn December 2017, we submitted our first NDA to the FDA for patisiran.  An NDA must include the results of extensive pre-clinical,nonclinical, clinical and other testing, as described above, a compilation of data relating to the product’s pharmacology, chemistry, manufacture and controls, proposed labeling and other information. In addition, an NDA for a new active ingredient, new indication, new dosage form, new dosing regimen, or new route of administration typically must contain data assessing the safety and effectiveness for the claimed indication in all relevant pediatric subpopulations, and support dosing and administration for each pediatric subpopulation for which the drug is shown to be safe and effective. In some circumstances, the FDA may grantalthough deferrals for the submission of some or all pediatric data, or full or partial waivers.waivers may be available in some circumstances.

The cost of preparing and submitting an NDA is substantial. Under federal law, NDAs are subject to substantial application user fees and the sponsor of an approved NDA is also subject to annual product and establishment user fees. Under the Prescription Drug User Fee Act, or PDUFA, as amended, each NDA must be accompanied by a user fee. For fiscal year 2018, the user fee for each NDA requiring clinical data is approximately $2.4 million. The PDUFA also imposes an annual program fee for each approved prescription drug, which is set at approximately $300,000 for fiscal year 2018. The FDA adjusts the PDUFA user fees on an annual basis. According to the FDA’s fee schedule, effective through September 30, 2015, the user fee for each NDA application requiring clinical data, is approximately $2.3 million. PDUFA also imposes an annual product fee for drugs and an annual establishment fee on facilities used to manufacture prescription drugs. Fee waivers or reductions are available in certain circumstances, including a waiver of the application fee for the first application filed by a small business. Additionally, no user fees are assessed on NDAs for products designated as orphan drugs, unless the product also includes a non-orphan indication.

The FDA conducts a preliminary review of all NDAs within the first 60 days after submission before accepting them for filing to determine whether they are sufficiently complete to permit substantive review. The FDA may request additional information rather than accept an NDA for filing. If the submission is accepted for filing, the FDA begins an in-depth review of the NDA. The FDA has agreed to specified performance goals

35


regarding the timing of its review of NDAs, although the FDA does not always meet these goals. The review process is often significantly extended by FDA requests for additional information or clarification regarding information already provided in the submission. The FDA may also refer applications for novel drug products or drug products that present difficult questions of safety or efficacy to an advisory committee, typically a panel that includes independent clinicians and other experts, for review, evaluation and a recommendation as to whether the application should be approved. The FDA is not bound by the recommendation of an advisory committee, but it generally follows such recommendations. The FDA normally conducts a pre-approval inspection to gain assurance that the manufacturing facility, methods and controls are


adequate to preserve the drug’s identity, strength, quality, purity and stability, and are in compliance with regulations governing cGMPs.current good manufacturing practice, or cGMP, requirements. In addition, the FDA often will conduct a bioresearch monitoring inspection of select clinical trial sites involved in conducting pivotal studies to assure data integrity and compliance with applicable GCP requirements.

If the FDA evaluation of the NDA and the various inspections of manufacturing facilities and clinical trial sites are favorable, the FDA may issue an approval letter, which authorizes commercial marketing of the drug with specific prescribing information for a specific indication. As a condition of NDA approval, the FDA may require post-approval testing, sometimes referred to as Phase 4 trials and surveillance to monitor the drug’s safety or effectiveness and may impose other conditions, including labeling restrictions, such as a Boxed Warning, and/or distribution and use restrictions through a Risk Evaluation and Mitigation Strategy, or REMS, all of which can materially impact the potential market and profitability of the drug. In addition, the FDA may impose distribution and use restrictions and other limitations on labeling and communication activities with respect to an approved drug product through a Risk Evaluation and Mitigation Strategy, or REMS, plan. Once granted, product approvals may be further limited or withdrawn if compliance with regulatory standards is not maintained or safety or other problems are identified following initial marketing.

Once an NDA is approved, a product will be subject to certain post-approval requirements, including requirements for adverse eventregistration and listing, AE reporting, submission of periodic reports, recordkeeping, product sampling and distribution. Additionally, the FDA also strictly regulates the promotional claims that may be made about prescription drug products and biologics. In particular, the FDA generally prohibits pharmaceutical companies from promoting their drugs or biologics for uses that are not approved by the FDA as reflected in the product’s approved labeling. In addition, the FDA requires substantiation of any safety or effectiveness claims, including claims that one product is superior in terms of safety or effectiveness to another. Superiority claims generally must be supported by two adequate and well-controlled head-to-head clinical trials. To the extent that market acceptance of our products may dependdepends on their superiority over existing therapies, any restriction on our ability to advertise or otherwise promote claims of superiority, or requirements to conduct additional expensive clinical trials to provide proof of such claims, could negatively affect the sales of our products or our costs. We must also notify the FDA of any change in an approved product beyond variations already allowed in the approval. Certain changes to the product, its labeling or its manufacturing require prior FDA approval and may require the conduct of further clinical investigations to support the change, which may require the payment of additional, substantial user fees.change. Such approvals may be expensive and time-consuming and, if not approved, the FDA will not allow the product to be marketedcommercially distributed as modified.

If the FDA’s evaluation of the NDA submission or manufacturing facilities is not favorable, the FDA may refuse to approve the NDA or issue a complete response letter. The complete response letter describes the deficiencies that the FDA has identified in an application and, when possible, recommends actions that the applicant might take to placeallow FDA to approve the application in condition for approval.application. Such actions may include, among other things, conducting additional safety or efficacy studies after which the sponsor may resubmit the application for further review.studies. Even with the completion of this additional testing or the submission of additional requested information, the FDA ultimately may decide that the application does not satisfy the regulatory criteria for approval. With limited exceptions, the FDA may withhold approval of an NDA regardless of prior advice it may have provided or commitments it may have made to the sponsor.

Some of our product candidates may need to be administered using specialized drug delivery systems/systems that are considered to be medical devices. We may rely on drug delivery systems that are already approved to deliver drugs like ours to similar physiological sites or, in some instances, we may need to modify the design or labeling of the legally available device for delivery of our product candidate. The FDA may regulate theour product candidate when used with a specialized drug delivery system as a combination product, or

36


which could permit the combination to be approved through a single application, such as an NDA.  Alternatively, the FDA could require separate, additional approvals or clearances for the modified device. In addition, to the extent the delivery device is owned by another company, we would need that company’s cooperation to implement the necessary changes to the device and to obtain any additional approvals or clearances. Obtaining such additional approvals or clearances, and cooperation of other companies, when necessary, could significantly delay, and increase the cost of obtaining marketing approval, which could reduce the commercial viability of a product candidate. To the extent that we rely on previously unapproved drug delivery systems, we may be subject to additional testing and approval requirements from the FDA above and beyond those described above.

Abbreviated Applications.

Once an NDA is approved, the product covered thereby becomes a listed drug that can, in turn, be relied upon by potential competitors in support of approval of an abbreviated new drug application, or ANDA, or 505(b)(2) application upon expiration of certain patent and non-patent exclusivity periods, if any.application. An approved ANDA generally provides an abbreviated approval pathway for marketing of a drug product that has the same active ingredients in the same strength, dosage form and route of administration as the listed drug and has been shown through appropriate testing (unless waived) to be bioequivalent to the listed drug. There is no requirement, other than the requirement for bioequivalence testing (which may be waived by the FDA), for an ANDA applicant to conduct or submit results of nonclinical or clinical tests to prove the safety or effectiveness of its drug product. Drugs approved in this way are commonly referred to as generic equivalents to the listed drug are listed as such by the FDA and can often be substituted by pharmacists under prescriptions written for the original listed drug. A 505(b)(2) application is a type of NDA that relies, in part, upon data the applicant does not own and to which it does not have a right of reference. Such applications typically are submitted for changes to previously approved drug products.


The approval of ANDAs and 505(b)(2) applications can be delayed by patents and non-patent exclusivity covering the listed drug. Federal law provides for a period of three years of exclusivity following approval of a listed drug that contains a previously approved active ingredient but is approved in, among other things, a new dosage, dosage form, route of administration or combination, or for a new use, if the FDA determines that new clinical investigations, other than bioavailability studies, that were conducted or sponsored by the applicant and are essential to the approval of the application. This three-year exclusivity covers only the conditions of use associated withapproval for which the new clinical investigations were essential, such as a new dosage form or indication.  Accordingly, three-year exclusivity generally protects changes to a previously approved drug product that require clinical testing for approval and, as a general matter, does not prohibit the FDA from approving ANDAs or 505(b)(2) applications for generic versions of the original, unmodified drug product.

Federal law also provides a five-year period of up to five yearsNCE exclusivity following approval of a drug containing no previously approvedthat contains a new chemical entity, or NCE.  An NCE is a drug that contains an active moiety which is the(the molecule or ion responsible for the action of the drug substance, during whichsubstance) that has never previously been approved by the FDA. If a listed drug has NCE exclusivity, ANDAs and 505(b)(2) applications referencing the protected listed drug cannot be submitted to the FDA for five years unless the submission accompaniesapplication contains a challenge tocertification challenging a listed patent, i.e., a paragraph IV certification (discussed further below), in which case the submissionANDA or 505(b)(2) application may be madesubmitted four years following approval of the original product approval.listed drug. Five-year and three-year exclusivity will not delay the submission or approval of a full NDA; however, an applicant submitting a full NDA would be required to conduct or obtain a right of reference to all of the pre-clinicalnonclinical studies and adequate and well-controlled clinical trials necessary to demonstrate safety and effectiveness.

Additionally, in the event that the sponsor of the listed drug has properly informed the FDA of patents covering its listed drug, applicants submitting an ANDA or 505(b)(2) application referencing thea listed drug generally are required to make onea certification with respect to each patent listed in the FDA’s publication Approved Drug Products with Therapeutic Equivalence Evaluations, commonly referred to as the Orange Book, for the listed drug.  The only exception is if the applicant is not seeking approval of foura use claimed by a method-of-use patent, in which case the applicant can submit a statement to that effect. These certifications for each listed patent, except for patents covering methods of use for which(and statements) determine when the FDA can approve the ANDA or 505(b)(2) application. If the ANDA or 505(b)(2) applicant iscertifies that it does not seeking approval.intend to market its generic product before a listed patent expires (i.e., a paragraph III certification), then the FDA cannot grant effective approval of the ANDA or 505(b)(2) application until the relevant patent expires.  If anthe ANDA or 505(b)(2) applicant certifies its belief that one or morea listed patents arepatent is invalid, unenforceable, or will not be infringed (and thereby indicatesby its proposed product, and thus that it is seeking approval prior to patent expiration)expiration (i.e., ita paragraph IV certification), the statute provides a process for litigating the patent infringement issues during the FDA’s review of the ANDA or 505(b)(2) application.  In particular, the applicant is required to provide notice of its filingpatent challenge to the NDA sponsor and the patent holder within certain time limits. If the patent holder then initiates a suit for patent infringement against the ANDA or 505(b)(2) applicant within 45 days of receipt of the notice, the FDA cannot grant effective approval of the ANDA or 505(b)(2) application until either 30 months have passed (which may be extended or shortened in certain cases) or there has been a court decision or settlement order holding or stating that the patents in question are invalid, unenforceable or not infringed. If the patent holder does not initiate a suit for patent infringement within the 45 days, the ANDA or 505(b)(2) application may be approved immediately upon successful completion of FDA review, unless blocked by another listed patent or regulatory exclusivity period. If the ANDA or 505(b)(2) applicant certifies that it does not intend to market its generic product before some or all listed patents on the listed drug expire, then the FDA cannot grant effective approval of the ANDA or 505(b)(2) application until those patents expire. The first of the ANDA applicants submitting substantially complete applications certifying that one or more listed patents for a

37


particular product are invalid, unenforceable, or not infringed may qualify for an exclusivity period of 180 days running from when the generic product is first marketed, during which subsequently submitted ANDAs containing similar certifications cannot be granted effective approval. The 180-day generic exclusivity can be forfeited in various ways, including if the first applicant does not market its product within specified statutory timelines. If more than one applicant files a substantially complete ANDA on the same day, each such first applicant will be entitled to share the 180-day exclusivity period, but there will only be one such period, beginning on the date of first marketing by any of the first applicants.

The Patient Protection and Affordable Care Act, also referred to as the PPACA or the Affordable Care Act, signed into law on March 23, 2010, includes a subtitle called the Biologics Price Competition and Innovation Act of 2009, or BPCI Act, which created an abbreviated approval pathway for biological products shown to be similar to, or interchangeable with, an FDA-licensed reference biological product. This amendment to the Public Health Service Act attempts to minimize duplicative testing. Biosimilarity, which requires that there be no clinically meaningful differences between the biological product and the reference product in terms of safety, purity, and potency, can be shown through analytical studies, animal studies, and a clinical study or studies. Interchangeability requires that a product is biosimilar to the reference product and the product must demonstrate that it can be expected to produce the same clinical results as the reference product and, for products administered multiple times, the biologic and the reference biologic may be switched after one has been previously administered without increasing safety risks or risks of diminished efficacy relative to exclusive use of the reference biologic. However, complexities associated with the larger, and often more complex, structure of biological products, as well as the process by which such products are manufactured, pose significant hurdles to implementation that are still being worked out by the FDA.

A reference biologic is granted twelve years of exclusivity from the time of first licensure of the reference product. The first biologic product submitted under the abbreviated approval pathway that is determined to be interchangeable with the reference product has exclusivity against other biologics submitting under the abbreviated approval pathway for the lesser of (i) one year after the first commercial marketing, (ii) 18 months after approval if there is no legal challenge, (iii) 18 months after the resolution in the applicant’s favor of a lawsuit challenging the biologics’ patents if an application has been submitted, or (iv) 42 months after the application has been approved if a lawsuit is ongoing within the 42-month period.Orphan Drug Designation (ODD).

Under the Orphan Drug Act, as amended, the FDA may grant ODD to a drug intended to treat a rare disease or condition, which is generally a disease or condition that affects fewer than 200,000 individuals in the United States or more than 200,000 individuals in the United States and for which there is no reasonable expectation that the cost of developing and making availablerecovering drug development costs in the United States a drug for this type of disease or condition will be recovered from sales in the United States for that drug.States. ODD must be requested before submitting an NDA. After the FDA grants ODD, the identity of the therapeutic agent and its potential orphan use are disclosed publicly by the FDA. We intend to request ODD designation for our product candidates, if applicable. For example, the FDA has granted ODD for patisiran as a therapeutic approach for the treatment of FAP and for ALN-AT3ATTR amyloidosis, givosiran as a therapeutic approach for hemophilia.AHPs, fitusiran as a therapeutic approach for hemophilia A and B, and inclisiran as a therapeutic approach for HoFH.

If a product that has ODD subsequently receives the first FDA approval for the disease for which it has such designation, the product is entitled to orphan productdrug exclusivity, which means that the FDA may not approve for seven years any other applications, including a full NDA, to market the same orphan drug for the same indication, except in very limited circumstances, for seven years.circumstances. For purposes of small molecule drugs, the FDA defines “same drug” as a drug that contains the same active moiety and is intended for the same use as the previously approved orphan drug. For purposes of large molecule drugs, the FDA defines “same drug” as a drug that contains the same principal molecular structural features, but not necessarily all of the same structural features, and is intended for the same use as the drug in question. Notwithstanding the above definitions, a drug that is clinically superior to an orphan drug will not be considered the “same drug” and thus will not be blocked by orphan drug exclusivity.

A designated orphan drug may not receive orphan drug exclusivity if it is approved for a use that is broader than the indication for which it received orphan designation. In addition, orphan drug exclusive marketing rights in the United States may be lost if the FDA later determines that the request for designation was materially defective or if the manufacturer is unable to assure sufficient quantities of the drug to meet the needs of patients with the rare disease or condition.


Pediatric Study Plans.

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The Orphan Products Grants Program in FDA’s Office of Orphan Products Development, or OOPD, with an annual budget of approximately $14.0 million, supports clinical development of products including drugs, biologics, medical devices and medical foods for use in rare diseases and conditions where no current therapy exists or where the proposed product will be superior to the existing therapy. This program provides grants for clinical studies on safety and/or effectiveness that will either result in, or substantially contribute to, market approval of these products. In addition, OOPD will administer a new grant program, the Pediatric Device Consortia Grant Program, resulting from the 2007 FDAAA legislation to support nonprofit consortia to facilitate pediatric medical device development. The future availability of such grants is subject to uncertainties regarding continued federal funding.

From time to time, legislation is drafted and introduced in Congress that could significantly change the statutory provisions governing the approval, manufacturing and marketing of drug products. In addition, FDA regulations and guidance are often revised or reinterpretedFDCA, as amended by the agency or reviewing courts in ways that may significantly affect our business and development of our product candidates and any products that we may commercialize. It is impossible to predict whether additional legislative changes will be enacted, or FDA regulations, guidance or interpretations changed, or what the impact of any such changes may be. Federal budget uncertainties or spending reductions may reduce the capabilities of the FDA, extend the duration of required regulatory reviews, and reduce the availability of clinical research grants.

Recently, the Food and Drug Administration Safety and Innovation Act, or FDASIA, which was signed into law on July 9, 2012, amended the FDCA. FDASIA, requires that a sponsor who is planning to submit a marketing application for a drug or biological product that includes a new active ingredient, new indication, new dosage form, new dosing regimen or new route of administration submit an initial Pediatric Study Plan, or PSP, within sixty days of an end-of-phase 2 meeting or as may be agreed between the sponsor and the FDA. Drugs with ODD are exempt from these requirements. The initial PSP must include an outline of the pediatric study or studies that the sponsor plans to conduct, including study objectives and design, age groups, relevant endpoints and statistical approach, or a justification for not including such detailed information, and any request for a deferral of pediatric assessments or a full or partial waiver of the requirement to provide data from pediatric studies along with supporting information. The FDA and the sponsor must reach agreement on the PSP. A sponsor can submit amendments to an agreed-upon initial PSP at any time if changes to the pediatric plan need to be considered based on data collected from nonclinical studies, early phase clinical trials, and/or other clinical development programs.

Fast Track Program.

The FDA has a Fast Track program that is intended to expedite or facilitate the process for reviewing new drugs and biological products that meet certain criteria. Specifically, new drugs and biological products are eligible for Fast Track designation if they are intended to treat a serious or life-threatening condition and demonstrate the potential to address unmet medical needs for the condition. Fast Track designation applies to the combination of the product and the specific indication for which it is being studied. The sponsor of a new drug or biological product may request the FDA to designate the drug or biologic as a Fast Track product at any time during the clinical development of the product. Unique to aproduct, but ideally no later than the pre-NDA or –biologics license application, or BLA, meeting. Fast Track product,designation provides opportunities for frequent interactions with FDA to expedite drug development and review as well as the FDA may consideropportunity for priority and/or rolling review sections of the marketing application on a rolling basis before the complete application is submitted, if the sponsor provides a schedule for the submission of the sections of the application, the FDA agrees to accept sections of the application and determines that the schedule is acceptable, and the sponsor pays any required user fees upon submission of the first section of the application.NDA. We intend to request Fast Track designation for our product candidates, if applicable. For example, the FDA granted Fast Track designation to patisiran for the treatment of FAP.hATTR amyloidosis.

Any product submitted to the FDA for marketing, including under a Fast Track program, may be eligible for other types of FDA programs intended to expedite development and review, such as priority review and accelerated approval. Any product is eligible for priority review if it has the potential totreats a serious condition and, if approved, would provide safe and effective therapy where no satisfactory alternative therapy exists or a significant improvement in the safety or effectiveness of treatment, diagnosis or prevention of a disease compared to marketed products. The FDA will attempt to direct additional resources to the evaluation ofFDA’s goal for taking action on an application forwith a new drug or biological product designatedPriority Review designation is six months instead of ten months. The FDA granted our request for priority review infor patisiran and has set an effort to facilitateaction date of August 11, 2018 under the review.PDUFA. Additionally, a product may be eligible for accelerated approval. Drug or biological products studied for their safety and effectiveness in treating serious or life-threatening illnesses and

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that provide meaningful therapeutic benefit over existing treatments may receive accelerated approval, which means that they may be approved on the basis of adequate and well-controlled clinical studies establishing that the product has an effect on a surrogate endpoint that is reasonably likely to predict a clinical benefit, or on the basis of an effect on a clinical endpoint other than survivalirreversible morbidity or mortality that is reasonably likely to predict an effect on irreversible morbidity.morbidity or mortality or other clinical benefits. As a condition of approval, the FDA may require that a sponsor of a drug or biological product receiving accelerated approval perform adequate and well-controlled post-marketing clinical studies.studies to verify the predicted clinical benefit. In addition, the FDA currently requires as a condition for accelerated approval pre-approval of promotional materials, which could adversely impact the timing of the commercial launch of the product. Fast Track designation, priority review and accelerated approval do not change the standards for approval but may expedite the development or approval process.

The Food and Drug Administration Safety and Innovation Act of 2012Breakthrough Therapy Designation.

FDASIA also amended the FDCA to require the FDA to expedite the development and review of a “breakthrough therapy.” A drug or biological product can be designated as a breakthrough therapy if it is intended to treat a serious or life-threatening disease or condition and preliminary clinical evidence indicates that it may demonstrate substantial improvement over existing therapies on one or more clinically significant endpoints. A sponsor may request that a drug or biological product be designated as a breakthrough therapy at any time during the clinical development of the product. If so designated, the FDA shall act to expedite the development and review of the product’s marketing application, including by meeting with the sponsor throughout the product’s development, providing timely advice to the sponsor to ensure that the development program to gather nonclinical, manufacturing/controls and clinical data is as efficient as practicable, involving senior managers and experienced review staff in a cross-disciplinary review, assigning a cross-disciplinary project lead for the FDA review team to facilitate an efficient review of the development program and to serve as a scientific liaison between the review team and the sponsor, and taking steps to ensure that the design of the clinical trials is as efficient as practicable.practicable, and allowing a rolling review. The FDA granted Breakthrough Therapy designation for patisiran and givosiran. We intend to request “breakthrough therapy” designation for our other product candidates, if applicable.


Foreign Regulation of New Drug Compounds

In addition to regulations in the United States, we are subject to a variety of regulations in other jurisdictions governing, among other things, clinical trials and any commercial sales and distribution of our products.

Whether or not we obtain FDA approval for a product, we must obtain the requisite approvals from regulatory authorities in all or most foreign countries prior to the commencement of clinical trials or marketing of the product in those countries. Certain countries outside of the United States have a similar process that requires the submission of a clinical trial application, or CTA, much like the IND prior to the commencement of human clinical trials. In Europe, for example, a CTA must be submitted to each country’s national health authority and an independent ethics committee, much like the FDA and IRB, respectively. Once the CTA is approved in accordance with a country’s requirements, clinical trial development may proceed. Similarly, all clinical trials in Australia require, among other things, review and approval of clinical trial proposals by an ethics committee, which provides a combined ethical and scientific review process.

The requirements and process governing the conduct of clinical trials, product licensing, pricing and reimbursement vary from country to country. In all cases, the clinical trials must be conducted in accordance with GCP, which have their origin in the World Medical Association’s Declaration of Helsinki, the applicable regulatory requirements, and guidelines developed by the International Conference on Harmonization for GCP practices in clinical trials.

The approval procedure also varies among countries and can involve requirements for additional testing. The time required may differ from that required for FDA approval and may be longer than that required to obtain FDA approval. Although there are some procedures for unified filings in the EU, in general, each country has its own procedures and requirements, many of which are time consuming and expensive. Thus, there can be substantial delays in obtaining required approvals from foreign regulatory authorities after the relevant applications are filed.

In Europe, marketing authorizations may be submitted under a centralized or decentralized procedure. The centralized procedure is mandatory for the approval of biotechnology and many pharmaceutical products and

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provides for the grant of a single marketing authorization that is valid in all EU member states. The decentralized procedure is a mutual recognition procedure that is available at the request of the applicant for medicinal products that are not subject to the centralized procedure. We intend to strive to choose the appropriate route of European regulatory filing to accomplish the most rapid regulatory approvals. However, our chosen regulatory strategy may not secure regulatory approvals on a timely basis or at all.

If we fail to comply with applicable foreign regulatory requirements, we may be subject to, among other things, fines, suspension or withdrawal of regulatory approvals, product recalls, seizure of products, operating restrictions and criminal prosecution.

Pharmaceutical Coverage, Pricing and ReimbursementReimbursement.

Significant uncertainty exists as to the coverage and reimbursement status of any drug products for which we obtain regulatory approval. In the United States and markets in other countries, sales of any products for which we may receive regulatory approval for commercial sale will depend in part on the availability of reimbursement from third-party payors. Third-party payors include government health administrative authorities,healthcare programs, managed care providers, private health insurers and other organizations. The process for determining whether a payor will provide coverage for a drug product may be separate from the process for setting the price or reimbursement rate that the payor will pay for the drug product. Third-party payors may limit coverage to specific drug products on an approved list, or formulary, which might not include all of the FDA-approved drugs for a particular indication. Third-party payors may provide coverage, but place stringent limitations on such coverage, such as requiring alternative treatments to be tried first. These third-party payors are increasingly challenging the price and examining the medical necessity and cost-effectiveness of medical products and services, in addition to their safety and efficacy. In addition, significant uncertainty exists as to the reimbursement status of newly approved healthcare product candidates.products. We may need to conduct expensive pharmacoeconomic studies in order to demonstrate the medical necessity and cost-effectiveness of our products, in addition to incurring the costs required to obtain FDA approvals. Our product candidates may not be considered medically reasonable or necessary or cost-effective. Even if a drug product is covered, a payor’s decision to provide coverage for a drug product does not imply that an adequate reimbursement rate will be approved. Adequate third-party reimbursement may not be available to enable us to maintain price levels sufficient to realize an appropriate return on our investment in product development.

Federal, state and local governments in the United States and foreign governments continue to consider legislation to limit the growth of healthcare costs, including the cost of prescription drugs. Specifically, there have been several recent U.S. Congressional inquiries and proposed federal and state legislation designed to, among other things, bring more transparency to drug pricing, reduce the cost of prescription drugs under Medicare, review the relationship between pricing and manufacturer patient programs, and reform government program reimbursement methodologies for drugs.  On January 2, 2013, the American Taxpayer Relief Act of 2012 was signed into law, which, among other things, further reduced Medicare payments to several types of providers. Future legislation could limit payments for pharmaceuticals such as the drug candidates that we are developing.

Different pricing and reimbursement schemes exist in other countries. In the EU, governments influence the price of pharmaceuticaldrug products through their pricing and reimbursement rules and control of national health care systems that fund a large part of the cost of those products to consumers. Some jurisdictions operate systems under which products may be marketed only after a reimbursement price has been agreed. To obtain reimbursement or pricing approval, some of these countries may require the completion of clinical trials that compare the cost-effectiveness of a particular product candidate to currently available therapies. Other member states allow companies to set their own prices for medicines, but monitor and control company profits. The downward pressure on health care costs in general, particularly prescription drugs, has become very intense. As a result, increasingly high barriers are being erected to the entry of new products. In addition, in some countries, cross-border imports from low-priced markets exert competitive pressure that may reduce pricing within a country.

The marketability of any products for which we receive regulatory approval for commercial sale may suffer if the government and third-party payors fail to provide adequate coverage and reimbursement. In addition, the emphasis on managed care in the United States has increased and we expect will continue to exert downward pressure on pharmaceutical pricing. Coverage policies, third-party reimbursement rates and pharmaceutical pricing regulations may change at any time. Even if favorable coverage and reimbursement status is attained for one or more products for which we receive regulatory approval, less favorable coverage policies and reimbursement rates may be implemented in the future.

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In March 2010, the PPACA,Patient Protection and Affordable Care Act, also referred to as amended by the HealthAffordable Care and Education Reconciliation Act of 2010,or the PPACA, was enacted, which includes measures that have or will significantly change the way health care is financed by both governmental and private insurers. Among the provisions of the PPACA of greatest importance to the pharmaceutical industry are the following:

The Medicaid Drug Rebate Program requires pharmaceutical manufacturers to enter into and have in effect a national rebate agreement with the Secretary of the Department of Health and Human Services as a condition for states to receive federal matching funds for the manufacturer’s outpatient drugs furnished to Medicaid patients. Effective in 2010, the PPACA made several changes to the Medicaid Drug Rebate Program, including increasing pharmaceutical manufacturers’ rebate liability by raising the minimum basic Medicaid rebate on most branded prescription drugs and biologic agentsproducts from 15.1%15.1 percent of average manufacturer price, or AMP, to 23.1%23.1 percent of AMP and adding a new rebate calculation for “line extensions” (i.e., new formulations, such as extended release formulations) of solid oral dosage forms of branded products, as well as potentially impacting their rebate liability by modifying the statutory definition of AMP. PPACA also expanded the universe of Medicaid utilization subject to drug rebates by requiring pharmaceutical manufacturers to pay rebates on Medicaid managed care utilization as of 2010 and by expanding the population potentially eligible for Medicaid drug benefits, to be phased-in by 2014. The Centers for Medicare and Medicaid Services, or CMS, have proposed to expand Medicaid rebate liability to the territories of the United States as well. In addition, the PPACA provides for the public availability of retail survey prices and certain weighted average AMPs under the Medicaid program. The implementation of this requirement by the Centers for Medicare and Medicaid Services, or CMS, may also provide for the public availability of pharmacy acquisition of cost data, which could negatively impact our sales.

In order for a pharmaceutical product to receive federal reimbursement under the Medicare Part B and Medicaid programs or to be sold directly to U.S. government agencies, the manufacturer must extend discounts to entities eligible to participate in the 340B drug pricing program. The required 340B discount on a given product is calculated based on the AMP and Medicaid rebate amounts reported by the manufacturer. Effective in 2010, PPACA expanded the types of entities eligible to receive discounted 340B pricing, although, under the current state of the law, with the exception of children’s hospitals, these newly eligible entities will not be eligible to receive discounted 340B pricing on orphan drugs when used for the orphan indication. In addition, as 340B drug pricing is determined based on AMP and Medicaid rebate data, the revisions to the Medicaid rebate formula and AMP definition described above could cause the required 340B discount to increase.


 

In order for a drug product to receive federal reimbursement under the Medicare Part B and Medicaid programs or to be sold directly to U.S. government agencies, the manufacturer must extend discounts to entities eligible to participate in the 340B drug pricing program. The required 340B discount on a given product is calculated based on the AMP and Medicaid rebate amounts reported by the manufacturer. Effective in 2010, the PPACA expanded the types of entities eligible to receive discounted 340B pricing, although, under the current state of the law, with the exception of children’s hospitals, these entities will not be eligible to receive discounted 340B pricing on orphan drugs. In addition, as 340B drug pricing is determined based on AMP and Medicaid rebate data, the revisions to the Medicaid rebate formula and AMP definition described above could cause the required 340B discount to increase.

Effective in 2011, the PPACA imposed a requirement on manufacturers of branded drugs and biologic agentsproducts to provide a 50%50 percent discount off the negotiated price of branded drugs dispensed to Medicare Part D patients in the coverage gap (i.e., “donut hole”).

Effective in 2011, the PPACA imposed an annual, nondeductible fee on any entity that manufactures or imports certain branded prescription drugs and biologic agents,products, apportioned among these entities according to their market share in certain government healthcare programs, although this fee would not apply to sales of certain products approved exclusively for orphan indications.

Effective in 2012, the PPACA required pharmaceuticalcertain manufacturers to track certain financial arrangements with physicians and teaching hospitals, including any “transfer of value” made or distributed to such entities, as well as any investment interests held by physicians and their immediate family members. Manufacturers were required to begin tracking this information in 2013 and toannually report this information to CMS, beginning in 2014.which posts this information on its website.

As of 2010, a new Patient-Centered Outcomes Research Institute was established pursuant to the PPACA to oversee, identify priorities in, and conduct comparative clinical effectiveness research, along with funding for such research. The research conducted by the Patient-Centered Outcomes Research Institute may affect the market for certain pharmaceuticaldrug products.

The PPACA created the Independent Payment Advisory Board which, beginning in 2014, will havehas authority to recommend certain changes to the Medicare program to reduce expenditures by the program that could result in reduced payments for prescription drugs. Under certain circumstances, these recommendations will become law unless Congress enacts legislation that will achieve the same or greater Medicare cost savings.

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result in reduced payments for prescription drugs. Under certain circumstances, these recommendations will become law unless Congress enacts legislation that will achieve the same or greater Medicare cost savings.

The PPACA established the Center for Medicare and Medicaid Innovation within CMS to test innovative payment and service delivery models to lower Medicare and Medicaid spending, potentially including prescription drug spending. Funding has been allocated to support the mission of the Center for Medicare and Medicaid Innovation from 2011 to 2019.

The law expands eligibility criteria for Medicaid programs by, among other things, allowing states to offer Medicaid coverage to certain individuals with income at or below 133 percent of the federal poverty level, thereby potentially increasing a manufacturer's Medicaid rebate liability.

Possible Change in Laws or Policies.

From time to time, legislation is drafted and introduced in Congress that could significantly change the statutory provisions governing the approval, manufacturing and marketing of drug products. In addition, FDA regulations and guidance are often revised or reinterpreted by the agency or reviewing courts in ways that may significantly affect our business and development of our product candidates and any products that we may commercialize. It is impossible to predict whether additional legislative changes will be enacted, or FDA regulations, guidance or interpretations will be changed, or what the impact of any such changes may be. Federal budget uncertainties or spending reductions may reduce the capabilities of the FDA, extend the duration of required regulatory reviews, and reduce the availability of clinical research grants.

EU Regulatory Considerations

In the EU medicinal products are subject to extensive pre- and post-market regulation by regulatory authorities at both the EU and national levels.

Clinical Trials.

Clinical trials of medicinal products in the EU must be conducted in accordance with EU and national regulations and the International Conference on Harmonization, or ICH, guidelines on GCP. If the sponsor of the clinical trial is not established within the EU, it must appoint an entity within the EU to act as its legal representative. The sponsor must take out a clinical trial insurance policy, and in most EU countries the sponsor is liable to provide ‘no fault’ compensation to any study subject injured in the clinical trial.


Prior to commencing a clinical trial, the sponsor must obtain a CTA from the competent authority, and a positive opinion from an independent ethics committee. The application for a CTA must include, among other things, a copy of the trial protocol and an investigational medicinal product dossier containing information about the manufacture and quality of the medicinal product under investigation. Any substantial changes to the trial protocol or other information submitted with the clinical trial applications must be notified to or approved by the relevant competent authorities and ethics committees.

Currently, CTAs must be submitted to the competent authority in each EU member state in which the trial will be conducted. Under the new Regulation on Clinical Trials, which is currently expected to come into application in the second half of 2019, there will be a centralized application procedure where one national authority leads the scientific review of the application leading to increased information-sharing and decision-making between member states.  Each concerned member state will continue to complete an ethical review of any CTA.

Information related to the product, patient population, phase of investigation, study sites and investigators, and other aspects of the clinical trial is made public by the competent authority once the CTA is approved. The results of the clinical trial must be submitted by the sponsor to the competent authorities and, with the exception of non-pediatric Phase 1 trials, will be made public at the latest within six months of the end of a pediatric clinical trial, or otherwise within 12 months after the end of the trial.

During the development of a medicinal product, the EMA and national medicines regulators within the EU provide the opportunity for dialogue and guidance on the development program. At the EMA level, this is usually done in the form of scientific advice, which is given by the Scientific Advice Working Party of the Committee for Medicinal Products for Human Use, or CHMP. A fee is incurred with each scientific advice procedure. Advice from the EMA is typically provided based on questions concerning, for example, quality (chemistry, manufacturing and controls testing), nonclinical testing and clinical studies, and pharmacovigilance plans and risk-management programs. Advice is not legally binding with regard to any future marketing authorisation application of the product concerned.

Marketing Authorisations.

After completion of the required clinical testing, we must obtain a marketing authorisation before we may place a medicinal product on the market in the EU. There are various application procedures available, depending on the type of product involved. All application procedures require an application in the common technical document, or CTD, format, which includes the submission of detailed information about the manufacturing and quality of the product, and nonclinical study and clinical trial information. There is an increasing trend in the EU towards greater transparency and, while the manufacturing or quality information is currently generally protected as confidential information, the EMA and national regulatory authorities are now liable to disclose much of the nonclinical and clinical information in marketing authorisation dossiers, including the full clinical study reports, in response to freedom of information requests after the marketing authorisation has been granted. In October 2014, the EMA adopted a policy under which clinical study reports would be posted on the agency’s website following the grant, denial or withdrawal of a marketing authorisation application, subject to procedures for limited redactions and protection against unfair commercial use. A similar requirement is contained in the new Regulation on Clinical Trials that is currently expected to take effect in the second half of 2019.

The centralized procedure gives rise to marketing authorisations that are valid throughout the EU and, by extension (after national implementing decisions), in Norway, Iceland and Liechtenstein, which, together with the EU member states, comprise the European Economic Area, or EEA. Applicants file MAAs with the EMA, where they are reviewed by relevant scientific committees, including the CHMP. The EMA forwards CHMP opinions to the European Commission, or EC, which uses them as the basis for deciding whether to grant a marketing authorisation. The centralized procedure is compulsory for medicinal products that (1) are derived from biotechnology processes, (2) contain a new active substance (not yet approved on November 20, 2005) indicated for the treatment of certain diseases, such as HIV/AIDS, cancer, diabetes, neurodegenerative disorders, viral diseases or autoimmune diseases and other immune dysfunctions, (3) are orphan medicinal products or (4) are advanced therapy medicinal products, such as gene or cell therapy medicines. For medicines that do not fall within these categories, an applicant may voluntarily submit an application for a centralized marketing authorisation to the EMA, as long as the CHMP agrees that (i) the medicine concerned contains a new active substance (not yet approved on November 20, 2005), (ii) the medicine is a significant therapeutic, scientific, or technical innovation, or (iii) if its authorization under the centralized procedure would be in the interest of public health. In December 2017, we submitted our first MAA for patisiran under the centralized procedure, which has been accepted by the EMA.

For those medicinal products for which the centralized procedure is not available, the applicant must submit MAAs to the national medicines regulators through one of three procedures: (1) a national procedure, which results in a marketing authorisation in a single EU member state; (2) the decentralized procedure, in which applications are submitted simultaneously in two or more EU member states; and (3) the mutual recognition procedure, which must be used if the product has already been authorized in at least one other EU member state, and in which the EU member states are required to grant an authorization recognizing the existing authorization in the other EU member state, unless they identify a serious risk to public health. A national procedure is only possible


for one member state; as soon as an application is submitted in a second member state the mutual recognition or decentralized procedure will be triggered.

Under the centralized procedure in the EU, the maximum timeframe for the evaluation of an MAA is 210 days. However, this timeline excludes clock stops, when additional written or oral information is to be provided by the applicant in response to questions asked by the CHMP, so the overall process typically takes a year or more. Accelerated evaluation might be granted by the CHMP in exceptional cases, when a medicinal product is expected to be of a major interest for public health and therapeutic intervention, defined by the absence or insufficiency of an appropriate alternative therapeutic approach for the disease to be treated; and anticipation of high therapeutic benefit of the new product. In this circumstance, EMA ensures that the opinion of the CHMP is given within 150 days. In November 2017, the EMA granted an accelerated assessment for patisiran.

Data Exclusivity.

MAAs for generic medicinal products do not need to include the results of pre-clinical studies and clinical trials, but instead can refer to the data included in the marketing authorisation of a reference product for which regulatory data exclusivity has expired. If a marketing authorisation is granted for a medicinal product containing a new active substance, that product benefits from eight years of data exclusivity, during which generic MAAs referring to the data of that product may not be accepted by the regulatory authorities, and a further two years of market exclusivity, during which such generic products may not be placed on the market. The two-year period may be extended to three years if during the first eight years a new therapeutic indication with significant clinical benefit over existing therapies is approved.

There is a special regime for biosimilars, or biological medicinal products that are similar to a reference medicinal product but that do not meet the definition of a generic medicinal product, for example, because of differences in raw materials or manufacturing processes. For such products, the results of appropriate pre-clinical studies or clinical trials must be provided, and guidelines from the EMA detail the type of quantity of supplementary data to be provided for different types of biological product. There are no such guidelines for complex biological products, such as gene or cell therapy medicinal products, and so it is unlikely that biosimilars of those products will currently be approved in the EU. However, guidance from the EMA states that they will be considered in the future in light of the scientific knowledge and regulatory experience gained at the time.

Orphan Medicinal Products.

The EMA’s COMP may recommend orphan medicinal product designation to promote the development of products that are intended for the diagnosis, prevention or treatment of life-threatening or chronically debilitating conditions affecting not more than five in 10,000 persons in the EU. Additionally, designation is granted for products intended for the diagnosis, prevention or treatment of a life-threatening, seriously debilitating or serious and chronic condition and when, without incentives, it is unlikely that sales of the product in the EU would be sufficient to justify the necessary investment in developing the medicinal product. The COMP may only recommend orphan medicinal product designation when the product in question offers a significant clinical benefit over existing approved products for the relevant indication. Following a positive opinion by the COMP, the EC adopts a decision granting orphan status. The COMP will reassess orphan status in parallel with EMA review of an MAA and orphan status may be withdrawn at that stage if it no longer fulfills the orphan criteria (for instance because in the meantime a new product was approved for the indication and no convincing data are available to demonstrate a significant benefit over that product). Orphan medicinal product designation entitles a party to financial incentives such as reduction of fees or fee waivers and ten years of market exclusivity is granted following marketing authorisation. During this period, the competent authorities may not accept or approve any similar medicinal product for the same therapeutic indication, unless the second medicinal product is safer, more effective or otherwise clinically superior. This period may be reduced to six years if the orphan medicinal product designation criteria are no longer met, including where it is shown that the product is sufficiently profitable not to justify maintenance of orphan designation.  Patisiran, givosiran and fitusiran have been granted orphan medicinal product designation.

Post-Approval Controls.

The holder of a marketing authorisation must establish and maintain a pharmacovigilance system and appoint an individual qualified person for pharmacovigilance, or QPPV, who is responsible for oversight of that system. Key obligations include expedited reporting of suspected serious adverse reactions and submission of periodic safety update reports, or PSURs.

All new MAAs must include a risk management plan, or RMP, describing the risk management system that the company will put in place and documenting measures to prevent or minimize the risks associated with the product. The regulatory authorities may also impose specific obligations as a condition of the marketing authorisation. Such risk-minimization measures or post-authorization obligations may include additional safety monitoring, more frequent submission of PSURs, or the conduct of additional clinical trials


or post-authorization safety studies. RMPs and PSURs are routinely available to third parties requesting access, subject to limited redactions.

All advertising and promotional activities for the product must be consistent with the approved summary of product characteristics, and therefore all off-label promotion is prohibited. Direct-to-consumer advertising of prescription medicines is also prohibited in the EU. Although general requirements for advertising and promotion of medicinal products are established under EU directives, the details are governed by regulations in each member state and can differ from one country to another.

Manufacturing.

Medicinal products may only be manufactured in the EU, or imported into the EU from another country, by the holder of a manufacturing authorization from the competent national authority. The manufacturer or importer must have a qualified person, or QP, who is responsible for certifying that each batch of product has been manufactured in accordance with EU standards of cGMP before releasing the product for commercial distribution in the EU or for use in a clinical trial. Manufacturing facilities are subject to periodic inspections by the competent authorities for compliance with cGMP.

Pricing and Reimbursement.

Governments influence the price of medicinal products in the EU through their pricing and reimbursement rules and control of national healthcare systems that fund a large part of the cost of those products to consumers. Some jurisdictions operate positive and negative list systems under which products may only be marketed once a reimbursement price has been agreed. To obtain reimbursement or pricing approval, some of these countries may require the completion of clinical trials that compare the cost-effectiveness of a particular product candidate to currently available therapies. Other member states allow companies to fix their own prices for medicines, but monitor and control company profits. The downward pressure on healthcare costs in general, particularly prescription medicines, has become very intense. As a result, increasingly high barriers are being erected to the entry of new products.

Foreign Regulation of New Drug Compounds

In addition to regulations in the United States and the EU, we are subject to a variety of regulations in other jurisdictions governing, among other things, clinical trials and any commercial sales and distribution of our products. In particular, we plan to file for regulatory approval in Japan in mid-2018 and in one or more additional countries by the end of the year, and will have to follow the specific regulations in Japan and such other countries, which are complex.

Whether or not we obtain FDA approval for a product, we must obtain the requisite approvals from regulatory authorities in all or most foreign countries prior to the commencement of clinical trials or marketing of the product in those countries. Certain countries outside of the United States have a similar process that requires the submission of a CTA, much like the IND prior to the commencement of human clinical trials. Once the CTA is approved in accordance with a country’s requirements, clinical trial development may proceed. Similarly, all clinical trials in Australia require, among other things, review and approval of clinical trial proposals by an ethics committee, which provides a combined ethical and scientific review process.

The requirements and process governing the conduct of clinical trials, product licensing, pricing and reimbursement vary from country to country. In all cases, the clinical trials must be conducted in accordance with GCP, which have their origin in the World Medical Association’s Declaration of Helsinki, the applicable regulatory requirements, and guidelines developed by the ICH for GCP in clinical trials.

The approval procedure also varies among countries and can involve requirements for additional testing. The time required may differ from that required for FDA approval and may be longer than that required to obtain FDA approval. Thus, there can be substantial delays in obtaining required approvals from foreign regulatory authorities after the relevant applications are filed.

If we fail to comply with applicable foreign regulatory requirements, we may be subject to, among other things, fines, suspension or withdrawal of regulatory approvals, product recalls, seizure of products, operating restrictions and criminal prosecution.

Hazardous Materials

Our research, development and manufacturing processes involve the controlled use of hazardous materials, chemicals and radioactive materials and produce waste products. We are subject to federal, state and local laws and regulations governing the use, manufacture, storage, handling and disposal of hazardous materials and waste products. We do not expect the cost of complying with these laws and regulations to be material.


Manufacturing

To date, we have manufactured only limited supplies of drug substance for use in IND-enabling toxicology studies in animals at our own facility, as well as patisiran formulated bulk drug product for use in clinical trials, and if approved, for commercial sale.  We have contracted with several third-party contract manufacturing organizations, or CMOs, for the supply of drug substance and finished product, other than patisiran, to meet our testing needs for pre-clinical toxicology and clinical testing. We expect to continue to rely on third-party contract manufacturing organizationsCMOs for the supply of drug substance and certain drug product, including siRNAs and siRNA conjugates, for our product candidates for at least the foreseeable future. next several years, including to support the launch of our first several products and to supply Sanofi Genzyme with fitusiran under the AT3 License Terms. During 2015, we amended our manufacturing agreement with Agilent Technologies, Inc., or Agilent, to provide for Agilent to supply, subject to any conflicting obligations under our third-party agreements, a specified percentage of the active pharmaceutical ingredients required for certain of our products in clinical development, as well as other products the parties may agree upon in the future, over an initial term of four years. We are required to provide rolling forecasts for products on a quarterly basis, a portion of which will be considered a binding, firm order. Agilent is required to reserve sufficient capacity to ensure that it can supply products in the amounts specified under such firm orders, as well as up to a certain percentage of the remaining, non-binding portions of each forecast. Subject to any conflicting obligations under our third-party agreements, we have also agreed to negotiate in good faith to enter into a separate commercial manufacturing supply agreement with Agilent for certain products, consistent with certain specified terms, including a specified minimum purchase commitment. Currently, Agilent is the sole manufacturer of the active pharmaceutical ingredients for patisiran for clinical and commercial use. In April 2016, we completed our purchase of a parcel of land in Norton, Massachusetts. We have commenced construction of a cGMP manufacturing facility at this site for drug substance, including siRNAs and siRNA conjugates, for clinical and commercial use, which we currently expect to be operational in 2020.

During 2012, we established a manufacturing facility and have developed cGMP capabilities and processes for the manufacture of patisiran formulated bulk drug product for late-stagelate stage clinical trials and commercial use. During 2013, we manufactured our first cGMP batches of patisiran for use in our Phase 2 OLE and Phase 3 clinical trials. We expect towill manufacture late-stage clinical and commercial supply for patisiran formulated bulk drug product in our facility. Infacility for the future, we may also develop our own capabilities to manufacture drug substance, including siRNAs and siRNA conjugates for human clinical use.foreseeable future. Commercial quantities of any drugs that we may seek to develop will have to be manufactured in facilities, and by processes, that comply with FDA regulations and other federal, state and local regulations, as well as comparable foreign regulations.

We believe we have sufficient manufacturing capacity through our third-party contract manufacturersCMOs and our current internal cGMP manufacturing facility to meet our current research, clinical and early-stage commercial needs.needs and the needs of Sanofi Genzyme for clinical supply. We believe that the supply capacity we have established externally, together with the internal capacity we developed to support pre-clinical trials, our existing facility for patisiran formulated bulk drug product and the new facility we are building, will be sufficient to meet our and Sanofi Genzyme’s anticipated needs for the next several years. We monitor the capacity availability for the manufacture of drug substance and drug product and believe that our supply agreements with our contract manufacturesCMOs and the lead times for new supply agreements would allow us to access additional capacity to meet our and Sanofi Genzyme’s currently anticipated needs. We also believe that our products can be manufactured at a scale and with production and procurement efficiencies that will result in commercially competitive costs.

Commercial Operations

After successfully overcoming various challenges associated with developing a potential new class of innovative medicines - such as solving the issue of drug delivery, optimizing our RNAi therapeutics to exhibit potency and durability of effect, and designing and carrying out comprehensive clinical trials to demonstrate the safety and clinical efficacy of our investigational products - we now embark on the next part of the journey; introducing our RNAi therapeutics to as many eligible patients in need as possible. To meet that new challenge, we have started to build a global commercial operation which will be fully integrated and ready to sequentially manage the potential of multiple product launches across multiple geographies. As a commercial-stage biopharmaceutical company, we intend to leverage the internal knowledge accumulated at Alnylam as well as hire talented people from industry to commercialize our products ourselves in key countries globally. The conduct of these commercial activities will be dependent upon regulatory approvals and on agreements that we have made or may make in the future with strategic collaborators, currently as follows with respect to our late-stage clinical programs:

For patisiran, we now have global rights to develop and commercialize patisiran, pending approval by regulatory authorities, and other TTR products, including ALN-TTRsc02 and any back-ups, as a result of the 2018 amendment to the Sanofi Genzyme collaboration and the related Exclusive TTR License;

For givosiran, we retain global rights to develop and commercialize;

For fitusiran, Sanofi Genzyme has global rights to develop and commercialize fitusiran and any back-ups as a result of the 2018 amendment to the Sanofi Genzyme collaboration and the related AT3 License Terms; and

For inclisiran, we have granted MDCO global rights to develop and commercialize.


Scientific AdvisorsThroughout the development of our product candidates, we have remained focused on keeping patients at the center of everything we do. This patient focus will continue as we transition towards commercialization. Moreover, the late stage programs we are advancing to commercialization are focused on orphan diseases, and these patients and their families are often in need of more than just a product. It is our goal to identify information, education solutions and services that benefit these patients and their families, and to have a rich patient services approach in these orphan diseases. In addition, we are focused early in the product development cycle on establishing evidence that we can bring to payors about the overall burden of disease and pharmacoeconomic opportunities that our product candidates represent to ensure access for patients.

We seek advice from our scientific advisory board, which consistsare assembling the key components of a numberglobal commercial organization with a focus on preparation for the anticipated commercial launch of leading scientistspatisiran in 2018, assuming regulatory approval is obtained. We have already initiated a staged build of commercial capabilities with the planned hire of approximately 250 employees deployed in customer facing activities across the world, initially in the United States and physicians, on scientificmajor European countries, followed by Canada and medical matters.Switzerland, with a phased approach to the Asia Pacific, Latin American and Middle Eastern regions. We plan to build a focused commercial team with broad experience in marketing, sales, patient access, patient services, distribution and product reimbursement, in particular for orphan diseases.  In the coming months, we will continue to expand our footprint in major European markets and beyond.  During 2017, as we prepared for a potential patisiran commercial launch in the United States and Europe in 2018, we continued to expand our commercial organization, incorporating the appropriate quality systems, compliance policies, systems and procedures, as well as implementing internal systems and infrastructure in order to support commercial sales, and the establishment of patient-focused programs. Given our accelerated global commercial opportunity, we intend to expand these capabilities more broadly during 2018 as we strategically assess the global opportunity for patisiran. Ultimately, we intend to leverage the commercial infrastructure that we build to support the potential launches of givosiran and ALN-TTRsc02.  Our scientific advisory board meets regularlyobjective is to assess:

our research and development programs;

be ready to execute successful product launches. For many territories/countries, we may also elect to utilize strategic partners, distributors or contract sales forces to assist in the design and implementationcommercialization of our clinical programs;

our patent and publication strategies;

new technologies relevant to our research and development programs; and

specific scientific and technical issues relevant to our business.

products.

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The current members of our scientific advisory board are:

Name

Position/Institutional Affiliation

Dennis A. Ausiello, M.D.

Director/Center for Assessment Technology and Continuous Health (CATCH); Jackson Distinguished Professor of Clinical Medicine/Harvard Medical School; Physician-in-Chief Emeritus/Massachusetts General Hospital

David P. Bartel, Ph.D.

Member/Whitehead Institute for Biomedical Research; Professor/Massachusetts Institute of Technology; Investigator/Howard Hughes Medical Institute

Robert S. Langer, Ph.D.

Institute Professor/Massachusetts Institute of Technology

Judy Lieberman, M.D., Ph.D.

Senior Investigator/Immune Disease Institute — Harvard Medical School;

Professor/Harvard Medical School

Paul R. Schimmel, Ph.D.

Ernest and Jean Hahn Professor/Skaggs Institute for Chemical Biology, The Scripps Research Institute

Phillip A. Sharp, Ph.D.

Institute Professor/The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology

Daniel J. Rader, M.D.

Professor of Molecular Medicine and Chief, Division of Translational Medicine and Human Genetics/Perelman School of Medicine, University of Pennsylvania

Markus Stoffel, M.D., Ph.D.

Professor/Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich

Thomas H. Tuschl, Ph.D.

Professor/Rockefeller University; Investigator/Howard Hughes Medical Institute

Phillip D. Zamore, Ph.D.

Gretchen Stone Cook Professor/University of Massachusetts Medical School;

Co-Director/RNA Therapeutics Institute, University of Massachusetts Medical School; Investigator/Howard Hughes Medical Institute

Employees

At January 31, 2015,2018, we had 256 employees, 220 of whom were engaged in research and development.749 employees. None of our employees are represented by a labor union or covered by a collective bargaining agreement, nor have we experienced work stoppages. We believe that relations with our employees are good.

Financial Information About Geographic Areas

See the section entitled “Segment Information” appearing in Note 2 to our consolidated financial statements for financial information about geographic areas. The Notes to our consolidated financial statements are contained in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K.

Corporate Information

The company comprises seven entities, Alnylam Pharmaceuticals, Inc. and six wholly owned subsidiaries (Alnylam U.S., Inc., Alnylam Europe AG, Alnylam (Bermuda) Ltd., Alnylam UK Limited, Alnylam Securities Corporation and Sirna Therapeutics, Inc.). Alnylam Pharmaceuticals, Inc. is a Delaware corporation that was formed in May 2003. Alnylam U.S., Inc., one of our wholly owned subsidiaries, is also a Delaware corporation that was formed in June 2002. Alnylam Securities Corporation is a Massachusetts corporation that was formed in December 2006. Alnylam Europe AG, which was incorporated in Germany in June 2000 under the name Ribopharma AG, was acquired by Alnylam Pharmaceuticals, Inc. in July 2003. Alnylam (Bermuda) Ltd., an entity organized under the laws of Bermuda, was formed in August 2013. Alnylam UK Limited, an entity organized under the laws of the United Kingdom, was formed in January 2014. Sirna Therapeutics, Inc. is a Delaware corporation that was acquired by Alnylam Pharmaceuticals, Inc. from Merck in March 2014.2002 as our initial corporate entity. Our principal executive office is located at 300 Third Street, Cambridge, Massachusetts 02142, and our telephone number is (617) 551-8200.

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Investor Information

We maintain an internet website athttp://www.alnylam.com. The information on our website is not incorporated by reference into this annual report on Form 10-K and should not be considered to be a part of this annual report on Form 10-K. Our website address is included in this annual report on Form 10-K as an inactive technical reference only. Our reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended, including our annual reports on Form 10-K, our quarterly reports on Form 10-Q and our current reports on Form 8-K, and amendments to those reports, are accessible through our website, free of charge, as soon as reasonably practicable after these reports are filed electronically with, or otherwise furnished to, the United States Securities and Exchange Commission, or SEC. We also make available on our website the charters of our audit committee, compensation committee, nominating and corporate governance committee, and science and technology committee, as well as our corporate governance guidelines and our code of business conduct and ethics. In addition, we intend to disclose on our web site any amendments to, or waivers from, our code of business conduct and ethics that are required to be disclosed pursuant to the SEC rules.


You may read and copy any materials we file with the SEC at the SEC’s Public Reference Room at 100 F Street, NE, Washington, DC 20549. You may obtain information on the operation of the Public Reference Room by calling the SEC at 1-800-SEC-0330. The SEC also maintains an Internet website that contains reports, proxy and information statements, and other information regarding Alnylam and other issuers that file electronically with the SEC. The SEC’s Internet website address ishttp://www.sec.gov.

Executive Officers of the Registrant

Set forth below is information about our executive officers, as of December 31, 2014.

Name

Age

Position

John M. Maraganore, Ph.D

52Chief Executive Officer and Director

Barry E. Greene

51President and Chief Operating Officer

Akshay K. Vaishnaw, M.D., Ph.D.

52Executive Vice President and Chief Medical Officer

Laurie B. Keating

60Senior Vice President, General Counsel and Secretary

Michael P. Mason

40Vice President of Finance and Treasurer

John M. Maraganore, Ph.D.has served as our Chief Executive Officer and as a member of our board of directors since December 2002. Dr. Maraganore also served as our President from December 2002 to December 2007. From April 2000 to December 2002, Dr. Maraganore served as Senior Vice President, Strategic Product Development at Millennium Pharmaceuticals, Inc., a biopharmaceutical company (now Millennium: The Takeda Oncology Company). Dr. Maraganore serves as a member of the board of directors of Agios Pharmaceuticals, Inc., a biotechnology company and bluebird bio, Inc., a biotechnology company.

Barry E. Greenehas served as our President and Chief Operating Officer since December 2007, as our Chief Operating Officer since he joined us in October 2003, and from February 2004 through December 2005, as our Treasurer. From February 2001 to September 2003, Mr. Greene served as General Manager of Oncology at Millennium Pharmaceuticals, Inc., a biopharmaceutical company (now Millennium: The Takeda Oncology Company). Mr. Greene serves as a member of the board of directors of Acorda Therapeutics, Inc., a biotechnology company and Karyopharm Therapeutics Inc., a clinical-stage pharmaceutical company.

Akshay K. Vaishnaw, M.D., Ph.D.has served as our Executive Vice President of Research and Development since December 2014 and has served as our Chief Medical Officer since June 2011. He served as our Executive Vice President from June 2012 to December 2014 and prior to that as our Senior Vice President from June 2011 to June 2012. He served as our Senior Vice President, Clinical Research from December 2008 to June 2011, and prior to that served as our Vice President, Clinical Research from the time he joined us in January 2006. From December 1998 through December 2005, Dr. Vaishnaw held various positions at Biogen Idec Inc. (formerly Biogen, Inc.), a biopharmaceutical company. Dr. Vaishnaw is a Member of the Royal College of Physicians, United Kingdom.

 

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Laurie B. Keatinghas served as our Senior Vice President, General Counsel and Secretary since September 2014. Prior to joining Alnylam, Ms. Keating served as Senior Vice President, General Counsel and Secretary of Millennium: The Takeda Oncology Company, a biopharmaceutical company, from September 2004 to January 2014. Prior to Millennium, Ms. Keating was co-founder and the first chief executive officer of Hydra Biosciences, Inc. Before co-founding Hydra, she served as an executive at several high growth technology companies. Upon graduating from law school, Ms. Keating practiced law at McCutchen, Doyle, Brown and Enersen (which became Bingham McCutchen and is now a part of Morgan, Lewis & Bockius).

Michael P. Mason has served as our Vice President of Finance and Treasurer since February 2011. From December 2005 to February 2011, Mr. Mason served as our Corporate Controller, and from August 2009 to February 2011, as our Senior Director of Finance. From June 2006 to July 2009, Mr. Mason served as our Director of Finance. From May 2000 through November 2005, Mr. Mason served in several finance and commercial roles at Praecis Pharmaceuticals Incorporated, a public biotechnology company, most recently as Corporate Controller. Prior to Praecis, Mr. Mason worked in the audit practice at KPMG LLP, a national audit, tax and advisory services firm. Mr. Mason has an MBA and is a certified public accountant.

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ITEM 1A.

RISK FACTORS

Our business is subject to numerous risks. We caution you that the following important factors, among others, could cause our actual results to differ materially from those expressed in forward-looking statements made by us or on our behalf in filings with the SEC, press releases, communications with investors and oral statements. All statements other than statements relating to historical matters should be considered forward-looking statements. When used in this report, the words “believe,” “expect,” “plan,” “anticipate,” “estimate,” “predict,” “may,” “could,” “should,” “intend,” “will,” “target,” “goal” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these words. Any or all of our forward-looking statements in this annual report on Form 10-K and in any other public statements we make may turn out to be wrong. They can be affected by inaccurate assumptions we might make or by known or unknown risks and uncertainties. Many factors mentioned in the discussion below will be important in determining future results. Consequently, no forward-looking statement can be guaranteed. Actual future results may vary materially from those anticipated in forward-looking statements. We explicitly disclaim any obligation to update any forward-looking statements to reflect events or circumstances that arise after the date hereof. You are advised, however, to consult any further disclosure we make in our reports filed with the SEC.

Risks Related to Our Business

Risks Related to Being a Clinical Stage Company

BecauseAlthough we arehave several product candidates in late stage clinical development, including one in registration, there is limited information about our ability to successfully overcome many of the risks and uncertainties encountered by companies in the biopharmaceutical industry.

As a companyAlthough we have product candidates in late stage clinical development and one product under regulatory review for approval in the United States and the EU, we have limited experience and have not yet demonstrated an ability to successfully overcome many of the risks and uncertainties frequently encountered by companies in new and rapidly evolving fields, particularly in the biopharmaceutical area. For example, to execute our business plan, we will need to successfully:

execute product development activities using unproven technologies related to both RNAi and to the delivery of siRNAs to the relevant tissues and cells;

build and maintain a strong intellectual property portfolio;

gain regulatory acceptance for the development and commercialization of our product candidates and market success for any products we commercialize;

develop and maintain successful strategic alliances; and

manage our spending as costs and expenses increase due to clinical trials, regulatory approvals and commercialization.

If we are unsuccessful in accomplishing these objectives, we may not be able to develop product candidates, commercialize products, raise capital, expand our business or continue our operations.

The approach we are taking to discover and develop novel RNAi therapeutics is unproven and may never lead to marketable products.

We have concentrated our efforts and therapeutic product research and development on RNAi technology and our future success depends on the successful development of this technology and products based on it. Neither we nor any other company has received regulatory approval to market therapeutics utilizing siRNAs, the class of molecule we are trying to develop into drugs. The scientific discoveries that form the basis for our efforts to discover and develop new drugs are relatively new. The scientific evidence to support the feasibility of developing drugs based on these discoveries is both preliminary andstill limited. Skepticism as to the feasibility of developing RNAi therapeutics has been expressed in scientific literature. For example, there are potential challenges to achieving safe RNAi therapeutics based on theso-calledoff-target so-called off-target effects and activation of the interferon response. In

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addition, decisions by other companies with respect to their RNAi development efforts or their adoption of different or related technologies and the potential success of any such different or related technologies may increase skepticism in the marketplace regarding the potential for RNAi therapeutics.


Relatively few product candidates based on these discoveries have ever been tested in humans. siRNAs may not naturally possess the inherent properties typically required of drugs, such as the ability to be stable in the body, long enough to reach the tissues in which their effects are required, noror the ability to enter cells within theserelevant tissues in order to exert their effects. We currently have only limited data,spent and no conclusive evidence,expect to suggest that we can introduce thesedrug-like properties into siRNAs. We maycontinue to spend large amounts of money tryingdeveloping siRNAs that possess the properties typically required of drugs, and to introduce these properties,date, we have only taken one product candidate through Phase 3 development and may never succeedfiled for regulatory approval in doing so.the United States and the EU. In addition, these compounds may not demonstrate in patients the chemical and pharmacological properties ascribed to them in laboratory studies, and they may interact with human biological systems in unforeseen, ineffective or harmful ways. AsFor example, in October 2016, we discontinued development of revusiran, an investigational RNAi therapeutic that was in development for the treatment of patients with cardiomyopathy due to hATTR amyloidosis, due to safety concerns. We conducted a comprehensive evaluation of the revusiran data and reported the results of this evaluation in August 2017, however, our investigation did not result in a conclusive explanation regarding the cause of the mortality imbalance observed in the ENDEAVOUR Phase 3 study. If we may neverdo not succeed in developing a marketable product,products that gain regulatory approval and succeed in the marketplace, we may not become profitable and the value of our common stock will decline.

Further, our focus solely on RNAi technology for developing drugs, as opposed to multiple, more proven technologies for drug development, increases the risks associated with the ownership of our common stock. If we are not successful in developing a product candidateand commercializing one or more products using RNAi technology, we may be required to change the scope and direction of our product development activities. In that case, we may not be able to identify and implement successfully an alternative product development strategy.

Risks Related to Our Financial Results and Need for Financing

We have a history of losses and may never become and remain consistently profitable.

We have experienced significant operating losses since our inception. At December 31, 2014,2017, we had an accumulated deficit of $956.6 million.$2.15 billion. To date, we have not developedreceived regulatory approval to market or sell any products nor generated any revenues from the sale of products. Further, we do not expect to generate any product revenues inuntil at the foreseeable future.earliest mid- to late-2018, assuming we receive marketing approval for patisiran. We expect to continue to incur annual net operating losses over the next several years and will require substantial resources over the next several years as we expand our efforts to discover, develop and commercialize RNAi therapeutics. WeUntil we are successful in obtaining regulatory approval for our product candidates and successful in commercializing such products, we anticipate that the majoritya significant portion of any revenues we generate over the next several years will be from alliances with pharmaceutical and biotechnology companies, but cannot be certain that we will be able to maintain our existing alliances or secure orand maintain thesenew alliances, or meet the obligations or achieve any milestones that we may be required to meet or achieve to receive payments. We anticipate that revenues derived from such sources will not be sufficient to make us consistently profitable.

We believe that to become and remain consistently profitable, we must succeed in discovering, developing and commercializing novel drugs with significant market potential. This will require us to be successful in a range of challenging activities, includingpre-clinical testing and clinical trial stages of development, obtaining regulatory approval and reimbursement for these novel drugs and manufacturing, marketing and selling them. We may never succeed in these activities, and may never generate revenues that are significant enough to achieve profitability. Even if we do achieve profitability, we may not be able to sustain or increase profitability on a quarterly or annual basis. If we cannot become and remain consistently profitable, the market price of our common stock could decline. In addition, we may be unable to raise capital, expand our business, develop additional product candidates or continue our operations.

We will require substantial additional funds to complete our research, development and developmentcommercialization activities and if additional funds are not available, we may need to critically limit, significantly scale back or cease our operations.

We have used substantial funds to develop our RNAi technologies and will require substantial funds to conduct further research and development, includingpre-clinical testing and clinical trials of our product candidates, and to manufacture, market and marketsell any products that are approved for commercial sale. Because we cannot be certain of the length of time or activities associated with successful development of our product candidates, we are unable to estimate the actual funds we will require to develop and commercialize them.

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Our future capital requirements and the period for which we expect our existing resources to support our operations may vary from what we expect. We have based our expectations on a number of factors, many of which are difficult to predict or are outside of our control, including:

our progress in demonstrating that siRNAs can be active as drugs and achieve desired clinical effects;

our ability to develop relatively standard procedures for selecting and modifying siRNA product candidates;

progress in our research and development programs, as well as what may be required by regulatory bodies to advance these programs;

the timing, receipt and amount of milestone and other payments, if any, from present and future collaborators, if any;


 

the timing, receipt and amount of milestone and other payments, if any, from present and future collaborators, if any;

our ability to maintain and establish additional collaborative arrangements and/or new business initiatives;

the resources, time and costs required to successfully initiate and complete ourpre-clinical and clinical studies, obtain regulatory approvals, prepare for commercialization of our product candidates and obtain and maintain licenses tothird-party intellectual property;

our ability to establish, maintain and operate our own manufacturing facilities in a timely and cost effective manner;

our ability to manufacture, or contract with third parties for the manufacture of, our product candidates for clinical testing and commercial sale;

the resources, time and cost required for the preparation, filing, prosecution, maintenance and enforcement of patent claims;

the costs associated with legal activities, including litigation, arising in the course of our business activities and our ability to prevail in any such legal disputes;

progress in the research and development programs of Regulus; and

the timing, receipt and amount of sales and royalties, if any, from our potential products.

If our estimates and predictions relating to these factors are incorrect, we may need to modify our operating plan.

Even if our estimates are correct, we will be required to seek additional funding in the future and intend to do so through either collaborative arrangements, public or private equity offerings or debt financings, or a combination of one or more of these funding sources. Additional funds may not be available to us on acceptable terms or at all.

In April 2016, our subsidiary, Alnylam U.S., Inc., entered into an aggregate of $150.0 million in term loan agreements related to the build out of our new drug substance manufacturing facility. In December 2017, we repaid in full $120.0 million outstanding under one such term loan agreement.  We are the guarantor under the remaining term loan agreement, which matures in April 2021.  Interest on the borrowings is calculated based on LIBOR plus 0.45 percent. During an event of default under the remaining agreement, the obligations under such agreement will bear interest at a rate per annum equal to the interest rate then in effect plus two percent. The obligations under the term loan agreement are secured by cash collateral in an amount equal to, at any given time, at least 100 percent of the principal amount outstanding under such agreement at such time. The remaining agreement includes restrictive covenants that could limit our flexibility in conducting future business activities and further limit our ability to change the nature of our business and, in the event of insolvency, the lenders would be paid before holders of equity securities received any distribution of corporate assets. If an event of default occurs, the interest rate would increase and the lender would be entitled to take various actions, including the acceleration of amounts due under the loan. Our ability to satisfy our obligations under this agreement and meet our debt service obligations will depend upon our future performance, which will be subject to financial, business and other factors affecting our operations, many of which are beyond our control.

In addition, the terms of any financing may adversely affect the holdings or the rights of our stockholders. For example, if we raise additional funds by issuing equity securities, under our shelf registration statement or otherwise, further dilution to our existing stockholders will result. In addition, as a condition to providing additional fundsfunding to us, future investors may demand, and may be granted, rights superior to those of existing stockholders. Moreover, our investor agreement with Sanofi Genzyme provides Sanofi Genzyme with the right, subject to certain exceptions, generally to maintain its ownership position in us until Sanofi Genzyme owns less than 7.5%7.5 percent of our outstanding common stock, subject to certain additional limited rights of Sanofi Genzyme to maintain its ownership percentage. In accordance with the investor agreement, as a result of our issuance of shares in connection with our acquisition of Sirna in March 2014,to date, Sanofi Genzyme has exercised its right to purchase an additional 344,448 shares of our common stock. In January 2015, Genzyme also exercised its right to purchase 196,251stock in connection with our acquisition of Sirna in March 2014, an aggregate of 401,281 shares of our common stock based on its 2014 compensatory right and its right to purchase 744,5662015 compensation-related rights and an aggregate of 1,042,067 shares of our common stock in connection with our public offering.offerings in January 2015 and May 2017. These purchases allowed Sanofi Genzyme to maintain its ownership level of our outstanding common stock. Sanofi Genzyme currently holds approximately 12%11 percent of our outstanding common stock. While the exercise of these rights by Sanofi Genzyme has provided us with an additional $112.0$147.7 million in cash to date, and while we expect theany exercise of these rights by Sanofi Genzyme in the future will provide us with further additional cash, these exercises have caused, and any future exercise of these rights by Sanofi Genzyme will also cause further, dilution to our stockholders. Debt financing, if available, may involve restrictive covenants that could limitSanofi Genzyme elected not to exercise its compensation-related rights for 2016 and 2017. Additionally, Sanofi Genzyme elected not to exercise its right to purchase additional shares in connection with our flexibilitypublic offering in conducting future business activities and, in the event of insolvency, would be paid before holders of equity securities received any distribution of corporate assets.November 2017. 


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If we are unable to obtain additional funding on a timely basis, we may be required to significantly delay or curtail one or more of our research or development programs, delay the build-out of our global commercial infrastructure or undergo future reductions in our workforce or other corporate restructuring activities.activities, and our ability to achieve our strategy for 2020 may be delayed or diminished. We also could be required to seek funds through arrangements with collaborators or others that may require us to relinquish rights to some of our technologies, product candidates or products that we would otherwise pursue on our own.

If the estimates we make, or the assumptions on which we rely, in preparing our consolidated financial statements prove inaccurate, our actual results may vary from those reflected in our projections and accruals.

Our consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America, or GAAP. The preparation of these consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of our assets, liabilities, revenues and expenses, the amounts of charges accrued by us and related disclosure of contingent assets and liabilities. We base our estimates on historical experience and on various other assumptions that we believe to be reasonable under the circumstances. We cannot assure you, however, that our estimates, or the assumptions underlying them, will be correct.

The investment of our cash, cash equivalents and fixed income marketable securities is subject to risks which may cause losses and affect the liquidity of these investments.

At December 31, 2014,2017, we had $881.9 million$1.70 billion in cash, cash equivalents and fixed income marketable securities.securities, excluding the $30.0 million of restricted investments related to our term loan agreement. We historically have invested these amounts in high–grade corporate bonds,notes, commercial paper, securities issued or sponsored by the U.S. government, certificates of deposit and money market funds meeting the criteria of our investment policy, which is focused on the preservation of our capital. Corporate notes may also include foreign bonds denominated in U.S. dollars. These investments are subject to general credit, liquidity, market and interest rate risks. We may realize losses in the fair value of these investments or a complete loss of these investments, which would have a negative effect on our consolidated financial statements. In addition, should our investments cease paying or reduce the amount of interest paid to us, our interest income would suffer. The market risks associated with our investment portfolio may have an adverse effect on our results of operations, liquidity and financial condition.

The effect of comprehensive U.S. tax reform legislation on us, our subsidiaries and our affiliates, whether adverse or favorable, is uncertain.              

Our business is subject to numerous international, federal, state, and other governmental laws, rules, and regulations that may adversely affect our operating results, including, taxation and tax policy changes, tax rate changes, new tax laws, or revised tax law interpretations, which individually or in combination may cause our effective tax rate to increase. For example, on December 22, 2017, the President of the United States signed into law the Tax Cuts and Jobs Act of 2017, or the TCJA. Among a number of significant changes to the current U.S. federal income tax rules, the TCJA reduces the marginal U.S. corporate income tax rate from 35 percent to 21 percent, introduces a capital investment deduction, limits the current deduction for net interest expense, limits the use of net operating losses to offset future taxable income, and makes extensive changes in the way in which income earned outside the United States is taxed in the United States. The TCJA is complex and far-reaching and we cannot predict with certainty the impact its enactment will have on us. Moreover, that effect, whether adverse or favorable, may not become evident for some period of time.

Risks Related to Our Dependence on Third Parties

Our license and collaboration agreements with pharmaceutical companies are important to our business. If these pharmaceutical companies do not successfully develop drugs pursuant to these agreements or we develop drugs targeting the same diseases as ournon-exclusive licensees, our business could be adversely affected.

In July 2007, we entered into a license and collaboration agreement with Roche. Under the license and collaboration agreement we granted Roche anon-exclusive license to our intellectual property to develop and commercialize therapeutic products that function through RNAi, subject to our existing contractual obligations to third parties. In November 2010, Roche announced the discontinuation of certain activities in research and early development, including their RNAi research efforts. In October 2011, Arrowhead announced its acquisition of RNA therapeutics assets from Roche, including our license and collaboration agreement with Roche. As a result of the assignment, Arrowhead now has all of the rights and obligations of Roche under that agreement. The license is limited to four therapeutic areas and may be expanded to include additional therapeutic areas, upon payment to us by Arrowhead of an additional $50.0 million for each additional therapeutic area, if any. In addition, for each RNAi therapeutic product developed by Arrowhead, its affiliates, or sublicensees under the collaboration agreement, we are entitled to receive milestone payments upon achievement of specified development and sales events, totaling up to an aggregate of $100.0 million per therapeutic target, together with royalty payments based on worldwide annual net sales, if any. Our receipt of milestone payments under this agreement is dependent upon Arrowhead’s ability to successfully develop and commercialize RNAi therapeutic products.

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In May 2008, we entered into a similar license and collaboration agreement with Takeda, which is limited to two therapeutic areas, and which may be expanded to include additional therapeutic areas, upon payment to us by Takeda of an additional $50.0 million for each additional therapeutic area, if any. For each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, we are entitled to receive specified development and commercialization milestone payments, totaling up to $171.0 million per product, together with royalty payments based on worldwide annual net sales, if any.

In September 2010, Novartis exercised its right under our collaboration and license agreement to select 31 designated gene targets, for which Novartis has exclusive rights to discover, develop and commercialize RNAi therapeutic products using our intellectual property and technology. Under the terms of the collaboration and license agreement, for any RNAi therapeutic products Novartis develops against these targets, we are entitled to receive milestone payments upon achievement of certain specified development and annual net sales events, up to an aggregate of $75.0 million per therapeutic product, as well as royalties on annual net sales of any such product, if any. During 2014, Novartis publically indicated that they no longer intend to invest in the development of certain RNAi therapeutics and intend to divest certain of their RNAi assets. Novartis has the right to assign our collaboration and license agreement to athird-party that acquires substantially all of its assets relating to RNAi.

If Takeda, Arrowhead or any assignee of Novartis fails to successfully develop products using our technology, we may not receive any milestone or royalty payments under our agreements with them. Finally, Takeda or Arrowhead could become a competitor of ours in the development ofRNAi-based drugs targeting the same diseases that we choose to target. Takeda has significantly greater financial resources than we do and far more experience in developing and marketing drugs, which could put us at a competitive disadvantage if we were to compete with them in the development ofRNAi-based drugs targeting the same disease.

We may not be able to execute our business strategy if we are unable to enter into alliances with other companies that can provide business and scientific capabilities and funds for the development and commercialization of our product candidates. If we are unsuccessful in forming or maintaining these alliances on terms favorable to us, our business may not succeed.

We do not currently have any capabilityare developing capabilities for sales or distribution and also have early capabilitycapabilities for marketing, sales and market access, andas well as limited capacity for drug development due to our growing pipeline of RNAi therapeutic opportunities. Accordingly, we have entered into alliances with other companies and collaborators that we believe can provide such capabilities in certain territories, and we intend to enter into additional such alliances in the future. Our collaboration strategy is to form alliances that create significant value for ourselvesus and our collaborators in the advancement of RNAi therapeutics as a new class of innovative medicines. Specifically, with respect to our Genetic Medicine pipeline, we formed a broad strategic alliance with Sanofi Genzyme in 2014 pursuant to which we retain development and commercial rights for our current and future Genetic Medicine products in North Americathe United States, Canada and Western Europe, and Sanofi Genzyme willhas the right to develop and commercialize our current and future Genetic Medicine products principally in territories outsidethe rest of North America and Western Europe,the world, subject to certain broader rights. In January 2018, we and Sanofi Genzyme amended our 2014 collaboration to provide that we would develop and commercialize patisiran globally and Sanofi Genzyme would develop and commercialize fitusiran globally.  With respect to ourCardio-Metabolic and Hepatic Infectious Disease pipelines,pipeline, we intend to seek future


strategic alliances for these programs, while retaining significantunder which we may retain certain product development and commercialization rights, or we may structure as global alliances, as we did in the United States and EU. We currently have a global allianceour collaboration with MDCO to advance ourALN-PCS program.inclisiran. In October 2017, we announced an exclusive licensing agreement with Vir Biotechnology for the development and commercialization of RNAi therapeutics for infectious diseases, including chronic hepatitis B virus infection.

In such alliances, we expect our current, and may expect our future, collaborators to provide substantial capabilities in clinical development, regulatory affairs, and/or marketing, sales and distribution. Under certain of our alliances, we also may expect our collaborators to develop, market and/or sell certain of our product candidates. We may have limited or no control over the development, sales, marketing and distribution activities of these third parties. Our future revenues may depend heavily on the success of the efforts of these third parties. For example, we will rely entirely on (i) Sanofi Genzyme for the development and commercialization of patisiran, revusiranfitusiran worldwide and potentially other of our Genetic Medicine programs in territories outside of North Americathe United States, Canada and Western Europe, under the 2014 Genzyme collaboration, and (ii) MDCO for later stageall future development and commercialization ofALN-PCSsc inclisiran worldwide. If Sanofi Genzyme and/or MDCO are not successful in their development and/or commercialization efforts, our future revenues from RNAi therapeutics for these indications may be adversely affected. Sanofi Genzyme also has the right to elect one global license for a future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of our 2014 collaboration. Sanofi Genzyme could elect its one global license for lumasiran, an investigational RNAi therapeutic targeting GO for the treatment of PH1. If Sanofi Genzyme elects to take a global license to lumasiran or another of our programs, we will no longer control the development and potential commercialization of such program and any revenues we receive will depend solely on the success of Sanofi Genzyme’s efforts. In addition, Sanofi Genzyme may elect not to opt into one or more of our Genetic Medicine programs. For example, during 2016, Sanofi Genzyme elected not to take a regional license for our givosiran and cemdisiran programs. While we intend to advance these programs independently, retaining global development and commercial rights, our ability to advance these programs and successfully develop and commercialize these product candidates may be adversely affected as a result of Sanofi Genzyme’s decision. 

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We may not be successful in entering into suchfuture alliances on terms favorable to us due to various factors, including our ability to successfully demonstrate proof of conceptproof-of-concept for our technology in humans, our ability to demonstrate the safety and efficacy of our specific drug candidates, our ability to manufacture or have third parties manufacture RNAi therapeutics, the strength of our intellectual property and/or concerns around challenges to our intellectual property. For example, our decision in October 2016 to discontinue development of revusiran could make it more difficult for us to attract collaborators due to concerns around the safety and/or efficacy of our technology platform or product candidates. In addition, our decision in September 2017 to temporarily suspend dosing in all ongoing fitusiran studies pending further review of a fatal thrombotic SAE and agreement with regulatory authorities on a risk mitigation strategy could, notwithstanding the alignment reached with the FDA on a risk mitigation strategy in November 2017, contribute to further concerns about the safety of our therapeutic candidates. Even if we do succeed in securing any such alliances, we may not be able to maintain them if, for example, development or approval of a product candidate is delayed, challenges are raised as to the validity or scope of our intellectual property, we are unable to secure adequate reimbursement from payors or sales of an approved drug are lower than we expected. In the case of the Monsanto agreement, if we cease to own or otherwise exclusively control certain licensed patent rights in the agriculture field, resulting in the loss of exclusivity with respect to Monsanto’s rights to such patent rights, and such loss of exclusivity has a material adverse effect on the licensed products (as defined in the agreement), we would be required to pay Monsanto up to $5.0 million in liquidated damages, and Monsanto’s royalty obligations to us would be reduced or, under certain circumstances, terminated.

Furthermore, any delay in entering into collaboration agreements would likely either delay the development and commercialization of certain of our product candidates and reduce their competitiveness even if they reach the market, or prevent the development of certain product candidates. Any such delay related to our collaborations could adversely affect our business.

For certain product candidates that we may develop, we have formed collaborations to fund all or part of the costs of drug development and commercialization, such as our collaborationcollaborations with MDCO.Sanofi Genzyme, MDCO and Vir Biotechnology. We may not, however, be able to enter into additional collaborations for certain other programs, and the terms of any collaboration agreement we do secure may not be favorable to us. If we are not successful in our efforts to enter into future collaboration arrangements with respect to one or more of our product candidates, we may not have sufficient funds to develop that or other product candidates internally, or to bring our product candidates to market. If we do not have sufficient funds to develop and bring our product candidates to market, we will not be able to generate revenues from these product candidates, and this will substantially harm our business.

If any collaborator terminates or fails to perform its obligations under agreements with us, the development and commercialization of our product candidates could be delayed or terminated.

Our dependence on collaborators for capabilities and funding means that our business could be adversely affected if any collaborator terminates its collaboration agreement with us or fails to perform its obligations under that agreement. Our current or future collaborations, if any, may not be scientifically or commercially successful. Disputes may arise in the future with respect to the ownership of rights to technology or products developed with collaborators, which could have an adverse effect on our ability to develop and commercialize any affected product candidate.


Our current collaborations allow, and we expect that any future collaborations will allow, either party to terminate the collaboration for a material breach by the other party. In addition, our collaborators may have additional termination rights for convenience with respect to the collaboration or a particular program under the collaboration, under certain circumstances. For example, Sanofi Genzyme has the right to terminate our 2014 collaboration on a product-by-product basis in the event of certain safety concerns. Sanofi Genzyme also has the right to terminate its global license agreement for fitusiran at any time upon six months’ prior written notice.  If Sanofi Genzyme were to terminate a particular program, we may have to expend significantly more on the development and commercialization of such product candidate. Moreover, our agreement with MDCO relating to the development and commercialization ofALN-PCS inclisiran worldwide may be terminated by MDCO at any time upon four months’ prior written notice. If we were to lose a commercialization collaborator, we would have to attract a new collaborator or develop internalexpanded sales, distribution and marketing capabilities internally, which would require us to invest significant amounts of financial and management resources.

In addition, if we have a dispute with a collaborator over the ownership of technology or other matters, or if a collaborator terminates its collaboration with us, for breach or otherwise, or determines not to pursue the research, and development and/or commercialization of RNAi therapeutics, it could delay our development of product candidates, result in the need for additional company resources to develop product candidates, require us to expend time and resources to develop expanded sales and marketing capabilities outside of the United States and EU,on a more expedited timeline, make it more difficult for us to attract new collaborators and could adversely affect how we are perceived in the business and financial communities. For example, in March 2011, TekmiraArbutus filed a civil complaint against us claiming, among other things, misappropriation of its confidential and proprietary information and trade secrets. As a result of the litigation, which was settled in November 2012, we were required to expend resources and management attention

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that would otherwise have been engaged in other activities. In addition, in August 2013, we initiated binding arbitration proceedings to resolve a disagreement with TekmiraArbutus regarding the achievement by TekmiraArbutus of a $5.0 million milestone payment under ourcross-license agreement relating to the manufacture ofALN-VSP clinical trial material for use in China. We currently expect that the TekmiraThe Arbutus arbitration hearing will bewas held in May 2015. In March 2016, the second quarter of 2015.arbitration panel ruled in our favor and as a result, no milestone payment is due to Arbutus at this time. Arbutus did not appeal this ruling.

Moreover, a collaborator, or in the event of a change in control of a collaborator or the assignment of a collaboration agreement to a third party, the successor entity or assignee, could determine that it is in its interests to:

pursue alternative technologies or develop alternative products, either on its own or jointly with others, that may be competitive with the products on which it is collaborating with us or which could affect its commitment to the collaboration with us;

pursuehigher-priority programs or change the focus of its development programs, which could affect the collaborator’s commitment to us; or

if it has marketing rights, choose to devote fewer resources to the marketing of our product candidates, if any are approved for marketing, than it does for product candidates developed without us.

If any of these occur, the development and commercialization of one or more product candidates could be delayed, curtailed or terminated because we may not have sufficient financial resources or capabilities to continue such development and commercialization on our own.

We rely on third parties to conduct our clinical trials, and if they fail to fulfill their obligations, our development plans may be adversely affected.

We rely on independent clinical investigators, contract research organizations, or CROs, and otherthird-party service providers to assist us in managing, monitoring and otherwise carrying out our clinical trials. We have contracted, and we plan to continue to contract with, certain third parties to provide certain services, including site selection, enrollment, monitoring, auditing and data management services. Although we depend heavily on these parties, we do not control themonly certain aspects of their activity and therefore, we cannot be assured that these third parties will adequately perform all of their contractual obligations to us.us in compliance with regulatory and other legal requirements and our internal policies and procedures. Nevertheless, we are responsible for ensuring that each of our studies is conducted in accordance with the applicable protocol, legal, regulatory and scientific standards, and our reliance on third parties does not relieve us of our regulatory responsibilities. We and our CROs are required to comply with GCP requirements, which are regulations and guidelines enforced by the FDA and comparable foreign regulatory authorities for all of our product candidates in clinical development. Regulatory authorities enforce these GCP requirements through periodic inspections of trial sponsors, principal investigators and trial sites. If we or any of our CROs fail to comply with applicable GCP requirements, the clinical data generated in our clinical trials may be deemed unreliable and the FDA, the EMA, the PMDA in Japan or comparable foreign regulatory authorities may require us to perform additional clinical trials before approving our marketing applications. We cannot assure you that upon inspection by a given regulatory authority, such regulatory authority will determine that any of our clinical trials comply with GCP regulations.


If our third-party service providers cannot adequately and timely fulfill their obligations to us, or if the quality and accuracy of our clinical trial data is compromised due to failure by such third party to adhere to our protocols or regulatory requirements or if such third parties otherwise fail to meet deadlines, our development plans and/or regulatory reviews for marketing approvals may be delayed or terminated.terminated, including, for example, review of our NDA and MAA filings for patisiran. As a result, our results of operations and the commercial prospects for our product candidates would be harmed, our costs could increase and our ability to generate revenues could be delayed.

We have very limited manufacturing experience orand resources and we must incur significant costs to develop this expertise and/or rely on third parties to manufacture our products.

We have very limited manufacturing experience. In order to develop our product candidates, apply for regulatory approvals and commercialize our products, if approved, we will need to develop, contract for, or otherwise arrange for the necessary manufacturing capabilities. Historically, our internal manufacturing capabilities were limited tosmall-scale production of material for use in in vitro and in vivo experiments that is not required to be produced under current cGMP standards. During 2012, we developed cGMP capabilities and processes for the manufacture of patisiran formulated bulk drug product forlate-stage late stage clinical trial use and early commercial supply. In addition, in April 2016, we completed our purchase of a parcel of land in Norton, Massachusetts, where we have commenced construction of a cGMP manufacturing facility for drug substance, including siRNAs and siRNA conjugates, for clinical and commercial use.

We may manufacture limited quantities of clinical trial materials ourselves, but otherwise we currently rely on third parties to manufacture the materialsdrug substance and, with the exception of patisiran, the finished product we will require for any clinical trials that we initiate.initiate and to support the commercial launch of our first several products. There are a limited number of manufacturers that supply synthetic siRNAs. We currently rely on a few contract manufacturerslimited number of CMOs for our supply of synthetic siRNAs. For example, in July 2015, we amended our manufacturing agreement with Agilent, to provide for Agilent to supply, subject to any conflicting obligations under our third-party agreements, a specified percentage of the active pharmaceutical ingredients required for certain of our products in clinical development, as well as other products the parties may agree upon in the future. We will also rely on Agilent to supply the active pharmaceutical ingredients to support the commercial launch of patisiran.  There are risks inherent in pharmaceutical manufacturing that could affect the ability of our contract manufacturersCMOs, including Agilent, to meet our delivery time requirements or provide adequate amounts of material to meet our needs. Included in these risks are potential synthesis and purification failures andand/or contamination during the manufacturing process, as well as other issues with the CMO’s facility and ability to comply with the applicable manufacturing requirements, which could result in unusable product and cause delays in our manufacturing timelines and ultimately delay our clinical trials and potentially put at risk commercial supply, as well as result in additional expense to us. To fulfill our siRNA requirements, we maywill likely need to secure alternative suppliers of synthetic siRNAs and such alternative

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suppliers are limited and may not be readily available, or we may be unable to enter into agreements with them on reasonable terms and in a timely manner. As noted above, in order to ensure long-term supply capabilities for our RNAi therapeutics, we are developing our own capabilities to manufacture drug substance, including siRNAs and siRNA conjugates, for clinical and commercial use.

In addition to the manufacture of the synthetic siRNAs, we may have additional manufacturing requirements related to the technology required to deliver the siRNA to the relevant cell or tissue type, such as LNPs or conjugates. In some cases, the delivery technology we utilize is highly specialized or proprietary, and for technical andand/or legal reasons, we may have access to only one or a limited number of potential manufacturers for such delivery technology. In addition, the scale upscale-up of our delivery technologies could be very difficult.difficult and/or take significant time. We also have very limited experience in suchscale-up and manufacturing, requiring us to depend on a limited number of third parties, who might not be able to deliver in a timely manner, or at all. Failure by manufacturers to properly manufacture our delivery technology and/or formulate our siRNAs for delivery could result in unusable product. Furthermore, competition for supply from our manufacturers from other companies, a breach by such manufacturers of their contractual obligations or a dispute with such manufacturers would cause delays in our discovery and development efforts, as well as additional expense to us.

Given the limited number of suppliers for our delivery technology and other materials,drug substance, we have developed cGMP capabilities and processes for the manufacture of patisiran formulated bulk drug product forlate-stage late stage clinical use and early commercial supply. During 2015, we scaled our cGMP manufacturing capacity for patisiran and believe we should have adequate resources to supply and in the future,our commercial needs. In addition, as noted above, we may also developare developing our own capabilities to manufacture drug substance, including siRNAs and siRNA conjugates, for human clinical and commercial use. In developing these manufacturing capabilities by building our own manufacturing facility,facilities, we have incurred substantial expenditures.expenditures, and expect to incur significant additional expenditures in the future. In addition, the construction and qualification of our drug substance facility is expected to take several years to complete and there are many risks inherent in the construction of a new facility that could result in delays and additional costs, including the need to obtain access to necessary equipment and third-party technology, if any. Also, we have had to, and will likely need to continue to, hire and train qualified employees to staff our new facility.facilities. We do not currently have a second source of supply for patisiran formulated bulk


drug product. If we are unable to manufacture sufficient quantities of material or if we encounter problems with our facilityfacilities in the future, we may also need to secure alternative suppliers of patisiran formulated bulk drug product and drug substance, and such alternative suppliers may not be available, or we may be unable to enter into agreements with them on reasonable terms and in a timely manner.  Any delay or setback in the manufacture of patisiran could, assuming approval, delay the launch or ongoing commercial supply, which could significantly impact our revenues and operating results.

The manufacturing process for any products that we may develop is subject to the FDA and foreign regulatory authority approval process and we will need to meet, and will need to contract with manufacturersCMOs who can meet, all applicable FDA and foreign regulatory authority requirements on an ongoing basis. In addition, if we receive the necessary regulatory approval for any product candidate, we also expect to rely on third parties, including potentially our commercial collaborators, to produce materials required for commercial supply. We may experience difficulty in obtaining adequate manufacturing capacity for our needs.needs and the needs of our collaborators, who we have, in some instances, the obligation to supply. If we are unable to obtain or maintain contract manufacturingCMOs for these product candidates, or to do so on commercially reasonable terms, we may not be able to successfully develop and commercialize our products.

To the extent that we have existing, or enter into future, manufacturing arrangements with third parties, we depend, and will depend in the future, on these third parties, including Agilent, to perform their obligations in a timely manner and consistent with contractual and regulatory requirements, including those related to quality control and quality assurance. The failure of athird-party manufacturerAgilent or any other CMO to perform its obligations as expected, or, to the extent we manufacture all or a portion of our product candidates ourselves, our failure to execute on our manufacturing requirements, could adversely affect our business in a number of ways, including:

we or our current or future collaborators may not be able to initiate or continue clinical trials of product candidates that are under development;

we or our current or future collaborators may be delayed in submitting regulatory applications, or receiving regulatory approvals, for our product candidates;candidates, including patisiran;

we may lose the cooperation of our collaborators;

our facilities and those of our third party manufacturers,CMOs, and our products could be the subject of inspections by regulatory authorities that could have a negative outcome and result in delays in supply;

we may be required to cease distribution or recall some or all batches of our products or take action to recover clinical trial material from clinical trial sites; and

ultimately, we may not be able to meet commercial demands for our products.

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If anythird-party manufacturer CMO with whom we contract, including Agilent, fails to perform its obligations, we may be forced to manufacture the materials ourselves, for which we may not have the capabilities or resources, or enter into an agreement with a differentthird-party manufacturer, CMO, which we may not be able to do on reasonable terms, if at all. In either scenario, our clinical trials or commercial distribution could be delayed significantly as we establish alternative supply sources. In some cases, the technical skills required to manufacture our products or product candidates may be unique or proprietary to the original manufacturerCMO and we may have difficulty, or there may be contractual restrictions prohibiting us from, transferring such skills to aback-up or alternate supplier, or we may be unable to transfer such skills at all. In addition, if we are required to change manufacturersCMOs for any reason, we will be required to verify that the new manufacturerCMO maintains facilities and procedures that comply with quality standards and with all applicable regulations and guidelines. We will also need to verify, such as through a manufacturing comparability study, that any new manufacturing process will produce our product according to the specifications previously submitted to or approved by the FDA or another regulatory authority. The delays associated with the verification of a new manufacturerCMO could negatively affect our ability to develop product candidates in a timely manner or within budget. Furthermore, a manufacturerCMO may possess technology related to the manufacture of our product candidate that such manufacturerCMO owns independently. This would increase our reliance on such manufacturerCMO or require us to obtain a license from such manufacturerCMO in order to have another third partyCMO manufacture our products or product candidates.

We have no sales or distribution experience and only early capabilities for marketing, sales and market access, and expect to invest significant financial and management resources to establish these capabilities.capabilities and to establish a global commercial infrastructure.

We have no sales or distribution experience and only early capabilities for marketing, sales and market access. We currently expect to rely heavily on third parties to launch and market certain of our product candidates in certain geographies, if approved. However, we intend to commercialize the majorityseveral of our late-stage products on our own inglobally, including patisiran, as a result of the United StatesJanuary 2018 amendment to our Sanofi Genzyme collaboration, and EU, and accordingly,givosiran. Accordingly, we will need to develop internal sales, distribution and marketing capabilities as part of our core product strategy initially in the United States and the EU, then Canada and Switzerland, Central and Eastern Europe, Japan and in other major markets in the rest of the world, which will require significant


financial and management resources. For our Genetic Medicine programs wherethose products for which we will perform sales, marketing and distribution functions ourselves, in North Americaincluding patisiran and Western Europe,givosiran, if approved, and for futureCardio-Metabolic and Hepatic Infectious Disease products we successfully develop where we intend tomay retain significantcertain product development and commercialization rights, in the United States and EU, we could face a number of additional risks, including:

we may not be able to attract and build a significant marketing or sales force;

we may not be able to establish our global capabilities and infrastructure in a timely manner;

the cost of establishing a marketing or sales force may not be justifiable in light of the revenues generated by any particular product;product and/or in any specific geographic region; and

our direct sales and marketing efforts may not be successful.

If we are unable to develop our own global sales, marketing and distribution capabilities for patisiran and other products, we will not be able to successfully commercialize our Genetic Medicine pipeline or our futureCardio-Metabolic and Hepatic Infectious Disease pipelines in our sales territoriesproducts without reliance on third parties.

Credit and financial market conditions may exacerbate certain risks affecting our business from time to time.

Due to tightening of global credit, there may be a disruption or delay in the performance of ourthird-party contractors, suppliers or collaborators. We rely on third parties for several important aspects of our business, including significant portions of our manufacturing needs, development of product candidates and conduct of clinical trials. If such third parties are unable to satisfy their commitments to us, our business could be adversely affected.

Our ability to secure additional financing in addition to our term loan agreement and to satisfy our financial obligations under indebtedness outstanding from time to time will depend upon our future operating performance, which is subject to then prevailing general economic and credit market conditions, including interest rate levels and the availability of credit generally, and financial, business and other factors, many of which are beyond our control. In light of periodic uncertainty in the capital and credit markets, there can be no assurance that sufficient financing will be available on desirable or even any terms to fund investments, acquisitions, stock repurchases, dividends, debt refinancing or extraordinary actions.

Risks Related to Managing Our Operations

If we are unable to attract and retain qualified key management and scientists, development, medical and commercial staff, consultants and advisors, our ability to implement our business plan may be adversely affected.

We are highly dependent upon our senior management and our scientific, clinical and medical staff. The loss of the service of any of the members of our senior management, including Dr. John Maraganore, our Chief

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Executive Officer, may significantly delay or prevent the achievement of product development and commercialization, and other business objectives. Our employment agreementsarrangements with our key personnel are terminable without notice. We do not carry key person life insurance on any of our employees.

We have grown our workforce significantly over the past yearseveral years and expect to continueanticipate continuing to add a significant number of additional employees during 2015.as we focus on achieving our Alnylam 2020 strategy. We face intense competition for qualified individuals from numerous pharmaceutical and biotechnology companies, universities, governmental entities and other research institutions, many of which have substantially greater resources with which to reward qualified individuals than we do. WeIn addition, due to the risks associated with developing a new class of medicine, we may experience disappointing results in a clinical program and our stock price may decline as a result, as was the case following our decision in October 2016 to discontinue our revusiran program, and, to less of an extent, following our temporary suspension of dosing in our fitusiran program in September 2017. As a result, we may face additional challenges in attracting and retaining employees. Accordingly, we may be unable to attract and retain suitably qualified individuals in order to support our growing research, development and commercialization efforts and initiatives, and our failure to do so could have an adverse effect on our ability to implement our future business plan.

We may have difficulty expanding our operations successfully as we evolve from a U.S.-based company primarily involved in discovery,pre-clinical testing and clinical development into onea global company that develops and commercializes multiple drugs.

We expect that asAs we increase the number of product candidates we are developing we will also need to expand our operations. operations in the United States and continue to build operations in the EU and other geographies, including Japan. Based on the positive data reported from our APOLLO Phase 3 study of patisiran, we filed an NDA and an MAA for patisiran in December 2017. Assuming regulatory approvals, we are preparing to commercialize patisiran in 2018 and now have global development and commercialization rights for patisiran as a result of the January 2018 amendment to our Sanofi Genzyme collaboration. We also plan to file for regulatory approval in Japan in mid-2018 and in one or more additional countries by the end of the year.


As noted above, we have growngrew our workforce significantly over the past yearduring 2016 and expect2017, and anticipate continuing to continue to add a significant number ofhire additional employees, during 2015.including employees in the EU, Japan and other territories, as we focus on the potential commercial launch of patisiran and achieving our Alnylam 2020 strategy. This expected growth will likely placeis placing a strain on our administrative and operational infrastructure, and we will likely need to develop additional and/or new infrastructure and capabilities to support our growth and obtain additional space to conduct our operations.operations in the United States, the EU, Japan and other geographies. If we are unable to develop such additional infrastructure or obtain sufficient space to accommodate our growth in a timely manner and on commercially reasonable terms, our business could be negatively impacted. As product candidates we develop enter and advance through clinical trials, we will need to expand our global development, regulatory, manufacturing, quality, compliance, and marketing and sales capabilities, or contract with other organizations to provide these capabilities for us. In addition, as our operations expand due to our development progress, we expect that we will need to manage additional relationships with various collaborators, suppliers and other organizations. Our ability to manage our operations and future growth will require us to continue to improve our operational, financial and management controls and systems, reporting systems and infrastructure, and policies and procedures. We may not be able to implement improvements to our management information and control systems in an efficient or timely manner and may discover deficiencies in existing systems and controls.

The increasing use of social media platforms presents new risks and challenges.

Social media is increasingly being used to communicate about our clinical development programs and the diseases our investigational RNAi therapeutics are being developed to treat, and we intend to utilize appropriate social media in connection with our commercialization efforts following approval of our drug candidates. Social media practices in the biopharmaceutical industry continue to evolve and regulations relating to such use are not always clear. This evolution creates uncertainty and risk of noncompliance with regulations applicable to our business. For example, patients may use social media channels to comment on their experience in an ongoing blinded clinical study or to report an alleged AE. When such disclosures occur, there is a risk that we fail to monitor and comply with applicable AE reporting obligations or we may not be able to defend our business or the public’s legitimate interests in the face of the political and market pressures generated by social media due to restrictions on what we may say about our investigational products. There is also a risk of inappropriate disclosure of sensitive information or negative or inaccurate posts or comments about us on any social networking website. If any of these events were to occur or we otherwise fail to comply with applicable regulations, we could incur liability, face regulatory actions or incur other harm to our business.

Our business and operations could suffer in the event of system failures.

Despite the implementation of security measures, our internal computer systems and those of our contractors and consultants are vulnerable to damage from computer viruses, unauthorized access, natural disasters, terrorism, war, and telecommunication and electrical failures. Such events could cause interruption of our operations. For example, the loss ofpre-clinical trial data or data from completed or ongoing clinical trials for our product candidates could result in delays in our regulatory filings and development efforts, as well as delays in the commercialization of our products, and significantly increase our costs. To the extent that any disruption or security breach were to result in a loss of or damage to our data, or inappropriate disclosure of confidential or proprietary information, we could incur liability and the development and potential commercialization of our product candidates could be delayed.

The results of the United Kingdom’s referendum on withdrawal from the EU may have a negative effect on global economic conditions, financial markets and our business.

In June 2016, the United Kingdom, or UK, held a referendum in which voters approved an exit from the EU, commonly referred to as “Brexit.” This referendum has created political and economic uncertainty, particularly in the UK and the EU, and this uncertainty may persist for years. A withdrawal could, among other outcomes, disrupt the free movement of goods, services and people between the UK and the EU, and result in increased legal and regulatory complexities, as well as potential higher costs of conducting business in Europe. The UK’s vote to exit the EU could also result in similar referendums or votes in other European countries in which we do business. Given the lack of comparable precedent, it is unclear what financial, trade and legal implications the withdrawal of the UK from the EU would have and how such withdrawal would affect us.

For example, Brexit could result in the UK or the EU significantly altering its regulations affecting the clearance or approval of our product candidates that are developed in the UK. Any new regulations could add time and expense to the conduct of our business, as well as the process by which our products receive regulatory approval in the UK, the EU and elsewhere. In addition, the announcement of Brexit and the withdrawal of the UK from the EU have had and may continue to have a material adverse effect on global economic conditions and the stability of global financial markets, and may significantly reduce global market liquidity and restrict the ability of key market participants to operate in certain financial markets. Any of these effects of Brexit, among others, could adversely affect our business, our results of operations, liquidity and financial condition.


Risks Related to Our Industry

Risks Related to Development, Clinical Testing and Regulatory Approval of Our Product Candidates

Any product candidates we develop may fail in development or be delayed to a point where they do not become commercially viable.

Before obtaining regulatory approval for the commercial distribution of our product candidates, we must conduct, at our own expense, extensivepre-clinical nonclinical tests and clinical trials to demonstrate the safety and efficacy in humans of our product candidates.Pre-clinical Nonclinical and clinical testing is expensive, difficult to design and implement, can take many years to complete and is uncertain as to outcome, and the historical failure rate for

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product candidates is high. In October 2016, we discontinued development of one of our product candidates, which included a Phase 3 clinical trial. We currently have severalmultiple other programs in clinical development, including patisiranseveral internal programs and two partnered programs currently in aPhase 3 development, as well as several earlier stage clinical programs. In November 2017, we reported positive complete results from our APOLLO Phase 3 clinical trial revusiranfor our lead product candidate, patisiran, and in a Phase 3 clinical trial,ALN-AT3 in a Phase 1 clinical trial,ALN-PCSsc in a Phase 1 clinical trialDecember 2017, we filed an NDA and ALN-CC5 in a Phase 1/2 clinical trial. Assuming regulatory clearance, we expect to initiate a Phase 1 clinical trialan MAA forALN-AS1 in mid-2015. patisiran. However, we may not be able to further advance these or any other product candidate through clinical trials.trials and regulatory approval.

If we enter into clinical trials, the results frompre-clinical nonclinical testing or early clinical trials of a product candidate may not predict the results that will be obtained in subsequent subjects or in subsequent human clinical trials of that product candidate or any other product candidate. For example, in early 2015,June 2017, we announced updated results from our Phase 1 clinical trial ofALN-AT3, including initial givosiran. Although the clinical data on three subjects with hemophilia from the second dose cohort of this study. Although the initial clinical data on these three subjectstrial are encouraging, the data are preliminary in nature, based on a limited number of subjects and theALN-AT3 Phase 1 study is not complete.patients with AIP. These data, or other positive data, may not continue for these subjects or occur for any future subjects in this study,patients with AIP, and may not be repeated or observed in any future studies.our ENVISION Phase 3 study. There can be no assurance that this studyour studies with givosiran will ultimately be successful or support further clinical advancement or regulatory approval of this product candidate. There is a high failure rate for drugs proceeding through clinical studies. A number of companies in the pharmaceutical and biotechnology industries have suffered significant setbacks in clinical development even after achieving promising results in earlier studies, and any such setbacks in our clinical development could have a material adverse effect on our business and operating results. Moreover, patisiran, revusirangivosiran, fitusiran, inclisiran andALN-AT3 our other product candidates each employ novel delivery technologies that have yet to be extensively evaluated in human clinical trials and proven safe and effective. In May 2014, we reported the first human study results for our Enhanced Stabilization Chemistry, orESC-GalNAc conjugate technology, which enables subcutaneous dosing with increased potency, durability and a wide therapeutic index. While these initial clinical results ofALN-AT3 demonstrated a greater than50-fold potency improvement withESC-GalNAc conjugates relative to standard template chemistry conjugates, we cannot assure you that we will see similar results with other clinical candidates.

In addition, we, the FDA or other applicable regulatory authorities, or an institutional review board, or IRB or similar foreign review board or committee, may delay initiation of or suspend clinical trials of a product candidate at any time for various reasons, including if we or they believe the healthy volunteer subjects or patients participating in such trials are being exposed to unacceptable health risks. Among other reasons, adverse side effects of a product candidate or related product on healthy volunteer subjects or patients in a clinical trial could result in our decision, or a decision by the FDA or foreign regulatory authorities, suspendingto suspend or terminatingterminate the trial, and refusingor, in the case of regulatory agencies, a refusal to approve a particular product candidate for any or all indications of use. For example, in October 2016, we announced our decision to discontinue development of revusiran, an investigational RNAi therapeutic that was being developed for the treatment of patients with cardiomyopathy due to hATTR amyloidosis. Our decision followed the recommendation of the revusiran ENDEAVOUR Phase 3 study Data Monitoring Committee, or DMC, to suspend dosing and the observation of an imbalance in mortality in revusiran-treated patients as compared to those on placebo. We conducted a comprehensive evaluation of the revusiran data and reported the results of our evaluation on August 9, 2017. Following our evaluation, we continue to believe that the decision to discontinue development of revusiran does not affect patisiran, which is under regulatory review for the treatment of hATTR amyloidosis, or any of our other investigational RNAi therapeutic programs in development. In September 2017, we announced that we had temporarily suspended dosing in all ongoing fitusiran studies pending further review of a fatal thrombotic SAE and agreement with regulatory authorities on a risk mitigation strategy. We have reached alignment with study investigators and the FDA on safety measures and a risk mitigation strategy to enable resumption of dosing in clinical studies with fitusiran, including our Phase 2 OLE study and the ATLAS Phase 3 program, including protocol-specified guidelines and additional investigator and patient education concerning reduced doses of replacement factor or bypassing agent to treat any breakthrough bleeds in fitusiran studies. Based on this, amended protocols were submitted to the regulatory authorities and in December 2017, the FDA lifted the clinical hold.  Dosing has resumed in the Phase 2 OLE study and we expect to begin dosing patients in the ATLAS Phase 3 program in early 2018.

Clinical trials of a new product candidate require the enrollment of a sufficient number of patients, including patients who are suffering from the disease the product candidate is intended to treat and who meet other eligibility criteria. Rates of patient enrollment are affected by many factors, including the size of the patient population, the age and condition of the patients, the stage and severity of disease, the availability of clinical trials for other investigational drugs for the same disease or condition, the nature of the protocol, the proximity of patients to clinical sites, the availability of effective treatments for the relevant disease, and the eligibility criteria for the clinical trial. For example, we or our partners may experience difficulty enrolling our clinical trials, including, but not limited to, our clinical trials for patisiran,fitusiran, due to the small population of ATTR patients suffering from FAP and the availability of existing approved treatments, as well as other investigational treatments in development. Moreover, given the recent temporary suspension of dosing in our fitusiran studies due to a fatal thrombotic SAE, people with hemophilia may be more reluctant to enroll in the ATLAS Phase 3 program of fitusiran. Delays or difficulties in patient


enrollment or difficulties retaining trial participants, including as a result of the availability of existing or other investigational treatments or safety concerns, can result in increased costs, longer development times or termination of a clinical trial.

Although our investigational RNAi therapeutics have been generally well tolerated in our clinical trials to date, new safety findings may emerge. For example, as noted above, in September 2017, we announced that we had temporarily suspended dosing in all ongoing fitusiran studies pending further review of a fatal thrombotic SAE that occurred in a patient with hemophilia A without inhibitors who was receiving fitusiran in our Phase 2 OLE study. In addition, in October 2016, we made the decision to discontinue our revusiran program. Following reports in the revusiran Phase 2 OLE study of new onset or worsening peripheral neuropathy, the revusiran ENDEAVOUR Phase 3 study DMC assembled in early October 2016 at our request to review these reports and ENDEAVOUR safety data on an unblinded basis. The DMC did not find conclusive evidence for a drug-related neuropathy signal in the ENDEAVOUR trial, but informed us that the benefit-risk profile for revusiran no longer supported continued dosing. We subsequently reviewed unblinded ENDEAVOUR data which revealed an imbalance of mortality in the revusiran arm as compared to placebo. Further, a review by us in 2017 of the ENDEAVOUR results subsequent to the completion of follow-up of the patients post-dosing discontinuation revealed an imbalance in new onset or worsening peripheral neuropathy in the revusiran arm as compared to placebo. We had previously reported, in July 2016, preliminary data from our revusiran Phase 2 OLE study for 12 patients who had reached the 12-month endpoint as of the data transfer date of May 26, 2016. SAEs were observed in 14 patients, one of which, a case of lactic acidosis, was deemed possibly related to the study drug and the patient discontinued treatment. There were a total of seven deaths reported at that time in the revusiran OLE study, all of which were unrelated to the study drug. The majority of the AEs were mild or moderate in severity; ISRs were reported in 12 patients. In August 2015, we reported that three patients had discontinued from the revusiran Phase 2 OLE study due to recurrent localized reactions at the injection site or a diffuse rash; no further discontinuations due to ISRs had occurred as of May 26, 2016.

In our patisiran APOLLO Phase 3 study in patients with polyneuropathy due to hATTR amyloidosis, the most commonly reported AEs that occurred more frequently in patisiran patients were peripheral edema and IRRs. These were generally mild to moderate in severity and only one patient discontinued from the APOLLO study due to an IRR. Compared to placebo, patisiran treatment was associated with fewer treatment discontinuations and fewer study withdrawals due to AEs. The incidence of SAEs across the patisiran and placebo groups was similar and the SAEs reported in two or more patients in the patisiran group included: diarrhea, cardiac failure, congestive cardiac failure, orthostatic hypotension, pneumonia and atrioventricular block complete. These were all considered unrelated to patisiran, except for one SAE of diarrhea. SAEs occurred with similar frequency in the placebo group, except for diarrhea. Deaths were recorded with a similar incidence across the patisiran and placebo treatment groups and no deaths were considered related to the study drug.

In addition, in our ALN-VSP clinical trial, one patient with advanced pancreatic neuroendocrine cancer with extensive involvement of the liver developed hepatic failure five days following the second dose ofALN-VSP and subsequently died; this was deemed possibly related to the study drug. In our patisiran Phase 2 open label extension study in FAP patients, infusion reactions occurred in approximately 15%As demonstrated by the discontinuation of patients, were mild in severity and did not result in any discontinuations. In our revusiran Phase 1 clinical trial, we observed injection site reactions, or ISRs,program in a minorityOctober 2016 and the temporary suspension of subjects receiving revusiran or placebo. These were reported as being clinically mild and consisteddosing in September 2017 in our fitusiran studies, the occurrence of transient erythema associated in a minority of cases with edemaSAEs and/or pain. In

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all cases, these reactions wereself-limiting and resolved within approximately two hours of onset. In our revusiran Phase 2 trial in FAC and SSA patients, the most common adverse event was ISRs that occurred in 23% of patients. These were all mild in severity and were similar to the ISRs observed and previously reported in the revusiran Phase 1 study. The next most common adverse event was a low incidence of transient mild liver function test changes (15%) that, in all cases, resolved without discontinuing therapy. In three of four patients, these elevations appeared to be clinically insignificant and were less than one and a half times the upper limit of normal. One patient had an approximatefour-fold elevation in liver transaminases that was deemed a serious adverse event and mild in severity; this event resolved during continued dosing. The occurrence of adverse eventsAEs can result in the suspension or termination of clinical trials of a product candidate by us or the FDA or a foreign regulatory authority, or refusal to approve a particular product candidate for any or all indications of use.

Clinical trials also require the review, oversight and approval of IRBs or, outside of the United States, an independent ethics committee, which continually review clinical investigations and protect the rights and welfare of human subjects. Inability to obtain or delay in obtaining IRB or ethics committee approval can prevent or delay the initiation and completion of clinical trials, and the FDA or foreign regulatory authorities may decide not to consider any data or information derived from a clinical investigation not subject to initial and continuing IRB or ethics committee review and approval, as the case may be, in support of a marketing application.

Our product candidates that we develop may encounter problems during clinical trials that will cause us, an IRB, ethics committee or regulatory authorities to delay, suspend or terminate these trials, or that will delay or confound the analysis of data from these trials. If we experience any such problems, we may not have the financial resources to continue development of the product candidate that is affected, or development of any of our other product candidates. We may also lose, or be unable to enter into, collaborative arrangements for the affected product candidate and for other product candidates we are developing.

A failure of one or more of our clinical trials can occur at any stage of testing. We may experience numerous unforeseen events during, or as a result of,pre-clinical nonclinical testing and the clinical trial process that could delay or prevent regulatory approval or our ability to commercialize our product candidates, including:

ourpre-clinical nonclinical tests or clinical trials may produce negative or inconclusive results, and we may decide, or regulators may require us, to conduct additionalpre-clinical nonclinical testing or clinical trials, or we may abandon projects that we expect to be promising;

delays in filing INDs or comparable foreign applications or delays or failure in obtaining the necessary approvals from regulators or IRBs in order to commence a clinical trial at a prospective trial site, or their suspension or termination of a clinical trial once commenced;


 

delays in filing IND applications or comparable foreign applications or delays or failure in obtaining the necessary approvals from regulators or IRBs/ethics committees in order to commence a clinical trial at a prospective trial site, or their suspension or termination of a clinical trial once commenced;

conditions imposed on us by an IRB or ethics committee, or the FDA or comparable foreign authorities regarding the scope or design of our clinical trials;

problems in engaging IRBs or ethics committees to oversee clinical trials or problems in obtaining or maintaining IRB or ethics committee approval of trials;

delays in enrolling patients and volunteers into clinical trials, and variability in the number and types of patients and volunteers available for clinical trials;

highdrop-out rates for patients and volunteers in clinical trials;

negative or inconclusive results from our clinical trials or the clinical trials of others for product candidates similar to ours;

inadequate supply or quality of product candidate materials or other materials necessary for the conduct of our clinical trials;

greater than anticipated clinical trial costs;

serious and unexpecteddrug-related side effects experienced by participants in our clinical trials or by individuals using drugs similar to our product candidates;

poor or disappointing effectiveness of our product candidates during clinical trials;

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unfavorable FDA or other regulatory agency inspection and review of a clinical trial site or records of any clinical orpre-clinical nonclinical investigation;

failure of ourthird-party contractors or investigators to comply with regulatory requirements or otherwise meet their contractual obligations in a timely manner, or at all;

governmental or regulatory delays and changes in regulatory requirements, policy and guidelines, including the imposition of additional regulatory oversight around clinical testing generally or with respect to our technology in particular; or

varying interpretations of data by the FDA and similar foreign regulatory agencies.

Even if we successfully complete clinical trials of our product candidates, as is the case with patisiran, any given product candidate may not prove to be a safe and effective treatment for the disease for which it was being tested.

We may be unable to obtain United States or foreign regulatory approval and, as a result, unable to commercialize our product candidates.

Our product candidates are subject to extensive governmental regulations relating to, among other things, research, testing, development, manufacturing, safety, efficacy, approval, recordkeeping, reporting, labeling, storage, packaging, advertising and promotion, pricing, marketing and distribution of drugs. Rigorouspre-clinical nonclinical testing and clinical trials and an extensive regulatory approval process are required to be successfully completed in the United States and in many foreign jurisdictions before a new drug can be marketed. Satisfaction of these and other regulatory requirements is costly, time consuming, uncertain and subject to unanticipated delays. It is possible that none of the product candidates we may develop will obtain the regulatory approvals necessary for us or our collaborators to begin selling them.

We have limited experience in conducting and managing the clinical trials necessary to obtain regulatory approvals, including approval by the FDA. The time required to obtain FDA and other regulatory approvals is unpredictable but typically takes many years following the commencement of clinical trials, depending upon the type, complexity and novelty of the product candidate. The standards that the FDA and its foreign counterparts use when regulating us are not always applied predictably or uniformly and can change. Any analysis we perform of data frompre-clinical nonclinical and clinical activities is subject to confirmation and interpretation by regulatory authorities, which could delay, limit or prevent regulatory approval. We may also encounter unexpected delays or increased costs due to new government regulations, for example, from future legislation or administrative action, or from changes in FDA policy during the period of product development, clinical trials and FDA regulatory review. It is impossible to predict whether legislative changes will be enacted, or whether FDA or foreign regulations, guidance or interpretations will be changed, or what the impact of such changes, if any, may be.


Because the drugs we are developing may represent a new class of drug, the FDA and its foreign counterparts have not yet established any definitive policies, practices or guidelines in relation to these drugs. The lack of policies, practices or guidelines may hinder or slow review by the FDA of any regulatory filings that we may submit. Moreover, the FDA may respond to these submissions by defining requirements we may not have anticipated. Such responses could lead to significant delays in the clinical development of our product candidates. In addition, because there may be approved treatments for some of the diseases for which we may seek approval, in order to receive regulatory approval, we may need to demonstrate through clinical trials that the product candidates we develop to treat these diseases, if any, are not only safe and effective, but safer or more effective than existing products. Furthermore, in recent years, there has been increased public and political pressure on the FDA with respect to the approval process for new drugs, and the FDA’s standards, especially regarding drug safety, appear to have become more stringent.

In November 2017, we reported positive complete results from our APOLLO Phase 3 clinical trial and generally encouraging safety data, and in December 2017, we completed the submission of our first NDA and submitted our first MAA for patisiran. In January 2018, we announced that the EMA has accepted the MAA and initiated its review. Patisiran was previously granted an accelerated assessment by the EMA.  In early February 2018, we announced that the FDA has accepted our NDA and granted our request for priority review, with an action date of August 11, 2018.  We also plan to file for regulatory approval in Japan in mid-2018 and in one or more additional countries by the end of the year. Any delay or failure in obtaining required approvals could have a material adverse effect on our ability to generate revenues from the particularpatisiran or any product candidate for which we are seeking approval.may seek approval in the future. Furthermore, any regulatory approval to market apatisiran or any other product may be subject to limitations on the approved uses for which we may market the product or the labeling or other restrictions. In addition, the FDA has the authority to require a REMS plan as part of a new drug application, oran NDA, or after approval, which may impose further requirements or

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restrictions on the distribution or use of an approved drug, such as limiting prescribing to certain physicians or medical centers that have undergone specialized training, limiting treatment to patients who meet certainsafe-use criteria and requiring treated patients to enroll in a registry. TheseIn the EU, we could be required to adopt a similar plan, known as a risk management plan, and our products could be subject to specific risk minimization measures, such as restrictions on prescription and supply, the conduct of post-marketing safety or efficacy studies, or the distribution of patient and/or prescriber educational materials. In either instance, these limitations and restrictions may limit the size of the market for the product and affect reimbursement bythird-party payors.

We are also subject to numerous foreign regulatory requirements governing, among other things, the conduct of clinical trials, manufacturing and marketing authorization,authorisation, pricing andthird-party reimbursement. The foreign regulatory approval process varies among countries and includes all of the risks associated with FDA approval described above as well as risks attributable to the satisfaction of local regulations in foreign jurisdictions. Approval by the FDA does not ensure approval by regulatory authorities outside the United States and vice versa.

Even if we obtain regulatory approvals, our marketed drugs will be subject to ongoing regulatory oversight. If we fail to comply with continuing U.S. and foreign requirements, our approvals could be limited or withdrawn, we could be subject to other penalties, and our business would be seriously harmed.

Following any initial regulatory approval of patisiran and any other drugs we may develop, we will also be subject to continuing regulatory oversight, including the review of adverse drug experiences and clinical results that are reported after our drug products are made commercially available. This would include results from anypost-marketing tests or surveillance to monitor the safety and efficacy of thepatisiran or other drug productproducts required as a condition of approval or agreed to by us. Any regulatory approvals that we receive for patisiran or our other product candidates may also be subject to limitations on the approved uses for which the product may be marketed. Other ongoing regulatory requirements include, among other things, submissions of safety and otherpost-marketing information and reports, registration and listing, as well as continued compliance with cGMP requirements and good clinical practicesGCP requirements for any clinical trials that we conductpost-approval. In addition, we are conducting, and intend to continue to conduct, clinical trials for our product candidates, and we intend to seek approval to market our product candidates, in jurisdictions outside of the United States, and therefore will be subject to, and must comply with, regulatory requirements in those jurisdictions.

The FDA has significantpost-market authority, including, for example, the authority to require labeling changes based on new safety information and to requirepost-market studies or clinical trials to evaluate serious safety risks related to the use of a drug and to require withdrawal of the product from the market. The FDA also has the authority to require a REMS plan after approval, which may impose further requirements or restrictions on the distribution or use of an approved drug.

The manufacturerCMO and manufacturing facilities we use to make our product candidates, including our Cambridge facility, our future Norton facility, and Agilent and other CMOs, will also be subject to periodic review and inspection by the FDA and other regulatory agencies. To date, our Cambridge manufacturing facility has not been subject to an inspection by any regulatory authority. We expect Agilent will undergo regulatory inspection by the FDA and potentially other regulatory authorities in connection with the review of our NDA and MAA, as well as any subsequent applications for regulatory approval in other territories. The discovery of any new or previously unknown problems with us or ourthird-party manufacturers, CMOs, or our or their manufacturing processes or facilities, may result in restrictions on


the drug or manufacturerCMO or facility, including delay in approval or, in the future, withdrawal of the drug from the market. We have developed cGMP capabilities and processes for the manufacture of patisiran formulated bulk drug product for Phase 3 clinical and earlycommercial use. In addition, in April 2016, we completed our purchase of a parcel of land in Norton, Massachusetts, where we have commenced construction of a cGMP manufacturing facility for drug substance, including siRNAs and siRNA conjugates, for clinical and commercial use. We may not have the ability or capacity to manufacture material at a broader commercial scale in the future. We may manufacture clinical trial materials or we may contract a third party to manufacture these materials for us. Reliance onthird-party manufacturers CMOs entails risks to which we would not be subject if we manufactured products ourselves, including reliance on thethird-party manufacturer CMO for regulatory compliance. Our product promotion and advertising will also be subject to regulatory requirements and continuing regulatory review.

If we or our collaborators, manufacturersCMOs or service providers fail to comply with applicable continuing regulatory requirements in the United States or foreign jurisdictions in which we may seek to market our products, we or they may be subject to, among other things, fines, warning letters, holds on clinical trials, refusal by the FDA or foreign regulatory authorities to approve pending applications or supplements to approved applications, suspension or withdrawal of regulatory approval, product recalls and seizures, refusal to permit the import or export of products, operating restrictions, injunction, civil penalties and criminal prosecution.

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Even if we receive regulatory approval to market our product candidates, the market may not be receptive to our product candidates upon their commercial introduction, which will prevent us from becoming profitable.

The product candidates that we are developing are based upon new technologies or therapeutic approaches. Key participants in pharmaceutical marketplaces, such as physicians,third-party payors and consumers, may not accept a product intended to improve therapeutic results based on RNAi technology. As a result, it may be more difficult for us to convince the medical community andthird-party payors to accept and use our product, or to provide favorable reimbursement.

Other factors that we believe will materially affect market acceptance of our product candidates include:

the timing of our receipt of any marketing approvals, the terms of any approvals and the countries in which approvals are obtained;

the safety and efficacy of our product candidates, as demonstrated in clinical trials and as compared with alternative treatments, if any;

relative convenience and ease of administration of our product candidates;

the willingness of patients to accept potentially new routes of administration;administration or new or different therapeutic approaches and mechanisms of action;

the success of our physician education programs;

the availability of adequate government andthird-party payor reimbursement;

the pricing of our products, particularly as compared to alternative treatments;treatments, and the market perception of such prices and any price increase that we may implement in the future; and

availability of alternative effective treatments for the diseases that product candidates we develop are intended to treat and the relative risks, benefits and costs of thethose treatments.

For example, patisiran utilizes an intravenous mode of administration that physicians and/or patients may not readily adopt or which may not compete with other potentially available options. In addition, fitusiran represents a new approach to treating hemophilia which may not be readily accepted by patients and their caregivers.

In addition, our estimates regarding the potential market size for patisiran or our other product candidates may be materially different from what we currently expect at the time we commence commercialization, which could result in significant changes in our business plan and may have a material adverse effect on our results of operations and financial condition.

If we or our collaborators, manufacturersCMOs or service providers fail to comply with healthcare laws and regulations, we or they could be subject to enforcement actions, which could affect our ability to develop, market and sell our products and may harm our reputation.

As a manufacturer of pharmaceuticals, we are subject to federal, state, and comparable foreign healthcare laws and regulations pertaining to fraud and abuse and patients’ rights. These laws and regulations include:

theThe U.S. federal healthcare programanti-kickback law,Anti-Kickback statute, which prohibits, among other things, persons from soliciting, receiving, offering or providingpaying remuneration, directly or indirectly, to induce either the referral of an individual for a healthcare item or service, or the purchasing or ordering of an item or service, for which payment may be made under a federal healthcare program such as Medicare or Medicaid;Medicaid.


 

The U.S. federal false claims laws, including the False Claims Act, or FCA, which prohibit, among other things, individuals or entities from knowingly presenting or causing to be presented, claims for payment by government-funded programs such as Medicare or Medicaid that are false or fraudulent, and which may apply to us by virtue of statements and representations made to customers or third parties, and, making, using or causing to be made or used a false record or statement material to a false or fraudulent claim to the federal government. Manufacturers can be held liable under the FCA even when they do not submit claims directly to government payors if they are deemed to “cause” the submission of false or fraudulent claims. The FCA also permits a private individual acting as a “whistleblower” to bring actions on behalf of the federal government alleging violations of the FCA and to share in any monetary recovery; and which may apply to us by virtue of statements and representations made to customers or third parties.

the U.S. federal false claims law, which prohibits, among other things, individuals or entities from knowingly presenting or causing to be presented, claims for payment bygovernment-funded programs such as Medicare or Medicaid that are false or fraudulent, and which may apply to us by virtue of statements and representations made to customers or third parties;

the U.S.The federal Health Insurance Portability and Accountability Act of 1996, or HIPAA, which created federal criminal statutes that prohibit knowingly and willfully executing, or attempting to execute, a scheme to defraud any healthcare benefit program or obtain, by means of false or fraudulent pretenses, representations, or promises, any of the money or property owned by, or under the custody or control of, any healthcare benefit program, regardless of the payor (e.g., public or private) and knowingly and willfully falsifying, concealing or covering up by any trick or device a material fact or making any materially false statements in connection with the delivery of, or payment for, healthcare benefits, items or services relating to healthcare matters.  Similar to the federal Anti-Kickback Statute, a person or entity can be found guilty of violating HIPAA without actual knowledge of the statute or specific intent to violate it.

HIPAA as amended by the Health Information Technology for Economic and Clinical Health Act, which impose requirements relating to the privacy, security, and transmission of individually identifiable health information; and require notification to affected individuals and regulatory authorities of certain breaches of security of individually identifiable health information;information.

theThe U.S. federal Open Payments requirements were implemented by the CMS, pursuant to the PPACA. Under the National Physician Payment TransparencyOpen Payments Program, manufacturers of medical devices, medical supplies, biological products and drugs covered by Medicare, Medicaid and the Children’s Health Insurance Programs must report all transfers of value, including consulting fees, travel reimbursements, research grants, and other payments or gifts with values over $10 made to physicians and teaching hospitals.

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products and drugs covered by Medicare, Medicaid and Children’s Health Insurance Programs report all transfers of value, including consulting fees, travel reimbursements, research grants, and other payments or gifts with values over $10 made to physicians and teaching hospitals; and

stateFederal consumer protection and unfair competition laws, which broadly regulate marketplace activities and activities that potentially harm consumers.

State and foreign laws comparable to each of the above federal laws, suchincluding in the EU laws prohibiting giving healthcare professionals any gift or benefit in kind as for example,an inducement to prescribe our products, national transparency laws requiring the public disclosure of payments made to healthcare professionals and institutions, and data privacy laws, in addition to anti-kickback and false claims laws applicable to commercial insurers and othernon-federal payors, requirements for mandatory corporate regulatory compliance programs, and laws relating to government reimbursement programs, patient data privacy and security.

If our operations are found to be in violation of any such requirements, we may be subject to penalties, including civil or criminal penalties, criminal prosecution, monetary damages, the curtailment or restructuring of our operations, loss of eligibility to obtain approvals from the FDA, or exclusion from participation in government contracting, healthcare reimbursement or other government programs, including Medicare and Medicaid, or the imposition of a corporate integrity agreement with the Office of Inspector General of the Department of Health and Human Services, any of which could adversely affect our financial results. We are establishing our global compliance infrastructure as we prepare for the potential launch of patisiran in 2018 in the United States and the EU. Although effective compliance programs can mitigate the risk of investigation and prosecution for violations of these laws, these risks cannot be entirely eliminated. Any action against us for an alleged or suspected violation could cause us to incur significant legal expenses and could divert our management’s attention from the operation of our business, even if our defense is successful. In addition, achieving and sustaining compliance with applicable laws and regulations may be costly to us in terms of money, time and resources.

If we or our collaborators, manufacturersCMOs or service providers fail to comply with applicable federal, state or foreign laws or regulations, we could be subject to enforcement actions, which could affect our ability to develop, market and sell patisiran or our other products successfully and could harm our reputation and lead to reduced acceptance of our products by the market. These enforcement actions include, among others:

adverse regulatory inspection findings;

warning letters;

voluntary or mandatory product recalls or public notification or medical product safety alerts to healthcare professionals;

restrictions on, or prohibitions against, marketing our products;


 

restrictions on, or prohibitions against, marketing our products;

restrictions on, or prohibitions against, importation or exportation of our products;

suspension of review or refusal to approve pending applications or supplements to approved applications;

exclusion from participation ingovernment-funded healthcare programs;

exclusion from eligibility for the award of government contracts for our products;

suspension or withdrawal of product approvals;

product seizures;

injunctions; and

civil and criminal penalties, up to and including criminal prosecution resulting in fines, exclusion from healthcare reimbursement programs and imprisonment.

Moreover, federal, state or foreign laws or regulations are subject to change, and while we, our collaborators, manufacturersCMOs and/or service providers currently may be compliant, that could change due to changes in interpretation, prevailing industry standards or the legal structure.

Any drugs we develop may become subject to unfavorable pricing regulations,third-party reimbursement practices or healthcare reform initiatives, thereby harming our business.

The regulations that govern marketing approvals, pricing and reimbursement for new drugs vary widely from country to country. Some countries require approval of the sale price of a drug before it can be marketed. In

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many countries, the pricing review period begins after marketing or product licensing approval is granted. In some foreign markets, prescription pharmaceutical pricing remains subject to continuing governmental control even after initial approval is granted. We are actively monitoring these regulations as we await potential regulatory approval for patisiran in the U.S. and the EU and several of our other programs move into laterlate stages of development, however, manya number of our programs are currently in the earlier stages of development and we will not be able to assess the impact of price regulations for such programs for a number of years. As a result, weWe might obtain regulatory approval for a product, including patisiran, in a particular country, but then be subject to price regulations that delay our commercial launch of the product and negatively impact the revenues we are able to generate from the sale of the product in that country and potentially in other countries due to reference pricing.

Our ability to commercialize patisiran or any other products successfully also will depend in part on the extent to which reimbursement for these products and related treatments will be available from government health administration authorities, private health insurers and other organizations. Even if we succeed in bringing onepatisiran or moreother products to the market, thesepatisiran and such other products may not be consideredcost-effective, and the amount reimbursed for any products may be insufficient to allow us to sell patisiran or our other products on a competitive basis. Increasingly, thethird-party payors who reimburse patients or healthcare providers, such as government and private insurance plans, are requiring that drug companies provide them with predetermined discounts from list prices, and are seeking to reduce the prices charged or the amounts reimbursed for pharmaceuticaldrug products. If the price we are able to charge for patisiran or any other products we develop, or the reimbursement provided for such products, is inadequate in light of our development and other costs, or if reimbursement is denied, our return on investment could be adversely affected. In addition, we have stated publicly that we intend to grow through continued scientific innovation rather than arbitrary price increases. Specifically, we have stated that we will not raise the price of any product for which we receive marketing approval over the rate of inflation, as determined by the consumer price index for urban consumers (approximately 2.2 percent currently). Our patient access philosophy could also negatively impact the revenues we are able to generate from the sale of one or more of our products in the future.

We currently expect that anysome of the drugs we develop may need to be administered under the supervision of a physician or other healthcare professional on an outpatient basis.basis, including patisiran. Under currently applicable U.S. law, certain drugs that are not usuallyself-administered (including injectable drugs) may be eligible for coverage under the Medicare Part B program if:

they are incident to a physician’s services;

 

they are reasonable and necessary for the diagnosis or treatment of the illness or injury for which they are administered according to accepted standards of medical practice; and

they have been approved by the FDA and meet other requirements of the statute.


There may be significant delays in obtaining coverage fornewly-approved drugs, and coverage may be more limited than the purposes for which the drug is approved by the FDA or foreign regulatory authorities. Moreover, eligibility for coverage does not imply that any drug will be reimbursed in all cases or at a rate that covers our costs, including research, development, manufacture, sale and distribution.distribution or that covers a particular provider’s cost of acquiring the drug. Interim payments for new drugs, if applicable, may also not be sufficient to cover our costs and may not be made permanent. Reimbursement may be based on payments allowed forlower-cost drugs that are already reimbursed, may be incorporated into existing payments for other services and may reflect budgetary constraints or imperfections in Medicare data. Net prices for drugs may be reduced by mandatory discounts or rebates required by government healthcare programs or private payors and by any future relaxation of laws that presently restrict imports of drugs from countries where they may be sold at lower prices than in the United States.Third-party payors often rely upon Medicare coverage policy and payment limitations in setting their own reimbursement rates. Our inability to promptly obtain coverage and adequate reimbursement rates from bothgovernment-funded and private payors for patisiran or other new drugs that we develop and for which we obtain regulatory approval could have a material adverse effect on our operating results, our ability to raise capital needed to commercialize products, and our overall financial condition.

We believe that the efforts of governments andthird-party payors to contain or reduce the cost of healthcare and legislative and regulatory proposals to broaden the availability of healthcare will continue to affect the business and financial condition of pharmaceutical and biopharmaceutical companies. Specifically, there have been several recent U.S. Congressional inquiries and proposed federal and state legislation designed to, among other things, bring more transparency to drug pricing, reduce the cost of prescription drugs under Medicare, review the relationship between pricing and manufacturer patient programs, and reform government program reimbursement methodologies for drugs.

On January 2, 2013, the American Taxpayer Relief Act of 2012 was signed into law, which, among other things, further reduced Medicare payments to several types of providers.

A number of other legislative and regulatory changes in the healthcare system in the United States and other major healthcare markets have been proposed in recent years, and such efforts have expanded substantially in recent years. These developments have included prescription drug benefit legislation that was enacted in 2003 and took effect in January 2006, healthcare reform legislation enacted by certain states, and major healthcare reform legislation that was passed by

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Congress and enacted into law in the United States in 2010. These developments could, directly or indirectly, affect our ability to sell our products, if approved, at a favorable price.

In particular, in March 2010, the PPACA was signed into law. This new legislation changeschanged the current system of healthcare insurance and benefits intended to broaden coverage and control costs. The new law also contains provisions that will affect companies in the pharmaceutical industry and other healthcare related industries by imposing additional costs and changes to business practices. Provisions affecting pharmaceutical companies include the following:

Mandatory rebates for drugs sold into the Medicaid program have beenwere increased, and the rebate requirement has beenwas extended to drugs used inrisk-based Medicaid managed care plans.

The 340B Drug Pricing Program under the Public Health Service Act has beenwas extended to require mandatory discounts for drug products sold to certain critical access hospitals, cancer hospitals and other covered entities.

Pharmaceutical companies are required to offer discounts onbrand-name drugs to patients who fall within the Medicare Part D coverage gap, commonly referred to as the “Donut Hole.“donut hole.

Pharmaceutical companies are required to pay an annualnon-tax deductible fee to the federal government based on each company’s market share of prior year total sales of branded products to certain federal healthcare programs, such as Medicare, Medicaid, Department of Veterans Affairs and Department of Defense. Since we expect our branded pharmaceutical sales to constitute a small portion of the total federal healthhealthcare program pharmaceutical market, we do not expect this annual assessment to have a material impact on our financial condition.

The new law provides that approval of an application for afollow-on biologic product may not become effective until 12 years after the date on which the reference innovator biologic product was first licensed by the FDA, with a possiblesix-month extension for pediatric products. After this exclusivity ends, it will be easier for generic manufacturers to enter the market, which is likely to reduce the pricing for such products and could affect our profitability.

The law creates a new methodology by which rebates owed by manufacturers under the Medicaid Drug Rebate Program are calculated for drugs that are inhaled, infused, instilled, implanted or injected.

The law expands eligibility criteria for Medicaid programs by, among other things, allowing states to offer Medicaid coverage to certain individuals with income at or below 133 percent of the federal poverty level, thereby potentially increasing a manufacturer’s Medicaid rebate liability.


The law expands the entities eligible for discounts under the Public Health Service Act pharmaceutical pricing program.

The law establishes new requirements to report financial arrangements with physicians and teaching hospitals and to annually report drug samples that manufacturers and distributors provide to physicians.

The law establishes a new Patient-Centered Outcomes Research Institute to oversee, identify priorities in, and conduct comparative clinical effectiveness research, along with funding for such research.

The full effects of the U.S. healthcare reform legislation cannot be known until the new law is fully implemented through regulations or guidance issued by the CMS and other federal and state healthcare agencies. The financial impact of the U.S. healthcare reform legislation over the next few years will depend on a number of factors, including, but not limited, to the policies reflected in implementing regulations and guidance, and changes in sales volumes for products affected by the new system of rebates, discounts and fees. The newThis legislation may also have a positive impact on our future net sales, if any, by increasing the aggregate number of persons with healthcare coverage in the United States.

Moreover, weAs a result of the 2016 election in the United States, there is great political uncertainty concerning the fate of the PPACA and other healthcare laws. Members of the United States Congress and the Trump Administration have expressed an intent to pass legislation or adopt executive orders to fundamentally change or repeal parts of the PPACA. While Congress has not passed repeal legislation to date, the TCJA includes a provision repealing the individual insurance coverage mandate included in PPACA, effective January 1, 2019.  Further, on January 20, 2017, the President signed an Executive Order directing federal agencies with authorities and responsibilities under the PPACA to waive, defer, grant exemptions from, or delay the implementation of any provision of the PPACA that would impose a fiscal burden on states or a cost, fee, tax, penalty or regulatory burden on individuals, healthcare providers, health insurers, or manufacturers of pharmaceuticals or medical devices. On October 13, 2017, the President signed an Executive Order terminating the cost-sharing subsidies that reimburse insurers under the PPACA. Several state Attorneys General filed suit to stop the administration from terminating the subsidies, but their request for a restraining order was denied by a federal judge in California on October 25, 2017.  In addition, CMS has recently proposed regulations that would give states greater flexibility in setting benchmarks for insurers in the individual and small group marketplaces, which may have the effect of relaxing the essential health benefits required under the PPACA for plans sold through such marketplaces. Congress may consider other legislation to replace elements of the PPACA.  The implications of the PPACA, its possible repeal, any legislation that may be proposed to replace the PPACA, or the political uncertainty surrounding any repeal or replacement legislation for our business and financial condition, if any, are not yet clear.

We cannot predict what healthcare reform initiatives may be adopted in the future. Further federal and state legislative and regulatory developments are likely, and we expect ongoing initiatives in the United States to increase pressure on drug pricing. Such reforms could have an adverse effect on anticipated revenues from product candidates that we may successfully develop and for which we may obtain regulatory approval and may affect our overall financial condition and ability to develop drug candidates.

Our ability to obtain services, reimbursement or funding from the federal government may be impacted by possible reductions in federal spending.

Under the Budget Control Act of 2011, the failure of Congress to enact deficit reduction measures of at least $1.2 trillion for the years 2013 through 2021 triggered automatic cuts to most federal programs. These cuts included aggregate reductions to Medicare payments to providers of up to 2%2 percent per fiscal year, starting in 2013. Under the American Taxpayer Relief Act of 2012, which was enacted on January 1, 2013, the imposition of these automatic cuts was delayed until March 1, 2013. As required by law, President Obama issued a sequestration order on March 1, 2013. Certain of these automatic cuts have been implemented resulting in reductions in Medicare payments to physicians, hospitals, and other healthcare providers, among other things. The full impact on our business of these automatic cuts is uncertain.

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If other federal spending is reduced, any budgetary shortfalls may also impact the ability of relevant agencies, such as the FDA or National Institutes of HealthNIH to continue to function. Amounts allocated to federal grants and contracts may be reduced or eliminated. These reductions may also impact the ability of relevant agencies to timely review and approve drug research and development, manufacturing, and marketing activities, which may delay our ability to develop, market and sell any products we may develop.

There is a substantial risk of product liability claims in our business. If we are unable to obtain sufficient insurance, a product liability claim against us could adversely affect our business.

Our business exposes us to significant potential product liability risks that are inherent in the development, testing, manufacturing and marketing of human therapeutic products. Product liability claims could delay or prevent completion of our clinical development programs. Following the decision to discontinue clinical development of revusiran, we conducted a comprehensive evaluation of available revusiran data. We reported the results of this evaluation on August 9, 2017, however, our investigation did not result in a conclusive explanation regarding the cause of the mortality imbalance observed in the ENDEAVOUR Phase 3 study. In addition, in September 2017, we announced that we had temporarily suspended dosing in all ongoing fitusiran studies pending further


review of a fatal thrombotic SAE and agreement with regulatory authorities on a risk mitigation strategy. Notwithstanding the risks undertaken by all persons who participate in clinical trials, and the information on risks provided to study investigators and patients participating in revusiran and fitusiran studies, it is possible that product liability claims will be asserted against us relating to the worsening of a patient’s condition, injury or death alleged to have been caused by revusiran or fitusiran. Such claims might not be fully covered by product liability insurance. If we succeed in marketing products, suchincluding patisiran, product liability claims could result in an FDA investigation of the safety and effectiveness of our products, our manufacturing processes and facilities or our marketing programs, and potentially a recall of our products or more serious enforcement action, limitations on the approved indications for which they may be used, or suspension or withdrawal of approvals. Regardless of the merits or eventual outcome, liability claims may also result in decreased demand for our products, injury to our reputation, costs to defend the related litigation, a diversion of management’s time and our resources, substantial monetary awards to trial participants or patients and a decline in our stock price. We currently have product liability insurance that we believe is appropriate for our stage of development and may need to obtain higher levels prior to marketing any of our product candidates. Any insurance we have or may obtain may not provide sufficient coverage against potential liabilities. Furthermore, clinical trial and product liability insurance is becoming increasingly expensive. As a result, we may be unable to obtain sufficient insurance at a reasonable cost to protect us against losses caused by product liability claims that could have a material adverse effect on our business.

If we do not comply with laws regulating the protection of the environment and health and human safety, our business could be adversely affected.

Our research, development and manufacturing involvesinvolve the use of hazardous materials, chemicals and various radioactive compounds. We maintain quantities of various flammable and toxic chemicals in our facilities in Cambridge that are required for our research, development and manufacturing activities. We are subject to federal, state and local laws and regulations governing the use, manufacture, storage, handling and disposal of these hazardous materials. We believe our procedures for storing, handling and disposing these materials in our Cambridge facilities comply with the relevant guidelines of the City of Cambridge, the Commonwealth of Massachusetts and the Occupational Safety and Health Administration of the U.S. Department of Labor. Although we believe that our safety procedures for handling and disposing of these materials comply with the standards mandated by applicable regulations, the risk of accidental contamination or injury from these materials cannot be eliminated. If an accident occurs, we could be held liable for resulting damages, which could be substantial. We are also subject to numerous environmental, health and workplace safety laws and regulations, including those governing laboratory procedures, exposure toblood-borne pathogens and the handling of biohazardous materials.

Although we maintain workers’ compensation insurance to cover us for costs and expenses we may incur due to injuries to our employees resulting from the use of these materials, this insurance may not provide adequate coverage against potential liabilities. We do not maintain insurance for environmental liability or toxic tort claims that may be asserted against us in connection with our storage or disposal of biological, hazardous or radioactive materials. Additional federal, state and local laws and regulations affecting our operations may be adopted in the future. We may incur substantial costs to comply with, and substantial fines or penalties if we violate, any of these laws or regulations.

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Risks Related to Patents, Licenses and Trade Secrets

If we are not able to obtain and enforce patent protection for our discoveries, our ability to develop and commercialize our product candidates will be harmed.

Our success depends, in part, on our ability to protect proprietary methods and technologies that we develop under the patent and other intellectual property laws of the United States and other countries, so that we can prevent others from unlawfully using our inventions and proprietary information. However, we may not hold proprietary rights to some patents required for us to manufacture and commercialize our proposed products. Because certain U.S. patent applications are confidential until the patents issue, such as applications filed prior to November 29, 2000, or applications filed after such date which will not be filed in foreign countries, third parties may have filed patent applications for technology covered by our pending patent applications without our being aware of those applications, and our patent applications may not have priority over those applications. For this and other reasons, we may be unable to secure desired patent rights, thereby losing desired exclusivity. Further, we may be required to obtain licenses underthird-party patents to market our proposed products or conduct our research and development or other activities. If licenses are not available to us on acceptable terms, we willmay not be able to market the affected products or conduct the desired activities.

Our strategy depends on our ability to rapidly identify and seek patent protection for our discoveries. In addition, we may rely onthird-party collaborators to file patent applications relating to proprietary technology that we develop jointly during certain collaborations. The process of obtaining patent protection is expensive andtime-consuming. If our present or future collaborators fail to file and prosecute all necessary and desirable patent applications at a reasonable cost and in a timely manner, our business willmay be adversely affected. Despite our efforts and the efforts of our collaborators to protect our proprietary rights, unauthorized parties may


be able to obtain and use information that we regard as proprietary. While issued patents are presumed valid, this does not guarantee that the patent will survive a validity challenge or be held enforceable. Any patents we have obtained, or obtain in the future, may be challenged, invalidated, adjudged unenforceable or circumvented by parties attempting to design around our intellectual property. Moreover, third parties or the USPTO may commence interference proceedings involving our patents or patent applications. Any challenge to, finding of unenforceability or invalidation or circumvention of, our patents or patent applications, would be costly, would require significant time and attention of our management, could reduce or eliminate royalty payments to us from third party licensors and could have a material adverse effect on our business.

Our pending patent applications may not result in issued patents. The patent position of pharmaceutical or biotechnology companies, including ours, is generally uncertain and involves complex legal and factual considerations. The standards that the USPTO and its foreign counterparts use to grant patents are not always applied predictably or uniformly and can change. Similarly, the ultimate degree of protection that will be afforded to biotechnology inventions, including ours, in the United States and foreign countries, remains uncertain and is dependent upon the scope of the protection decided upon by patent offices, courts and lawmakers. Moreover, there are periodic discussions in the Congress of the United States and in international jurisdictions about modifying various aspects of patent law. For example, the America Invents Act includesincluded a number of changes to the patent laws of the United States. If any of the enacted changes do not provide adequate protection for discoveries, including our ability to pursue infringers of our patents for substantial damages, our business could be adversely affected. One major provision of the America Invents Act, which took effect in March 2013, changed United States patent practice from afirst-to-invent to afirst-to-file system. If we fail to file an invention before a competitor files on the same invention, we no longer have the ability to provide proof that we were in possession of the invention prior to the competitor’s filing date, and thus would not be able to obtain patent protection for our invention. There is also no uniform, worldwide policy regarding the subject matter and scope of claims granted or allowable in pharmaceutical or biotechnology patents.

Accordingly, we do not know the degree of future protection for our proprietary rights or the breadth of claims that will be allowed in any patents issued to us or to others. We also rely to a certain extent on trade secrets,know-how and technology, which are not protected by patents, to maintain our competitive position. If any trade secret,know-how or other technology not protected by a patent were to be disclosed to or

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independently developed by a competitor, our business and financial condition could be materially adversely affected.

We license patent rights fromthird-party owners. If such owners do not properly or successfully obtain, maintain or enforce the patents underlying such licenses, our competitive position and business prospects willmay be harmed.

We are a party to a number of licenses that give us rights tothird-party intellectual property that is necessary or useful for our business. In particular, we have obtained licenses from, among others, CRT, Isis,Ionis, MIT, Whitehead, Max Planck Innovation Tekmira and Arrowhead.Arbutus. We also intend to enter into additional licenses tothird-party intellectual property in the future.

Our success will depend in part on the ability of our licensors to obtain, maintain and enforce patent protection for our licensed intellectual property, in particular, those patents to which we have secured exclusive rights. Our licensors may not successfully prosecute the patent applications to which we are licensed. Even if patents issue in respect of these patent applications, our licensors may fail to maintain these patents, may determine not to pursue litigation against other companies that are infringing these patents, or may pursue such litigation less aggressively than we would. Without protection for the intellectual property we license, other companies might be able to offer substantially identical products for sale, which could adversely affect our competitive business position and harm our business prospects. In addition, we sublicense our rights under variousthird-party licenses to our collaborators. Any impairment of these sublicensed rights could result in reduced revenues under our collaboration agreements or result in termination of an agreement by one or more of our collaborators.

Other companies or organizations may challenge our patent rights or may assert patent rights that prevent us from developing and commercializing our products.

RNAi is a relatively new scientific field, the commercial exploitation of which has resulted in many different patents and patent applications from organizations and individuals seeking to obtain patent protection in the field. We have obtained grants and issuances of RNAi patents and have licensed many of these patents from third parties on an exclusive basis. The issued patents and pending patent applications in the United States and in key markets around the world that we own or license claim many different methods, compositions and processes relating to the discovery, development, manufacture and commercialization of RNAi therapeutics.

Specifically, we have a portfolio of patents, patent applications and other intellectual property covering: fundamental aspects of the structure and uses of siRNAs, including their manufacture and use as therapeutics, andRNAi-related mechanisms; chemical modifications to siRNAs that improve their suitability for therapeutic and other uses; siRNAs directed to specific targets as treatments for particular diseases; and delivery technologies, such as in the fieldfields of carbohydrate conjugates and cationic liposomes.liposomes; and all aspects of our specific development candidates.


As the field of RNAi therapeutics is maturing, patent applications are being fully processed by national patent offices around the world. There is uncertainty about which patents will issue, and, if they do, as to when, to whom, and with what claims. It is likely that there will be significant litigation and other proceedings, such as interference, reexamination and opposition proceedings, as well as inter partes and post-grant review proceedings introduced by provisions of the America Invents Act, which became available to third party challengers on September 16, 2012, in various patent offices relating to patent rights in the RNAi field. For example, various third parties have initiated oppositions to patents in our McSwiggen, Kreutzer-Limmer and Tuschl II series in the EPO and in other jurisdictions. We expect that additional oppositions will be filed in the EPO and elsewhere, and other challenges will be raised relating to other patents and patent applications in our portfolio. In many cases, the possibility of appeal exists for either us or our opponents, and it may be years before final, unappealable rulings are made with respect to these patents in certain jurisdictions. The timing and outcome of these and other proceedings is uncertain and may adversely affect our business if we are not successful in defending the patentability and scope of our pending and issued patent claims. In addition, third parties may attempt to invalidate our intellectual property rights. Even if our rights are not directly challenged, disputes could lead to the weakening of our intellectual property rights. Our defense against any attempt by third parties to circumvent or invalidate our intellectual property rights could be costly to us, could require significant

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time and attention of our management and could have a material adverse effect on our business and our ability to successfully compete in the field of RNAi.

There are many issued and pending patents that claim aspects of oligonucleotide chemistry and modifications that we may need to apply tofor our siRNA therapeutic candidates. There are also many issued patents that claim targeting genes or portions of genes that may be relevant for siRNA drugs we wish to develop. In addition, there may be issued and pending patent applications that may be asserted against us in a court proceeding or otherwise based upon the asserting party’s belief that we may need such patents for our siRNA therapeutic candidates. Thus, it is possible that one or more organizations will hold patent rights to which we willmay need a license.license, or hold patent rights which could be asserted against us. If those organizations refuse to grant us a license to such patent rights on reasonable terms and/or a court rules that we need such patent rights that have been asserted against us and we are not able to obtain a license on reasonable terms, we may not be ableunable to market products or perform research and development or other activities covered by thesesuch patents. For example, Silence issued and has now served, a claim in the High Court of England and Wales, naming us, our wholly owned subsidiary Alnylam UK Ltd., and The Medicines Company UK Ltd as co-defendants. The claim seeks a declaration that Silence is entitled to supplementary protection certificates, or SPCs, based on a European patent held by Silence, that Silence alleges covers certain of our product candidates. An SPC is an intellectual property right that could extend the life of the Silence patent in relation to a specified product for a period of up to five additional years bringing the potential expiration date to 2028. On October 27, 2017, we, through our affiliate Alnylam UK Ltd., and The Medicines Company UK Ltd filed and served a claim against Silence Therapeutics GmbH and Silence in the High Court of England and Wales seeking revocation of Silence’s patent, as well as a declaration of non-infringement by each of the products of such patent, and costs and interest among other potential remedies.  On November 30, 2017, we and The Medicines Company UK Ltd filed our defense to Silence’s claim against us denying that the products that are the subject of Silence’s claim against us fall under the Silence patent or that they are entitled to an SPC based on that patent.  Both cases are expected to be tried in the High Court of England and Wales in December 2018.  Although we believe Silence’s patent is invalid and not infringed by our product candidates and that, therefore, Silence would not be entitled to obtain an SPC based on any of our product candidates, litigation is subject to inherent uncertainty, and a court could ultimately rule against us.

If we become involved in patent litigation or other proceedings related to a determination of rights, we could incur substantial costs and expenses, substantial liability for damages or be required to stop our product development and commercialization efforts.

Third parties may sue us for infringing their patent rights. Likewise, we may need to resort to litigation to enforce a patent issued or licensed to us or to determine the scope and validity of proprietary rights of others. In addition,others or protect our proprietary information and trade secrets. For example, during the second quarter of 2015, we filed a trade secret misappropriation lawsuit against Dicerna , to protect our rights in the RNAi assets we purchased from Merck. A third party may also claim that we have improperly obtained or used its confidential or proprietary information. For example, in March 2011, TekmiraArbutus (formerly Tekmira) filed a civil complaint against us alleging, among other things, misappropriation of the plaintiffs’its confidential and proprietary information and trade secrets. In November 2012, we settled this litigation and restructured our contractual relationship with Tekmira.Arbutus. In connection with this restructuring, we incurred a $65.0 million charge to operating expenses during the quarter ended December 31, 2012.

In protecting our intellectual patent rights through litigation or other means, a third party may claim that we have improperly asserted our rights against them.  For example, in August 2017, Dicerna successfully added counterclaims against us in the above-referenced trade secret lawsuit alleging that our lawsuit represented abuse of process and claiming tortious interference with its business.  In addition, duringin August 2017, Dicerna filed a lawsuit against us in the pendencyUnited States District Court of Massachusetts alleging
attempted monopolization by us under
the Sherman Antitrust Act
.  Although we believe we have meritorious claims against Dicerna and meritorious defenses and responses to the counterclaims and federal claim being asserted by Dicerna, litigation is subject to inherent uncertainty, we incurredwill incur significant costs in defending against such claims and the defense of this litigation diverted the attention of our management and other resources that would otherwise have been engaged in other activities.a court could rule against us awarding unspecified money damages.


Furthermore, third parties may challenge the inventorship of our patents or licensed patents. For example, in March 2011, The University of Utah, or Utah, filed a complaint in the United States District Court for the District of Massachusetts against us, Max Planck Gesellschaft Zur Foerderung Der Wissenschaften e.V. and Max Planck Innovation, together, Max Planck, Whitehead, MIT and UMass, claiming that a professor of Utah iswas the sole inventor, or in the alternative, a joint inventor of certain of ourin-licensed patents. Utah iswas seeking correction of inventorship of the Tuschl patents, unspecified damages and other relief. In October 2011, we, Max Planck, Whitehead, MITAfter several years of court proceedings and UMass filed a motion to dismiss and UMass filed a motion to dismiss on separate grounds, which we, Max Planck, Whitehead and MIT have joined. In December 2011, Utah filed a second amended complaint dropping UMass as a defendant and adding as defendants several UMass officials. In June 2012,discovery, the Court denied both motions to dismiss. We, Max Planck, Whitehead, MIT and UMass filed an appeal of the Court’s ruling on the motion to dismiss for lack of jurisdiction and a motion requesting that the Court stay the case pending the outcome of the appeal. In July 2012, the Court stayed discovery in the case pending the outcome of the defendants’ appeal. In August 2013, the United States Court of Appeals for the Federal Circuit, or CAFC, affirmed the lower Court’s ruling, in a split decision. In September 2013, we filed a petition with the CAFC for rehearing or rehearing en banc. In November 2013, the CAFC denied our petition for rehearing or rehearing en banc and remanded the case back to the lower Court. In February 2014, we filed a petition for writ of certiorari from the Supreme Court and a motion to stay the lower Court proceedings pending a decision from the Supreme Court on our petition. The lower Courtcourt granted our motion to staymotions for summary judgment, and dismissed Utah’s state law damages claims as well. During the proceedings, however,pendency of this litigation, as well as the Arbutus litigation described above, we incurred significant costs, and in June 2014,each case, the Supreme Court deniedlitigation diverted the attention of our petition for certiorarimanagement and remanded the case back to the United States District Court for the District of Massachusetts for trial, which is now scheduled to begin on November 2, 2015.other resources that would otherwise have been engaged in other activities.

In addition, in connection with certain license and collaboration agreements, we have agreed to indemnify certain third parties for certain costs incurred in connection with litigation relating to intellectual property rights or the subject matter of the agreements. The cost to us of any litigation or other proceeding relating to intellectual property rights, even if resolved in our favor, could be substantial, and litigation would divert our management’s efforts. Some of our competitors may be able to sustain the costs of complex patent litigation more effectively than we can because they have substantially greater resources. Uncertainties resulting from the initiation and continuation of any litigation could delay our research and development efforts and limit our ability to continue our operations.

 

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If any parties successfully claim that our creation or use of proprietary technologies infringes upon or otherwise violates their intellectual property rights, we might be forced to pay damages, potentially including treble damages, if we are found to have willfully infringed on such parties’ patent rights. In addition to any damages we might have to pay, a court could require us to stop the infringing activity or obtain a license. Any license required under any patent may not be made available on commercially acceptable terms, if at all. In addition, such licenses are likely to benon-exclusive and, therefore, our competitors may have access to the same technology licensed to us. If we fail to obtain a required license and are unable to design around a patent, we may be unable to effectively market some of our technology and products, which could limit our ability to generate revenues or achieve profitability and possibly prevent us from generating revenue sufficient to sustain our operations. Moreover, we expect that a number of our collaborations will provide that royalties payable to us for licenses to our intellectual property may be offset by amounts paid by our collaborators to third parties who have competing or superior intellectual property positions in the relevant fields, which could result in significant reductions in our revenues from products developed through collaborations.

If we fail to comply with our obligations under any licenses or related agreements, we may be required to pay damages and could lose license or other rights that are necessary for developing and protecting our RNAi technology and any related product candidates that we develop, or we could lose certain rights to grant sublicenses.

Our current licenses impose, and any future licenses we enter into are likely to impose, various development, commercialization, funding, milestone, royalty, diligence, sublicensing, insurance, patent prosecution and enforcement, and other obligations on us. If we breach any of these obligations, or use the intellectual property licensed to us in an unauthorized manner, we may be required to pay damages and the licensor may have the right to terminate the license or render the licensenon-exclusive, which could result in us being unable to develop, manufacture, market and sell products that are covered by the licensed technology or enable a competitor to gain access to the licensed technology. For example, Tekmira hasin 2013, Arbutus (formerly Tekmira) notified us that it believesbelieved it hashad achieved a $5.0 million milestone payment under ourcross-license agreement relating to the manufacture ofALN-VSP clinical trial material for use in China. We have notified TekmiraArbutus that we dodid not believe that the milestone has been achieved under the terms of thecross-license agreement. In August 2013, we initiated binding arbitration proceedings seeking a declaratory judgment that Tekmira hasArbutus had not yet met the conditions of the milestone and iswas not entitled to payment at the time. The Arbutus arbitration hearing was held in May 2015. On March 9, 2016, the arbitration panel ruled in our favor and as a result, no milestone payment is due to Arbutus at this time. If it is determined through arbitration that Tekmira has met the requirements of the milestone, we will have to pay Tekmira the milestone. We currently expect that the Tekmira arbitration hearing will be held in the second quarter of 2015.Arbutus did not appeal this ruling.

Moreover, our licensors may own or control intellectual property that has not been licensed to us and, as a result, we may be subject to claims, regardless of their merit, that we are infringing or otherwise violating the licensor’s rights. In addition, while we cannot currently determine the amount of the royalty obligations we will be required to pay on sales of future products, if any, the amounts may be significant. The amount of our future royalty obligations will depend on the technology and intellectual property we use in products that we successfully develop and commercialize, if any. Therefore, even if we successfully develop and commercialize products, we may be unable to achieve or maintain profitability.

Confidentiality agreements with employees and others may not adequately prevent disclosure of trade secrets and other proprietary information.

In order to protect our proprietary technology and processes, we rely in part on confidentiality agreements with our collaborators, employees, consultants, outside scientific collaborators and sponsored researchers, and other advisors. These agreements may not effectively prevent disclosure of confidential information and may not provide an adequate remedy in the event of


unauthorized disclosure of confidential information. In addition, others may independently discover trade secrets and proprietary information, and in such cases we could not assert any trade secret rights against such party. Costly andtime-consuming litigation could be necessary to enforce and determine the scope of our proprietary rights, and failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

 

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Risks Related to Competition

The pharmaceutical market is intensely competitive. If we are unable to compete effectively with existing drugs, new treatment methods and new technologies, we may be unable to commercialize successfully any drugs that we develop.

The pharmaceutical market is intensely competitive and rapidly changing. Many large pharmaceutical and biotechnology companies, academic institutions, governmental agencies and other public and private research organizations are pursuing the development of novel drugs for the same diseases that we are targeting or expect to target. Many of our competitors have:

much greater financial, technical and human resources than we have at every stage of the discovery, development, manufacture and commercialization of products;

more extensive experience inpre-clinical testing, conducting clinical trials, obtaining regulatory approvals, and in manufacturing, marketing and selling pharmaceuticaldrug products;

product candidates that are based on previously tested or accepted technologies;

products that have been approved or are in late stages of development; and

collaborative arrangements in our target markets with leading companies and research institutions.

We will face intense competition from drugs that have already been approved and accepted by the medical community for the treatment of the conditions for which we may develop drugs. We also expect to face competition from new drugs that enter the market. We believe a significant number of drugs are currently under development, and may become commercially available in the future, for the treatment of conditions for which we may try to develop drugs. These drugs may be more effective, safer, less expensive, or marketed and sold more effectively, than any products we develop. For example, we are developing patisiran for the treatment of ATTR patients sufferinghATTR amyloidosis. In November 2017, we reported positive complete results from FAP.our APOLLO Phase 3 clinical trial and generally encouraging safety data, and in December 2017, we submitted our first NDA and MAA for patisiran.  In January 2018, we announced that the EMA has accepted the MAA and initiated its review. Patisiran was previously granted an accelerated assessment by the EMA.  In early February 2018, we announced that the FDA has accepted our NDA and granted our request for priority review, with an action date of August 11, 2018. We are aware of other approved products used to treat this disease, including tafamidis, marketed by Pfizer in Europe and certain countries outside the United States, as well as product candidates in various stages of clinical development. Patisiran maydevelopment, including an investigational drug being developed by Ionis. In October and November 2017, Ionis reported positive efficacy data as well as safety data from its Phase 3 clinical trial in hATTR amyloidosis, including thrombocytopenia and renal insufficiency SAEs. In November 2017, Ionis reported that it has filed its NDA and MAA for this investigational drug and in January 2018, reported that the FDA had accepted its NDA for priority review and set a PDUFA date of July 6, 2018. While we believe that patisiran will have a competitive product profile, it is possible it will not compete favorably with these products and product candidates, or others, and even if approved, it may not achieve commercial success.

If we successfully develop product candidates, and obtain approval for them, we will face competition based on many different factors, including:

the safety and effectiveness of our products relative to alternative therapies, if any;

the ease with which our products can be administered and the extent to which patients accept relatively new routes of administration;

the timing and scope of regulatory approvals for these products;

the availability and cost of manufacturing, marketing and sales capabilities;

price;

reimbursement coverage; and

patent position.

Our competitors may develop or commercialize products with significant advantages over any products we develop based on any of the factors listed above or on other factors. Our competitors may therefore be more successful in commercializing their products than we are, which could adversely affect our competitive position and business. Competitive products may make any


products we develop obsolete or noncompetitive before we can recover the expenses of developing and commercializing our product candidates. Such competitors could also recruit our employees, which could negatively impact our level of expertise and the ability to execute on our business plan. Furthermore, we also face competition from existing and new treatment methods that reduce or eliminate the need for drugs, such as the use of advanced medical devices. The development of new medical devices or other treatment methods for the diseases we are targeting could make our product candidates noncompetitive, obsolete or uneconomical.

70


We face competition from other companies that are working to develop novel drugs and technology platforms using technology similar to ours. If these companies develop drugs more rapidly than we do or their technologies, including delivery technologies, are more effective, our ability to successfully commercialize drugs may be adversely affected.

In addition to the competition we face from competing drugs in general, we also face competition from other companies working to develop novel drugs using technology that competes more directly with our own. We are aware of multipleseveral other companies that are working into develop RNAi therapeutic products. Some of these companies are seeking, as we are, to develop chemically synthesized siRNAs as drugs. Others are following a gene therapy approach, with the fieldgoal of RNAi.treating patients not with synthetic siRNAs but with synthetic, exogenously-introduced genes designed to produce siRNA-like molecules within cells. Companies working on chemically synthesized siRNAs include Takeda, Marina, Arrowhead, and its subsidiary, Calando, Quark, Silence, Arbutus, Sylentis, Dicerna, WAVE and Arcturus. In addition, we granted licenses or options for licenses to Isis,Ionis, Benitec, Arrowhead, and its subsidiary, Calando, Tekmira,Arbutus, Quark, Sylentis and others under which these companies may independently develop RNAi therapeutics against a limited number of targets. Any one of these companies may develop its RNAi technology more rapidly and more effectively than us.

In addition, as a result of agreements that we have entered into, Arrowhead, as the assignee of Roche, and Takeda have obtainednon-exclusive licenses, and Arrowhead, as the assignee of Novartis Pharma AG, has obtained specific exclusive licenses for 3130 gene targets, that include access to certain aspects of our technology that give them the right to compete with us in certain circumstances. We also compete with companies working to developantisense-based drugs. Like RNAi therapeutics, antisense drugs target mRNAs in order to suppress the activity of specific genes. IsisIonis is currently marketing anseveral antisense drugdrugs and has severalmultiple antisense product candidates in clinical trials, including one for the treatment of ATTR.hATTR amyloidosis that is currently under regulatory review in the United States and the EU. Ionis is also developing antisense drugs using ligand-conjugated GalNAc technology licensed from us, and these drugs have been shown to have increased potency at lower doses in clinical and pre-clinical studies, compared with antisense drugs that do not use such licensed GalNAc technology. The development of antisense drugs is more advanced than that of RNAi therapeutics, and antisense technology may become the preferred technology for drugs that target mRNAs to silence specific genes.

In addition to competition with respect to RNAi and with respect to specific products, we face substantial competition to discover and develop safe and effective means to deliver siRNAs to the relevant cell and tissue types. Safe and effective means to deliver siRNAs to the relevant cell and tissue types may be developed by our competitors, and our ability to successfully commercialize a competitive product would be adversely affected. In addition, substantial resources are being expended by third parties in the effort to discover and develop a safe and effective means of delivering siRNAs into the relevant cell and tissue types, both in academic laboratories and in the corporate sector. Some of our competitors have substantially greater resources than we do, and if our competitors are able to negotiate exclusive access to those delivery solutions developed by third parties, we may be unable to successfully commercialize our product candidates.

Risks Related to Our Common Stock

If our stock price fluctuates, purchasers of our common stock could incur substantial losses.

The market price of our common stock has fluctuated significantly and may continue to fluctuate significantly in response to factors that are beyond our control. The stock market in general has recentlyfrom time to time experienced extreme price and volume fluctuations, and the biotechnology in particular has experienced extreme price and volume fluctuations. The market prices of securities of pharmaceutical and biotechnology companies have been extremely volatile, and have experienced fluctuations that often have been unrelated or disproportionate to the clinical development progress or operating performance of these companies.companies, including as a result of adverse development events. These broad market and sector fluctuations have resulted and could in the future result in extreme fluctuations in the price of our common stock, which could cause purchasers of our common stock to incur substantial losses.

We may incur significant costs from class action litigation due to stock volatility.

Our stock price may fluctuate for many reasons, including as a result of public announcements regarding the progress of our development and commercialization efforts or the development and commercialization efforts of our collaborators and/or competitors, the addition or departure of our key personnel, variations in our quarterly operating results and changes in market valuations of


pharmaceutical and biotechnology companies. For example, in October 2016, we announced that we were discontinuing the development of revusiran and our stock price declined significantly as a result and in September 2017, following our temporary suspension of dosing in our fitusiran program, our stock also declined, although to a lesser extent. When the market price of a stock has been volatile as our stock price may be,has been, holders of that stock have occasionally brought securities class action litigation against the company that issued the stock. If any of our stockholders were to bring a lawsuit of this type against us, even if the lawsuit is without merit, we could incur substantial costs defending the lawsuit. The lawsuit could also divert the time and attention of our management.

71


Sales of additional shares of our common stock, including by us or our directors and officers, could cause the price of our common stock to decline.

Sales of substantial amounts of our common stock in the public market, or the availability of such shares for sale, by us or others, including the issuance of common stock upon exercise of outstanding options, could adversely affect the price of our common stock.

Sanofi Genzyme’s ownership of our common stock could delay or prevent a change in corporate control.

Sanofi Genzyme currently holds approximately 12%11 percent of our outstanding common stock and has the right to increase its ownership up to 30%,30 percent, as well as the right to maintain its then current ownership percentage through the term of our collaboration, subject to certain limitations. This concentration of ownership may harm the market price of our common stock by:

delaying, deferring or preventing a change in control of our company;

impeding a merger, consolidation, takeover or other business combination involving our company; or

discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control of our company.

Anti-takeover provisions in our charter documents and under Delaware law and our stockholder rights plan could make an acquisition of us, which may be beneficial to our stockholders, more difficult and may prevent attempts by our stockholders to replace or remove our current management.

Provisions in our certificate of incorporation and our bylaws may delay or prevent an acquisition of us or a change in our management. In addition, these provisions may frustrate or prevent any attempts by our stockholders to replace or remove our current management by making it more difficult for stockholders to replace members of our board of directors. Because our board of directors is responsible for appointing the members of our management team, these provisions could in turn affect any attempt by our stockholders to replace current members of our management team. These provisions include:

a classified board of directors;

a prohibition on actions by our stockholders by written consent;

limitations on the removal of directors; and

advance notice requirements for election to our board of directors and for proposing matters that can be acted upon at stockholder meetings.

In addition, our board of directors has adopted a stockholder rights plan, the provisions of which could make it difficult for a potential acquirer of Alnylam to consummate an acquisition transaction. Moreover, because we are incorporated in Delaware, we are governed by the provisions of Section 203 of the Delaware General Corporation Law, which prohibits a person who owns in excess of 15%15 percent of our outstanding voting stock from merging or combining with us for a period of three years after the date of the transaction in which the person acquired in excess of 15%15 percent of our outstanding voting stock, unless the merger or combination is approved in a prescribed manner. These provisions would apply even if the proposed merger or acquisition could be considered beneficial by some stockholders.

 

72


ITEM 1B.

UNRESOLVED STAFF COMMENTS

Not applicable.

 


ITEM 2.

PROPERTIESPROPERTIES

Our operations are based primarily in Cambridge, Massachusetts. AsMassachusetts; Zug, Switzerland; and Maidenhead, United Kingdom. A description of certain of the facilities we lease as of January 31, 2015,2018 is included in the table below.

Location

Primary Use

Approximate
Square Footage

Lease
Expiration Date

Renewal Option

300 Third Street Cambridge, Massachusetts

Corporate headquarters and primary research facility

129,000

September 2021

One five-year term

101 Main Street

Cambridge, Massachusetts

Additional office space

72,000

March 2019 and June 2021

One five-year term on each lease

675 West Kendall Street Cambridge, Massachusetts

Future corporate headquarters and research facility*

295,000

On or around February 2034

Two five-year terms

665 Concord Avenue

Cambridge, Massachusetts

cGMP manufacturing

15,000

August 2022

One five-year term

Grafenauweg 4

6300 Zug

International headquarters

14,500

March 2023

One five-year term

Braywick Gate

Braywick Road, Maidenhead

Berkshire, United Kingdom

Office space

21,500

May 2026

None

*

We intend to move our corporate headquarters and research facility to this location in early 2019. The term will commence on May 1, 2018 and rent payments will become due commencing upon substantial completion of the building improvements, which is currently expected to be on or around February 2019, and will continue for 15 years from the rent commencement date.

In addition to the locations above, we leased approximately 129,000 square feetalso maintain small offices in multiple locations in and outside of officethe United States to support our operations and laboratory spacegrowth.

In April 2016, we completed the purchase of 12 acres of undeveloped land in Cambridge, Massachusetts for our corporate headquarters and primary research facility, of which approximately 18,000 square feet is under sublease to a third party through September 2016. The term of our lease ends in September 2021, and we have the option to extend the lease for one additional five-year period. We also lease approximately 15,000 square feet of additional office and laboratory space in Cambridge, Massachusetts for our cGMP manufacturing facility. The lease for this property expires in August 2017, and we have the option to extend this lease for two successive five-year periods.

Norton, Massachusetts.  We have growncommenced construction of a manufacturing facility at this site for drug substance, including siRNAs and siRNA conjugates, for clinical and commercial use.

In the future, we may lease, operate, purchase or construct additional facilities in which to conduct expanded research, development and manufacturing activities and support future commercial operations. We believe that the total space available to us under our workforce significantly overcurrent leases will meet our needs for the past yearforeseeable future and expect to continue to add a significant number of additional employees during 2015. We expect to obtain additional space to accommodate our growth and we believe that additional space willwould be available to us on commercially reasonable terms asif required.

 

ITEM  3.

LEGAL PROCEEDINGS

UniversityFor a discussion of Utahmaterial pending legal proceedings, please read Note 7, Commitments and Contingencies – Litigation,

On March 22, 2011, Utah filed a civil complaint to our consolidated financial statements included in the United States District Court for the DistrictPart II, Item 8, “Financial Statements and Supplementary Data,” of Massachusetts against us, Max Planck, Whitehead, MIT and UMass, claiming a professor at Utah is the sole inventor or, in the alternative, a joint inventor, of the Tuschl patents. Utah did not serve the original complaintthis annual report on us or the other defendants. On July 6, 2011, Utah filed an amended complaint alleging substantially the same claims against us, Max Planck, Whitehead, MIT and UMass. The amended complaint was served on us on July 14, 2011. Utah is seeking changes to the inventorship of the Tuschl patents, unspecified damages and other relief. On October 31, 2011, we, Max Planck, Whitehead, MIT and UMass filed a motion to dismiss. Also on October 31, 2011, UMass filed a motion to dismiss on separate grounds, which we, Max Planck, Whitehead and MIT joined. On December 31, 2011, Utah filed a second amended complaint dropping UMass as a defendant and adding as defendants several UMass officials. In June 2012, the Court denied both motions to dismiss. We, Max Planck, Whitehead, MIT and UMass filed an appeal of the Court’s ruling on the motion to dismiss for lack of jurisdiction and a motion requesting that the Court stay the case pending the outcome of the appeal. In July 2012, the Court stayed discovery in the case pending the outcome of the defendants’ appeal. Oral arguments in the appeal were heard in early March 2013 in the CAFC. In August 2013, the CAFC affirmed the lower Court’s ruling, in a split decision. We believe the majority made an error in law when affirming the lower Court’s decision, and in September 2013, we filed a petition with the CAFC for rehearing or rehearing en banc. In October 2013, the CAFC invited Utah to file an answer to the petition. In November 2013, the CAFC denied our petition for rehearing or rehearing en banc and remanded the case back to the lower Court. In February 2014, we filed a petition for writ of certiorari from the Supreme Court and a motion to stay the lower Court proceedings pending a decision from the Supreme Court on our petition. The lower Court granted our motion to stay the proceedings, however, in June 2014 the Supreme Court denied our petition for certiorari and remanded the case back to the United States District Court for the District of Massachusetts for trial,Form 10-K, which is now scheduled to begin on November 2, 2015.

Although we believe we have meritorious defenses and intend to vigorously defend ourselves inincorporated into this matter, litigation is subject to inherent uncertainty and a court could ultimately rule against us. In addition, the defense of litigation and related matters are costly and may divert the attention of our management and other resources that would otherwise be engaged in other activities. We have not recorded an estimate of the possible loss associated with this legal proceeding due to the uncertainties related to both the likelihood and the amount of any possible loss or range of loss.item by reference.

 

ITEM  4.

MINE SAFETY DISCLOSURES

Not applicable.


PART II

 

73


PART II

ITEM  5.

MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

Market Information

Our common stock began tradingtrades on The NASDAQ Global Select Market on May 28, 2004 under the symbol “ALNY.” Prior to that time, there was no established public trading market for our common stock. The following table sets forth the high and low sale prices per share for our common stock on The NASDAQ Global Select Market for the periods indicated:

 

Year Ended December 31, 2013:

  High   Low 

Year Ended December 31, 2016:

 

High

 

 

Low

 

First Quarter

  $25.80    $18.61  

 

$

98.00

 

 

$

51.51

 

Second Quarter

  $31.79    $21.60  

 

$

75.08

 

 

$

49.96

 

Third Quarter

  $65.83    $31.75  

 

$

80.11

 

 

$

53.56

 

Fourth Quarter

  $67.97    $48.16  

 

$

71.67

 

 

$

31.38

 

 

 

 

 

 

 

 

 

Year Ended December 31, 2014:

  High   Low 

Year Ended December 31, 2017:

 

High

 

 

Low

 

First Quarter

  $112.57    $60.24  

 

$

60.41

 

 

$

35.98

 

Second Quarter

  $71.40    $47.03  

 

$

86.92

 

 

$

46.90

 

Third Quarter

  $79.88    $51.93  

 

$

119.02

 

 

$

70.76

 

Fourth Quarter

  $111.49    $72.80  

 

$

147.63

 

 

$

111.25

 

Holders of record

At January 30, 2015,31, 2018, there were 3733 holders of record of our common stock. Because many of our shares are held by brokers and other institutions on behalf of stockholders, we are unable to estimate the total number of beneficial holders represented by these record holders.

Dividends

We have never paid or declared any cash dividends on our common stock. We currently intend to retain any earnings for future growth and, therefore, do not expect to pay cash dividends in the foreseeable future.

Securities Authorized for Issuance Under Equity Compensation Plans

We intend to file with the SEC a definitive Proxy Statement, which we refer to herein as the Proxy Statement, not later than 120 days after the close of the fiscal year ended December 31, 2014.2017. The information required by this item relating to our equity compensation plans is incorporated herein by reference to the information contained under the section captioned “Equity Compensation Plan Information” of the Proxy Statement.


74


Stock Performance Graph

The following performance graph and related information shall not be deemed “soliciting material” or to be “filed” with the SEC, nor shall such information be incorporated by reference into any future filing under the Securities Act of 1933 or Securities Exchange Act of 1934, each as amended, except to the extent that we specifically incorporate it by reference into such filing.

The comparative stock performance graph below compares the five-year cumulative total stockholder return (assuming reinvestment of dividends, if any) from investing $100 on December 31, 2009,2012, to the close of the last trading day of 2014,2017, in each of  (i) our common stock (ii)and selected indices. We changed the comparison, for the years presented, from the NASDAQ US Benchmark TR Index and (iii) the NQ US Benchmark Pharma TR Index.Index, to the NASDAQ Composite Total Return Index and NASDAQ Biotechnology Total Return, respectively, because we believe these indices reflect a better comparison of our performance relative to the broader market and our peers. In this transition year, we have retained the previous indices for comparison but will not include them in our stock performance graph in subsequent annual filings. The stock price performance reflected in the graph below is not necessarily indicative of future price performance.

Comparison of Five-Year Cumulative Total Return

Among Alnylam Pharmaceuticals, Inc.,

NASDAQ US Benchmark TR Index, and NQ US Benchmark Pharma TR Index,

NASDAQ Composite Total Return and NASDAQ Biotechnology Total Return

 

 

 12/31/2009  12/31/2010  12/30/2011  12/31/2012  12/31/2013  12/31/2014 

12/31/2012

 

 

12/31/2013

 

 

12/31/2014

 

 

12/31/2015

 

 

12/30/2016

 

 

12/29/2017

 

Alnylam Pharmaceuticals, Inc.

 $100.00   $55.96   $46.25   $103.58   $364.93   $550.51  

$

100.00

 

 

$

352.33

 

 

$

531.51

 

 

$

515.84

 

 

$

205.15

 

 

$

696.16

 

NASDAQ US Benchmark TR Index

 $100.00   $117.55   $117.91   $137.29   $183.26   $206.09  

$

100.00

 

 

$

133.48

 

 

$

150.12

 

 

$

150.84

 

 

$

170.46

 

 

$

206.91

 

NQ US Benchmark Pharma TR Index

 $100.00   $102.60   $120.54   $137.81   $186.98   $227.77  

$

100.00

 

 

$

135.68

 

 

$

165.28

 

 

$

174.27

 

 

$

172.37

 

 

$

205.33

 

NASDAQ Composite Total Return

$

100.00

 

 

$

140.12

 

 

$

160.78

 

 

$

171.97

 

 

$

187.22

 

 

$

242.71

 

NASDAQ Biotechnology Total Return

$

100.00

 

 

$

165.97

 

 

$

223.07

 

 

$

249.32

 

 

$

196.09

 

 

$

238.51

 

 

75



ITEM 6.

SELECTED CONSOLIDATEDCONSOLIDATED FINANCIAL DATA

The following selected consolidated financial data for each of the five years in the period ended December 31, 20142017 are derived from our audited consolidated financial statements. The selected consolidated financial data set forth below should be read in conjunction with “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and the financial statements, and the related Notes, included elsewhere in this annual report on Form 10-K. Historical results are not necessarily indicative of future results.

Selected Consolidated Financial Data

(In thousands, except per share data)

 

 Year Ended December 31, 

 

Year Ended December 31,

 

 2014 2013 2012 2011 2010 

 

2017

 

 

2016

 

 

2015

 

 

2014

 

 

2013

 

Statements of Comprehensive Loss Data:

     

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Net revenues from collaborators

 $50,561   $47,167   $66,725   $82,757   $100,041  

 

$

89,912

 

 

$

47,159

 

 

$

41,097

 

 

$

50,561

 

 

$

47,167

 

Operating expenses(1)

  455,541    140,109    196,181    137,575    144,111  

Operating expenses(1) (2)

 

 

590,000

 

 

 

471,746

 

 

 

337,105

 

 

 

455,541

 

 

 

140,109

 

Loss from operations

  (404,980  (92,942  (129,456  (54,818  (44,070

 

 

(500,088

)

 

 

(424,587

)

 

 

(296,008

)

 

 

(404,980

)

 

 

(92,942

)

Net loss

  (360,395  (89,225  (106,014  (57,649  (43,515

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

 

$

(360,395

)

 

$

(89,225

)

Net loss per common share — basic and diluted

 $(4.85 $(1.45 $(2.11 $(1.36 $(1.04

 

$

(5.42

)

 

$

(4.79

)

 

$

(3.45

)

 

$

(4.85

)

 

$

(1.45

)

Weighted-average common shares outstanding — basic and diluted

  74,278    61,551    50,286    42,410    42,040  

 

 

90,554

 

 

 

85,596

 

 

 

83,992

 

 

 

74,278

 

 

 

61,551

 

(1) Non-cash stock-based compensation expenses included in operating expenses

 $33,061   $20,703   $12,360   $16,676   $19,118  

__________

(1) Stock-based compensation expenses included in operating expenses

 

$

92,819

 

 

$

75,528

 

 

$

45,783

 

 

$

33,061

 

 

$

20,703

 

The increase in operating(2) Operating expenses for the year ended December 31, 2014 resulted primarily fromincluded a $220.8 million charge to operatingin process research and development expenses in connection with our acquisition of the Sirna RNAi assets from Merck, which is described below in Management’s Discussion and Analysis of Financial Condition and Results of Operations — Discussion of Results of Operations for 2014 and 2013 under the heading “In-process research and development.” Operating expenses for the year ended December 31, 2012 included a $65.0 million charge to operating expenses in connection with the restructuring of our license agreement with Tekmira in November 2012.

  December 31, 
  2014  2013  2012  2011  2010 

Balance Sheet Data:

     

Cash, cash equivalents and fixed income marketable securities

 $881,929   $350,472   $226,228   $260,809   $349,904  

Working capital

  651,033    200,164    77,212    71,038    152,093  

Total assets

  1,079,595    420,530    287,520    281,917    393,265  

Total stockholders’ equity

  936,267    270,347    134,053    117,997    158,233  
Merck.

 

76

 

 

December 31,

 

 

 

2017

 

 

2016

 

 

2015

 

 

2014

 

 

2013

 

Balance Sheet Data:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Cash, cash equivalents and fixed income marketable

   securities

 

$

1,704,537

 

 

$

942,601

 

 

$

1,280,951

 

 

$

881,929

 

 

$

350,472

 

Restricted investments

 

 

30,000

 

 

 

150,000

 

 

 

 

 

 

 

 

 

 

Working capital

 

 

1,620,489

 

 

 

540,178

 

 

 

1,043,289

 

 

 

651,033

 

 

 

200,164

 

Total assets

 

 

1,994,730

 

 

 

1,262,810

 

 

 

1,386,510

 

 

 

1,079,595

 

 

 

420,530

 

Long-term debt

 

 

30,000

 

 

 

150,000

 

 

 

 

 

 

 

 

 

 

Total stockholders’ equity

 

 

1,766,431

 

 

 

920,221

 

 

 

1,264,714

 

 

 

936,267

 

 

 

270,347

 



ITEM 7.

MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Overview

We are a global biopharmaceutical company developing novel therapeutics based on RNAi. RNAi is a naturally occurring biological pathway within cells for selectivelysequence-specific silencing and regulatingregulation of gene expression. We are harnessing the expressionRNAi pathway to develop a potential new class of specific genes. Since many diseasesinnovative medicines, known as RNAi therapeutics. RNAi therapeutics are causedcomprised of siRNA, and function upstream of today’s medicines by the inappropriate activity of specific genes, the ability to silence genes selectively through RNAi could providepotently silencing mRNA that encode for disease-causing proteins, thus preventing them from being made. This is a new way to treat a wide range of human diseases. We believe that drugs that work through RNAi haverevolutionary approach with the potential to become a broad new classtransform the care of drugs, like small molecule, proteinpatients with genetic and antibody drugs. Using our intellectual property and expertise, we are developing what we believe to be a reproducible and modular approach to develop RNAi therapeutics for a variety of humanother diseases.

Our research and development strategy is focused primarily on use of our proprietary GalNAc-conjugate strategy for delivery of siRNAs — the molecules that mediate RNAi — towardto target genetically validated liver-expressed genes involvedthat have been implicated in the cause or pathway of human diseases.disease. We are also focusedutilize a LNP or GalNAc conjugate approach to enable hepatic delivery of siRNAs. Our focus is on clinical indications where there areis a high unmet medical needs,need, early biomarkers for the assessment of clinical activity in Phase 1 clinical studies, and a definable path for drug development, regulatory approval, patient access and commercialization.

Specifically, our broad pipeline of investigational RNAi therapeutics is focused in three STArs: Genetic Medicines, with a broad pipeline of RNAi therapeutics for the treatment of rare diseases;Medicines; Cardio-Metabolic Disease, with a pipeline of RNAi therapeutics toward genetically validated, liver-expressed disease targets for unmet needs in cardiovascular and metabolic diseases such as dyslipidemia, hypertension, NASH and type 2 diabetes;Diseases; and Hepatic Infectious Disease, with a pipeline of RNAi therapeutics designedDiseases. We are committed to address the major global health challenges of hepatic infectious diseases, including but not limited to HBV. In early 2015, we launched our guidance for 2020 for the advancement and commercialization of RNAi therapeutics as a whole new class of innovative medicines. Specifically, by the end ofour Alnylam 2020 we expect strategy, which is to achieve a company profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs.STArs by the end of 2020.  In December 2017, we filed our first NDA and MAA for patisiran. In January 2018, we announced that the EMA has accepted the MAA and initiated its review. Patisiran was previously granted an accelerated assessment by the EMA.  In early February 2018, we announced that the FDA has accepted our NDA and granted our request for priority review, with an action date of August 11, 2018. If approved, we expect to launch patisiran and begin generating product revenues in 2018.

In May 2017, we sold an aggregate of 5,000,000 shares of our common stock through an underwritten public offering at a price to the public of $71.87 per share. As a result of the offering, we received aggregate net proceeds of $355.2 million, after deducting underwriting discounts and commissions and other offering expenses of $4.2 million. In November 2017, we sold an aggregate of 6,440,000 shares of our common stock through an underwritten public offering at a price to the public of $125.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of $784.5 million, after deducting underwriting discounts and commissions and other offering expenses of $20.5 million.  We have used and intend to continue to use these proceeds for general corporate purposes, focused on achieving our Alnylam 2020 strategy.

In addition, in April 2016, our subsidiary, Alnylam U.S., Inc., entered into an aggregate of $150.0 million of term loan agreements with Bank of America N.A., or BOA, and Wells Fargo Bank, National Association, or Wells, related to the build out of our new drug substance manufacturing facility. In December 2017, we repaid in full $120.0 million outstanding under the BOA term loan agreement. Please read Note 7 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for a description of these term loan agreements. 

We have incurred significant losses since we commenced operations in 2002 and expect such losses to continue for the foreseeable future. At December 31, 2014,2017, we had an accumulated deficit of $956.6 million.$2.15 billion. Historically, we have generated losses principally from costs associated with research and development activities, acquiring, filing and expanding intellectual property rights and general administrative costs. As a result of planned expenditures for research and development activities relating to our research platform, our drug development programs, including the optimization of drug delivery technologies, clinical trial and manufacturing costs, the establishment of late-stagelate stage clinical and commercial capabilities, including global operations, continued management and growth of our patent portfolio, collaborations and general corporate activities, we expect to incur additional operating losses for the foreseeable future. We also anticipate that our operating results will fluctuate for the foreseeable future. Therefore, period-to-period comparisons should not be relied upon as predictive of the results in future periods.

Although weWe currently have programs focused on a number of therapeutic areas and, in December 2017, submitted our first NDA and MAA for marketing approval for patisiran.  However, our development efforts may not be successful and we are unable to predict when, if ever, we will successfully develop ormay not be able to commence sales of patisiran or any other product. To date, aIf we gain approval for and successfully launch patisiran in 2018, we may begin to generate net revenues from product sales. A substantial portion of our total net revenues in recent years has been derived from collaboration revenues from strategic alliances with Roche/Arrowhead, Takeda, Cubist, Novartis, MonsantoSanofi Genzyme and MDCO, andMDCO. In addition to potential revenues from the United States government in connection with our developmentcommercial sale of treatments for hemorrhagic fever viruses, including Ebola. Wepatisiran and future product candidates, we expect our sources of potential funding for the next several years to be derived primarily from newexisting and existingnew strategic alliances, which may include license and other fees, funded research and development, and milestone payments and royalties on product sales by our licensors, and proceeds from the sale of equity or debt.


In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $496.4 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $21.1 million. We intend to use these proceeds for general corporate

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purposes, focused on achieving our Alnylam 2020 profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs, by the end of 2020.

Significant 2014 Events

Acquisition of Sirna Therapeutics.    In March 2014, we purchased from Merck all of Merck’s right, title and interest in and to all of the outstanding shares of common stock of Sirna. Sirna possesses intellectual property and RNAi assets including pre-clinical therapeutic candidates, chemistry, and siRNA-conjugate and other delivery technologies that we are integrating into our platform for delivery of RNAi therapeutics. We did not acquire any employees, manufacturing or other facilities, developed processes or clinical-stage assets as part of the acquisition of Sirna. In consideration for the Sirna common stock, we (i) paid Merck $25.0 million in cash and (ii) issued to Merck an aggregate of 2,520,044 shares of our common stock, having a value of $150.0 million as calculated under the terms of the stock purchase agreement on the date of execution.

Merck is also eligible to receive the following consideration from us: (i) up to an aggregate of $10.0 million upon the achievement by us or our related parties of specified regulatory milestones for RNAi products covered by Sirna intellectual property, and (ii) up to an aggregate of $105.0 million upon the achievement by us or our related parties of specified development and regulatory ($40.0 million) and commercial ($65.0 million) milestones associated with the clinical development progress of certain pre-clinical candidates discovered by Sirna, together with low single-digit royalties for our products and single-digit royalties for Sirna products, in each case based on annual worldwide net sales, if any, by us and our related parties of any such products.

Genzyme Collaboration.    In January 2014, we entered into a global, strategic collaboration with Genzyme to discover, develop and commercialize RNAi therapeutics as Genetic Medicines to treat orphan diseases. The 2014 Genzyme collaboration superseded and replaced our 2012 agreement with Genzyme. The 2014 Genzyme collaboration is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of Genetic Medicines, which includes our current and future Genetic Medicine programs that reach Human POP by the end of 2019, subject to extension to the end of 2021 in various circumstances. We will retain product rights in North America and Western Europe, which we refer to as the Alnylam Territory, while Genzyme will obtain exclusive rights to develop and commercialize collaboration products in the rest of the world, which we refer to as the Genzyme Territory, together with certain broader co-development/co-promote or worldwide rights for certain products. Genzyme’s regional, co-development/co-promote and worldwide rights are structured as an opt-in that is triggered upon achievement of Human POP. We will maintain development control for all programs prior to Genzyme’s opt-in and maintain development and commercialization control after Genzyme’s opt-in for all programs in our territory.

Upon the effective date of the 2014 Genzyme collaboration, Genzyme expanded the scope of its regional license and collaboration for patisiran for the Genzyme Territory. We retain full product rights in the Alnylam Territory. We and Genzyme have also expanded our current collaboration on revusiran, so that we and Genzyme are co-developing and will co-promote revusiran in the Alnylam Territory. We maintain development and commercialization control with revusiran in the Alnylam Territory. Genzyme will develop and commercialize the product in the Genzyme Territory. In addition to its regional rights for our current and future Genetic Medicine programs in the Genzyme Territory, Genzyme has the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other RBD in our territory, with us maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme may exercise this selection right upon completion of Human POP for both the ALN-AT3 andALN-AS1 programs. Finally, Genzyme has the right for a global license to a single, future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. We will retain global rights to any RNAi therapeutic Genetic Medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions. We retain full rights to all current and future RNAi therapeutic programs outside of the field of Genetic Medicines, including the right to form new collaborations.

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Pursuant to the terms of a stock purchase agreement, we sold Genzyme 8,766,338 shares of our common stock and Genzyme paid us $700.0 million in aggregate cash consideration. Our investor agreement with Genzyme provides Genzyme with the right, subject to certain exceptions, generally to maintain its ownership position in us until Genzyme owns less than 7.5% of our outstanding common stock, subject to certain additional limited rights of Genzyme to maintain its ownership percentage. In accordance with our investor agreement with Genzyme, as a result of our issuance of shares in connection with our acquisition of Sirna in March 2014, on March 25, 2014, Genzyme exercised its right to purchase an additional 344,448 shares of our common stock, at a purchase price of $66.88, the closing price of our common stock that day, and paid us approximately $23.0 million. Genzyme also has the right each January to purchase a number of shares of our common stock based on the number of shares we issued during the previous year for compensatory purposes. Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock on January 22, 2015 for approximately $18.3 million. The sale of these shares to Genzyme was consummated as a private placement. In January 2015, in connection with our public offering described above, Genzyme exercised its right to purchase directly from us, in concurrent private placements, 744,566 shares of common stock, at the public offering price of $95.00 per share, resulting in proceeds to us of approximately $70.7 million. The sales of common stock to Genzyme were not registered as part of the public offering, though they were consummated simultaneously with the public offering. Each of these purchases allowed Genzyme to maintain its ownership level of our outstanding common stock of approximately 12%.

A description of our 2014 Genzyme collaboration and the related stock purchase and investor agreements is included in Part I, Item 1, “Strategic Alliances — Product Alliances — Genzyme.”

Research and Development

Since our inception, we have focused on drug discovery and development programs. Research and development expenses represent a substantial percentage of our total operating expenses. In early 2015, we launchedexpenses, as reflected by our guidance forbroad pipeline of clinical development programs, which includes several programs in late-stage development and one product in registration in the advancementUnited States and commercialization of RNAi therapeutics as a whole new class of innovative medicines. Specifically, by the end of 2020, we expect to achieve a company profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs.EU.

There is a risk that any drug discovery or development program may not produce revenue for a variety of reasons, including the possibility that we will not be able to adequately demonstrate the safety and effectiveness of the product candidate. For example, in October 2016, we announced the discontinuation of our revusiran clinical development program due to safety concerns and in September 2017, we announced that we had temporarily suspended dosing in all ongoing fitusiran studies.Moreover, there are uncertainties specific to any new field of drug discovery, including RNAi. The successful developmentsuccess of any product candidate we develop is highly uncertain. Due to the numerous risks associated with developing drugs, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts necessary to complete the development of, or the period, if any, in which material net cash inflows will commence from, any potential product candidate. These risks include the uncertainty of:

our ability to discover new product candidates;

our ability to progress product candidates into pre-clinical and clinical trials;

the scope, rate of progress and cost of our pre-clinical trials and other research and development activities, including those related to developing safe and effective ways of delivering siRNAs into cells and tissues;

the scope, rate of progress and cost of any clinical trials we commence;

clinical trial results;

the cost of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights;

the terms, timing and success of any collaboration, licensing and other arrangements that we may establish;

the cost, timing and success of regulatory filings and approvals or potential changes in regulations that govern our industry or the way in which they are interpreted or enforced;

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the cost and timing of establishing sufficient sales, marketing and distribution capabilities;

the cost and timing of establishing sufficient clinical and commercial supplies for any product candidates and products that we may develop and ultimately commercialize;

limits on our ability to research, develop or manufacture our product candidates as a result of contractual obligations to third parties or intellectual property held by third parties;

the costs associated with legal activities, including litigation, arising in the course of our business activities and our ability to prevail in any such legal disputes; and

the effect of competing technological and market developments.

Any failure to complete any stage of the development of any potential products in a timely manner could have a material adverse effect on our operations, financial position and liquidity. A discussion of some of the risks and uncertainties associated with completing our projects on schedule, or at all, and the potential consequences of failing to do so, are set forth in Part I, Item 1A of this annual report on Form 10-K under the heading “Risk Factors.”

Strategic Alliances

A significant component of our business plan is to enter into strategic alliances and collaborations with leading pharmaceutical and life sciences companies, academic institutions, research foundations and others, as appropriate, to gain access to funding, capabilities, technical resources and intellectual property to further our research, development and commercialization efforts and to generate revenues. We may also seek to form or advance new ventures and opportunities in areas outside our primary focus on RNAi therapeutics.

To generate revenues fromOur collaboration strategy is to form alliances that create significant value for ourselves and our intellectual propertycollaborators in the advancement of RNAi therapeutics as a potential new class of innovative medicines. Specifically, with respect to our Genetic Medicine pipeline, we formed a broad strategic alliance with Sanofi Genzyme in 2014 pursuant to which we retain development and commercial rights for our current and future Genetic Medicine products in the United States, Canada and Western Europe, and Sanofi Genzyme will develop and commercialize our current and future Genetic Medicine products for which it elects to opt-in, in the rest of the world, subject to certain broader rights. In January 2018, we also grant licensesand Sanofi Genzyme amended our 2014 Sanofi Genzyme collaboration to biotechnology companiesprovide that we would develop and commercialize patisiran globally and Sanofi Genzyme would develop and commercialize fitusiran globally. With respect to our Cardio-Metabolic pipeline, we intend to seek future strategic alliances for these programs, under which we may retain certain product development and commercialization rights, or we may structure as global alliances, as we did in our InterfeRx programcollaboration with MDCO to advance inclisiran. With respect to our Hepatic Infectious Disease pipeline, in October 2017, we announced an exclusive licensing agreement with Vir Biotechnology for the development and commercialization of RNAi therapeutics for specified targets in which we have no direct strategic interest. We also license key aspects of our intellectual property to companies active in the research products and services market, which includes the manufacture and sale of reagents. We expect our InterfeRx and research product licenses to generate modest revenues that we can re-invest in the development of our proprietary RNAi therapeutics pipeline. At January 31, 2015, we had granted such licenses, on both an exclusive and non-exclusive basis, to approximately 20 companies.infectious diseases, including chronic hepatitis B virus infection.

Since delivery of RNAi therapeutics has historically been an important objective of our research activities, we have also evaluated potential collaboration and licensing arrangements with other companies and academic institutions to gain access to delivery technologies. For example, we have entered into agreements with Tekmira and Acuitas, among others, to focus on various delivery strategies. We have also entered into license agreements with Isis, Max Planck Innovation, Tekmira, CRT and Whitehead, as well as a number of other entities, to obtain rights to intellectual property in the field of RNAi. Finally, we have sought, and may seek in the future, funding for the development of our proprietary RNAi therapeutics pipeline from the government and foundations.

Critical Accounting Policies and Estimates

Our discussion and analysis of our financial condition and results of operations is based on our consolidated financial statements, which have been prepared in accordance with GAAP. The preparation of our consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses and disclosure of contingent assets and liabilities in our consolidated financial statements. Actual results may differ from these estimates under different assumptions or conditions and could have a material impact on our reported results. While our significant accounting policies are more fully described in the Notes to our consolidated financial statements included elsewhere in this annual report on Form 10-K, we believe the following accounting policies to be the most critical in understanding the judgments and estimates we use in preparing our consolidated financial statements:

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Revenue Recognition

Our business strategy includes entering into collaborative license and development agreements with leading pharmaceutical and life sciences companies for the development and commercialization of our product candidates. WeFor example, we have entered into collaboration agreements with Novartis, Biogen Idec, Roche/Arrowhead, Takeda, Kyowa Hakko Kirin Cubist, Ascletis,Co., Ltd., or Kyowa Hakko Kirin, Monsanto, Sanofi Genzyme and MDCO. The terms of the agreements typically include deliverables such as non-refundable license fees, funding of research and development, payments based upon achievement of clinical and pre-clinical development milestones, regulatory milestones, manufacturing services, sales milestones and royalties on product sales. These agreements are generally referred to as multiple element arrangements.


In January 2011, we adopted new authoritative guidanceWe apply the accounting standard on revenue recognition for multiple element arrangements. The guidance, which applies to multiple element arrangements entered into or materially modified on or after January 1, 2011, amends the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence is not available. Deliverables under the arrangement will be separate units of accounting provided that (i) a delivered item has value to the customer on a standalone basis and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The new guidance did not change the criteria for standalone value. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, we have been unable to demonstrate standalone value in our multiple element arrangements. For example, we applied the new rules to collaborations executed with Monsanto and Genzyme during 2012, but we were unable to demonstrate standalone value for the delivered license element. In addition, we have not materially modified any of our multiple element arrangements entered into prior to 2011.

Non-refundable license fees are recognized as revenue upon delivery of the license only if we have a contractual right to receive such payment, the contract price is fixed or determinable, the collection of the resulting receivable is reasonably assured and we have no further performance obligations under the license agreement. Multiple element arrangements, such as license and development arrangements, are analyzed to determine whether the deliverables, which often include a license and performance obligations such as research and steering committee services, can be separated or whether they must be accounted for as a single unit of accounting. We recognize upfront license payments as revenue upon delivery of the license only if the license has standalone value and the fair value of the undelivered performance obligations, typically including research and/or steering committee services, that can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations would then be accounted for separately as performed. If the license is considered to either not have standalone value, or have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be accounted for as a single unit of accounting and the license payments and payments for performance obligations are recognized as revenue over the estimated period of when the performance obligations are performed or deferred indefinitely until the undelivered performance obligation can be determined. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, we have been unable to demonstrate standalone value in our multiple element arrangements.

Whenever we determine that an arrangement should be accounted for as a single unit of accounting, we must determine the period over which the performance obligations will be performed and revenue will be recognized. We recognize revenue using either  a proportional performance or a straight-line method. We recognize revenue using the proportional performance method when we can reasonably estimate the level of effort required to complete our performance obligations under an arrangement and such performance obligations are provided on a best-efforts basis. Direct labor hours or full-time equivalents are typically used as the measure of performance. The amount of revenue recognized under the proportional performance method is determined by multiplying the total payments under the contract, excluding royalties and payments contingent upon achievement of milestones, by the ratio of level of effort incurred to date to estimated total level of effort required to complete our performance obligations under the arrangement. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the proportional performance method, as of the period ending date.

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If we cannot reasonably estimate the level of effort required to complete our performance obligations under an arrangement, we recognize revenue under the arrangement on a straight-line basis over the period we expect to complete our performance obligations. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method, as of the period ending date.

Significant management judgment is required in determining the level of effort required under an arrangement and the period over which we are expected to complete our performance obligations under an arrangement. Steering committee services that are not inconsequential or perfunctory and that are determined to be performance obligations are combined with other research services or performance obligations required under an arrangement, if any, in determining the level of effort required in an arrangement and the period over which we expect to complete our aggregate performance obligations.

Many of our collaboration agreements entitle us to additional payments upon the achievement of performance-based milestones. These milestones are generally categorized into three types; development milestones which are generally based on the advancement of our pipeline and initiation of clinical trials, regulatory milestones which are generally based on the submission, filing or approval of regulatory applications such as an NDA in the United States, and commercialization milestones which are generally based on meeting specific thresholds of sales in certain geographic areas. If the achievement of a milestone is considered probable at the inception of the collaboration, the related milestone payment is included with other collaboration consideration, such as upfront fees and research funding, in our revenue model. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in our revenue model until the performance conditions are met. Upfront and ongoing development milestones per our collaboration agreements are not subject to refund if the development activities are not successful.

We perform an assessment to determine whether a substantive milestone exists at the inception of our collaborative arrangements. In evaluating if a milestone is substantive, we consider whether uncertainty exists as to the achievement of the milestone event at the inception of the arrangement, the achievement of the milestone involves substantive effort and can only be achieved based in whole or part on the performance or the occurrence of a specific outcome resulting from our performance, the amount of the milestone payment appears reasonable either in relation to the effort expected to be expended or to the projected enhancement of the value of the delivered items, there is any future performance required to earn the milestone, and the consideration is reasonable relative to all deliverables and payment terms in the arrangement. When a substantive milestone is achieved, the accounting rules permit us to recognize revenue related to the milestone payment in its entirety.


To date, we have not recorded any substantive milestones under our collaborations because we have not identified any milestones that meet the required criteria listed above. We have deferred recognition of payments for achievement of non-substantive milestones and recognized revenue over the estimated period of performance applicable towith each collaborative arrangement. As these milestones are achieved, we will recognize as revenue a portion of the milestone payment, which is equal to the percentage of the performance period completed, when the milestone is achieved, multiplied by the amount of the milestone payment, upon achievement of such milestone. We will recognize the remaining portion of the milestone payment over the remaining performance period under the proportional performance method or on a straight-line basis.

For revenue generating arrangements where we, as a vendor, provide consideration to a licensor or collaborator, as a customer, we apply the accounting standard that governs such transactions. This standard addresses the accounting for revenue arrangements where both the vendor and the customer make cash payments to each other for services and/or products. A payment to a customer is presumed to be a reduction of the selling price unless we receive an identifiable benefit for the payment and we can reasonably estimate the fair value of the benefit received. Payments to a customer that are deemed a reduction of selling price are recorded first as a reduction of revenue, to the extent of both cumulative revenue recorded to date and probable future revenues, which include any unamortized deferred revenue balances, under all arrangements with such customer, and then as an expense. Payments that are not deemed to be a reduction of selling price are recorded as an expense.

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We evaluate our collaborative agreements for proper classification in our consolidated statements of comprehensive loss based on the nature of the underlying activity. Transactions between collaborators recorded in our consolidated statements of comprehensive loss are recorded on either a gross or net basis, depending on the characteristics of the collaborative relationship. We generally reflect amounts due under our collaborative agreements related to cost-sharing of development activities as revenue.

Amounts received prior to satisfying the above revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets. Although we follow detailed guidelines in measuring revenue, certain judgments affect the application of our revenue policy. For example, in connection with our existing collaboration agreements, we have recorded on our consolidated balance sheet short-term and long-term deferred revenue based on our best estimate of when such revenue will be recognized. Short-term deferred revenue consists of amounts that are expected to be recognized as revenue in the next 12 months. Amounts that we expect will not be recognized prior to the next 12 months are classified as long-term deferred revenue. However, this estimate is based on our current operating plan and, if our operating plan should change in the future, we may recognize a different amount of deferred revenue over the next 12-month period.

The estimate of deferred revenue also reflects management’s estimate of the periods of our involvement in certain of our collaborations. Our performance obligations under these collaborations consist of participation on steering committees and the performance of other research and development services. In certain instances, the timing of satisfying these obligations can be difficult to estimate. Accordingly, our estimates may change in the future. Such changes to estimates would result in a change in revenue recognition amounts. If these estimates and judgments change over the course of these agreements, it may affect the timing and amount of revenue that we recognize and record in future periods. For example, in connection with our collaboration with Sanofi Genzyme, our estimate of the period to satisfy our performance obligations changed from approximately six years to approximately five years, effective October 2016. This change in our estimate was due to the discontinuation of our revusiran clinical development program. Beginning in the fourth quarter of 2016, due to the adjustment to the performance period made on a prospective basis in October 2016, we began to recognize an additional $1.8 million of revenue per quarter related to the consideration earned in connection with these programs related to the license to our patisiran and revusiran clinical programs. At December 31, 2014,2017, we had short-term and long-term deferred revenue of $23.9$41.7 million and $43.0$43.1 million, respectively, related to our collaborations.

The new accounting standard related to revenue recognition effective as of January 1, 2018 will have a material impact on our consolidated financial statements. Please read Note 2 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for our discussion of recent accounting pronouncements for the expected impact of this new accounting standard.

Sanofi Genzyme.Genzyme.    In January 2014, we entered into a global, strategic collaboration with Sanofi Genzyme to discover, develop and commercialize RNAi therapeutics as Genetic Medicines to treat orphan diseases. Thediseases, referred to as the 2014 Sanofi Genzyme collaborationcollaboration. It superseded and replaced the previous collaboration between us and Sanofi Genzyme entered into in October 2012, referred to as the 2012 Sanofi Genzyme agreement, to develop and commercialize RNAi therapeutics targeting TTR for the treatment of ATTR,hATTR amyloidosis, including patisiran and revusiran, in Japan and the Asia-Pacific region.In January 2018, we and Sanofi Genzyme amended the 2014 Sanofi Genzyme collaboration and entered into the Exclusive TTR License and the AT3 License Terms. The January 2018 transaction is subject to customary closing conditions and clearances, including clearance under the Hart-Scott-Rodino Antitrust Improvements Act.  We expect the transaction to close during the first quarter of 2018.


Sanofi Genzyme paid us an upfront cash payment of $22.5 million under the 2012 Sanofi Genzyme agreement. We were also entitled to receive certain milestone payments under the 2012 Sanofi Genzyme agreement. In the fourth quarter of 2013, we earned a milestone of $7.0 million based upon the completion of a successful patisiran Phase 2 clinical trial and a milestone of $4.0 million based upon the initiation of the Phase 3 clinical trial for patisiran. The parties agreed to collaborate in thetwo development and commercialization of licensed products, with Genzyme assuming primary responsibility in the Genzyme territory, which included Japan and the Asia-Pacific region, and us retaining primary responsibility in the rest of the world.

milestones totaling $11.0 million.  We determined that the deliverables under the 2012 Sanofi Genzyme agreement included the license, a joint steering committee and any additional TTR-specific RNAi therapeutic compounds that comprised the ALN-TTR program. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered joint steering committee and any additional TTR-specific RNAi therapeutic compounds did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Sanofi Genzyme had the ability to grant sublicenses, it could not sublicense all or substantially all of its rights under the 2012 Sanofi Genzyme agreement. The uniqueness of our services and the limited sublicense right were indicators that standalone value was not present in the arrangement. Therefore the deliverables were not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. We were unable to reasonably estimate the period of performance under the 2012 Sanofi Genzyme agreement, as we were unable to estimate the timeline of our deliverables related to the deliverable for any additional TTR-specific RNAi therapeutic compounds. Through December 31, 2013, we had deferred all revenue, or $33.5 million, under the 2012 Sanofi Genzyme agreement.

In January 2014, we entered into the 2014 Sanofi Genzyme collaboration. As noted above, the 2014 Sanofi Genzyme collaboration superseded and replaced the 2012 Sanofi Genzyme agreement.agreement and was amended in January 2018, at which time we also entered into the Exclusive TTR License and the AT3 License Terms. Under the 2014 Sanofi Genzyme collaboration, we retain full product rights in the Alnylam Territory, while Sanofi Genzyme will obtain exclusive rights to develop and commercialize collaboration products in the Sanofi Genzyme Territory, together with worldwide rights for one product. Upon the effective date of the 2014

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Sanofi Genzyme collaboration, Sanofi Genzyme expanded the scope of its regional license and collaboration for patisiran for the Sanofi Genzyme Territory. We retain full product rightsand Sanofi Genzyme also expanded our existing collaboration on revusiran, to include a co-development/co-commercialize license and collaboration in the Alnylam Territory. WeIn October 2016, we discontinued our revusiran clinical development program. In September 2015, Sanofi Genzyme elected to opt into our fitusiran clinical development program under the regional license terms and began funding the program under the regional license terms in January 2016. In November 2016, Sanofi Genzyme also expanded our current collaboration on revusiran, so that weexercised its right to co-develop and Genzyme are co-developing and will co-promote revusiran in the Alnylam Territory. We maintain development and commercialization control with revusiranco-commercialize fitusiran in the Alnylam Territory, and Genzyme willwhile retaining its rights to exclusively develop and commercialize the product in the Sanofi Genzyme Territory. Sanofi Genzyme shared in fifty percent of the global development costs for fitusiran in accordance with the co-development/co-commercialize license terms. In connection with the exercise of this right, Sanofi Genzyme paid us approximately $6.0 million in January 2017 for its incremental share of co-development costs incurred from January 2016 through September 2016.

Sanofi Genzyme’s rights with respect to patisiran and fitusiran will be modified in connection with the 2018 amendment, the Exclusive TTR License and the AT3 License Terms.  Sanofi Genzyme continues to have the right to opt into our future rare genetic disease programs for development and commercialization in the Sanofi Genzyme Territory as contemplated in the 2014 Sanofi Genzyme collaboration, as well as one right to a global license. In connection with the 2018 amendment, the Exclusive TTR License and the AT3 License Terms, we and Sanofi Genzyme agreed to terminate the co-development and co-commercialization rights related to revusiran, ALN-TTRsc02 and fitusiran under the original 2014 Sanofi Genzyme collaboration. No future rights will be granted to Sanofi Genzyme for co-development and co-commercialization under the 2014 Sanofi Genzyme collaboration, as amended. Please read Note 3 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for our discussion of the terms of the Exclusive TTR License and the AT3 License Terms.

In connection with the 2014 Sanofi Genzyme collaboration, we sold to Sanofi Genzyme 8,766,338 shares of our common stock and Sanofi Genzyme paid us $700.0 million in aggregate cash consideration. Based on the common stock price of $85.72, the fair value of the shares issued was $751.5 million, which was $51.5 million in excess of the proceeds received from Sanofi Genzyme for the issuance of our common stock. This $51.5 million is being amortized on a straight-line basis over the performance period which is currently approximately six years as described below.for the ALN-TTR programs.

In addition, Genzyme will be required to make payments totaling up to $50.0 million upon the achievement of certain patisiran development milestones. We could potentially earn the next patisiran milestone payment, ranging between $5.0 million and $20.0 million based on the geographic region, upon the achievement of specified events in connection with a regulatory filing or approval. In addition,Sanofi Genzyme will be required to make payments totaling up to $75.0 million per regional product, other than patisiran, includingconsisting of up to $55.0 million in development milestones and $20.0 million in commercial milestones. Sanofi Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each regional product based on annual net sales, if any, of such regional product by Sanofi Genzyme, its affiliates and sublicensees. In consideration for the rights granted to Sanofi Genzyme under the co-development/co-promoteco-commercialize license terms, Sanofi Genzyme will bewas required to make certain milestone payments totaling upfor fitusiran, and, prior to $75.0 million inthe discontinuation of our revusiran clinical development milestonesprogram, was required to make certain milestone payments for each of revusiran and ALN-AT3, if selected.revusiran. In December 2014, we earned a development milestone payment of $25.0 million based upon the initiation of the first global Phase 3 clinical trial for revusiran. We could potentially earn the next revusiran milestone payment, ranging between $5.0Finally, with respect to its one global product right, Sanofi Genzyme will be required to make payments totaling up to $200.0 million for such global product, including up to $100.0 million in development milestones and $25.0$100.0 million based on the geographic region, upon the achievement of specified events in connection with regulatory approval.commercial milestones. Sanofi Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each co-development/co-promote product based on annual net sales, if any, in the Genzyme Territory for such co-development/co-promote product by Genzyme, its affiliates and sublicensees. The parties will share profits equally and we expect to book product sales in the Alnylam Territory. Finally, with respect to global products, Genzyme will be required to make payments totaling up to $200.0 million per product, including up to $60.0 million in development milestones and $140.0 million in commercial milestones. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each global product based on annual net sales, if any, of eachsuch global product by Sanofi Genzyme, its affiliates and sublicensees.


Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Sanofi Genzyme under the 2014 Sanofi Genzyme collaboration.collaboration, as amended, or the AT3 License Terms.

We determined that the deliverables for the programs on which Sanofi Genzyme is currentlywas collaborating with us on includeupon initiation of the 2014 collaboration included the licenses to our patisiran and revusiran clinical programs, which licenses were delivered to Sanofi Genzyme upon the closing date of the transaction, and the associated development activities, joint steering committee participation and information exchange for these clinical programs. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and associated undelivered development activities, joint steering committee participation and information exchange activities did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Sanofi Genzyme has the ability to grant sublicenses, it cannot sublicense all or substantially all of its rights under the 2014 Sanofi Genzyme collaboration. The uniqueness of our services and the limited sublicense rights are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition model on the final deliverable. Under the 2014 Sanofi Genzyme collaboration, the last deliverables for patisiran and revusiran arewere expected to be completed within approximately six years from the closing date of the transaction and the last deliverables for fitusiran were expected to be completed within approximately five years from the date  Sanofi Genzyme elected to opt into our fitusiran program under the regional license terms. Our estimate regarding the performance period under the 2014 Sanofi Genzyme collaboration related to the license to our patisiran and revusiran clinical programs was adjusted in October 2016 due to our decision to discontinue development of revusiran. As a result, with respect to these programs, we currently expect the last deliverables to be completed within approximately five years from the closing date of the transaction as compared to an initial expectation of approximately six years. Our estimate regarding the performance period under the 2014 Sanofi Genzyme collaboration related to the license to our fitusiran program was adjusted in September 2017 due to our temporary suspension of dosing in all ongoing fitusiran studies. As a result, with respect to the fitusiran program, we currently expect the last deliverables to be completed within approximately six years  from the date Sanofi Genzyme elected to opt into the program under the regional license terms as compared to an initial expectation of approximately five years.  Beginning in September 2017, we are prospectively recognizing the remaining deferred revenue as of August 31, 2017 related to the license to our fitusiran program over this adjusted performance period.

We determined that the total cash received from Sanofi Genzyme under the now superseded 2012 Sanofi Genzyme agreement reflects consideration for certain of the performance obligations for ALN-TTR programs included in

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the 2014 Sanofi Genzyme collaboration. Therefore, we are recognizing the $33.5 million of deferred revenue under the 2012 Sanofi Genzyme agreement on a straight-line basis over the period of performance of the ALN-TTR programs which, as noted above, is currently approximately sixfive years. In addition, during the fourth quarterThrough December 31, 2017, we have earned a milestone payment of 2014, we recognized as revenue a portion of the $25.0 million milestone payment earned in December 2014and an aggregate of $140.1 million of expense reimbursement due to us from Sanofi Genzyme. We recognized these amounts as revenue equal to the percentage of the performance period completed when the milestone or development cost reimbursement was earned. As future consideration, including any milestones or reimbursement for development activities, are achieved, we will recognize as revenue a portion of these payments equal to the percentage of the performance period completed when the milestone or activities have been satisfied, multiplied by the amount of the payment. We will recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014,2017, deferred revenue under the 2014 Sanofi Genzyme collaboration was $6.7$49.2 million.

We determined that the opt-in rights that Sanofi Genzyme has for future Genetic Medicine programs represent separate and additional deliverables that Sanofi Genzyme may receive from us in future periods. Upon each initial opt-in by Sanofi Genzyme, we have determined that each program and the related activities will represent a single unit of accounting and, consistent with our accounting policies, we base our revenue recognition period on the final deliverable associated with each future opt-in.

The Medicines Company.    In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9 for the treatment of hypercholesterolemia and other human diseases, including ALN-PCSsc.inclisiran. MDCO paid us an upfront cash payment of $25.0 million. In addition, MDCO is required to make payments to us upon achievement of certain milestones, up to an aggregate of $180.0 million, including up to $30.0 million in specified development milestones, $50.0 million in specified regulatory milestones and $100.0 million in specified commercialization milestones. In December 2014, we earned a development milestone payment of $10.0 million under the MDCO agreement based upon the initiation of our Phase 1 clinical trial for ALN-PCSsc.inclisiran. In addition, in December 2014,November 2017, we also earned $4.8 million of development costs reimbursable from MDCO. We could potentially earn the nexta development milestone payment of $20.0 million under the MDCO agreement based upon the initiation by MDCO of a pivotal study for inclisiran. In addition, in 2017, 2016 and 2015, we were reimbursed an aggregate of $12.2 million of development costs from MDCO. We could potentially earn the next development milestone payment of $25.0 million based upon regulatory approval of an ALN-PCSsc pivotal study.NDA for inclisiran in the United States. In addition, we will be entitled to royalties ranging from the low- to high- teens based on annual worldwide net sales, if any, of ALN-PCSscinclisiran by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from MDCO.


Under the MDCO agreement, we retain responsibilitywere responsible for the development of ALN-PCSscinclisiran until Phase 1 Completion (as defined in the MDCO agreement) at our cost, up to an agreed upon initial development cost cap. MDCO will assume all other responsibilityis responsible for theleading and funding development andfrom Phase 2 forward, as well as potential commercialization, of ALN-PCSsc, at its sole cost. Under the terms of the MDCO agreement, during 2015 we transferred the development leadership of inclisiran to MDCO. The collaboration between us and MDCO is governed by a joint steering committee that is comprised of an equal number of representatives from each party. We arewere solely responsible for obtaining supply of finished product reasonably required for the conduct of our obligations through Phase 1 Completion, and were responsible for supplying MDCO with finished product reasonably required for the first Phase 2 clinical trial of an ALN-PCSscinclisiran conducted by MDCO, at our expense, provided such costs do not exceed the development costs cap, subject to certain exceptions. After such time,caps. In April 2016, we and MDCO will haveentered into a supply and technical transfer agreement to provide for our supply of inclisiran to MDCO, in accordance with the terms of the MDCO agreement. MDCO now has the sole right and responsibility to manufacture and supply ALN-PCSscinclisiran for development and commercialization under the MDCO development plan, subject to the terms of the MDCO agreement and the supply and technical transfer agreement.

We have determined that the significant deliverables under the MDCO agreement include the license, the joint steering committee, technology transfer obligations, development activities through Phase 1 Completion and supply of product for a Phase 2 clinical trial. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and collective undelivered activities and services do not have standalone value due to the specialized nature of the activities and services to be provided by us. In addition, while MDCO has the ability to grant sublicenses, it must receive our prior written consent to sublicense all or substantially all of its rights. The uniqueness of our services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition pattern on the final deliverable. Under the MDCO agreement, all deliverables are expected to be completed within approximately five years. We are recognizing revenue under the MDCO agreement on a straight-line basis over approximately five years. We are not utilizing a proportional performance model since we are unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the development activities is largely unknown.

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The initial upfront payment of $25.0 million from MDCO was initially recorded as deferred revenue. WeDuring the fourth quarter of 2014, we recognized as revenue a portion of the $10.0 million milestone and $4.8 million in expense reimbursementpayment earned in December 2014 equal to the percentage of the performance period completed when the milestone was earned. During the fourth quarter of 2017, we recognized as revenue a portion of the $20.0 million milestone payment earned in November 2017 equal to the percentage of the performance period completed when the milestone was earned. During 2017, 2016 and 2015, we also recognized as revenue a portion of the $5.4 million, $3.0 million and $3.8 million, respectively, of expense reimbursement due to us under the terms of the MDCO agreement equal to the percentage of the performance period completed upon the invoice date. As future consideration, including any milestones or reimbursement for development activities, are earned, if any, we will recognize as revenue a portion of the milestone paymentthese payments equal to the percentage of the performance period completed when the milestone is achieved or service has been provided, multiplied by the amount of the milestone payment. We recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014,2017, deferred revenue under the MDCO agreement was $24.7$5.7 million.

Monsanto.Monsanto.    In August 2012, we and Monsanto entered into a license and collaboration agreement, pursuant to which we granted to Monsanto a worldwide, exclusive, royalty bearing right and license, including the right to grant sublicenses, to our RNAi platform technology and intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. The Monsanto agreement also includesincluded the transfer of technology from us to Monsanto and initially included a collaborative research project. Under the Monsanto agreement, Monsanto will be our exclusive collaborator in the agriculture field for a ten-year period.

Monsanto paid us $29.2 million in upfront cash payments, and was also required to make near-term milestone payments to us upon the achievement of specified technology transfer and patent-related milestones. We were also entitled to receive additional funding for collaborative research efforts. In the aggregate, we had the ability to earn up to $5.0 million in milestone payments and research funding under the Monsanto alliance. We received a total of $4.0 million in milestone payments from Monsanto based upon the achievement of a specified patent-related event and the completion of technology transfer activities. In September 2014, we and Monsanto mutually determined not to pursue the discovery collaboration originally contemplated under the terms of the Monsanto agreement. Accordingly, Monsanto will not be required to pay us the final milestone of $1.0 million. There are no remaining milestones under the Monsanto agreement. Monsanto is required to pay to us a percentage of specified fees from certain sublicense agreements Monsanto may enter into that include access to our intellectual property, as well as low single-digit royalty payments on worldwide, net sales by Monsanto, its affiliates and sublicensees of certain licensed products, as defined in the Monsanto agreement, if any. Due to the uncertainty of the application of RNAi technology in the field of agriculture, we may not receive any license fees or royalty payments from Monsanto.


Under the terms of the Monsanto agreement, in the event that during the exclusivity period we cease to own or otherwise exclusively control certain licensed patent rights in the agriculture field, for any reason other than Monsanto’s breach of the Monsanto agreement or its negligence or willful misconduct, resulting in the loss of exclusivity with respect to Monsanto’s rights to such patent rights, and such loss of exclusivity has a material adverse effect on the licensed products, then we would be required to pay Monsanto liquidated damages of up to $2.5 million, which amount was reduced from $5.0 million as liquidated damages,during the fourth quarter of 2017, and Monsanto’s royalty obligations to us under the Monsanto agreement would be reduced or, under certain circumstances, terminated. We have the right to cure any such loss of patent rights under the Monsanto agreement.

We haveinitially determined that the significant deliverables under the Monsanto agreement includeincluded the license, the technology transfer activities and the services that we willwould be obligated to perform under the Monsanto discovery collaboration. We have also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered technical transfer activities and Monsanto discovery collaboration services dodid not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Monsanto has the ability to grant sublicenses, it cannot grant access to certain of our proprietary technology. The uniqueness of our services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered technical transfer activities and Monsanto discovery collaboration services arewere being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition model on the final deliverable. Under the Monsanto agreement, the last deliverable expected to be completed was the discovery collaboration, which was originally to be completed within five years. Therefore, prior to the September 2014 amendment, we were recognizing revenue under the Monsanto agreement on a straight-line basis over five years. However, as a result of the September 2014

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amendment, we have determined that the final deliverable in the collaboration iswas the technology transfer activities, know-how exchange and access to intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. Consequently, we are now recognizingrecognized the remaining deferred revenue of $16.8 million at the date of the amendment on a prospective basis from September 2014 through February 2015, the date which iswas the end of the 30-month obligation, which excludesexcluded $5.0 million related to a potential refund due to Monsanto under certain circumstances pursuant to the original terms of the Monsanto agreement. In 2017, we recognized an additional $2.5 million in revenue following the reduction of such potential refund by $2.5 million. We will continue to recognize this revenue on a straight-line basis over the remaining obligation period. We cannotcould not use a proportional performance model since we arewere unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the potential effort required iswas unknown. At December 31, 2014,2017, deferred revenue under the Monsanto agreement was $10.6$2.5 million of which $5.6 million will be recognized through February 2015 and $5.0 millionthat will be recognized when the potential refund obligation ceases and can be considered fixed or determinable.

Takeda.Takeda.    In May 2008, we entered into a license and collaboration agreement with Takeda to pursue the development and commercialization of RNAi therapeutics. Under the Takeda agreement, we granted to Takeda a non-exclusive, worldwide, royalty-bearing license to our intellectual property, including delivery-related intellectual property, controlled by us as of the date of the Takeda agreement or during the five years thereafter, to develop, manufacture, use and commercialize RNAi therapeutics, subject to our existing contractual obligations to third parties. The license initially is limited to the fields of oncology and metabolic disease and may be expanded at Takeda’s option to include other therapeutic areas, subject to specified conditions.

Takeda paid us an upfront payment of $100.0 million and an additional $50.0 million upon achievement of specified technology transfer milestones. In addition, for each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, we are entitled to receive specified development, regulatory and commercialization milestone payments, totaling up to $171.0 million per product, together with a double-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments per product include up to $26.0 million for the achievement of specified development milestones, up to $40.0 million for the achievement of specified regulatory milestones and up to $105.0 million for the achievement of specified commercialization milestones. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Takeda.

Pursuant to the Takeda agreement, we and Takeda also agreed to collaborate on the research of RNAi therapeutics directed to one or two disease targets agreed to by the parties, subject to our existing contractual obligations with third parties. The collaboration is governed by a joint technology transfer committee, a joint research collaboration committee and a joint delivery collaboration committee, each of which is comprised of an equal number of representatives from each party.

We have determined that the deliverables under the Takeda agreement includeincluded the license, the joint committees, the technology transfer activities and the services that we were obligated to perform under the research collaboration with Takeda. We also have determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered services (i.e., the joint committees and the research collaboration) arewere not separable and, accordingly, the license and services arewere being treated as a single unit of accounting. Under the Takeda agreement, the last elements to be delivered arewere the joint technology transfer committee and joint delivery collaboration committee services, each of which hashad a life of no more than seven years. We are recognizinghave fully recognized the upfront payment of $100.0 million and the technology transfer milestones of $50.0 million,


the receipt of which we believed was probable at the commencement of the collaboration, on a straight-line basis over seven years because we arewere unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the research collaboration iswas largely unknown, and therefore, cannotwe could not utilize a proportional performance model. As future milestones are achieved, we will recognize as revenue a portion of the milestone payment equal toamount in its entirety because all performance obligations for the percentageTakeda agreement have been delivered. As of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment. At December 31, 2014,2017, there was no remaining deferred revenue balance under the Takeda agreement was $8.9 million. This remaining deferred revenue will be recognizedas all of our contractual performance obligations were met in full through May 30, 2015.

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Accounting for Income Taxes

We recognize the tax benefit from an uncertain tax position only if it is more likely than not that the tax position will be sustained upon examination by the taxing authorities, based on the technical merits of the tax position. The tax benefits recognized in our financial statements from such a position are measured based on the largest benefit that has a greater than 50%50 percent likelihood of being realized upon ultimate resolution. Our policy is to accrue interest and penalties related to unrecognized tax positions in income tax expense. As of December 31, 2014,2017, we have not recorded significant interest and penalty expense related to uncertain tax positions.

On December 22, 2017, the President of the United States signed into law the TCJA tax reform legislation. The TCJA makes significant changes in U.S. tax law including a reduction in the corporate tax rates, changes to net operating loss carryforwards and carrybacks, and a repeal of the corporate alternative minimum tax. The TCJA reduced the U.S. corporate tax rate from the current rate of 35 percent down to 21 percent starting on January 1, 2018. As a result of the enacted law, we were required to revalue deferred tax assets and liabilities at 21 percent. This revaluation resulted in a provision of $227.9 million to income tax expense in continuing operations and a corresponding reduction in the valuation allowance.  As a result, there was no impact to our consolidated statements of comprehensive loss due to the reduction in tax rates.  The other provisions of the TCJA did not have a material impact on our consolidated financial statements.

Our preliminary estimate of the TCJA and the remeasurement of our deferred tax assets and liabilities is subject to the finalization of management’s analysis related to certain matters, such as developing interpretations of the provisions of the TCJA, changes to certain estimates and the filing of our tax returns. U.S. Treasury regulations, administrative interpretations or court decisions interpreting the TJCA may require further adjustments and changes in our estimates. The final determination of the TCJA and the remeasurement of our deferred assets and liabilities will be completed as additional information becomes available, but no later than one year from the enactment of the TCJA.

We operate in the United States, as well as in several countries outside of the United States, where our income tax returns are subject to audit and adjustment by local tax authorities. The nature of the uncertain tax positions is often very complex and subject to change, and the amounts at issue can be substantial. We develop our cumulative probability assessment of the measurement of uncertain tax positions using internal experience, judgment and assistance from professional advisors. We refine estimates as we become aware of additional information. Any outcome upon settlement that differs from our current estimate may result in additional tax expense in future periods. At December 31, 2014,2017, we had no unrecognized tax benefits that, if recognized, would favorably impact our effective income tax rate in future periods.benefits.

We recognize income taxes when transactions are recorded in our consolidated statements of comprehensive loss, with deferred taxes provided for items that are recognized in different periods for financial statement and tax reporting purposes. We record a valuation allowance to reduce the deferred tax assets to the amount that is more likely than not to be realized.

ForThere was no benefit to income taxes recorded during the years ended December 31, 2014, 2013 and 2012, we recorded a benefit from income taxes of $40.2 million, $2.7 million and $10.6 million, respectively. A benefit of $19.5 million, $2.7 million and $10.6 million for the years ended December 31, 2014, 2013, and 2012, respectively, is due primarily to our recognition of the corresponding income tax benefit associated with the increase in the value of our investment in Regulus that we carried at fair market value during the same respective period. In addition, for the year ended December 31, 2014, we recorded a benefit of $20.7 million due to the recognition of corresponding income tax expense associated with the excess of the proceeds received from Genzyme for the issuance of our common stock. The corresponding income tax expense has been recorded in other comprehensive income and additional paid-in capital, respectively.2017, 2016 or 2015.  

At December 31, 2014,2017, we had a valuation allowance against our net deferred tax assets to the extent it is more likely than not that the assets will not be realized. At December 31, 2014,2017, we had federal and state net operating loss carryforwards of $639.3 million$1.47 billion and $701.8 million,$1.55 billion, respectively, to reduce future taxable income that will expire at various dates through 2034.2037. At December 31, 2014,2017, we had federal and state research and development and investment tax credit carryforwards of $32.3$180.0 million and $10.1$15.3 million, respectively, available to reduce future tax liabilities that expire at various dates through 2034.2037. At December 31, 2014, we had foreign tax credit carryforwards of $3.2 million available to reduce future tax liabilities that expire in 2017. At December 31, 2014,2017, we had alternative minimum tax credits of $0.8 million that will either be available to reduce future regular tax liabilities to the extent such regular tax less other non-refundable credits exceeds the tentative minimum tax.or be fully refundable in 2021. We have a valuation allowance against the net operating loss and credit deferred tax assets as it is unlikely that we will realize these assets. Ownership changes, as defined in the Internal Revenue Code, including those resulting from the issuance of common stock in connection with our public offerings, may limit the amount of net operating loss and tax credit carryforwards that can be utilized to offset future taxable income or tax liability. The amount of the limitation is determined in accordance with Section 382 of the Internal Revenue Code. We have determinedperformed an analysis of ownership changes through December 31, 2017.  Based on this analysis, we do not believe that based onany of our value, in the event there was an annual limitation undertax attributes will expire unutilized due to Section 382 all net operating loss and tax credit carryforwards would still be available to offset taxable income.limitations.


Accounting for Stock-Based Compensation

We have stock incentive plans and an employee stock purchase plan under which we grant equity instruments. We may also grant inducement stock grants outside of our stock incentive plans. We account for all stock-based awards granted to employees at their fair value and generally recognize compensation expense over the vesting period of the award. Determining the amount of stock-based

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compensation to be recorded requires us to develop estimates of fair values of stock options as of the grant date. We calculate the grant date fair values of stock options using the Black-Scholes valuation model. Our expected stock price volatility assumption is based on the historical volatility of our publicly traded stock.

For stock option awards granted during the year ended December 31, 2014,2017, we used a weighted-average expected stock-price volatility assumption of 55%.66 percent. Our expected life assumption is based on our historical data. Our weighted-average expected term was 5.8 years for the year ended December 31, 2014.2017. We utilize a dividend yield of zero based on the fact that we have never paid cash dividends and currently have no intention to pay cash dividends. The risk-free interest rate used for each grant is based on the U.S. Treasury yield curve in effect at the time of grant for instruments with a similar expected life.

The fair value of restricted stock awards granted to employees is based upon the quoted closing market price per share on the date of grant, adjustedgrant. Expense for assumed forfeitures. Expensetime-based restricted stock awards is recognized over the vesting period, commencing whenperiod.

We have performance conditions included in certain of our stock option and restricted stock awards that are based upon the achievement of pre-specified clinical development, regulatory and/or commercial events. As the outcome of each event has inherent risk and uncertainties and a positive outcome may not be known until the event is achieved, we determine that it is probable that the awards will vest.

For performance-based stock awards,begin to recognize the value of the performance-based stock option and restricted stock awards is measured when we determine the achievement of sucheach performance conditionscondition is deemed probable.probable, which often is not until the condition is achieved.  This determination requires significant judgment by management. Expense is recognizedAt the probable date, we record a cumulative expense catch-up, with remaining expense amortized over the vesting period, commencing when we determine that it is probable that the awards will vest.remaining service period.

At December 31, 2014,2017, the estimated fair value of time-based unvested employee stock options and restricted stock awards was $61.4$124.3 million, net of estimated forfeitures. We will recognize this amount over the weighted-average remaining vesting period of approximately three years for these awards. At December 31, 2017, the estimated fair value of performance-based unvested employee stock options and restricted stock units was $74.1 million, net of estimated forfeitures. Stock-based employee compensation expense was $33.1$92.8 million for the year ended December 31, 2014.2017. However, we cannot currently predict the total amount of stock-based compensation expense to be recognized in any future period because such amounts will depend on levels of stock-based payments granted in the future as well as the portion of the awards that actually vest. The stock compensation accounting standard requiresvest, including our performance-based awards. We estimate forfeitures to be estimated at the time of grant and revised,revise, if necessary, in subsequent periods if actual forfeitures differ from those estimates. The term “forfeitures” is distinct from “cancellations” or “expirations” and represents only the unvested portion of the surrendered stock option. We have applied an annual forfeiture rate to all unvested employee stock options and restricted stock awards at December 31, 20142017 based on an analysis of our historical forfeitures. Ultimately, the actual expense recognized over the vesting period will only be for those shares that vest.

Estimated Liability for Development Costs

We record accrued liabilities related to expenses for which service providers have not yet billed us with respect to products we have received or services that we have incurred, specifically related to ongoing pre-clinical studies and clinical trials. These costs primarily relate to third-party clinical management costs, laboratory and analysis costs, toxicology studies and investigator fees. We have multiple product candidates in concurrent pre-clinical studies and clinical trials at multiple clinical sites throughout the world. In order to ensure that we have adequately provided for ongoing pre-clinical and clinical development costs during the period in which we incur such costs, we maintain an accrual to cover these expenses. We update our estimate for this accrual on at least a quarterly basis. The assessment of these costs is a subjective process that requires judgment. Upon settlement, these costs may differ materially from the amounts accrued in our consolidated financial statements. Our historical accrual estimates have not been materially different from our actual costs.


Results of Operations

The following data summarizes the results of our operations for the periods indicated, in thousands:

 

   Year Ended December 31, 
   2014   2013   2012 

Net revenues from collaborators

  $50,561    $47,167    $66,725  

Operating expenses

   455,541     140,109     196,181  

Loss from operations

   (404,980   (92,942   (129,456

Net loss

  $(360,395  $(89,225  $(106,014

 

 

Year Ended December 31,

Description

 

2017

 

 

2016

 

 

2015

 

 

Net revenues from collaborators

 

$

89,912

 

 

$

47,159

 

 

$

41,097

 

 

Operating expenses

 

 

590,000

 

 

 

471,746

 

 

 

337,105

 

 

Loss from operations

 

 

(500,088

)

 

 

(424,587

)

 

 

(296,008

)

 

Net loss

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

 

 

89


The increase in operating expenses for the year ended December 31, 2014 resulted primarily from a $220.8 million charge to operating expenses in connection with our acquisition of the Sirna RNAi assets from Merck, which is described below under the heading “In-process research and development.” Operating expenses for the year ended December 31, 2012 included a $65.0 million charge to operating expenses in connection with the restructuring of our license agreement with Tekmira in November 2012.

Discussion of Results of Operations  for 2014 and 2013

Net revenues from collaborators

We generate revenues through research and development collaborations. The following table summarizes our total consolidated net revenues from collaborators, for the periods indicated, in thousands, together with the changes, in thousands:

 

 

Year Ended December 31,

 

 

Dollar Change

 

  Year Ended
December 31,
 
  2014   2013 

Description

 

2017

 

 

2016

 

 

2015

 

 

2017 compared

to 2016

 

 

2016 compared

to 2015

 

Sanofi Genzyme

 

$

54,625

 

 

$

32,015

 

 

$

11,005

 

 

$

22,610

 

 

$

21,010

 

MDCO

 

 

30,217

 

 

 

11,220

 

 

 

10,301

 

 

 

18,997

 

 

 

919

 

Takeda

  $21,973    $21,973  

 

 

 

 

 

 

 

 

8,867

 

 

 

 

 

 

(8,867

)

Monsanto

   14,985     5,640  

 

 

2,500

 

 

 

 

 

 

5,621

 

 

 

2,500

 

 

 

(5,621

)

MDCO

   10,753     4,604  

Roche/Arrowhead

   1,000       

Cubist

        9,721  

Other

   1,850     5,229  

 

 

2,570

 

 

 

3,924

 

 

 

5,303

 

 

 

(1,354

)

 

 

(1,379

)

  

 

   

 

 

Total net revenues from collaborators

  $50,561    $47,167  

 

$

89,912

 

 

$

47,159

 

 

$

41,097

 

 

$

42,753

 

 

$

6,062

 

  

 

   

 

 

Net revenues from collaborators increased during the year ended December 31, 2017 as compared to the year ended December 31, 2016 due primarily to increased services performed by us in connection with our clinical development programs for which Sanofi Genzyme had opted in and the achievement of a $20.0 million milestone under our agreement with MDCO upon initiation of its Phase 3 study for inclisiran in early November 2017.

Net revenues from collaborators increased for the year ended December 31, 20142016 as compared to the year ended December 31, 20132015 due primarily to revenue recognizedservices performed by us in connection with our clinical development programs for which Sanofi Genzyme had opted in, partially offset by the September 2014 amendmentcompletion of our remaining performance obligations under the Monsanto agreement. In addition, net revenues from collaborators increased for the year ended December 31, 2014 as a result of the achievement of a milestone as well as expense reimbursement under our MDCO agreement. This increase was partially offset by recognition of the remaining deferred revenue under the Cubist agreement of $9.7 million due to the termination of the Cubist agreement in February 20132015 and the endcompletion of our performance obligations thereunder.revenue amortization under the Takeda agreement in May 2015.

We expect net revenues from collaborators to decrease during 2015 on a comparative basis2018 as compared to 2017 due primarily to decreased revenues under the planned completion of our performance obligations under each of the Monsanto agreement in February 2015 and the Takeda agreement in May 2015.

MDCO agreement. We had $66.9$84.8 million and $82.9 million of deferred revenue at December 31, 2014,2017 and 2016, respectively, which consists primarily of payments we have received from collaborators, primarily Sanofi Genzyme, MDCO and Kyowa Hakko Kirin, Monsanto, Takeda and Genzyme, but have not yet recognized pursuant to our revenue recognition policies. As a result of our adoption of the new standard related to revenue recognition on January 1, 2018, we expect to record a cumulative reduction of $68.3 million of deferred revenue with a corresponding adjustment to accumulated deficit in the first quarter of 2018. Please read Note 2 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for our discussion of recent accounting pronouncements for the expected impact of this new accounting standard.

For the foreseeable future,During 2018, if we are successful in obtaining regulatory approval and commercializing patisiran, we expect to begin to recognize net product revenues. Until we are successful in obtaining regulatory approval for patisiran and our other product candidates and in commercializing such products, we expect our revenues to continue to be derived primarily from our alliances with Sanofi Genzyme and MDCO, andas well as other strategic alliances as well asand potential new collaborations and licensing activities.activities, which may include license and other fees, funded research and development, milestone payments and royalties on product sales by our licensors.


90


Operating expenses

The following table summarizes our operating expenses for the periods indicated, in thousands and as a percentage of total operating expenses, together with the changes, in thousands and percentages:thousands:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Dollar Change

 

  2014   % of
Total
Operating
Expenses
  2013   % of
Total
Operating
Expenses
  Increase
(Decrease)
 
      $   % 

Description

 

2017

 

 

% of Total

Operating

Expenses

 

 

2016

 

 

% of Total

Operating

Expenses

 

 

2015

 

 

% of Total

Operating

Expenses

 

 

2017

compared

to 2016

 

 

2016

compared

to 2015

 

Research and development

  $190,249     42 $112,957     81 $77,292     68

 

$

390,635

 

 

 

66

%

 

$

382,392

 

 

 

81

%

 

$

276,495

 

 

 

82

%

 

$

8,243

 

 

$

105,897

 

In-process research and development

   220,766     48     �� 0  220,766     N/A  

General and administrative

   44,526     10  27,152     19  17,374     64

 

 

199,365

 

 

 

34

%

 

 

89,354

 

 

 

19

%

 

 

60,610

 

 

 

18

%

 

 

110,011

 

 

 

28,744

 

  

 

   

 

  

 

   

 

  

 

   

Total operating expenses

  $455,541     100 $140,109     100 $315,432     225

 

$

590,000

 

 

 

100

%

 

$

471,746

 

 

 

100

%

 

$

337,105

 

 

 

100

%

 

$

118,254

 

 

$

134,641

 

  

 

   

 

  

 

   

 

  

 

   

Research and development.    The following table summarizes the components of our research and development expenses for the periods indicated, in thousands and as a percentage of total research and development expenses, together with the changes, in thousands and percentages:thousands:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Dollar Change

 

 2014  % of
Expense
Category
  2013  % of
Expense
Category
  Increase
(Decrease)
 
 $ % 

Description

 

2017

 

 

% of

Expense

Category

 

 

2016

 

 

% of

Expense

Category

 

 

2015

 

 

% of

Expense

Category

 

 

2017

compared

to 2016

 

 

2016

compared

to 2015

 

Research and development

      

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Clinical trial and manufacturing

 $64,195    34 $27,415    24 $36,780    134

Compensation and related

  39,993    21  25,518    23  14,475    57

 

$

100,728

 

 

 

26

%

 

$

87,124

 

 

 

23

%

 

$

60,803

 

 

 

22

%

 

$

13,604

 

 

$

26,321

 

Clinical trial

 

 

87,730

 

 

 

22

%

 

 

92,383

 

 

 

24

%

 

 

68,240

 

 

 

25

%

 

 

(4,653

)

 

 

24,143

 

Manufacturing

 

 

54,681

 

 

 

14

%

 

 

56,348

 

 

 

15

%

 

 

45,388

 

 

 

16

%

 

 

(1,667

)

 

 

10,960

 

Stock-based compensation

 

 

51,872

 

 

 

13

%

 

 

42,946

 

 

 

11

%

 

 

27,086

 

 

 

10

%

 

 

8,926

 

 

 

15,860

 

External services

  27,432    14  15,320    14  12,112    79

 

 

38,675

 

 

 

10

%

 

 

48,624

 

 

 

13

%

 

 

35,259

 

 

 

13

%

 

 

(9,949

)

 

 

13,365

 

Non-cash stock-based compensation

  18,233    10  14,369    13  3,864    27

Facilities-related

  18,068    10  14,299    13  3,769    26

 

 

31,022

 

 

 

8

%

 

 

30,032

 

 

 

8

%

 

 

21,525

 

 

 

8

%

 

 

990

 

 

 

8,507

 

License fees

  12,064    6  7,968    7  4,096    51

Lab supplies and materials

  5,908    3  4,983    4  925    19

 

 

10,513

 

 

 

3

%

 

 

8,917

 

 

 

2

%

 

 

7,494

 

 

 

2

%

 

 

1,596

 

 

 

1,423

 

Other

  4,356    2  3,085    2  1,271    41

 

 

15,414

 

 

 

4

%

 

 

16,018

 

 

 

4

%

 

 

10,700

 

 

 

4

%

 

 

(604

)

 

 

5,318

 

 

 

  

 

  

 

  

 

  

 

  

Total research and development expenses

 $190,249    100 $112,957    100 $77,292    68

 

$

390,635

 

 

 

100

%

 

$

382,392

 

 

 

100

%

 

$

276,495

 

 

 

100

%

 

$

8,243

 

 

$

105,897

 

 

 

  

 

  

 

  

 

  

 

  

Research and development expenses increased slightly during the year endended December 31, 20142017 as compared to the year ended December 31, 20132016 due primarily to additional expenses for clinical trial and manufacturing and external services resulting primarily from the significant advancement of certain of our clinical and pre-clinical programs. In addition,increased compensation and related expense increased during the year ended December 31, 2014expenses as compared to the year ended December 31, 2013 due primarily to a significantresult of an increase in headcount during the period as we expand and advance our development pipeline. Non-cashpipeline, partially offset by decreases in external services expenses related to pre-clinical activities and clinical trial expenses as a result of our decision in October 2016 to discontinue development of revusiran. In addition, stock-based compensation expenses increased during the year ended December 31, 20142017 as a result of increased expense related to the accounting for performance-based stock option awards.

Research and development expenses increased during the year ended December 31, 2016 as compared to the year ended December 31, 20132015 due primarily to additional clinical trial and manufacturing and external services expenses as a result of the advancement of our Genetic Medicine pipeline. In addition, compensation and related expenses and stock-based compensation expenses increased during the year ended December 31, 2016 as compared to the prior year as a result of an increase in headcount during the period as we advanced our pipeline into later-stage development, as well as the vesting of certain performance-based stock option awards during 2016.


During the fourth quarter. License fees increased during the yearyears ended December 31, 2017, 2016 and 2015, in connection with advancing activities under our significant agreements, we incurred significant research and development expenses, primarily related to external development and manufacturing services. The 2018 amendment, together with the Exclusive TTR License and the AT3 License Terms, revise the terms and conditions of our 2014 as comparedSanofi Genzyme collaboration to provide us with the year ended December 31, 2013 dueexclusive right to paymentspursue the further global development and commercialization of all TTR products and any back-up products and provide Sanofi Genzyme with the exclusive right to certain entities, primarily fees paid to Isis aspursue the further global development and commercialization of all fitusiran and any back-up products. As a result, ofwe expect costs incurred under our significant agreements to decrease. The following table summarizes the 2014 Genzyme collaboration.expenses incurred under our significant agreements by collaboration partner for the periods indicated, in thousands:

 

 

2017

 

 

2016

 

 

2015

 

Sanofi Genzyme

 

$

184,703

 

 

$

160,580

 

 

$

115,768

 

MDCO

 

 

5,527

 

 

 

1,275

 

 

 

4,575

 

Ionis

 

 

3,250

 

 

 

525

 

 

 

3,300

 

Total

 

$

193,480

 

 

$

162,380

 

 

$

123,643

 

We expect to continue to devote a substantial portion of our resources to research and development expenses including for the advancement of our Genetic Medicine, Cardio-Metabolic Disease and Hepatic Infectious Disease STArs, to support the goal of three marketed products and ten programs in clinical development, including four late stage programs, byour goals for 2020. We expect that research and development expenses will increase significantly in 20152018 as compared to 2017 as we continue to develop our pipeline and advance our product candidates into later-stage development, hire additional employees and prepare regulatory submissions.  However, we expect that certain expenses will be variable depending on the timing of manufacturing batches, clinical trials.trial enrollment and results, regulatory review of our product candidates, and stock-based compensation expenses due to our determination regarding the probability of vesting for performance-based awards.

A significant portion of our research and development costs are not tracked by project as they benefit multiple projects or our technology platform. However, certain of our collaboration agreements contain cost-

91


sharingcost-sharing arrangements pursuant to which certain costs incurred under the project are reimbursed. Costs reimbursed under the agreements typically include certain direct external costs and a negotiated full-time equivalent labor rate for the actual time worked on the project. In addition, we have been reimbursed under government contracts for certain allowable costs including direct internal and external costs. As a result, although a significant portion of our research and development expenses are not tracked on a project-by-project basis, we do track direct external costs attributable to, and the actual time our employees worked on, our collaborations and government contracts.collaborations.

In-process research and development.    For the year ended December 31, 2014, we recorded $220.8 million to in-process research and development expense in connection with the purchase of the Sirna RNAi assets from Merck. Specifically, at the closing of the transaction, we paid Merck $25.0 million in cash and issued 2,142,037 shares of our common stock, resulting in a charge to in-process research and development expense of $199.3 million. We issued an additional 378,007 shares of common stock to Merck in May 2014 upon the completion of certain technology transfer activities during the second quarter of 2014. In the first quarter of 2014, we recorded a liability of $25.4 million associated with the then future obligation to issue these shares, which was also charged to in-process research and development expense. Upon completion of these technology transfer activities in the second quarter of 2014, we re-measured the expense recorded in connection with these shares using the then current price of our common stock, resulting in a credit of $3.9 million. In future periods, there will be no additional charges recorded to in-process research and development related to the purchase of the Sirna RNAi assets from Merck.

General and administrative.    The following table summarizes the components of our general and administrative expenses for the periods indicated, in thousands and as a percentage of total general and administrative expenses, together with the changes, in thousands and percentages:thousands: 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Dollar Change

 

  2014   % of
Expense
Category
  2013   % of
Expense
Category
  Increase
(Decrease)
 
      $   % 

Description

 

2017

 

 

% of

Expense

Category

 

 

2016

 

 

% of

Expense

Category

 

 

2015

 

 

% of

Expense

Category

 

 

2017

compared

to 2016

 

 

2016

compared

to 2015

 

General and administrative

          

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Consulting and professional services

  $15,068     34 $9,706     36 $5,362     55

 

$

68,847

 

 

 

35

%

 

$

25,310

 

 

 

28

%

 

$

21,451

 

 

 

35

%

 

$

43,537

 

 

$

3,859

 

Non-cash stock-based compensation

   14,828     33  6,334     23  8,494     134

Compensation and related

   9,539     21  7,102     26  2,437     34

 

 

60,289

 

 

 

30

%

 

 

20,967

 

 

 

24

%

 

 

12,721

 

 

 

21

%

 

 

39,322

 

 

 

8,246

 

Stock-based compensation

 

 

40,947

 

 

 

21

%

 

 

32,582

 

 

 

36

%

 

 

18,697

 

 

 

31

%

 

 

8,365

 

 

 

13,885

 

Facilities-related

   2,157     5  1,450     5  707     49

 

 

11,130

 

 

 

6

%

 

 

5,547

 

 

 

6

%

 

 

3,705

 

 

 

6

%

 

 

5,583

 

 

 

1,842

 

Other

   2,934     7  2,560     10  374     15

 

 

18,152

 

 

 

8

%

 

 

4,948

 

 

 

6

%

 

 

4,036

 

 

 

7

%

 

 

13,204

 

 

 

912

 

  

 

   

 

  

 

   

 

  

 

   

Total general and administrative expenses

  $44,526     100 $27,152     100 $17,374     64

 

$

199,365

 

 

 

100

%

 

$

89,354

 

 

 

100

%

 

$

60,610

 

 

 

100

%

 

$

110,011

 

 

$

28,744

 

  

 

   

 

  

 

   

 

  

 

   

General and administrative expenses increased significantly during the year ended December 31, 2017 as compared to the year ended December 31, 2016 due primarily to an increase in commercial and medical affairs headcount and commercial-related services to support corporate growth and prepare for potential commercial product launches. In addition, stock-based compensation expenses increased during the year ended December 31, 2017 as a result of increased expense related to the accounting for performance-based stock option awards.

General and administrative expenses increased during the year ended December 31, 20142016 as compared to the year ended December 31, 20132015 due primarily to an increase in non-cashcompensation and related expenses and stock-based compensation expenses. Thisexpenses resulting from an increase was due primarily toin headcount, as well as the vesting of certain performance-based stock option awards during 2016 and a one-time chargeexpense recorded for certainin connection with the acceleration of a stock options that were modified inoption award under the second quarterterms of 2014. Consulting and professional services increased duringour stock plan as the year ended December 31, 2014 as compared toresult of the year ended December 31, 2013 related to business development activities.unexpected death of an employee.


We expect that general and administrative expenses will increase slightlysignificantly in 20152018 as compared to 2017 as we continue to grow our operations.

Benefit from income taxes

Our benefit from income taxes was $40.2 million foroperations, including the year ended December 31, 2014 as compared to $2.7 million for the year ended December 31, 2013. The increase during the quarter and year ended December 31, 2014 as compared to the prior year periods was due primarily to our recognition of the corresponding income tax benefit associated with the increase in the valuecontinued build-out of our investmentglobal commercial infrastructure and field team, in Reguluspreparation for our anticipated first product launch in 2018, but expect that we carried at fair market value during the same respective period, as well as the difference between the value of

92


stock and the cash proceeds received from Genzyme for the issuance of our common stock. The corresponding income tax expense has been recorded in other comprehensive income and additional paid-in capital, respectively.

Discussion of Results of Operations for 2013 and 2012

Net revenues from collaborators

We generate revenues through research and development collaborations. The following table summarizes our total consolidated net revenues from collaborators, for the periods indicated, in thousands:

   Year Ended
December 31,
 
   2013   2012 

Takeda

  $21,973    $21,973  

Cubist

   9,721     2,777  

Monsanto

   5,640     1,954  

MDCO

   4,604       

Roche/Arrowhead

        37,318  

Other

   5,229     2,703  
  

 

 

   

 

 

 

Total net revenues from collaborators

  $47,167    $66,725  
  

 

 

   

 

 

 

Net revenues from collaborators decreased for the year ended December 31, 2013 as compared to the year ended December 31, 2012 due primarily to the completion of our remaining performance obligations under the Roche/Arrowhead alliance in August 2012. This decrease was partially offset by recognition of the remaining deferred revenue under the Cubist agreement of $9.7 million due to the termination of the Cubist agreement in February 2013 and the end of our performance obligations thereunder. In addition, the decrease was partially offset by revenues recorded under our agreements with Monsanto and MDCO.

We had $126.1 million of deferred revenue at December 31, 2013, which consisted of payments we had received from collaborators, primarily Takeda, Kyowa Hakko Kirin, Monsanto, MDCO and Genzyme, but have not yet recognized pursuant to our revenue recognition policies.

Operating expenses

The following table summarizes our operating expenses for the periods indicated, in thousands and as a percentage of total operating expenses, together with the changes, in thousands and percentages:

   2013   % of
Total
Operating
Expenses
  2012   % of
Total
Operating
Expenses
  Increase
(Decrease)
 
         $  % 

Research and development

  $112,957     81 $86,569     44 $26,388    30

General and administrative

   27,152     19  44,612     23  (17,460  (39)% 

Restructuring of Tekmira license agreement

        0  65,000     33  (65,000  (100)% 
  

 

 

   

 

 

  

 

 

   

 

 

  

 

 

  

Total operating expenses

  $140,109     100 $196,181     100 $(56,072  (29)% 
  

 

 

   

 

 

  

 

 

   

 

 

  

 

 

  

93


Research and development.    The following table summarizes the components of our research and development expenses for the periods indicated, in thousands and as a percentage of total research and development expenses, together with the changes, in thousands and percentages:

  2013  % of
Expense
Category
  2012  % of
Expense
Category
  Increase
(Decrease)
 
      $  % 

Research and development

      

Clinical trial and manufacturing

 $27,415    24 $15,930    18 $11,485    72

Compensation and related

  25,518    23  20,438    24  5,080    25

External services

  15,320    14  13,743    16  1,577    11

Non-cash stock-based compensation

  14,369    13  8,041    9  6,328    79

Facilities-related

  14,299    13  12,647    15  1,652    13

License fees

  7,968    7  5,693    7  2,275    40

Lab supplies and materials

  4,983    4  4,422    5  561    13

Restructuring

      0  2,817    3  (2,817  (100)% 

Other

  3,085    2  2,838    3  247    9
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

Total research and development expenses

 $112,957    100 $86,569    100 $26,388    30
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

Research and development expenses increased during the year ended December 31, 2013 as compared to the year ended December 31, 2012 due primarily to higher clinical trial and manufacturing costs related to our patisiran, revusiran and ALN-AT3 programs. In addition, stock-based compensation increased during the year ended December 31, 2013 as compared to the year ended December 31, 2012 due primarily to an increase in the Black-Scholes value and vesting of stock options granted in 2013. Compensation and related expenses also increased due primarily to the increase in workforce during the year. License fees increased for the year ended December 31, 2013 as compared to the year ended December 31, 2012 due primarily to payments to certain entities for the advancement of our patisiran program into a Phase 3 clinical trial during the fourth quarter, including a $5.0 million milestone paid to Tekmira. Partially offsetting these increases was a one-time charge related to our 2012 restructuring, including employee severance, benefits and other related cost.

General and administrative.    The following table summarizes the components of our general and administrative expenses for the periods indicated, in thousands and as a percentage of total general and administrative expenses, together with the changes, in thousands and percentages:

  2013  % of
Expense
Category
  2012  % of
Expense
Category
  Increase
(Decrease)
 
      $  % 

General and administrative

      

Consulting and professional services

 $9,706    36 $28,949    65 $(19,243  (66)% 

Compensation and related

  7,102    26  6,384    14  718    11

Non-cash stock-based compensation

  6,334    23  4,319    10  2,015    47

Facilities-related

  1,450    5  1,648    4  (198  (12)% 

Restructuring

      0  890    2  (890  (100)% 

Other

  2,560    10  2,422    5  138    6
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

Total general and administrative expenses

 $27,152    100 $44,612    100 $(17,460  (39)% 
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

The decrease in general and administrative expenses during the year ended December 31, 2013 as compared to the year ended December 31, 2012 was due primarily to a decrease in consulting and professional services expenses related to business activities, primarily legal activities related to litigation with Tekmira that was

94


resolved in November 2012. Also included in the year ended December 31, 2012 was a one-time charge related to our January 2012 strategic corporate restructuring, including employee severance, benefits and other related costs.

Other income (expense)

We incurred zero in equity in loss of joint venture (Regulus Therapeutics Inc.) for the year ended December 31, 2013 as compared to $4.5 million for the year ended December 31, 2012 related to our share of the net losses incurred by Regulus. In October 2012, Regulus completed an initial public offering, resulting in our ownership percentage decreasing from approximately 44% to 17% of Regulus’ outstanding common stock. As of December 31, 2013, our ownership percentage had decreased to approximately 15%.

Our benefit from income taxes was $2.7 million in 2013 as compared to $10.6 million for 2012. The change waswill be variable due to our recognitiondetermination regarding the probability of the corresponding income tax benefit associated with the increase in the value of our investment in Regulus that we carried at fair market value during the same respective period.vesting for performance-based awards.

Liquidity and Capital Resources

The following table summarizes our cash flow activities for the periods indicated, in thousands:

 

  Year Ended December 31, 

 

Year Ended December 31,

 

  2014 2013 2012 

 

2017

 

 

2016

 

 

2015

 

Net loss

  $(360,395 $(89,225 $(106,014

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

Adjustments to reconcile net loss to net cash used in operating activities

   224,155    28,686    (630

 

 

110,990

 

 

 

85,188

 

 

 

65,817

 

Changes in operating assets and liabilities

   (29,401  (8,118  (8,965

 

 

(2,902

)

 

 

17,219

 

 

 

35,116

 

  

 

  

 

  

 

 

Net cash used in operating activities

   (165,641  (68,657  (115,609

 

 

(382,786

)

 

 

(307,701

)

 

 

(189,140

)

Net cash (used in) provided by investing activities

   (548,814  (130,505  3,374  

 

 

(290,361

)

 

 

142,591

 

 

 

(321,321

)

Net cash provided by financing activities

   736,465    200,926    93,412  

 

 

1,124,891

 

 

 

177,832

 

 

 

616,177

 

  

 

  

 

  

 

 

Net increase (decrease) in cash and cash equivalents

   22,010    1,764    (18,823

Net increase in cash and cash equivalents

 

 

451,744

 

 

 

12,722

 

 

 

105,716

 

Cash and cash equivalents, beginning of period

   53,169    51,405    70,228  

 

 

193,617

 

 

 

180,895

 

 

 

75,179

 

  

 

  

 

  

 

 

Cash and cash equivalents, end of period

  $75,179   $53,169   $51,405  

 

$

645,361

 

 

$

193,617

 

 

$

180,895

 

  

 

  

 

  

 

 

Since we commenced operations in 2002, we have generated significant losses. At December 31, 2014,2017, we had an accumulated deficit of $956.6 million.$2.15 billion. At December 31, 2014,2017, we had cash, cash equivalents and fixed income marketable securities of $881.9 million, excluding our investment in equity securities of Regulus,$1.70 billion,  compared to cash, cash equivalents and fixed income marketable securities of $350.5$942.6 million at December 31, 2013.2016, in each case excluding the restricted investments related to our term loan agreements.

In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $496.4 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $21.1 million. We intend to use these proceeds for general corporate purposes, focused on achieving our Alnylam 2020 profile with three marketed products and ten RNAi therapeutic clinical programs, including four in late stages of development, across our three STArs, by the end of 2020. In January 2013,May 2017, we sold an aggregate of 9,200,0005,000,000 shares of our common stock through an underwritten public offering forat a price to the public of $71.87 per share. As a result of the offering, we received aggregate net proceeds of approximately $173.6$355.2 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $11.6$4.2 million. In February 2012,November 2017, we sold

95


an aggregate of 8,625,0006,440,000 shares of our common stock through an underwritten public offering forat a price to the public of $125.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $86.8$784.5 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $5.9$20.5 million.

We have used and intend to continue to use these proceeds for general corporate purposes, including clinical trial costs and other research and development expenses, continued growth of our manufacturing, quality, commercial and medical affairs capabilities to support our transition toward a commercial-stage biopharmaceutical company, the anticipated global commercial launches of patisiran and givosiran and other potential future products, the potential expansion of patisiran commercialization efforts in mixed phenotype populations, assuming consistent product labelling, potential repayment of outstanding indebtedness, potential acquisitions, investments or licenses in businesses, products or technologies that are complementary to our own, working capital, capital expenditures and general and administrative expenses.

Sanofi Genzyme has certain rights to purchase additional shares from us under our investor agreement. In February 2014, in connection with our 2014 Genzyme collaboration, we sold to Genzyme 8,766,338 shares of our common stock and Genzyme paid $700.0 million in aggregate cash consideration to us. In March 2014, as a result of our issuance of shares in connection with our acquisition of Sirna,public offerings described above, Sanofi Genzyme exercised its right under our investor agreement to purchase an additional 344,448directly from us, in concurrent private placements, 744,566 shares of our common stock in January 2015 at the public offering price resulting in $70.7 million in proceeds to us and paid us approximately $23.0 million.297,501 shares of common stock in May 2017 at the public offering price resulting in $21.4 million in proceeds to us. In addition, Sanofi Genzyme also has the right at the beginning of each Januaryyear to purchase a number of shares of our common stock based on the number of shares we issued during the previous year for compensatorycompensation-related purposes. Sanofi Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock onin January 22, 2015 for approximately $18.3 million. In January 2015, in connection with our public offering described above, Genzyme also exercised its right to purchase directly from us, in concurrent private placements, 744,566million and 205,030 shares of our common stock resulting in proceeds to us ofFebruary 2016 for $14.3 million. Sanofi Genzyme currently holds approximately $70.7 million. Each of these purchases allowed Genzyme to maintain its ownership level11 percent of our outstanding common stock of approximately 12%.stock.

We invest primarily in cash equivalents,money market funds, U.S. government-sponsored enterprise securities, U.S. treasury securities, high-grade corporate notes, certificates of deposit and commercial paper. Corporate notes may also include foreign bonds denominated in U.S. dollars. Our investment objectives are, primarily, to assure liquidity and preservation of capital and, secondarily, to obtain


investment income. All of our investments in debt securities are recorded at fair value and are available-for-sale. Fair value is determined based on quoted market prices and models using observable data inputs. We have not recorded any impairment charges to our fixed income marketable securities atduring the three years ended December 31, 2014.2017.

Operating activities

We have required significant amounts of cash to fund our operating activities as a result of net losses since our inception. Cash used in operating activities is adjusted for non-cash items to reconcile net loss to net cash provided by or used in operating activities. These non-cash adjustments have historically included stock-based compensation in-process research and development, intraperiod tax allocation and depreciation and amortization.

We expect that we will require significant amounts of cash to fund our operating activities for the foreseeable future as we continue to develop and advanceexecute on our Alnylam 2020 strategy through the advancement of our research, development, pre-commercial and developmentpotentially commercial initiatives. The actual amount of overall expenditures will depend on numerous factors, including the timing of expenses, the timing and terms of collaboration agreements or other strategic transactions, if any, and the timing and progress of our research, development and developmentcommercialization efforts.

The increase in net cash used in operating activities for the year ended December 31, 20142017 compared to the year ended December 31, 2013 was due primarily to our net loss adjusted for noncash activities, such as in-process research2016 and development expense of $220.8 million and partially offset by a benefit from intraperiod tax allocation of $40.2 million. The decrease in net cash used in operating activities for the year ended December 31, 20132016 compared to the year ended December 31, 20122015 was due primarily to our net lossloss.

Investing activities

For the years ended December 31, 2017, 2016 and other changes2015, net cash provided by or used in investing activities was due primarily to net purchases of fixed income marketable securities in accordance with management of our working capitalliquidity needs.  For the year ended December 31, 2017 and a decrease2016, there were purchases of property, plant and equipment of $104.2 million and $64.6 million, respectively, primarily in deferred revenueconnection with the construction of $6.2 million.our drug substance manufacturing facility. For the year ended December 31, 2016, there were $150.0 million of purchases of restricted investments related to our term loan agreements with BOA and Wells. In December 2017, we repaid in full $120.0 million outstanding under the BOA term loan agreement.

InvestingFinancing activities

For the year ended December 31, 2014,2017, net cash used in investingof $1.12 billion provided by financing activities of $548.8 million was due primarily to $514.9 millionproceeds of net purchases of fixed income marketable securities.$1.14 billion received from our May and November 2017 underwritten public offerings.  For the year ended December 31, 2013,2016, net cash used in investingof $177.8 million provided by financing activities of $130.5 million resultedwas due primarily from net purchases of fixed income marketable securities of $126.5 million.to our term loan agreements with BOA and Wells. For the year ended December 31, 2012, net cash provided by investing activities of $3.4 million resulted primarily from sales and maturities of fixed income marketable securities of $11.9 million offset by purchases of property and equipment of $8.3 million primarily in connection with the build-out of our cGMP manufacturing facility.

96


Financing activities

For the year ended December 31, 2014,2015, net cash of $736.5$616.2 million provided by financing activities was due primarily to proceeds of $723.0$496.4 million received from our January 2015 underwritten public offering, as well as proceeds of $89.0 million received from our issuances of common stock to Sanofi Genzyme as well as proceeds of $29.4 million from the issuance of common stock in connection with stock option exercises and other types of equity, partially offset by $16.0 million of payments for the repurchase of common stock for employee tax withholding. For the year ended December 31, 2013, net cash provided by financing activities of $200.9 million was due primarily to proceeds of $173.6 million received from our January 2013 underwritten public offering, as well as proceeds of $28.7 million from the issuance of common stock in connection with stock option exercises and other types of equity. For the year ended December 31, 2012, net cash of $93.4 million provided by financing activities was due primarily to proceeds of $86.8 million received from our February 2012 underwritten public offering, as well proceeds of $7.0 million from the issuance of common stock in connection with stock option exercises and other types of equity.2015.

Operating Capital Requirements

We docurrently have programs focused on a number of therapeutic areas and, in December 2017, submitted our first NDA and MAA for marketing approval for patisiran.  However, our development efforts may not know when, if ever,be successful and we will successfully develop ormay not be able to commence sales of patisiran or any other product. If we are able to gain approval and successfully launch patisiran in 2018, we may begin to generate net revenues from product sales. Therefore, we anticipate that we will continue to generate significant losses for the foreseeable future as a result of planned expenditures for research and development activities relating to our research platform, our drug development programs, including the optimization of drug delivery technologies, clinical trial and manufacturing costs, the establishment of late-stagelate stage clinical and commercial capabilities, including global operations, continued management and growth of our intellectual property including our patent portfolio, collaborations and general corporate activities. In addition, we are expanding our manufacturing capabilities, including through construction of a drug substance manufacturing facility in Norton, Massachusetts. In April 2016, our subsidiary, Alnylam U.S., Inc., entered into an aggregate of $150.0 million in term loan agreements with BOA and Wells, related to the build out of our new drug substance manufacturing facility. In December 2017, we repaid in full $120.0 million outstanding under the BOA term loan agreement. Interest on the borrowings under the BOA term loan agreement was, and interest under the Wells term loan agreement is, calculated based on LIBOR plus 0.45 percent. The obligations under the term loan agreements were, with respect to BOA, and are, with respect to Wells, secured by cash collateral in an amount equal to, at any given time, at least 100 percent of the principal amount of all term loans outstanding under the agreements at such time.  We are the guarantor under the Wells term loan agreement, which matures in April 2021.

Based on our current operating plan, we believe that our existing cash, cash equivalents and fixed income marketable securities, including the proceeds from our public offering and Genzyme’s purchases of additional shares of our common stock in January 2015, together with the cash we expect to generate under our current alliances, will be sufficient to enable us to achieveadvance our ‘Alnylam 2020’ guidance.Alnylam 2020


strategy for at least the next few years. For reasons discussed below, we may require significant additional funds earlier than we currently expect in order to develop, conduct clinical trials for, manufacture and commercialize any product candidates.

In the future, we may seek additional funding through additional collaborative arrangements and public or private financings. In December 2012, we filed an automatically effective shelf registration statement with the SEC for an indeterminate number of shares. Additional funding may not be available to us on acceptable terms or at all. In addition,Moreover, the terms of any additional financing may further adversely affect the holdings or the rights of our stockholders. For example, if we raise additional funds by issuing equity securities, further dilution to our existing stockholders maywill result. In addition, as a condition to providing additional funds to us, future investors may demand, and may be granted, rights superior to those of existing stockholders. If we are unable to obtain funding on a timely basis, we may be required to significantly delay or curtail one or more of our research or development programs.programs and our ability to achieve our goals for 2020 may be delayed or diminished. We also could be required to seek funds through arrangements with collaborators or others that may require us to relinquish rights to some of our technologies, or product candidates or products that we would otherwise pursue.pursue on our own.

Even if we are able to raise additional funds in a timely manner, our future capital requirements may vary from what we expect and will depend on many factors, including:

our progress in demonstrating that siRNAs can be active as drugs and achieve desired clinical effects;

our ability to develop relatively standard procedures for selecting and modifying siRNA product candidates;

progress in our research and development programs, as well as what may be required by regulatory bodies to advance these programs;

the timing, receipt and amount of milestone and other payments, if any, from present and future collaborators, if any;

our ability to maintain and establish additional collaborative arrangements and/or new business initiatives;

the resources, time and costs required to successfully initiate and complete our pre-clinical and clinical trials, obtain regulatory approvals, prepare for commercialization of our product candidates and obtain and maintain licenses to third-party intellectual property;

our ability to establish, maintain and operate our own manufacturing facilities in a timely and cost effective manner;

97


our ability to manufacture, or contract with third-parties for the manufacture of, our product candidates for clinical testing and commercial sale;

the resources, time and cost required for the preparation, filing, prosecution, maintenance and enforcement of patent claims;

the costs associated with legal activities, including litigation, arising in the course of our business activities and our ability to prevail in any such legal disputes;

progress in the research and development programs of Regulus; and

the timing, receipt and amount of sales and royalties, if any, from our potential products.

Off-Balance Sheet Arrangements

In connection with our license agreements with Max Planck relating to the Tuschl I and II patent applications, we are required to indemnify Max Planck for certain damages arising in connection with the intellectual property rights licensed under the agreements. Under this indemnification agreement with Max Planck, we are responsible for paying the costs of any litigation relating to the license agreements or the underlying intellectual property rights. In connection with the settlement of the litigation regarding the Tuschl patents, we also agreed to indemnify Whitehead, MIT and UMass for certain costs associated with defending the University of Utah litigation. In connection with our research agreement with Acuitas, we have agreed to indemnify Acuitas for certain legal costs, subject to certain exceptions and limitations. Amounts paid under the AcuitasThese indemnification agreement in connection with our previous litigation with Tekmira werecosts are charged to general and administrative expense. In addition, we are a party to a number of agreements entered into in the ordinary course of business, which contain typical provisions that obligate us to indemnify the other parties to such agreements upon the occurrence of certain events. These indemnification obligations are considered off-balance sheet arrangements in accordance with GAAP. To date, other than certain costs associated with the certain previously settled litigation related to the Tuschl patents and our disputes with Tekmira,Arbutus, and certain ongoingdefense costs related to the University of Utah litigation, we have not encountered material costs as a result of such obligations and have not accrued any liabilities related to such obligations in our consolidated financial statements. SeePlease read Note 7 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for further discussion of these indemnification agreements and guarantee obligations.agreements.


Contractual Obligations

In the table below, we set forth our enforceable and legally binding obligations and future commitments at December 31, 2014, as well as obligations related to contracts that we are likely to continue, regardless of the fact that they were cancelable at December 31, 2014.2017. Some of the figures that we include in this table are based on management’s estimates and assumptions about these obligations, including their duration, the possibility of renewal, anticipated actions by third parties and other factors. Because these estimates and assumptions are necessarily subjective, the obligations we will actually pay in future periods may vary from those reflected in the table.

 

   Payments Due by Period 

Contractual Obligations

  2015   2016 and
2017
   2018 and
2019
   After
2019
   Total 

Operating lease obligations(1)

  $6,810    $14,529    $14,995    $13,845    $50,179  

Purchase commitments(2)

   59,279     45,222     —       —       104,501  

Technology license commitments(3)

   7,379     1,468     1,516     8,592     18,955  
  

 

 

   

 

 

   

 

 

   

 

 

   

 

 

 

Total contractual cash obligations

  $73,468    $61,219    $16,511    $22,437    $173,635  
  

 

 

   

 

 

   

 

 

   

 

 

   

 

 

 

 

 

Payments Due by Period

 

Contractual Obligations

 

2018

 

 

2019 and 2020

 

 

2021 and 2022

 

 

After 2022

 

 

Total

 

Facility lease obligations(1)

 

$

14,464

 

 

$

67,016

 

 

$

53,978

 

 

$

297,726

 

 

$

433,184

 

Long-term debt(2)

 

 

614

 

 

 

1,229

 

 

 

30,252

 

 

 

 

 

 

32,095

 

Technology license and other commitments(3)

 

 

26,012

 

 

 

18,072

 

 

 

1,390

 

 

 

1,500

 

 

 

46,974

 

Total contractual cash obligations

 

$

41,090

 

 

$

86,317

 

 

$

85,620

 

 

$

299,226

 

 

$

512,253

 

 

(1)

Relates primarily to our Cambridge, Massachusetts non-cancelable operatingfacility lease agreements.

(2)

Includes commitments

In April 2016, our subsidiary, Alnylam U.S., Inc., entered into a $30.0 million term loan agreement with Wells, for which we are the guarantor, related to purchase orders, clinical,the build out of our new drug substance manufacturing facility, that matures in April 2021. Interest payments are included in the table above and pre-clinical agreements,are calculated based on LIBOR plus 0.45 percent. The obligations under the term loan agreement are secured by cash collateral in an amount equal to, at any given time, at least 100 percent of the principal amount of the term loan outstanding at such time. We include estimates for interest in “Long-term debt,” which are equivalent to our expectations for the probable outcome of variable interest rates that are dependent on various future events and other purchase commitments for goods or services.market interest rates.

(3)

Relates to our fixed payment obligations under license agreements, as well as other payments related to technology research and development.

98


The table above excludes approximately $333.3 million of cancellable commitments related to clinical and manufacturing-related agreements, including certain costs related to investment in the construction of our drug substance manufacturing facility and commitments that may be transitioned to Sanofi Genzyme under the AT3 License Terms. We in-license technology from a number of sources.sources, including Ionis and Merck. Pursuant to these in-license agreements, we will be required to make additional payments if and when we achieve specified development, regulatory and commercialization milestones. To the extent we are unable to reasonably predict the likelihood, timing or amount of such payments, we have excluded them from the table above.

Recent Accounting Pronouncements

SeePlease read Note 2 to our consolidated financial statements included in Part II, Item 8, “Financial Statements and Supplementary Data,” of this annual report on Form 10-K for a description of recent accounting pronouncements applicable to our business.

 

ITEM  7A.

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

As part of our investment portfolio, we own financial instruments that are sensitive to market risks. The investment portfolio is used to preserve our capital until it is required to fund operations, including our research, development and developmentearly commercial activities. Our fixed income marketable securities consist of primarily U.S. government-sponsored enterprise securities, U.S. treasury securities, high-grade corporate notes, and commercial paper. Corporate notes may also include foreign bonds denominated in U.S. dollars. All of our investments in debt securities are classified as available-for-sale and are recorded at fair value. Our available-for-sale investments in debt securities are sensitive to changes in interest rates and changes in the credit ratings of the issuers. Interest rate changes would result in a change in the net fair value of these financial instruments due to the difference between the market interest rate and the market interest rate at the date of purchase of the financial instrument. If market interest rates were to increase immediately and uniformly by 50 basis points, or one-half of a percentage point, from levels at December 31, 2014,2017, the net fair value of our interest-sensitive financial instruments would have resulted in a hypothetical decline of $3.2$2.7 million. We currently do not seek to hedge this exposure to fluctuations in interest rates. A downgrade in the credit rating of an issuer of a debt security or further deterioration of the credit markets could result in a decline in the fair value of the debt instruments. Our investment guidelines prohibit investment in auction rate securities and we do not believe we have any direct exposure to losses relating from mortgage-based securities or derivatives related thereto such as credit-default swaps. Historically, foreign currency fluctuations have not been material. We did not record any impairment charges to our fixed income marketable securities during the year ended December 31, 2014.

2017.

 

99



ITEM 8.

FINANCIAL STATEMENTSSTATEMENTS AND SUPPLEMENTARY DATA

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

 

Page

Management’s Annual Report on Internal Control Over Financial Reporting

101

87

Report of Independent Registered Public Accounting Firm

102

88

Consolidated Balance Sheets at December 31, 20142017 and 20132016

103

90

Consolidated Statements of Comprehensive Loss for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

104

91

Consolidated Statements of Stockholders’ Equity for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

105

92

Consolidated Statements of Cash Flows for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

106

93

Notes to Consolidated Financial Statements

107

94

 


100


Management’s Annual Report on InternalInternal Control Over Financial Reporting

TheOur management of the Company is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is defined in Rule 13a-15(f) or 15d-15(f) promulgated under the Securities Exchange Act of 1934 as a process designed by, or under the supervision of, the company’s principal executive and principal financial officers and effected by the company’s board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that:

Pertain to the maintenance of records that in reasonable detail accurately and fairly reflect the transactions and dispositions of the assets of the Company;our assets;

Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that our receipts and expenditures of the Company are being made only in accordance with authorizations of management and directors of the Company;directors; and

Provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of the Company’sour assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

The Company’sOur management assessed the effectiveness of the Company’sour internal control over financial reporting as of December 31, 2014.2017. In making this assessment, the Company’s management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission (COSO) in Internal Control-Integrated Framework (2013).

Based on itsour assessment, our management concluded that, as of December 31, 2014, the Company’s2017, our internal control over financial reporting is effective based on those criteria.

The effectiveness of the Company’sour internal control over financial reporting as of December 31, 20142017 has been audited by PricewaterhouseCoopers LLP, an independent registered public accounting firm, as stated in their report. This report appears on page 102.88.


101


Report of Independent RegisteredRegistered Public Accounting Firm

Tothe To the Board of Directors and Stockholders of Alnylam Pharmaceuticals, Inc.

In our opinion,

Opinions on the Financial Statements and Internal Control over Financial Reporting

We have audited the accompanying consolidated balance sheets of Alnylam Pharmaceuticals, Inc. and its subsidiaries as of December 31, 2017 and 2016, and the related consolidated statements of comprehensive loss, stockholders’ equity and cash flows for each of the three years in the period ended December 31, 2017, including the related notes (collectively referred to as the “consolidated financial statements”).  We also have audited the Company's internal control over financial reporting as of December 31, 2017, based on criteria established in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO).  

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of Alnylam Pharmaceuticals, Inc.and its subsidiariesatthe Company as of December 31, 20142017 and 2013,2016, and the results of their operations and their cash flows for each of the three years in the period ended December 31, 20142017 in conformity with accounting principles generally accepted in the United States of America.  Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2014,2017, based on criteria established inInternal Control - Integrated Framework (2013) (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). COSO.

Basis for Opinions

The Company’sCompany's management is responsible for these consolidated financial statements, for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control over Financial Reporting. Our responsibility is to express opinions on thesethe Company’s consolidated financial statements and on the Company’sCompany's internal control over financial reporting based on our integrated audits.  We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States).PCAOB.  Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud, and whether effective internal control over financial reporting was maintained in all material respects.  

Our audits of the consolidated financial statements included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks.  Such procedures included examining, on a test basis, evidence supportingregarding the amounts and disclosures in the consolidated financial statements, assessingstatements.  Our audits also included evaluating the accounting principles used and significant estimates made by management, andas well as evaluating the overall presentation of the consolidated financial statement presentation.statements.  Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk.  Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions.

Definition and Limitations of Internal Control over Financial Reporting

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles.  A company’s internal control over financial reporting includes those policies and procedures that (i) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (ii) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (iii) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.


Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements.  Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

/s/PricewaterhouseCoopers LLP

Boston, Massachusetts

February 13, 2015

15, 2018

 

102


We have served as the Company’s auditor since 2003.


ALNYLAM PHARMACEUTICALS, INC.

CONSOLIDATED BALANCE SHEETS

(In thousands, except share and per share amounts)

 

  December 31, 

 

December 31,

 

  2014 2013 

 

2017

 

 

2016

 

ASSETSASSETS  

 

 

 

 

 

 

 

 

Current assets:

   

 

 

 

 

 

 

 

 

Cash and cash equivalents

  $75,179   $53,169  

 

$

645,361

 

 

$

193,617

 

Marketable securities

   526,929    192,701  

 

 

1,045,257

 

 

 

424,185

 

Investment in equity securities of Regulus Therapeutics Inc

   94,583      

Investment in equity securities of Regulus Therapeutics Inc.

 

 

 

 

 

8,997

 

Billed and unbilled collaboration receivables

   39,937    4,248  

 

 

34,002

 

 

 

23,334

 

Prepaid expenses and other current assets

   9,739    3,910  

 

 

40,120

 

 

 

21,744

 

  

 

  

 

 

Total current assets

   746,367    254,028  

 

 

1,764,740

 

 

 

671,877

 

Marketable securities

   279,821    104,602  

 

 

13,919

 

 

 

324,799

 

Deferred tax assets

   31,667      

Investment in equity securities of Regulus Therapeutics Inc.

       45,452  

Property and equipment, net

   21,740    16,448  
  

 

  

 

 

Property, plant and equipment, net

 

 

181,900

 

 

 

114,572

 

Restricted investments

 

 

30,000

 

 

 

150,000

 

Other assets

 

 

4,171

 

 

 

1,562

 

Total assets

  $1,079,595   $420,530  

 

$

1,994,730

 

 

$

1,262,810

 

  

 

  

 

 
LIABILITIES AND STOCKHOLDERS’ EQUITYLIABILITIES AND STOCKHOLDERS’ EQUITY  

 

 

 

 

 

 

 

 

Current liabilities:

   

 

 

 

 

 

 

 

 

Accounts payable

  $15,111   $5,896  

 

$

28,355

 

 

$

54,465

 

Accrued expenses

   23,680    14,160  

 

 

72,203

 

 

 

42,118

 

Deferred tax liabilities

   31,667      

Deferred rent

   1,005    1,112  

 

 

1,988

 

 

 

1,576

 

Deferred revenue

   23,871    32,696  

 

 

41,705

 

 

 

33,540

 

  

 

  

 

 

Total current liabilities

   95,334    53,864  

 

 

144,251

 

 

 

131,699

 

Deferred rent, net of current portion

   5,011    2,925  

 

 

6,626

 

 

 

8,431

 

Deferred revenue, net of current portion

   42,983    93,394  

 

 

43,075

 

 

 

49,392

 

  

 

  

 

 

Long-term debt

 

 

30,000

 

 

 

150,000

 

Other liabilities

 

 

4,347

 

 

 

3,067

 

Total liabilities

   143,328    150,183  

 

 

228,299

 

 

 

342,589

 

  

 

  

 

 

Commitments and contingencies (Note 7)

   

 

 

 

 

 

 

 

 

Stockholders’ equity:

   

 

 

 

 

 

 

 

 

Preferred stock, $0.01 par value per share, 5,000,000 shares authorized and no shares issued and outstanding at December 31, 2014 and 2013

         

Common stock, $0.01 par value per share, 125,000,000 shares authorized; 77,202,753 shares issued and outstanding at December 31, 2014; 63,741,573 shares issued and outstanding at December 31, 2013

   772  �� 637  

Preferred stock, $0.01 par value per share, 5,000,000 shares authorized and no shares

issued and outstanding at December 31, 2017 and 2016

 

 

 

 

 

 

Common stock, $0.01 par value per share, 125,000,000 shares authorized; 99,666,549 shares issued and outstanding at December 31, 2017; 85,941,344 shares issued and

outstanding at December 31, 2016

 

 

997

 

 

 

859

 

Additional paid-in capital

   1,843,362    846,228  

 

 

3,947,552

 

 

 

2,609,614

 

Accumulated other comprehensive income

   48,763    19,717  

Accumulated other comprehensive loss

 

 

(34,433

)

 

 

(33,441

)

Accumulated deficit

   (956,630  (596,235

 

 

(2,147,685

)

 

 

(1,656,811

)

  

 

  

 

 

Total stockholders’ equity

   936,267    270,347  

 

 

1,766,431

 

 

 

920,221

 

  

 

  

 

 

Total liabilities and stockholders’ equity

  $1,079,595   $420,530  

 

$

1,994,730

 

 

$

1,262,810

 

  

 

  

 

 

The accompanying notes are an integral part of these consolidated financial statements.

 


103


ALNYLAM PHARMACEUTICALS, INC.

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(In thousands, except per share amounts)

 

  Year Ended December 31, 

 

Year Ended December 31,

 

  2014 2013 2012 

 

2017

 

 

2016

 

 

2015

 

Net revenues from collaborators

  $50,561   $47,167   $66,725  

 

$

89,912

 

 

$

47,159

 

 

$

41,097

 

  

 

  

 

  

 

 

Operating expenses:

    

 

 

 

 

 

 

 

 

 

 

 

 

Research and development(1)

   190,249    112,957    86,569  

 

 

390,635

 

 

 

382,392

 

 

 

276,495

 

In-process research and development

   220,766          

General and administrative(1)

   44,526    27,152    44,612  

 

 

199,365

 

 

 

89,354

 

 

 

60,610

 

Restructuring of Tekmira license agreement

           65,000  
  

 

  

 

  

 

 

Total operating expenses

   455,541    140,109    196,181  

 

 

590,000

 

 

 

471,746

 

 

 

337,105

 

  

 

  

 

  

 

 

Loss from operations

   (404,980  (92,942  (129,456

 

 

(500,088

)

 

 

(424,587

)

 

 

(296,008

)

  

 

  

 

  

 

 

Other income (expense):

    

 

 

 

 

 

 

 

 

 

 

 

 

Equity in loss of joint venture (Regulus Therapeutics Inc.)

           (4,522

Gain on issuance of stock by Regulus Therapeutics Inc.

           16,084  

Interest income

   2,559    1,069    977  

 

 

12,236

 

 

 

8,308

 

 

 

5,859

 

Other income (expense)

   1,817    (47  331  
  

 

  

 

  

 

 

Other (expense) income

 

 

(3,022

)

 

 

6,171

 

 

 

76

 

Total other income

   4,376    1,022    12,870  

 

 

9,214

 

 

 

14,479

 

 

 

5,935

 

  

 

  

 

  

 

 

Loss before income taxes

   (400,604  (91,920  (116,586

Benefit from income taxes

   40,209    2,695    10,572  
  

 

  

 

  

 

 

Net loss

  $(360,395 $(89,225 $(106,014

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

  

 

  

 

  

 

 

Net loss per common share — basic and diluted

  $(4.85 $(1.45 $(2.11

 

$

(5.42

)

 

$

(4.79

)

 

$

(3.45

)

  

 

  

 

  

 

 

Weighted-average common shares used to compute basic and diluted net loss per common share

   74,278    61,551    50,286  

 

 

90,554

 

 

 

85,596

 

 

 

83,992

 

  

 

  

 

  

 

 

Comprehensive loss:

    

 

 

 

 

 

 

 

 

 

 

 

 

Net loss

  $(360,395 $(89,225 $(106,014

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

Unrealized gain on marketable securities, net of tax

   31,127    4,055    15,827  

Reclassification adjustment for realized gain on marketable securities included in net loss

   (2,081        
  

 

  

 

  

 

 

Unrealized loss on marketable securities, net of tax

 

 

(2,886

)

 

 

(30,833

)

 

 

(44,394

)

Reclassification adjustment for realized loss (gain) on marketable securities

included in net loss

 

 

1,894

 

 

 

(6,977

)

 

 

 

Comprehensive loss

  $(331,349 $(85,170 $(90,187

 

$

(491,866

)

 

$

(447,918

)

 

$

(334,467

)

  

 

  

 

  

 

 

 

(1)

Non-cash stock-based

Stock-based compensation expenses included in operating expenses are as follows:

 

Research and development

  $18,233    $14,369    $8,041  

 

$

51,872

 

 

$

42,946

 

 

$

27,086

 

General and administrative

   14,828     6,334     4,319  

 

 

40,947

 

 

 

32,582

 

 

 

18,697

 

The accompanying notes are an integral part of these consolidated financial statements.

 


104


ALNYLAM PHARMACEUTICALS, INC.

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY

(In thousands, except share amounts)

 

  Common Stock  Additional
Paid-in
Capital
  Accumulated
Other
Comprehensive
Income (Loss)
  Accumulated
Deficit
  Total
Stockholders’
Equity
 
  Shares  Amount     

Balance at December 31, 2011

  42,721,942   $427   $518,731   $(165 $(400,996 $117,997  

Exercise of common stock options

  661,909    7    6,395            6,402  

Issuance of common stock under other types of equity plans

  97,459    1    878            879  

Issuance of restricted stock, net of cancellations and tax withholdings

  383,626    4    (523          (519

Issuance of common stock, net of offering costs

  8,625,000    86    86,714            86,800  

Stock-based compensation expense

          12,360            12,360  

Joint venture stock-based compensation expense (Regulus Therapeutics Inc.)

          321            321  

Other comprehensive income

              15,827        15,827  

Net loss

                  (106,014  (106,014
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

 

 

 

Balance at December 31, 2012

  52,489,936    525    624,876    15,662    (507,010  134,053  

Exercise of common stock options

  2,031,916    20    27,974            27,994  

Issuance of common stock under other types of equity plans

  60,180    1    1,183            1,184  

Tax withholdings and cancellations of restricted stock, net of issuances of new awards

  (40,459  (1  (1,988          (1,989

Issuance of common stock, net of offering costs

  9,200,000    92    173,480            173,572  

Stock-based compensation expense

          20,703            20,703  

Other comprehensive income

              4,055        4,055  

Net loss

                  (89,225  (89,225
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

 

 

 

Balance at December 31, 2013

  63,741,573    637    846,228    19,717    (596,235  270,347  

Exercise of common stock options

  1,972,204    20    28,429            28,449  

Issuance of common stock under other types of equity plans

  31,122    1    1,580            1,581  

Tax withholdings and cancellations of restricted stock, net of issuances of new awards

  (172,976  (2  (15,390          (15,392

Issuance of common stock to Genzyme

  9,110,786    91    774,396            774,487  

Issuance of common stock in connection with an asset acquisition

  2,520,044    25    195,741            195,766  

Stock-based compensation expense

          33,061            33,061  

Tax provision associated with intraperiod tax allocation

          (20,683          (20,683

Other comprehensive income before reclassifications, net of tax

              31,127        31,127  

Reclassification adjustment for realized gain on marketable securities included in net loss

              (2,081      (2,081

Net loss

                  (360,395  (360,395
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

 

 

 

Balance at December 31, 2014

  77,202,753   $772   $1,843,362   $48,763   $(956,630 $936,267  
 

 

 

  

 

 

  

 

 

  

 

 

  

 

 

  

 

 

 

 

 

Common Stock

 

 

Additional

Paid-in

 

 

Accumulated

Other

Comprehensive

 

 

Accumulated

 

 

Total

Stockholders’

 

 

 

Shares

 

 

Amount

 

 

Capital

 

 

Income (Loss)

 

 

Deficit

 

 

Equity

 

Balance at December 31, 2014

 

 

77,202,753

 

 

$

772

 

 

$

1,843,362

 

 

$

48,763

 

 

$

(956,630

)

 

$

936,267

 

Exercise of common stock options

 

 

1,461,237

 

 

 

15

 

 

 

29,410

 

 

 

 

 

 

 

 

 

29,425

 

Issuance of common stock under other types of equity plans

 

 

32,427

 

 

 

1

 

 

 

2,665

 

 

 

 

 

 

 

 

 

2,666

 

Issuance of common stock under equity plans, net of tax

   withholdings

 

 

6,366

 

 

 

 

 

 

(378

)

 

 

 

 

 

 

 

 

(378

)

Issuance of common stock to Sanofi Genzyme

 

 

940,817

 

 

 

9

 

 

 

89,009

 

 

 

 

 

 

 

 

 

89,018

 

Issuance of common stock, net of offering costs

 

 

5,447,368

 

 

 

54

 

 

 

496,346

 

 

 

 

 

 

 

 

 

496,400

 

Stock-based compensation expense related to equity-classified

   awards

 

 

 

 

 

 

 

 

45,783

 

 

 

 

 

 

 

 

 

45,783

 

Other comprehensive loss, net of tax

 

 

 

 

 

 

 

 

 

 

 

(44,394

)

 

 

 

 

 

(44,394

)

Net loss

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(290,073

)

 

 

(290,073

)

Balance at December 31, 2015

 

 

85,090,968

 

 

 

851

 

 

 

2,506,197

 

 

 

4,369

 

 

 

(1,246,703

)

 

 

1,264,714

 

Exercise of common stock options, net of tax withholdings

 

 

559,344

 

 

 

5

 

 

 

11,603

 

 

 

 

 

 

 

 

 

11,608

 

Issuance of common stock under other types of equity plans

 

 

75,453

 

 

 

1

 

 

 

3,647

 

 

 

 

 

 

 

 

 

3,648

 

Issuance of common stock under equity plans, net of tax

   withholdings

 

 

10,549

 

 

 

 

 

 

(314

)

 

 

 

 

 

 

 

 

(314

)

Issuance of common stock to Sanofi Genzyme

 

 

205,030

 

 

 

2

 

 

 

14,299

 

 

 

 

 

 

 

 

 

14,301

 

Stock-based compensation expense related to equity-classified

   awards

 

 

 

 

 

 

 

 

74,182

 

 

 

 

 

 

 

 

 

74,182

 

Other comprehensive loss, net of tax

 

 

 

 

 

 

 

 

 

 

 

(37,810

)

 

 

 

 

 

(37,810

)

Net loss

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(410,108

)

 

 

(410,108

)

Balance at December 31, 2016

 

 

85,941,344

 

 

 

859

 

 

 

2,609,614

 

 

 

(33,441

)

 

 

(1,656,811

)

 

 

920,221

 

Exercise of common stock options

 

 

1,841,566

 

 

 

19

 

 

 

80,527

 

 

 

 

 

 

 

 

 

80,546

 

Issuance of common stock under other types of equity plans

 

 

134,615

 

 

 

2

 

 

 

5,905

 

 

 

 

 

 

 

 

 

5,907

 

Issuance of common stock under equity plans, net of tax

   withholdings

 

 

11,523

 

 

 

 

 

 

(707

)

 

 

 

 

 

 

 

 

(707

)

Issuance of common stock to Sanofi Genzyme

 

 

297,501

 

 

 

3

 

 

 

21,378

 

 

 

 

 

 

 

 

 

21,381

 

Issuance of common stock, net of offering costs

 

 

11,440,000

 

 

 

114

 

 

 

1,139,511

 

 

 

 

 

 

 

 

 

1,139,625

 

Stock-based compensation expense related to equity-classified

   awards

 

 

 

 

 

 

 

 

91,324

 

 

 

 

 

 

 

 

 

91,324

 

Other comprehensive loss, net of tax

 

 

 

 

 

 

 

 

 

 

 

 

(992

)

 

 

 

 

 

(992

)

Net loss

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(490,874

)

 

 

(490,874

)

Balance at December 31, 2017

 

 

99,666,549

 

 

$

997

 

 

$

3,947,552

 

 

$

(34,433

)

 

$

(2,147,685

)

 

$

1,766,431

 

The accompanying notes are an integral part of these consolidated financial statements.

 


105


ALNYLAM PHARMACEUTICALS, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

 

  Year Ended December 31, 

 

Year Ended December 31,

 

  2014 2013 2012 

 

2017

 

 

2016

 

 

2015

 

Cash flows from operating activities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Net loss

  $(360,395 $(89,225 $(106,014

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

Adjustments to reconcile net loss to net cash used in operating activities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Depreciation and amortization

   11,926    10,229    9,035  

 

 

13,367

 

 

 

15,130

 

 

 

19,050

 

Non-cash stock-based compensation

   33,061    20,703    12,360  

Stock-based compensation

 

 

92,819

 

 

 

75,528

 

 

 

45,783

 

Charge for 401(k) company stock match

   692    449    364  

 

 

2,302

 

 

 

1,507

 

 

 

984

 

Equity in loss of joint venture (Regulus Therapeutics Inc.)

           4,522  

Realized gain on sale of marketable securities

   (2,081      (255

Gain on issuance of stock by joint venture

           (16,084

Benefit from intraperiod tax allocation

   (40,209  (2,695  (10,572

In-process research and development

   220,766          

Realized loss (gain) on sale of marketable equity securities

 

 

1,894

 

 

 

(6,977

)

 

 

 

Other

 

 

608

 

 

 

 

 

 

 

Changes in operating assets and liabilities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Proceeds from landlord tenant improvements

   1,941    204    1,780  

 

 

 

 

 

2,145

 

 

 

374

 

Billed and unbilled collaboration receivables

   (35,689  (4,144  1,364  

 

 

(10,668

)

 

 

(15,036

)

 

 

31,639

 

Prepaid expenses and other assets

   (5,829  (1,356  1,780  

 

 

(20,711

)

 

 

(5,276

)

 

 

(6,820

)

Accounts payable

   8,840    1,832    (1,736

 

 

(4,939

)

 

 

10,098

 

 

 

1,676

 

Accrued expenses and other

   9,122    1,547    (3,591

 

 

31,568

 

 

 

10,673

 

 

 

6,343

 

Deferred revenue

   (7,786  (6,201  (8,562

 

 

1,848

 

 

 

14,615

 

 

 

1,904

 

  

 

  

 

  

 

 

Net cash used in operating activities

   (165,641  (68,657  (115,609

 

 

(382,786

)

 

 

(307,701

)

 

 

(189,140

)

  

 

  

 

  

 

 

Cash flows from investing activities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Purchases of property and equipment

   (8,961  (4,006  (8,348

Increase in restricted cash

           (162

Purchases of property, plant and equipment

 

 

(104,209

)

 

 

(64,557

)

 

 

(12,950

)

Purchases of restricted investments and increase in restricted cash

 

 

 

 

 

(150,000

)

 

 

(1,471

)

Purchases of marketable securities

   (977,775  (364,305  (277,129

 

 

(903,457

)

 

 

(759,310

)

 

 

(1,033,843

)

Sales and maturities of marketable securities

   462,922    237,806    289,013  

 

 

597,305

 

 

 

1,116,458

 

 

 

726,943

 

Payment for asset acquisition

   (25,000        
  

 

  

 

  

 

 

Sale of restricted investments

 

 

120,000

 

 

 

 

 

 

 

Net cash (used in) provided by investing activities

   (548,814  (130,505  3,374  

 

 

(290,361

)

 

 

142,591

 

 

 

(321,321

)

  

 

  

 

  

 

 

Cash flows from financing activities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Proceeds from exercise of stock options and other types of equity

   29,420    28,743    6,971  

 

 

84,142

 

 

 

14,127

 

 

 

31,137

 

Proceeds from issuance of common stock, net of offering costs

       173,572    86,800  

 

 

1,139,625

 

 

 

 

 

 

496,400

 

Proceeds from issuance of common stock to Genzyme

   723,037          

Proceeds from issuance of common stock to Sanofi Genzyme

 

 

21,381

 

 

 

14,301

 

 

 

89,018

 

Proceeds from issuance of long-term debt

 

 

 

 

 

150,000

 

 

 

 

Repayment of long-term debt

 

 

(120,000

)

 

 

 

 

 

 

Payments for repurchase of common stock for employee tax withholding

   (15,992  (1,389  (359

 

 

(257

)

 

 

(596

)

 

 

(378

)

  

 

  

 

  

 

 

Net cash provided by financing activities

   736,465    200,926    93,412  

 

 

1,124,891

 

 

 

177,832

 

 

 

616,177

 

  

 

  

 

  

 

 

Net increase (decrease) in cash and cash equivalents

   22,010    1,764    (18,823

Net increase in cash and cash equivalents

 

 

451,744

 

 

 

12,722

 

 

 

105,716

 

Cash and cash equivalents, beginning of period

   53,169    51,405    70,228  

 

 

193,617

 

 

 

180,895

 

 

 

75,179

 

  

 

  

 

  

 

 

Cash and cash equivalents, end of period

  $75,179   $53,169   $51,405  

 

$

645,361

 

 

$

193,617

 

 

$

180,895

 

  

 

  

 

  

 

 

Supplemental disclosure of cash flows:

    

 

 

 

 

 

 

 

 

 

 

 

 

Net cash proceeds from income tax refunds (cash paid for income taxes)

  $517   $(11 $(17

Cash paid for interest

 

$

2,430

 

 

$

1,096

 

 

$

 

Cash paid for income taxes

 

$

114

 

 

$

111

 

 

$

66

 

Supplemental disclosure of noncash investing and financing activities:

    

 

 

 

 

 

 

 

 

 

 

 

 

Fixed asset expenditures included in accounts payable and accrued expenses

  $1,526   $161   $1,441  

 

$

8,176

 

 

$

33,153

 

 

$

1,333

 

Fair value of common stock issued for asset acquisition

  $195,766   $   $  

Fair value of common stock received for collaboration agreement in other

assets

 

$

2,700

 

 

$

 

 

$

 

Receipt of common stock for exercises of stock options

  $1,219   $   $  

 

$

653

 

 

$

1,260

 

 

$

686

 

Difference in fair value of common stock issued to Genzyme less cash proceeds received

  $51,450   $   $  

Repurchase of common stock for employee tax withholding in accrued expenses

  $   $600   $  

 

$

450

 

 

$

 

 

$

 

The accompanying notes are an integral part of these consolidated financial statements.

 


106


ALNYLAM PHARMACEUTICALS, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

 

1.

NATURE OF BUSINESS

We commenced operations on June 14, 2002 as a biopharmaceutical company seeking to develop and commercialize novel therapeutics based on RNA interference, or RNAi. We are focused on discovering, developing and commercializing RNAi therapeutics by establishing strategic alliances with leading pharmaceutical and life sciences companies, establishing and maintaining a strong intellectual property position in the RNAi field, generating revenues through licensing agreements, and ultimately developing and commercializing RNAi therapeutics for our own account.globally. We have devoted substantially all of our efforts to business planning, research, development and development,early commercial efforts, acquiring, filing and expanding intellectual property rights, recruiting management and technical staff, and raising capital. In late 2017, we filed a new drug application, or NDA, and a marketing authorisation application, or MAA, seeking regulatory approval of our first product in the United States and Europe, respectively. If one or both of such applications is approved, we expect to begin commercializing and generating product revenues in 2018.

We are subject to risks common to companies in our industry including, but not limited to, uncertainties relating to conducting clinical research and development, the manufacture and supply of products for clinical and commercial use, obtaining and maintaining regulatory approvals and pricing and reimbursement for our products, market acceptance, managing global growth and operating expenses, availability of additional capital, competition, obtaining and enforcing patents, stock price volatility, dependence on collaborative relationships and third-party service providers, dependence on key personnel, potential litigation, product liability claims and government investigations.

 

2.

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation and Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of Alnylam and our wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America, or GAAP, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Concentrations of Credit Risk and Significant Customers

Financial instruments that potentially expose us to concentrations of credit risk consist primarily of cash, cash equivalents and fixed income marketable securities. At December 31, 20142017 and 2013,2016, substantially all of our cash, cash equivalents and fixed income marketable securities were invested in money market mutual funds, certificates of deposit, commercial paper, corporate notes, municipal debt securities, U.S. government-sponsored enterprise securities and U.S. treasury securities through highly rated financial institutions. Corporate notes may also include foreign bonds denominated in U.S. dollars. Investments are restricted, in accordance with our investment policy, to a concentration limit per issuer.

In recent periods, our revenues from collaborations have been generated primarily from primarily F. Hoffmann-La Roche Ltd and certainSanofi Genzyme, the specialty care global business unit of its affiliates, collectively, Roche, which assigned its rights and obligations to Arrowhead Research Corporation,Sanofi, The Medicines Company, or Arrowhead, in 2011,MDCO, Takeda Pharmaceutical Company Limited, or Takeda, Cubist Pharmaceuticals, Inc., or Cubist,and Monsanto Company, or Monsanto, and The Medicines Company, or MDCO.Monsanto. For the year ended December 31, 2014,2017, our billed and unbilled collaboration receivables were composed primarily of amountsa milestone payment due from Genzyme Corporation, aMDCO and expense reimbursement due from Sanofi company, or Genzyme, and MDCO based upon the achievement of certain milestones and, also with respect to MDCO, expense reimbursement.Genzyme. For the year ended December 31, 2013,2016, our billed and unbilled collaboration receivables were composed primarily of an amountexpense reimbursement due from Genzyme based upon the initiation of a Phase 3 clinical trial.Sanofi Genzyme.


107


The following table summarizes customers that represent greater than 10%10 percent of our net revenues from collaborators, for the periods indicated:

 

 

Year Ended December 31,

 

  Year Ended
December 31,
 

 

2017

 

 

2016

 

 

2015

 

  2014 2013 2012 

Sanofi Genzyme

 

 

61

%

 

 

68

%

 

 

27

%

MDCO

 

 

34

%

 

 

24

%

 

 

25

%

Takeda

   43  47  33

 

*

 

 

*

 

 

 

22

%

Monsanto

   30  12  *  

 

*

 

 

*

 

 

 

14

%

MDCO

   21  *    *  

Cubist

   *    21  *  

Roche/Arrowhead

   *    *    56

The following table summarizes customers with amounts due that represent greater than 10%10 percent of our billed and unbilled collaboration receivables balance, at the periods indicated:

 

 

At December 31,

 

  At December 31, 

 

2017

 

 

2016

 

  2014 2013 

Genzyme

   63  94

MDCO

   37  *  

 

 

59

%

 

*

 

Sanofi Genzyme

 

 

39

%

 

 

97

%

 

*

Represents 10%10 percent or less

Fair Value Measurements

The fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices (adjusted), interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability. The fair value hierarchy level is determined by the lowest level of significant input.

Investments in Marketable Securities and Cash Equivalents

We invest our excess cash balances in short-term and long-term marketable debt and equity securities. We classify our investments in marketable debt securities as either held-to-maturity or available-for-sale based on facts and circumstances present at the time we purchased the securities. At each balance sheet date presented, we classified all of our investments in debt and equity securities as available-for-sale. We report available-for-sale investments at fair value at each balance sheet date and include any unrealized holding gains and losses (the adjustment to fair value) in accumulated other comprehensive income (loss), a component of stockholders’ equity. At December 31, 2014,2017, the balance in our accumulated other comprehensive incomeloss was composed solely of activity related to our available-for-sale marketable securities, including our investment in equity securities of Regulus Therapeutics Inc., or Regulus. Realized gains and losses are determined using the specific identification method and are included in other income.income (expense). We recognized $2.1$1.9 million of realized losses and $7.0 million of realized gains from sales of our Regulus available-for-sale securities as other income on(expense) in our consolidated statements of comprehensive loss during the yearyears ended December 31, 2014.2017 and 2016, respectively. If any adjustment to fair value reflects a decline in the value of the investment, we consider all available evidence to evaluate the extent to which the decline is “other than temporary,” including our intention to sell and, if so, mark the investment to market through a charge to our consolidated statements of comprehensive loss. We did not record any impairment charges related to our fixed income marketable securities during the years ended December 31, 2014, 20132017, 2016 or 2012.2015. Our marketable securities are classified as cash equivalents if the original maturity, from the date of purchase, is 90 days or less, and as marketable securities if the original maturity, from the date of purchase, is in excess of 90 days. Our cash equivalents are composed of commercial paper, corporate notes, U.S. government-sponsored enterprise securities, U.S. treasury securities and money market funds.

108


InDuring the fourthsecond quarter of 2012,2017, we began accountingsold all our remaining holdings in Regulus. We accounted for our investment in Regulus as an available-for-sale marketable security. Intraperiod tax allocation rules require us to allocate our provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income. In periods in which we have a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income, we must allocate the tax provision to the other categories of earnings. We then record a related tax benefit in continuing operations. Upon sales of our available-for-sale marketable securities, we apply the aggregate portfolio approach.approach to recognize the related tax provision or benefit into income (loss) from continuing operations. As a result, the disproportionate tax effect remains in accumulated other comprehensive income (loss) as long as we maintain an investment portfolio.


Property, Plant and Equipment

Property, plant and equipment are stated at cost, net of accumulated depreciation. Depreciation expense is recorded on a straight-line basis over the estimated useful life of the asset. Leasehold improvements are amortized over the shorter of the asset’s estimated useful life or the lease term. Construction in progress reflects amounts incurred for construction or improvements of property, plant or equipment that have not been placed in service. The cost and accumulated depreciation of assets retired or sold are removed from the respective asset category, and any gain or loss is recognized in our consolidated statements of comprehensive loss.

The estimated useful lives of property, plant and equipment are as follows:

Asset Category

Useful Life

Laboratory equipment

5 years

Computer equipment and software

3-10 years

Furniture and fixtures

5 years

Leasehold improvements

Shorter of asset life or lease term

Land

Construction in progress

Estimated Liability for Development Costs

We record accrued liabilities related to expenses for which service providers have not yet billed us with respect to products we have received or services that we have incurred, specifically related to ongoing pre-clinical studies and clinical trials. These costs primarily relate to third-party clinical management costs, laboratory and analysis costs, toxicology studies and investigator fees. We have multiple product candidates in concurrent pre-clinical studies and clinical trials at multiple clinical sites throughout the world. In order to ensure that we have adequately provided for ongoing pre-clinical and clinical development costs during the period in which we incur such costs, we maintain an accrual to cover these expenses. We update the estimate for this accrual on at least a quarterly basis. The assessment of these costs is a subjective process that requires judgment. Upon settlement, these costs may differ materially from the amounts accrued in our consolidated financial statements. Our historical accrual estimates have not been materially different from our actual costs.

Revenue Recognition

We have entered into collaboration agreements with leading pharmaceutical and life sciences companies, including Novartis Pharma AG and one of its affiliates, together, Novartis, Roche, Takeda, Kyowa Hakko Kirin Co., Ltd., or Kyowa Hakko Kirin, Cubist, Monsanto, Sanofi Genzyme and MDCO. The terms of our collaboration agreements typically include deliverables such as non-refundable license fees, funding of research and development, payments based upon achievement of clinical and pre-clinical development milestones, regulatory milestones, manufacturing services, sales milestones and royalties on product sales. These agreements are generally referred to as multiple element arrangements.

In January 2011, we adopted new authoritative guidanceWe apply the accounting standard on revenue recognition for multiple element arrangements. The guidance, which applied to multiple element arrangements entered into or materially modified on or after January 1, 2011, amended the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence is not available. Deliverables under the arrangement couldwill be considered separate units of accounting provided that (i) a delivered item has value to the customer on a standalone basis and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The new guidance did not change the criteria for standalone value. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, we have been unable to demonstrate standalone value in our multiple element arrangements. For example, we applied the new rules to collaborations executed with Monsanto and Genzyme during 2012, but we were unable to demonstrate standalone value for the delivered license element. In addition, we have not materially modified any of our multiple element arrangements entered into prior to 2011.

Non-refundable license fees are recognized as revenue upon delivery of the license only if we have a contractual right to receive such payment, the contract price is fixed or determinable, the collection of the resulting receivable is reasonably assured and we have no further performance obligations under the license agreement. Multiple element arrangements, such as license and development arrangements, are analyzed to determine whether the deliverables, which often include a license and performance obligations such as research and steering committee services, can be separated or whether they must be accounted for as a single unit of accounting. We recognize upfront license payments as revenue upon delivery of the license only if the license

109


has standalone value and the fair value of the undelivered performance obligations, typically including research and/or steering committee services, that can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations arewould then be accounted for separately as such obligations are fulfilled.performed. If the license is considered to either not have standalone value, or have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be accounted for as a single unit of accounting and the license payments and payments for performance obligations are recognized as revenue over the estimated period of when the performance obligations are performed and or deferred indefinitely until the undelivered performance obligation can be determined. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, we have been unable to demonstrate standalone value in our multiple element arrangements.

Whenever we determine that an arrangement should be accounted for as a single unit of accounting, we determine the period over which the performance obligations will be performed and revenue will be recognized. Revenue is recognized using either a proportional performance or a straight-line method. We recognize revenue using the proportional performance method when the level of effort required to complete our performance obligations under an arrangement can be reasonably estimated and such performance obligations are provided on a best-efforts basis. Direct labor hours or full-time equivalents are typically used as the measure of performance. The amount of revenue recognized under the proportional performance method is determined by multiplying the total


payments under the contract, excluding royalties and payments contingent upon achievement of milestones, by the ratio of level of effort incurred to date to estimated total level of effort required to complete our performance obligations under the arrangement. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the proportional performance method, as of the period ending date.

If we cannot reasonably estimate the level of effort to complete our performance obligations under an arrangement, we recognize revenue under the arrangement on a straight-line basis over the period we are expected to complete our performance obligations. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method, as of the period ending date.

Significant management judgment is required in determining the level of effort required under an arrangement and the period over which we are expected to complete our performance obligations under an arrangement. Steering committee services that are not inconsequential or perfunctory and that are determined to be performance obligations are combined with other research services or performance obligations required under an arrangement, if any, in determining the level of effort required in an arrangement and the period over which we expect to complete our aggregate performance obligations.

Many of our collaboration agreements entitle us to additional payments upon the achievement of performance-based milestones. These milestones are generally categorized into three types; development milestones which are generally based on the advancement of our pipeline and initiation of clinical trials, regulatory milestones which are generally based on the submission, filing or approval of regulatory applications such as a new drug applicationan NDA in the United States, and commercialization milestones which are generally based on meeting specific thresholds of sales in certain geographic areas. If the achievement of a milestone is considered probable at the inception of the collaboration, the related milestone payment is included with other collaboration consideration, such as upfront fees and research funding, in our revenue model. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in our revenue model until the performance conditions are met. Upfront and ongoing development milestones per our collaboration agreements are not subject to refund if the development activities are not successful.

We perform an assessment to determine whether a substantive milestone exists at the inception of our collaborative arrangements. In evaluating if a milestone is substantive, we consider whether uncertainty exists as to the achievement of the milestone event at the inception of the arrangement, the achievement of the milestone involves substantive effort and can only be achieved based in whole or part on the performance or the occurrence of a specific outcome resulting from our performance, the amount of the milestone payment appears reasonable either in relation to the effort expected to be expended or to the projected enhancement of the value of the

110


delivered items, there is any future performance required to earn the milestone, and the consideration is reasonable relative to all deliverables and payment terms in the arrangement. When a substantive milestone is achieved, the accounting rules permit us to recognize revenue related to the milestone payment in its entirety.

To date, we have not recorded any substantive milestones under our collaborations because we have not identified any milestones that meet the required criteria listed above. We have deferred recognition of payments for achievement of non-substantive milestones and recognized revenue over the estimated period of performance applicable towith each collaborative arrangement. As these milestones are achieved, we will recognize as revenue a portion of the milestone payment, which is equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment, upon achievement of such milestone. We will recognize the remaining portion of the milestone payment over the remaining performance period under the proportional performance method or on a straight-line basis.

For revenue generating arrangements where we, as a vendor, provide consideration to a licensor or collaborator, as a customer, we apply the accounting standard that governs such transactions. This standard addresses the accounting for revenue arrangements where both the vendor and the customer make cash payments to each other for services and/or products. A payment to a customer is presumed to be a reduction of the selling price unless we receive an identifiable benefit for the payment and it can reasonably estimate the fair value of the benefit received. Payments to a customer that are deemed a reduction of selling price are recorded first as a reduction of revenue, to the extent of both cumulative revenue recorded to date and probable future revenues, which include any unamortized deferred revenue balances, under all arrangements with such customer, and then as an expense. Payments that are not deemed to be a reduction of selling price are recorded as an expense.

We evaluate our collaborative agreements for proper classification in our consolidated statements of comprehensive loss based on the nature of the underlying activity. Transactions between collaborators recorded in our consolidated statements of comprehensive loss are recorded on either a gross or net basis, depending on the characteristics of the collaborative relationship. We generally reflect amounts due under our collaborative agreements related to cost-sharing of development activities as revenue.


Amounts received prior to satisfying the above revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets. Although we follow detailed guidelines in measuring revenue, certain judgments affect the application of our revenue policy. For example, in connection with our existing collaboration agreements, we have recorded on our consolidated balance sheet short-term and long-term deferred revenue based on our best estimate of when such revenue will be recognized. Short-term deferred revenue consists of amounts that are expected to be recognized as revenue in the next 12 months. Amounts that we expect will not be recognized within the next 12 months are classified as long-term deferred revenue. However, this estimate is based on our current operating plan and, if our operating plan should change in the future, we may recognize a different amount of deferred revenue over the next 12-month period.

The estimate of deferred revenue also reflects management’s estimate of the periods of our involvement in certain of our collaborations. Our performance obligations under these collaborations consist of participation on steering committees and the performance of other research and development services. In certain instances, the timing of satisfying these obligations can be difficult to estimate. Accordingly, our estimates may change in the future. Such changes to estimates would result in a change in revenue recognition amounts. If these estimates and judgments change over the course of these agreements, it may affect the timing and amount of revenue that we recognize and record in future periods. At December 31, 2014,2017, we had short-term and long-term deferred revenue of $23.9$41.7 million and $43.0$43.1 million, respectively, related to our collaborations. The new accounting standard related to revenue recognition effective as of January 1, 2018, discussed below under the heading “Recent Accounting Pronouncements,” will have a material impact on our consolidated financial statements.

Income Taxes

We use the asset and liability method of accounting for income taxes. Under the asset and liability method, deferred tax assets and liabilities reflect the impact of temporary differences between amounts of assets and liabilities for financial reporting purposes and such amounts as measured under enacted tax laws. A valuation allowance is required to offset any net deferred tax assets if, based upon the available evidence, it is more likely than not that some or all of the deferred tax asset will not be realized.

111


We account for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors that include, but are not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. Our policy is to accrue interest and penalties related to unrecognized tax positions in income tax expense. As of December 31, 2014,2017, we have not recorded significant interest and penalty expense related to uncertain tax positions.

Research and Development CostsExpenses

We expenserecord research and development costsexpenses as incurred. Included in research and development costsexpenses are wages, stock-based compensation expenses, benefits and other operating costs, facilities, supplies, external services, clinical trial and manufacturing costs, and overhead directly related to our research and development operations, as well as costs to acquire technology licenses.

We have entered into several license agreements for rights to utilize certain technologies. The terms of the licenses may provide for upfront payments, annual maintenance payments, milestone payments based upon certain specified events being achieved and royalties on product sales. We charge costs to acquire and maintain licensed technology that has not reached technological feasibility and does not have alternative future use to research and development expense as incurred. During the years ended December 31, 2014, 20132017, 2016 and 2012,2015, we charged to research and development expense costs associated with license fees of $12.1$7.7 million, $8.0$2.4 million and $5.7$3.5 million, respectively.

Accounting for Stock-Based Compensation

We have stock incentive plans and an employee stock purchase plan under which we grant equity instruments. We may also grant inducement stock grants outside of our stock incentive plans. We account for all stock-based awards granted to employees at their fair value and generally recognize compensation expense over the vesting period of the award. Determining the amount of stock-based compensation to be recorded requires us to develop estimates of fair values of stock options as of the grant date. We calculate the grant date fair values of stock options using the Black-Scholes valuation model. Our expected stock price volatility assumption is based on the historical volatility of our publicly traded stock.

For stock-based awards granted to non-employees, we generally recognize compensation expense over the vesting period of the award, which is generally the period during which services are rendered by such non-employees. At the end of each financial reporting period prior to vesting, we re-measure the value of these stock-based awards (as calculated using the Black-Scholes option-pricing model) using the then-current fair value of our common stock. Stock options granted by us to non-employees, other than members of our Board of Directors and Scientific Advisory Board members, generally vest over the service period.

The fair value of restricted stock awards   granted to employees is based upon the quoted closing market price per share on the date of grant, adjustedgrant. Expense for assumed forfeitures. Expensetime-based restricted stock awards is recognized over the vesting period, commencing when we determine that it is probable that the awards will vest.period.


For performance-based stock option and restricted stock awards, we begin to recognize expense is first recorded when we determine that the achievement of such performance conditions is deemed probable. This determination requires significant judgment by management. At the probable date, we record a cumulative expense catch-up, with remaining expense amortized over the remaining service period.

Comprehensive Loss

Comprehensive loss is comprised of net loss and certain changes in stockholders’ equity that are excluded from net loss. We include foreign currency translation adjustments in other comprehensive loss for Alnylam Europe AG, or Alnylam Europe, asif the functional currency is not the United States dollar. We include unrealized gains and losses on certain marketable securities in other comprehensive loss.

112


Net Loss Per Common Share

We compute basic net loss per common share by dividing net loss by the weighted-average number of common shares outstanding. We compute diluted net loss per common share by dividing net loss by the weighted-average number of common shares and dilutive potential common share equivalents then outstanding. Potential common shares consist of shares issuable upon the exercise of stock options (using(the proceeds of which are then assumed to have been used to repurchase outstanding shares using the treasury stock method), and unvested restricted stock awards.. Because the inclusion of potential common shares would be anti-dilutive for all periods presented, diluted net loss per common share is the same as basic net loss per common share.

The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:

 

  At December 31, 

 

At December 31,

 

  2014   2013   2012 

 

2017

 

 

2016

 

 

2015

 

Options to purchase common stock

   8,169     8,713     8,932  

 

 

11,239

 

 

 

12,270

 

 

 

9,960

 

Unvested restricted common stock

   30     500     604  

 

149

 

 

171

 

 

 

19

 

  

 

   

 

   

 

 

 

 

11,388

 

 

 

12,441

 

 

 

9,979

 

   8,199     9,213     9,536  
  

 

   

 

   

 

 

Segment Information

We operate in a single reporting segment, the discovery, development and commercialization of RNAi therapeutics.

Subsequent Events

We did not have any material recognized subsequent events. However, we did have the following nonrecognized subsequent events, which are more fully described in Notes 3 and 8:

In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. See Note 8.

In January 2015, in connection with our public offering, we sold an aggregate of 744,566 shares of our common stock to Genzyme through concurrent private placements at the public offering price of $95.00 per share. See Note 3.

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board, or FASB, issued a new revenue recognition standard which amends revenue recognition principles and provides a single, comprehensive set of criteria for revenue recognition within and across all industries. The new standard provides a five step framework whereby revenue is recognized when control of promised goods or services are transferred to a customer at an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The standard also requires enhanced disclosures pertaining to revenue recognition in both interim and annual periods. For public companies,In August 2015, the FASB deferred the effective date of the new revenue standard is effectivefrom January 1, 2017 to January 1, 2018. In March 2016, the FASB issued amendments to clarify the implementation guidance on principal versus agent considerations. In April 2016, the FASB issued amendments to clarify the guidance on accounting for interimlicenses of intellectual property and annual reporting periods beginning after December 15, 2016. Early adoption is not permitted.identifying performance obligations. In May 2016, the FASB issued amendments related to collectibility, non-cash consideration, the presentation of sales and other similar taxes collected from customers and transition. The standard allows for adoption using a full retrospective method or a modified retrospective method. On January 1, 2018, we adopted this standard using the modified retrospective method. Our implementation approach included performing a detailed review of our collaboration agreements. In addition, we designed internal controls to enable the preparation of financial information and have reached conclusions on key accounting assessments related to the new standard, including our assessment that the impact of accounting for costs incurred to obtain a contract is immaterial. We completed our assessment to quantify the expected impact that the new standard will have on our consolidated financial statements and related disclosures. We expect the adoption of the new standard to result in a cumulative reduction of $68.3 million of deferred revenue with a corresponding adjustment to the opening balance of accumulated deficit to be recorded in the first quarter of 2018. This adjustment is due primarily to the application of the new standard to our collaboration agreements with Sanofi Genzyme, MDCO and Kyowa Hakko Kirin. A substantial portion of the incremental $68.3 million adjustment is the result of the application of the new guidance regarding how entities should measure progress in satisfying performance obligations and the contract’s transaction price. In addition, as a result of the cumulative reduction in deferred revenue, our corresponding deferred tax asset will be reduced by approximately $13.6 million, which will be offset by a corresponding decrease to our valuation allowance. These offsetting adjustments will be recorded to accumulated deficit in the first quarter of 2018. We do not expect an impact to cash from or used in operating, financing or investing on our consolidated statement of cash flows as a result of the adoption of the new standard.  


In January 2016, the FASB issued new guidance on recognition and measurement of financial assets and financial liabilities. The new guidance will impact the accounting for equity investments, financial liabilities under the fair value option, and the presentation and disclosure requirements for financial instruments. All equity investments in unconsolidated entities (other than those accounted for under the equity method of accounting) will generally be measured at fair value with changes in fair value recognized through earnings. There will no longer be an available-for-sale classification (changes in fair value reported in other comprehensive income (loss)) for equity securities with readily determinable fair values. In addition, the FASB clarified the need for a valuation allowance on deferred tax assets resulting from unrealized losses on available-for-sale debt securities. In general, the new guidance will require modified retrospective application to all outstanding instruments, with a cumulative effect adjustment recorded to opening retained earnings. This guidance became effective for us on January 1, 2018. We currently do not expect this guidance to have a significant impact on our consolidated financial statements and related disclosures.

In February 2016, the FASB issued a new leasing standard that requires that all lessees recognize the assets and liabilities that arise from leases on the consolidated balance sheet and disclose qualitative and quantitative information about its leasing arrangements. The new standard will be effective for us on January 1, 2019. Early adoption is permitted. We are currently evaluating the methodtiming of our adoption and the expected impact that thethis standard could have on our consolidated financial statements and related disclosures.

In June 2014,October 2016, the FASB issued guidance that share-based payment awards with performance targets that affect vesting and could be achieved afteran entity should recognize the requisite service period should be accounted for as performance conditions. As a result, performance targets are not reflected in estimatingincome tax consequences of an intra-entity transfer of an asset other than inventory when the award’s grant date fair value. Stock-based compensation expense is recognized overtransfer occurs instead of deferring the requisite service period if the achievement of the

113


performance condition is probable.income tax effects. The standard isnew guidance became effective for interim and annual reporting periods beginning after December 15, 2015. Earlyus on a modified retrospective basis on January 1, 2018. The adoption is permitted. We doof this guidance did not expect the standard will have an impact on our consolidated financial statements and related disclosures sincedisclosures.

In November 2016, the FASB issued guidance that requires restricted cash and restricted cash equivalents be included with cash and cash equivalents when reconciling the total beginning and ending amounts for the periods shown on the consolidated statement of cash flows. The new standard became effective for us on January 1, 2018 using a retrospective transition method for each period presented. For the years ended December 31, 2017 and 2016, our accountingrestricted cash and restricted cash equivalents were not significant. We currently do not expect this guidance to have a significant impact on our consolidated financial statements and related disclosures.

In March 2017, the FASB issued guidance that amends the amortization period for share-based payment awardscertain purchased callable debt securities held at a premium by shortening the amortization period for the premium to the earliest call date.  The new standard will be effective for us on January 1, 2019. Early adoption is permitted. We are currently evaluating the timing of our adoption and the expected impact that this standard could have on our consolidated financial statements and related disclosures.

Subsequent Events  

We did not have any material recognized subsequent events. However, we did have a nonrecognized subsequent event with performance targetsrespect to our collaboration with Sanofi Genzyme, which is consistent with this guidance.more fully described in Note 3.

3.

SIGNIFICANT AGREEMENTS

The following table summarizes our total consolidated net revenues from collaborators, for the periods indicated, in thousands:

 

 

Year Ended December 31,

  Year Ended December 31, 
  2014   2013   2012 

Description

 

2017

 

 

2016

 

 

2015

 

 

Sanofi Genzyme

 

$

54,625

 

 

$

32,015

 

 

$

11,005

 

 

MDCO

 

 

30,217

 

 

 

11,220

 

 

 

10,301

 

 

Takeda

  $21,973    $21,973    $21,973  

 

 

 

 

 

 

 

 

8,867

 

 

Monsanto

   14,985     5,640     1,954  

 

 

2,500

 

 

 

 

 

 

5,621

 

 

MDCO

   10,753     4,604       

Roche/Arrowhead

   1,000          37,318  

Cubist

        9,721     2,777  

Other

   1,850     5,229     2,703  

 

 

2,570

 

 

 

3,924

 

 

 

5,303

 

 

  

 

   

 

   

 

 

Total net revenues from collaborators

  $50,561    $47,167    $66,725  

 

$

89,912

 

 

$

47,159

 

 

$

41,097

 

 

  

 

   

 

   

 

 


The following table provides the research and development expenses incurred by type that are directly attributable to each significant agreement for the periods indicated, in thousands:

 

 

Year Ended December 31,

 

 

 

2017

 

 

2016

 

 

2015

 

 

 

Sanofi Genzyme

 

 

MDCO

 

 

Ionis

 

 

Sanofi Genzyme

 

 

MDCO

 

 

Ionis

 

 

Sanofi Genzyme

 

 

MDCO

 

 

Ionis

 

Research and development

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Clinical trial and manufacturing

 

$

174,901

 

 

$

5,421

 

 

$

 

 

$

150,179

 

 

$

1,211

 

 

$

 

 

$

108,903

 

 

$

3,308

 

 

$

 

External services

 

 

4,475

 

 

 

 

 

 

3,250

 

 

 

7,366

 

 

 

 

 

 

 

 

 

3,151

 

 

 

770

 

 

 

 

Other

 

 

5,327

 

 

 

106

 

 

 

 

 

 

3,035

 

 

 

64

 

 

 

525

 

 

 

3,714

 

 

 

497

 

 

 

3,300

 

Total research and

   development expenses

 

$

184,703

 

 

$

5,527

 

 

$

3,250

 

 

$

160,580

 

 

$

1,275

 

 

$

525

 

 

$

115,768

 

 

$

4,575

 

 

$

3,300

 

The research and development expenses incurred for each significant agreement consist of costs incurred for external development and manufacturing services for which we are reimbursed and licensing payments made to the counterparty to such agreement. In addition, these expenses include a reasonable estimate of compensation and related costs as billed to our counterparties. There were no material research and development expenses incurred for Monsanto or Takeda during the years ended December 31, 2017, 2016 and 2015. For the years ended December 31, 2017, 2016 and 2015, we did not incur material general and administrative expenses related to our significant agreements.

Product Alliances

Sanofi Genzyme Collaboration

In January 2014, we entered into a global, strategic collaboration with Sanofi Genzyme to discover, develop and commercialize RNAi therapeutics as Genetic Medicines to treat orphan diseases.diseases, referred to as the 2014 Sanofi Genzyme collaboration. The 2014 Sanofi Genzyme collaboration superseded and replaced the previous collaboration between us and Sanofi Genzyme entered into in October 2012 to develop and commercialize RNAi therapeutics targeting transthyretin, or TTR, for the treatment of TTR-mediatedhereditary ATTR amyloidosis, or ATTR, including patisiran and revusiran, in Japan and the Asia-Pacific region.

On January 6, 2018, we and Sanofi Genzyme entered into an amendment to our 2014 Sanofi Genzyme collaboration. In connection and simultaneously with entering into the amendment to the 2014 Sanofi Genzyme collaboration, we and Sanofi Genzyme also entered into an Exclusive License Agreement with respect to all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, referred to as the Exclusive TTR License, and the ALN-AT3 Global License Terms with respect to fitusiran and any back-up products, referred to as the AT3 License Terms. As a result, we will have the exclusive right to pursue the further global development and commercialization of all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, and Sanofi Genzyme will have the exclusive right to pursue the further global development and commercialization of fitusiran and any back-up products.

The January 2018 transaction is subject to customary closing conditions and clearances, including clearance under the Hart-Scott-Rodino Antitrust Improvements Act.  We expect the transaction to close during the first quarter of 2018.

2012 Sanofi Genzyme Agreement

Under the 2012 Sanofi Genzyme agreement, Sanofi Genzyme paid us an upfront cash payment of $22.5 million. We were also entitled to receive certain milestone payments under the 2012 Sanofi Genzyme agreement. In the fourth quarter of 2013, we earned a milestone of $7.0$11.0 million based upon the completion of a successfulin patisiran Phase 2 clinical trial and a milestone of $4.0 million based upon the initiation of the Phase 3 clinical trial for patisiran.

Underdevelopment milestones under the 2012 Sanofi Genzyme agreement, the parties agreed to collaborate in the development and commercialization of licensed products, with Genzyme assuming primary responsibility in the Genzyme territory, which included Japan and the Asia-Pacific region, and us retaining primary responsibility in the rest of the world.agreement.

We determined that the deliverables under the 2012 Sanofi Genzyme agreement included the license, a joint steering committee and any additional TTR-specific RNAi therapeutic compounds that comprised the ALN-TTR program. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered joint steering committee and any additional TTR-specific RNAi therapeutic compounds did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Sanofi Genzyme had the ability to grant sublicenses, it could not sublicense all or substantially all of its rights under the 2012 Sanofi Genzyme agreement. The uniqueness of our services and the limited sublicense right were indicators that standalone value was not present in the arrangement. Therefore the deliverables were not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. We were unable to reasonably estimate the period of performance under the 2012 Sanofi Genzyme agreement, as we were unable to estimate the timeline


of our deliverables related to the deliverable for any

114


additional TTR-specific RNAi therapeutic compounds. Through December 31, 2013, we had deferred all revenue, or $33.5 million, under the 2012 Sanofi Genzyme agreement.

2014 Sanofi Genzyme Collaboration, as amended in January 2018

In January 2014, we entered into the 2014 Sanofi Genzyme collaboration. As noted above, the 2014 Sanofi Genzyme collaboration superseded and replaced the 2012 Sanofi Genzyme agreement.agreement and was amended in January 2018, at which time we also entered into the Exclusive TTR License and the AT3 License Terms.

The 2014 Sanofi Genzyme collaboration is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of Genetic Medicines, which includes our current and future Genetic Medicine programs that reach Human Proof-of-Principle Study Completion (as defined in the Sanofi Genzyme master agreement), or Human POP, by the end of 2019, subject to extension to the end of 2021 in various circumstances. We will retain product rights in North Americathe United States, Canada and Western Europe, referred to as the Alnylam Territory, while Sanofi Genzyme will obtain exclusive rights to develop and commercialize collaboration products in the rest of the world, referred to as the Sanofi Genzyme Territory, together with certain broader co-development/co-promote or worldwide rights for certain products.one product. Sanofi Genzyme’s rights under the 2014 Sanofi Genzyme collaboration, described in detail below, are structured as an opt-in that is triggered upon achievement of Human POP. We maintain development control for all programs prior to Sanofi Genzyme’s opt-in and maintain development and commercialization control after Sanofi Genzyme’s opt-in for all programs in the Alnylam Territory.

Specifically, in addition to its regional rights for our current and future Genetic Medicine programs in the Genzyme Territory, Genzyme has the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other rare bleeding disorders in the Alnylam Territory, with us maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme may exercise this selection right upon the completion of Human POP for both the ALN-AT3 andALN-AS1 programs. Finally, Genzyme has the right for a global license to a single, future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. We will retain global rights to any RNAi therapeutic Genetic Medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions. We retain full rights to all current and future RNAi therapeutic programs outside of the field of Genetic Medicines, including the right to form new collaborations.

Under the 2014 Sanofi Genzyme collaboration, Sanofi Genzyme’s specific license rights and the programs which Sanofi Genzyme opted into prior to the 2018 amendment include the following:

Regional license terms and programs — Upon opt-in, we will retain product rights in the Alnylam Territory, while Sanofi Genzyme will obtain exclusive rights to develop and commercialize the product in the Sanofi Genzyme Territory. Sanofi Genzyme can elect this license for any of our current and future Genetic Medicine programs that complete Human POP by the end of 2019, subject to limited extension. Development costs for products once Sanofi Genzyme exercises an option will be shared between Sanofi Genzyme and us, with Sanofi Genzyme responsible for twenty percent of the global development costs. Upon the effective date of the 2014 Genzyme collaboration, Genzyme expanded the scope of its regional license and collaboration for patisiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial, which was originally established under the 2012 Genzyme agreement. Genzyme will be required to make payments totaling up to $50.0 million upon the achievement of certain patisiran development milestones. In addition,Sanofi Genzyme will be required to make payments totaling up to $75.0 million per regional product, other than patisiran, includingconsisting of up to $55.0 million in development milestones and $20.0 million in commercial milestones. We could potentially earn the next patisiran milestone payment, ranging between $5.0 million and $20.0 million based on the geographic region, upon the achievement of specified events in connection with a regulatory filing or approval.Sanofi Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each regional product based on annual net sales, if any, of such regional product by Sanofi Genzyme, its affiliates and sublicensees.

Co-development/co-promote Upon the effective date of the 2014 Sanofi Genzyme collaboration, Sanofi Genzyme expanded the scope of its regional license terms — Upon opt-in, we will retain product rightsand collaboration for patisiran, which was originally established under the 2012 Sanofi Genzyme agreement. In September 2015, Sanofi Genzyme elected to opt into our fitusiran clinical development program for the treatment of hemophilia and other rare bleeding disorders under the regional license terms. Cost-sharing for the fitusiran program began in January 2016 under the regional license terms. Sanofi Genzyme also had the right to elect to co-develop and co-commercialize fitusiran in the Alnylam Territory whilepursuant to the co-development/co-commercialize license terms described below. In November 2016, Sanofi Genzyme will obtain exclusive rightsexercised this right and elected to developco-develop and commercialize the product in the Genzyme Territory, and will co-promote the productco-commercialize fitusiran in the Alnylam Territory. UponIn addition, during 2016, Sanofi Genzyme elected not to opt into the effective datedevelopment and commercialization of givosiran or cemdisiran in the Sanofi Genzyme Territory.

 

115Sanofi Genzyme’s rights with respect to patisiran and fitusiran will be modified in connection with the 2018 amendment, the Exclusive TTR License and the AT3 License Terms, as described below. Sanofi Genzyme continues to have the right to opt into our future rare genetic disease programs for development and commercialization in the Sanofi Genzyme Territory under the regional license terms.


Co-development/co-commercialize license terms and programs — Upon opt-in, we retained product rights in the Alnylam Territory, while Sanofi Genzyme obtained exclusive rights to develop and commercialize the product in the Sanofi Genzyme Territory, and to co-commercialize the product in the Alnylam Territory. Upon the effective date of the 2014 Sanofi Genzyme collaboration, Sanofi Genzyme expanded its regional rights for revusiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial, which were originally granted under the 2012 Sanofi Genzyme agreement, to include a co-development/co-promoteco-commercialize license and collaboration. In October 2016, we decided to discontinue development of revusiran. In our TTR program, we are also developing ALN-TTRsc02.  Sanofi Genzyme also has thehad a right to elect a co-development/co-promoteco-commercialize license and collaboration for ALN-AT3, if it does notALN-TTRsc02. As noted above, in November 2016, Sanofi Genzyme exercised its right to elect a globalco-development/co-commercialize license and collaboration for ALN-AS1.fitusiran. Development costs for co-development/co-promoteco-commercialize products, once Sanofi Genzyme exercisesexercised an option, will bewere shared between Sanofi Genzyme and us, with Sanofi Genzyme responsible for fifty percent of the global development costs. In connection with the exercise of its co-development/co-commercialize rights for fitusiran, Sanofi


Genzyme will bepaid us approximately $6.0 million in January 2017 for its incremental share of co-development costs incurred from January 2016 through September 2016. Sanofi Genzyme was required to make certain milestone payments  totaling upfor fitusiran, and, prior to $75.0 million in development milestonesthe discontinuation of the revusiran program, was required to make certain milestone payments for each of revusiran and ALN-AT3, if selected.revusiran. In December 2014, we earned a development milestone payment of $25.0 million based upon the initiation of the first global Phase 3 clinical trial for revusiran.  We could potentially earn the next revusiranSanofi Genzyme was also obligated to pay us a milestone payment, ranging between $5.0 million andof $25.0 million based on the geographic region, upon the achievementdosing of specified eventsthe first patient in connection with regulatory approval.our ATLAS Phase 3 program for fitusiran. In addition, Sanofi Genzyme will also bewas required to pay tiered double-digit royalties up to twenty percent for each co-development/co-promoteco-commercialize product based on annual net sales, if any, in the Sanofi Genzyme Territory for such co-development/co-promoteco-commercialize product by Sanofi Genzyme, its affiliates and sublicensees. The parties willwere to share profits equally and we expectexpected to book product sales in the Alnylam Territory.

In connection with the 2018 amendment, the Exclusive TTR License and the AT3 License Terms, as described below, we and Sanofi Genzyme agreed to terminate the co-development and co-commercialization rights related to revusiran, ALN-TTRsc02 and fitusiran under the 2014 Sanofi Genzyme collaboration. No future rights will be granted to Sanofi Genzyme for co-development and co-commercialization under the 2014 Sanofi Genzyme collaboration, as amended by the 2018 amendment.

Global license terms and programs Global license terms – Upon opt-in,Sanofi Genzyme will obtain a worldwide licensecontinues to develop and commercialize the product. Genzyme can elect a global license for ALN-AS1, if it does not elect a co-development/co-promote license for ALN-AT3. Genzyme will also have one right to a global license through 2019, subject to limited extension, for a future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Sanofi Genzyme collaboration. Sanofi Genzyme could elect its global license for lumasiran.  Upon opt-in, Sanofi Genzyme will obtain a worldwide license to develop and commercialize the product. Sanofi Genzyme shall be responsible for one hundred percent of global development costs.costs for a global license product. Sanofi Genzyme will be required to make payments totaling up to $200.0 million perfor such global product, including up to $60.0$100.0 million in development milestones and $140.0$100.0 million in commercial milestones. Sanofi Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for eachsuch global product based on annual net sales, if any, of eachsuch global product by Sanofi Genzyme, its affiliates and sublicensees.

Exclusive TTR License and AT3 License Terms

As noted above, the 2018 amendment, together with the Exclusive TTR License and the AT3 License Terms, revise the terms and conditions of the 2014 Sanofi Genzyme collaboration to (i) provide us the exclusive right to pursue the further global development and commercialization of all TTR products, including patisiran, ALN-TTRsc02 and any back-up products, (ii) provide Sanofi Genzyme the exclusive right to pursue the further global development and commercialization of fitusiran and any back-up products and (iii) terminate the previous co-development and co-commercialization rights related to revusiran, ALN-TTRsc02 and fitusiran under the 2014 Sanofi Genzyme collaboration. Going forward, we will fund all development and commercialization costs for patisiran and ALN-TTRsc02.  We also will fund development and commercialization costs for fitusiran through the transition period, up to a cap of $50.0 million, after which Sanofi Genzyme will fund all development and commercialization costs for fitusiran.  We expect to substantially complete the transition of the fitusiran program to Sanofi Genzyme by mid-2018. Each party will be responsible for its costs associated with the transfer of the respective program to the other party.

Under the 2018 amendment and the Exclusive TTR License, Sanofi Genzyme will be eligible to receive (i) royalties up to twenty-five percent, increasing over time, based on annual net sales of patisiran in territories excluding the United States, Canada and Western Europe, provided royalties on annual net sales of patisiran in Japan will be twenty-five percent beginning as of the effective date of the Exclusive TTR License, (ii) tiered royalties of fifteen to thirty percent based on global annual net sales of ALN-TTRsc02 (consistent with the royalties due to us from Sanofi Genzyme on fitusiran), and (iii) tiered royalties of up to fifteen percent based on global annual net sales of any back-up products, in each case by us, our affiliates and our sublicensees.  Except as described below, there will be no additional milestones due to either party with respect to patisiran, ALN-TTRsc02 or fitusiran.

In consideration for the rights granted to Sanofi Genzyme under the 2018 amendment and the AT3 License Terms, Sanofi Genzyme is required to make one milestone payment of $50.0 million following the dosing of the first patient in the ATLAS Phase 3 program for fitusiran.  In addition, we will be eligible to receive tiered royalties of fifteen to thirty percent based on global annual net sales of fitusiran and up to fifteen percent based on global annual net sales of any back-up products, in each case by Sanofi Genzyme, its affiliates and its sublicensees. We and Sanofi Genzyme intend to enter into a supply agreement to provide for the supply of fitusiran to Sanofi Genzyme for ongoing clinical studies, and, at Sanofi Genzyme’s request, commercial sales. Sanofi Genzyme also has the right to manufacture fitusiran.

Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Sanofi Genzyme under the 2014 Sanofi Genzyme collaboration.

Undercollaboration, as amended, or the master agreement, the parties will collaborate in the development of option products, with us leading development for all programs prior to Genzyme’s opt-in and also leading development and commercialization for all programs in the Alnylam Territory after Genzyme’s opt-in. If Genzyme does not exercise its option to license rights to a particular program, we will retain the exclusive right to develop and commercialize such program throughout the world, including the right to sublicense to third parties.AT3 License Terms.


The 2014 Sanofi Genzyme collaboration, isas amended, will continue to be governed by an alliance joint steering committee that is comprised of an equal number of representatives from each party. There will also beare additional committees to manage various aspects of each regional co-developed/co-promoted and global program. Weprogram and Genzyme intend to enter into supply agreements to provide for supply of collaboration products to Genzyme for clinical studies,oversee certain matters, including transition planning, that may arise under the Exclusive TTR License and at Genzyme’s request, commercial sales. Genzyme also has certain rights to manufacture collaboration products. Additionally, Genzyme has certain limited opt-out rights, as specified in the master agreement, upon which products revert fully back to us with no further obligations to Genzyme.AT3 License Terms.

The original master agreement (including the license terms appended thereto) contains, as well as the Exclusive TTR License and the AT3 License Terms, contain certain termination provisions, including for material breach by the other party. In addition, we have the right to terminate Exclusive TTR License without cause with respect to any or all licensed products at any time upon six months’ prior written notice and Sanofi Genzyme has the right to terminate the AT3 License Terms without cause with respect to any particular licensed product at any time upon six months’ prior written notice.

Unless terminated earlier pursuant to its terms, the master agreement will terminate upon the last to expire of any of the option periods under the master agreement or the license terms appended thereto. The term of the Exclusive TTR License expires on a licensed product-by-licensed product and country-by-country basis upon expiration of the last royalty term to expire under the agreement, where a royalty term is defined as the latest to occur of (a) expiration of the last valid claim of patent rights covering a licensed product; (b) the expiration of Regulatory Exclusivity for a licensed product, as defined in the Exclusive TTR License; or (c) the twelfth anniversary of the first commercial sale of the licensed product in such country. The term of the AT3 License Terms expires on a licensed product-by-licensed product and country-by-country basis upon expiration of the last royalty term to expire under the agreement, where a royalty term is defined as the latest to occur of (x) the expiration of the last valid claim of patent rights covering a licensed product; (y) the expiration of Regulatory Exclusivity for a licensed product, as defined in the AT3 License Terms; or (z) the twelfth anniversary of the first commercial sale of the licensed product in such country.

Upon the closing of the equity transaction in February 2014, we sold to Sanofi Genzyme 8,766,338 shares of our common stock and Sanofi Genzyme paid $700.0 million in aggregate cash consideration to us. As a condition to the closing of the equity transaction, Sanofi Genzyme entered into an investor agreement with us. Under the investor agreement, until the earlier of the fifth anniversary of the expiration or earlier termination of the 2014 Sanofi Genzyme

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collaboration and the date on which Sanofi Genzyme and its affiliates cease to beneficially own at least 5%5 percent of our outstanding common stock, Sanofi Genzyme and its affiliates are bound by certain “standstill” provisions. The standstill provisions include agreements not to acquire more than 30%30 percent of our outstanding common stock, call stockholder meetings, nominate directors other than those approved by our board of directors, subject to certain limited exceptions, or propose or support a proposal to acquire us. Further, Sanofi Genzyme has agreed to vote, and cause its affiliates to vote, all shares of our voting securities they are entitled to vote, up to a maximum of 20%20 percent of our outstanding common stock, in a manner either as recommended by our board of directors or proportionally with the votes cast by our other stockholders, except with respect to certain change of control transactions or our liquidation or dissolution. Until Sanofi Genzyme owns less than 7.5%7.5 percent of our outstanding common stock, subject to Sanofi Genzyme’s limited right to maintain its ownership percentage as described below, if we issue common stock or securities convertible into or exercisable for common stock to a third party that holds at least 30%30 percent of our outstanding common stock or, in connection with a collaboration or license transaction, to a third party that will initially hold at least the percentage of our outstanding common stock represented by the shares purchased by Sanofi Genzyme at the closing of the equity transaction, we will offer Sanofi Genzyme an opportunity to amend the standstill and voting provisions in the investor agreement to be consistent with the terms provided to such third party.

Under the investor agreement, Sanofi Genzyme has also agreed not to dispose of any shares of common stock beneficially owned by it immediately after the closing of the stock purchase until the earlier of (i) December 31, 2019 (subject to extension by up to two years if Sanofi Genzyme’s option to select additional compounds under the master agreement is extended beyond December 31, 2019) and (ii) six months after the expiration or earlier valid termination of the collaboration, in each case subject to earlier termination in the event certain clinical activities under the collaboration fail to occur. Following the expiration of this lock-up period, Sanofi Genzyme will be permitted to sell such shares of common stock subject to certain limitations, including volume and manner of sale restrictions. Notwithstanding the foregoing, following the two-year anniversary of the closing of the stock purchase, in the event that the market price per share of our common stock is at least 100%100 percent higher than the market price per share of our common stock at closing of the stock purchase (in each case based upon a ten-day trailing average), Sanofi Genzyme may sell up to 25%25 percent of its initial shares, subject to certain restrictions on post-lock-up period dispositions as described above.

Under the investor agreement, following the lock-up period, Sanofi Genzyme will have three demand rights to require us to conduct a registered underwritten public offering with respect to the shares of common stock beneficially owned by Sanofi Genzyme immediately after the closing of the stock purchase.purchase, subject to certain conditions. In addition, following the lock-up period, subject to certain conditions, Sanofi Genzyme will be entitled to participate in registered underwritten public offerings by us if other selling stockholders are included in the registration.


The investor agreement provides that, until Sanofi Genzyme owns less than 7.5%7.5 percent of our outstanding common stock, subject to Sanofi Genzyme’s limited right to maintain its ownership percentage as described herein, in connection with new issuances of common stock, subject to certain exceptions, Sanofi Genzyme will be entitled to a right of first offer to participate proportionally to maintain its then-current ownership percentage of our common stock. If Sanofi Genzyme is not entitled to a right of first offer with respect to a new issuance, Sanofi Genzyme will have the opportunity, on a post-transaction basis, to purchase additional shares sufficient to maintain its pre-transaction ownership percentage of our common stock (subject to the same 7.5%7.5 percent ownership threshold).

Finally, in the event Sanofi Genzyme and its affiliates acquire at least 20%20 percent or more of our outstanding common stock, Sanofi Genzyme will be entitled to appoint one individual to our board of directors. Sanofi Genzyme will also be entitled to certain information rights, including with respect to financial information in the event Sanofi Genzyme or its affiliates require such information for its own financial reporting purposes. The rights and restrictions under the investor agreement are subject to termination upon the occurrence of certain events.

We recorded the issuance of 8,766,338 shares of our common stock under the stock purchase agreement using the price of our common stock on the date the shares were issued to Sanofi Genzyme. Based on the common stock price of $85.72, the fair value of the shares issued was $751.5 million, which was $51.5 million in excess of the proceeds received from Sanofi Genzyme for the issuance of our common stock. This $51.5 million is being amortized on a straight-line basis over the performance period which is currently approximately six years as described

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below.for the ALN-TTR programs. In addition, due to intraperiod tax allocation rules, upon closing of the equity transaction we recorded a benefit from income taxes of $15.2 million due to the Sanofi Genzyme equity purchase being recorded in additional paid-in capital, net of tax. For the year ended December 31, 2014, we recorded a cumulative benefit from income taxes of $20.7 million.

In accordance with the investor agreement, as a result of our issuance of shares in connection with our acquisition of Sirna Therapeutics, Inc., or Sirna, in March 2014, Sanofi Genzyme exercised its right to purchase an additional 344,448 shares of our common stock for approximately $23.0 million. In addition, in January 2015, in connection with our public offering,offerings, Sanofi Genzyme exercised its right to purchase directly from us, in concurrent private placements, 744,566 shares of common stock in January 2015 at the public offering price resulting in approximately $70.7 million in proceeds to us and 297,501 shares of common stock in May 2017 at the public offering price resulting in $21.4 million in proceeds to us. Sanofi Genzyme elected not to purchase shares in connection with our November 2017 offering. The sales of common stock to Sanofi Genzyme were not registered as part of thethese public offering,offerings, though they were consummated simultaneously with thesuch public offering.offerings.

In addition, as part of these rights under our investor agreement withSanofi Genzyme Genzymealso has the right at the beginning of each Januaryyear to purchase a number of shares of our common stock based on the number of shares we issued during the previous year for compensatorycompensation-related purposes. Sanofi Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock on January 22, 2015 for approximately $18.3 million and 205,030 shares of our common stock on February 1, 2016 for $14.3 million. Sanofi Genzyme elected not to exercise its compensation-related right for 2016 or 2017. The salesales of these shares to Sanofi Genzyme waswere consummated as a private placement. In each instance, the purchase byplacements.

Sanofi Genzyme described above allowed Genzyme to maintain its ownership levelcurrently holds approximately 11 percent of our outstanding common stock of approximately 12%.stock.

We determined that the deliverables for the programs on which Sanofi Genzyme is currentlywas collaborating with us on includeupon initiation of the 2014 Sanofi Genzyme collaboration included the licenses to our patisiran and revusiran clinical programs, which licenses were delivered to Sanofi Genzyme upon the closing date of the transaction, and the associated development activities, joint steering committee participation and information exchange for these clinical programs. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and associated undelivered development activities, joint steering committee participation and information exchange activities did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Sanofi Genzyme has the ability to grant sublicenses, it cannot sublicense all or substantially all of its rights under the 2014 Sanofi Genzyme collaboration. The uniqueness of our services and the limited sublicense rights are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition model on the final deliverable. Under the 2014 Sanofi Genzyme collaboration, the last deliverables for patisiran and revusiran arewere expected to be completed within approximately six years from the closing date of the transaction and the last deliverables for fitusiran were expected to be completed within approximately five years from the date Sanofi Genzyme elected to opt into our fitusiran program under the regional license terms. Our estimate regarding the performance period under the 2014 Sanofi Genzyme collaboration related to the license to our patisiran and revusiran clinical programs was adjusted in October 2016 due to our decision to discontinue development of revusiran. As a result, with respect to these programs, we currently expect the last deliverables to be completed within approximately five years from the closing date of the transaction as compared to an initial expectation of  approximately six years. Our estimate regarding the performance period under the 2014 Sanofi Genzyme collaboration related to the license to our fitusiran program was adjusted in September 2017 due to our temporary suspension of dosing in all ongoing fitusiran studies. As a result, with respect to the fitusiran program, we currently expect the last deliverables to be completed within approximately six years from the date Sanofi Genzyme


elected to opt into the program under the regional license terms as compared to an initial expectation of approximately five years. Beginning in September 2017, we are prospectively recognizing the remaining deferred revenue as of August 31, 2017 related to the license to our fitusiran program over this adjusted performance period.

We determined that the total cash received from Sanofi Genzyme under the now superseded 2012 Sanofi Genzyme agreement reflects consideration for certain of the performance obligations for ALN-TTR programs included in the 2014 Sanofi Genzyme collaboration. Therefore we are recognizing the $33.5 million of deferred revenue under the 2012 Sanofi Genzyme agreement on a straight-line basis over the period of performance of the ALN-TTR programs, which, as noted above,programs. As consideration is currently approximately six years. In addition, during the fourth quarter of 2014, we recognized as revenue a portion of the $25.0 million milestone payment earned in December 2014 equal to the percentage of the performance period completed when the milestone was earned. As future consideration,achieved, including any milestones or reimbursement for development activities, are achieved, we will recognize as revenue a portion of these payments equal to the percentage of the performance period completed when the milestone or activities have been satisfied, multiplied by the amount of the payment. We will recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014, deferred revenue under

The following table presents information related to the 2014 Sanofi Genzyme collaboration, was $6.7 million.in thousands:

Excess of fair value of our common stock issued to Sanofi Genzyme in February 2014

 

$

(51,450

)

Deferred revenue remaining under the 2012 Sanofi Genzyme agreement upon execution of the

   2014 Sanofi Genzyme collaboration

 

 

33,500

 

Milestone payment received:

 

 

 

 

Year-ended December 31, 2014

 

 

25,000

 

Development expense reimbursement from Sanofi Genzyme:

 

 

 

 

Year-ended December 31, 2015

 

 

33,949

 

Year-ended December 31, 2016

 

 

54,337

 

Year-ended December 31, 2017

 

 

51,846

 

Total consideration at December 31, 2017

 

$

147,182

 

Cumulative revenue recognized at December 31, 2017

 

$

98,014

 

Deferred revenue at December 31, 2017

 

$

49,168

 

We determined that the opt-in rights that Sanofi Genzyme has for future Genetic Medicine programs represent separate and additional deliverables that Sanofi Genzyme may receive from us in future periods. Upon each initial opt-in by Sanofi Genzyme, we have determined that each program and the related activities will represent a single unit of accounting and, consistent with our accounting policies, we will base our revenue recognition period on the final deliverable associated with each future opt-in, if any.

opt-in.

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The Medicines Company Alliance

In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9 for the treatment of hypercholesterolemia and other human diseases, including ALN-PCSsc.inclisiran. MDCO paid us an upfront cash payment of $25.0 million. Upon achievement of certain events, we will be entitled to receive milestone payments, up to an aggregate of $180.0 million, including up to $30.0 million in specified development milestones, $50.0 million in specified regulatory milestones and $100.0 million in specified commercialization milestones. In addition, we will be entitled to royalties ranging from the low- to high- teens based on annual worldwide net sales, if any, of licensed products by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances. In December 2014, we earned a development milestone payment of $10.0 million under the MDCO agreement based upon the initiation of our Phase 1 clinical trial for ALN-PCSsc.inclisiran. In November 2017, we earned a development milestone payment of $20.0 million under the MDCO agreement based upon the initiation by MDCO of a pivotal study for inclisiran. In addition, in December 2014,2017, 2016 and 2015, we earned $4.8were reimbursed an aggregate of $12.2 million for reimbursement of costs incurred for certain development activities. We could potentially earn the next development milestone payment of $20.0$25.0 million based upon regulatory approval of an NDA for inclisiran in the initiation of a pivotal study for ALN-PCSsc.United States. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from MDCO.

Under the MDCO agreement, we and MDCO will collaborate in the further development of ALN-PCSsc.inclisiran. We will retainhad responsibility for the development of ALN-PCSscinclisiran until Phase 1 Completion, as defined in the MDCO agreement, at our cost, up to an agreed upon initial development cost cap. In late 2015, MDCO will assume all otherassumed responsibility for theall development and commercialization of ALN-PCSsc,inclisiran, at its sole cost. The collaboration between us and MDCO is governed by a joint steering committee comprised of an equal number of representatives from each party.


We arewere solely responsible for obtaining supply of finished product reasonably required for the conduct of our obligations under the initial development plan through Phase 1 Completion, and for supplying MDCO with finished product reasonably required for the first Phase 2 clinical trial of ALN-PCSscinclisiran conducted by MDCO, at our expense, provided such costs do not exceed the development costs cap, subject to certain exceptions. After such time,caps.  In April 2016, we and MDCO will haveentered into a supply and technical transfer agreement to provide for our supply of inclisiran to MDCO, in accordance with the terms of the MDCO agreement. MDCO now has the sole right and responsibility to manufacture and supply ALN-PCSscinclisiran for development and commercialization under the MDCO development plan, subject to the terms of the MDCO agreement. Weagreement and MDCO intend to enter into athe supply and technical transfer agreement to provide for supply of ALN-PCSsc to MDCO within a specified time following the effective date of the MDCO agreement.

Unless terminated earlier in accordance with the terms of the agreement, the MDCO Agreementagreement expires on a licensed product-by-licensed product and country-by-country basis upon expiration of the last royalty term for any licensed product in any country, where a royalty term is defined as the latest to occur of (1) the expiration of the last valid claim of patent rights covering a licensed product, (2) the expiration of the Regulatory Exclusivity, as defined in the MDCO Agreement,agreement, and (3) the twelfth anniversary of the first commercial sale of the licensed product in such country. We estimate that our fundamental RNAi patents covering licensed products under the MDCO Agreementagreement will expire both in and outside of the United States generally between 20152016 and 2028. We also estimate that our ALN-PCS product-specific patents covering licensed products under the MDCO Agreementagreement in the United States and elsewhere will expire at the end of 2033. These patent rights are subject to potential patent term extensions and/or supplemental protection certificates extending such terms in countries where such extensions may become available. In addition, more patent filings relating to the collaboration may be made in the future.

Either party may terminate the MDCO Agreementagreement in the event the other party fails to cure a material breach or upon patent-related challenges by the other party. In addition, MDCO has the right to terminate the agreement without cause at any time upon four months’ prior written notice.

During the term of the MDCO agreement, neither party will, alone or with an affiliate or third party, research, develop or commercialize, or grant a license to any third party to research, develop or commercialize, in any country, any product directed to the PCSK9 gene, other than a licensed product, without the prior written agreement of the other party, subject to the terms of the MDCO agreement.

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We have determined that the significant deliverables under the MDCO agreement include the license, the joint steering committee, technology transfer obligations, development activities through Phase 1 Completion and supply of product for a Phase 2 clinical trial. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and collective undelivered activities and services do not have standalone value due to the specialized nature of the activities and services to be provided by us. In addition, while MDCO has the ability to grant sublicenses, it must receive our prior written consent to sublicense all or substantially all of its rights. The uniqueness of our services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition pattern on the final deliverable. Under the MDCO agreement, all deliverables are expected to be completed within approximately five years. We are recognizing revenue under the MDCO agreement on a straight-line basis over approximately five years. We are not utilizing a proportional performance model since we are unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the development activities is largely unknown.

We received the upfront payment of $25.0 million from MDCO in February 2013, which was initially recorded as deferred revenue. During the fourth quarter of 2014, we recognized as revenue a portion of the $10.0 million milestone payment earned in December 2014 equal to the percentage of the performance period completed when the milestone was earned. During the fourth quarter of 2014,2017, we recognized as revenue a portion of the $20.0 million milestone payment earned in November 2017 equal to the percentage of the performance period completed when the milestone was earned. During the years ended December 31, 2017, 2016 and 2015, we also recognized as revenue a portion of the $4.8$5.4 million, $3.0 million and $3.8 million, respectively, of expense reimbursement due to us under the terms of the MDCO agreement equal to the percentage of the performance period completed upon the invoice date. As future consideration, including any milestones or reimbursement for development activities, are earned, we will recognize as revenue a portion of these payments equal to the percentage of the performance period completed when the milestone is achieved or service has been satisfied,provided, multiplied by the amount of the payment. We will recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014,2017, deferred revenue under the MDCO agreement was $24.7$5.7 million.


Vir Biotechnology, Inc. Alliance

In October 2017, we formed an exclusive licensing agreement with Vir Biotechnology, Inc. for the development and commercialization of RNAi therapeutics for infectious diseases, including chronic hepatitis B virus infection. We received an upfront payment, comprised of cash and shares of Vir Biotechnology common stock, which currently is not material to our consolidated financial statements.

Platform Alliances

Monsanto Alliance

In August 2012, we and Monsanto entered into a license and collaboration agreement, pursuant to which we granted to Monsanto a worldwide, exclusive, royalty bearing right and license, including the right to grant sublicenses, to our RNAi platform technology and intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. The Monsanto agreement also includesincluded the transfer of technology from us to Monsanto and initially included a collaborative research project. Under the Monsanto agreement, Monsanto will be our exclusive collaborator in the agriculture field for a ten-year period.

Monsanto paid us $29.2 million in upfront cash payments, and was also required to make near-term milestone payments to us upon the achievement of specified technology transfer and patent-related milestones. We were also entitled to receive additional funding for collaborative research efforts. In the aggregate, we had the ability to earn up to $5.0 million in milestone payments and research funding under the Monsanto alliance. We received a total of $4.0 million in milestone payments from Monsanto based upon the achievement of a specified patent-related event and the completion of technology transfer activities. In September 2014, we and Monsanto mutually determined not to pursue the discovery collaboration originally contemplated under the terms of the Monsanto agreement. Accordingly, Monsanto willwas not be required to pay us the final milestone of $1.0 million. There are no remaining milestones under the Monsanto agreement. Monsanto is required to pay to us a percentage of specified fees from certain sublicense agreements Monsanto may enter into that include access to our intellectual property, as well as low single-digit royalty payments on worldwide, net sales by Monsanto, its affiliates and sublicensees of certain licensed products, as defined in the Monsanto agreement, if any. Due to the uncertainty of the application of RNAi technology in the field of agriculture, we may not receive any license fees or royalty payments from Monsanto.

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The term of the Monsanto agreement generally ends upon the expiration of the last-to-expire patent licensed under the agreement. We estimate that our fundamental RNAi patents licensed under the Monsanto agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Monsanto may terminate the Monsanto agreement in its entirety upon30-days’ prior written notice to us, provided, however, that Monsanto is required to continue to make royalty payments to us if any royalties were payable on net sales of a licensed product during the previous 24 months. The Monsanto agreement may also be terminated by either party in the event the other party fails to cure a material breach under the Monsanto agreement.

Under the terms of the Monsanto agreement, in the event that during the exclusivity period we cease to own or otherwise exclusively control certain licensed patent rights in the agriculture field, for any reason other than Monsanto’s breach of the Monsanto agreement or its negligence or willful misconduct, resulting in the loss of exclusivity with respect to Monsanto’s rights to such patent rights, and such loss of exclusivity has a material adverse effect on the licensed products, then we would be required to pay Monsanto up to $5.0$2.5 million as liquidated damages, which amount was reduced from $5.0 million during the fourth quarter of 2017, and Monsanto’s royalty obligations to us under the Monsanto agreement would be reduced or, under certain circumstances, terminated. We have the right to cure any such loss of patent rights under the Monsanto agreement.

Under the Monsanto agreement, the last deliverable expected to be completed was the discovery collaboration, which was originally expected to be completed within five years. Therefore, prior to the September 2014 amendment, we were recognizing revenue under the Monsanto agreement on a straight-line basis over five years. However, as a result of the September 2014 amendment, we have determined that the final deliverable in the collaboration is the technology transfer activities, know-how exchange and access to intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. Consequently, we are now recognizingrecognized the remaining deferred revenue of $16.8 million at the date of the amendment on a prospective basis from September 2014 through February 2015, the date which iswas the end of the 30 month obligation, which excludesexcluded $5.0 million related to a potential refund due to Monsanto under certain circumstances pursuant to the original terms of the Monsanto agreement. In 2017, we recognized an additional $2.5 million in revenue following the reduction of such potential refund by $2.5 million. We will continue to recognize this revenue on a straight-line basis over the remaining obligation period. We cannotcould not use a proportional performance model since we arewere unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the potential effort required iswas unknown. At December 31, 2014,2017, deferred revenue under the Monsanto agreement was $10.6$2.5 million of which $5.6 million will be recognized through February 2015 and $5.0 million will be recognized when the potential refund obligation ceases and can be considered fixed or determinable.


Takeda Alliance

In May 2008, we entered into a license and collaboration agreement with Takeda to pursue the development and commercialization of RNAi therapeutics. Under the Takeda agreement, we granted to Takeda a non-exclusive, worldwide, royalty-bearing license to our intellectual property, including delivery-related intellectual property, controlled by us as of the date of the Takeda agreement or during the five years thereafter, to develop, manufacture, use and commercialize RNAi therapeutics, subject to our existing contractual obligations to third parties. The license initially is limited to the fields of oncology and metabolic disease and may be expanded at Takeda’s option to include other therapeutic areas, subject to specified conditions.

Takeda paid us an upfront payment of $100.0 million and an additional $50.0 million upon achievement of specified technology transfer milestones. In addition, for each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, we are entitled to receive specified development, regulatory and commercialization milestone payments, totaling up to $171.0 million per product, together with a double-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments per product include up to $26.0 million for the achievement of specified development milestones, up to $40.0 million for the achievement of specified regulatory milestones and up to $105.0 million for the achievement of specified commercialization milestones. We could potentially earn the next milestone payment of $2.0 million based upon the achievement of a specified pre-clinical event by Takeda for an RNAi therapeutic product. Due to the

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uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Takeda.

Pursuant to the Takeda agreement, we and Takeda also agreed to collaborate on the research of RNAi therapeutics directed to one or two disease targets agreed to by the parties, subject to our existing contractual obligations with third parties. The collaboration is governed by a joint technology transfer committee, a joint research collaboration committee and a joint delivery collaboration committee, each of which is comprised of an equal number of representatives from each party. The term of the Takeda agreement generally ends upon the later of (i) the expiration of our last-to-expire patent covering a licensed product and (ii) the last-to-expire term of a profit sharing agreement in the event we elect to enter into such an agreement. We estimate that our fundamental RNAi patents covered under the Takeda agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. The Takeda agreement may be terminated by either party in the event the other party fails to cure a material breach under the agreement. In addition, Takeda may terminate the agreement on a licensed product-by-licensed product or country-by-country basis upon 180-days’ prior written notice to us, provided, however, that Takeda is required to continue to make royalty payments to us for the duration of the royalty term with respect to a licensed product.

We have determined that the deliverables under the Takeda agreement includeincluded the license, the joint committees, the technology transfer activities and the services that we were obligated to perform under the research collaboration. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered services (i.e., the joint committees and the research collaboration) arewere not separable and, accordingly, the license and services arewere being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition pattern on the final deliverable. Under the Takeda agreement, the last elements to be delivered arewere the joint technology transfer committee and joint delivery collaboration committee services, each of which hashad a life of no more than seven years.

We are recognizinghave fully recognized the upfront payment of $100.0 million and the technology transfer milestones of $50.0 million, the receipt of which we believed was probable at the commencement of the collaboration, on a straight-line basis over seven years because we arewere unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the research collaboration iswas largely unknown, and therefore, cannotwe could not utilize a proportional performance model. As future milestones are achieved, if any, we will recognize as revenue a portion of the milestone payment equal toamount in its entirety because all performance obligations for the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment.Takeda agreement have been delivered. At December 31, 2014,2017, there was no deferred revenue under the Takeda agreement was $8.9 million. This remaining deferred revenue will be recognizedas all of our contractual performance obligations were met in full through May 30, 2015.

Other Strategic License Agreements

IsisIonis Collaboration and License Agreement

In January 2015, we and Ionis Pharmaceuticals, Inc., or Ionis (formerly Isis Pharmaceuticals, Inc.) entered into a second amended and restated strategic collaboration and license agreement.agreement, which we further amended in July 2015. The 2015 IsisIonis agreement provides for certain new exclusive target cross-licenses of intellectual property on foureight disease targets, providing each company with exclusive RNA therapeutic license rights for twofour programs, and extends the parties’ existing non-exclusive technology cross-license, which was originally entered into in 2004 and was amended and restated in 2009, through April 2019.


Pursuant to the 2015 IsisIonis agreement, IsisIonis granted to us an exclusive, low single-digit royalty-bearing license to its chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: antithrombin and aminolevulinic acid synthase-1.four targets. In exchange, we granted to IsisIonis an exclusive, low single-digit royalty-bearing license to our chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: Factor XI and apolipoprotein (a).four targets.

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In addition, under the 2015 IsisIonis agreement, the parties agreed to extend the existing non-exclusive technology cross-license through April 2019. Specifically, IsisIonis granted us a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for double-stranded RNAi therapeutics. In turn, we granted IsisIonis a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for single-stranded antisense therapeutics. This broad, non-exclusive cross-license includes chemistry, motif and mechanism patents, but excludes patent claims on formulations, manufacturing and specific targets.

Under the original 2004 agreement, IsisIonis licensed to us its patent estate related to antisense motifs and mechanisms and oligonucleotide chemistry for double-stranded RNAi products in exchange for a previously disclosed technology access fee, participation in fees for our partnering programs and future milestone and royalty payments from us for programs that incorporate Isis’Ionis’ intellectual property. We have the right to use Isis’Ionis’ intellectual property in our development programs or in collaborations and IsisIonis agreed not to grant licenses under these patents to any other organization for the discovery, development and commercialization of double-stranded RNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which IsisIonis plays an active role.

In turn, under the original 2004 agreement, we non-exclusively licensed to IsisIonis our patent estate relating to antisense motifs and mechanisms and oligonucleotide chemistry to research, develop and commercialize single-stranded antisense therapeutics, single stranded RNAi therapeutics and to research double-stranded RNAi compounds. IsisIonis also received a license to develop and commercialize double-stranded RNAi drugs targeting a limited number of therapeutic targets on a non-exclusive basis. We granted these licenses for RNAi therapeutics in exchange for option fees, and future milestone and royalty payments from IsisIonis for RNAi programs that incorporate certain of our intellectual property.

In August 2012, we and IsisIonis amended the agreement to provide certain terms for the discovery, development and commercialization of double-stranded RNA products by us or our sublicensees in the field of agriculture.

As set forth in the 2015 IsisIonis agreement, under the original 2004 agreement, we paid IsisIonis an upfront license fee of $5.0 million and we agreed to pay IsisIonis milestone payments, totaling up to approximately $3.4 million, upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each product that we or a collaborator develop using IsisIonis intellectual property. In addition, we agreed to pay to IsisIonis a percentage of specified fees from strategic collaborations we may enter into that include access to Isis’Ionis’ intellectual property.

IsisIonis has the right to elect up to ten non-exclusive target licenses under the agreement and has the right to purchase one additional non-exclusive target per year during the term of the collaboration. IsisIonis agreed to pay us, per therapeutic target, a license fee of $0.5 million, milestone payments for double-stranded RNAi products totaling approximately $3.4 million, payable upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each double-stranded RNAi or single-stranded RNAi product developed by IsisIonis or a collaborator that utilizes our intellectual property. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Isis.Ionis.

The term of the 2015 IsisIonis agreement generally ends upon the expiration of the last-to-expire patent licensed thereunder, whether such patent is a patent licensed by us to Isis,Ionis, or vice versa. Either party may terminate the 2015 IsisIonis agreement on 90 days’ prior written notice if the other party materially breaches the agreement and fails to cure the breach within the 90-day notice period and no substantial steps have otherwise been taken to cure the breach, provided, however, that neither party may terminate licenses granted to the other party to the extent necessary to develop or sell products that have at least reached investigational new drug-enabling studies (except for a party’s uncured failure of its payment obligations). Either party may also terminate the agreement in the event the other party undergoes specified bankruptcy events.

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During the years ended December 31, 2014, 20132017, 2016 and 2012,2015, as result of certain payments received by us in connection with the Sanofi Genzyme MDCO and MonsantoMDCO alliances, we paid $7.7$0.2 million, $0.7$0.2 million and $2.5$1.9 million to Isis,Ionis, respectively. In addition, as of December 31, 2014,2017 and 2016, we owed Isis $1.8Ionis $1.0 million and $0.2 million, respectively, for amounts incurred but not yet paid. These license fees were charged to research and development expense.

Asset acquisition

In-process research and development

In March 2014, we purchased from Merck Sharp & Dohme Corp., or Merck, all of Merck’s right, title and interest in and to all of the outstanding shares of common stock of Sirna. Sirna possesses intellectual property and RNAi assets including early-stage pre-clinical therapeutic candidates, chemistry, and siRNA-conjugate and other delivery technologies that we intend to integrate into our platform for delivery of RNAi therapeutics.

At the closing of the transaction, we paid Merck $25.0 million in cash and issued 2,142,037 shares of our common stock. We recorded this issuance using the price of our common stock on March 5, 2014, the date that these shares were issued to Merck. Based on the common stock price of $81.36, the fair value of the shares issued was $174.3 million. As a result of the cash payment and issuance of shares to Merck, we recorded a total of $199.3 million to in-process research and development expense. We issued an additional 378,007 shares of common stock to Merck on May 19, 2014 upon the completion of certain technology transfer activities during the second quarter of 2014. In the first quarter of 2014, we recorded a liability of $25.4 million associated with the then future obligation to issue these shares, based on the then current price of our common stock, which was also charged to in-process research and development expense. Upon completion of these technology transfer activities in the second quarter of 2014, we re-measured the expense recorded in connection with these shares using the then current price of our common stock, resulting in a credit of $3.9 million. We recorded an expense of $220.8 million to in-process research and development for the year ended December 31, 2014 as a result of this asset acquisition. In future periods, there will be no additional charges recorded to in-process research and development related to the purchase of the Sirna RNAi assets from Merck.

We accounted for this transaction as an acquisition of in-process research and development assets and recorded the entire amount to in-process research and development expense as we did not acquire any employees, manufacturing or other facilities, developed processes or clinical-stage assets as part of our acquisition of Sirna.

Pursuant to the Sirna agreement, Merck is also eligible to receive the following consideration from us: (i) up to an aggregate of $10.0 million upon the achievement by us or our related parties of specified regulatory milestones for RNAi products covered by Sirna intellectual property, and (ii) up to an aggregate of $105.0 million upon the achievement by us or our related parties of specified development and regulatory ($40.0 million) and commercial ($65.0 million) milestones associated with the clinical development progress of certain pre-clinical candidates discovered by Sirna, together with low single-digit royalties for our products and single-digit royalties for Sirna products, in each case based on annual worldwide net sales, if any, by us and our related parties of any such products. These amounts will be recorded as research and development expenses as incurred based on our accounting for this transaction as an asset acquisition.

Under the Sirna agreement, Merck also agreed not to dispose of (i) any shares of our common stock beneficially owned for a period of six months following the closing date, subject to certain limited exceptions, and (ii) 50% of the shares of our common stock beneficially owned for a period of six additional months following the termination of the initial lock-up, referred to as the Subsequent Lock-Up. During and following the expiration of the Subsequent Lock-Up, Merck will be permitted to sell such shares of our common stock subject to certain limitations, including certain volume and manner of sale restrictions.

 

124



4.

FAIR VALUE MEASUREMENTS

The following tables present information about our assets that are measured at fair value on a recurring basis at December 31, 20142017 and 2013,2016, and indicate the fair value hierarchy of the valuation techniques we utilized to determine such fair value, in thousands:

 

Description

  At
December 31,
2014
   Quoted
Prices in
Active
Markets
(Level 1)
   Significant
Observable
Inputs
(Level 2)
   Significant
Unobservable
Inputs
(Level 3)
 

 

At

December 31,

2017

 

 

Quoted

Prices in

Active

Markets

(Level 1)

 

 

Significant

Observable

Inputs

(Level 2)

 

 

Significant

Unobservable

Inputs

(Level 3)

 

Cash equivalents

  $56,203    $56,203    $    $  

Cash equivalents:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Commercial paper

 

$

82,262

 

 

$

 

 

$

82,262

 

 

$

 

Corporate notes

 

 

18,116

 

 

 

 

 

 

18,116

 

 

 

 

U.S. government-sponsored enterprise securities

 

 

231,122

 

 

 

 

 

 

231,122

 

 

 

 

U.S. treasury securities

 

 

62,855

 

 

 

 

 

 

62,855

 

 

 

 

Money market funds

 

 

122,986

 

 

 

122,986

 

 

 

 

 

 

 

Marketable securities (fixed income):

        

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Certificates of deposit

   24,300          24,300       

 

 

30,200

 

 

 

 

 

 

30,200

 

 

 

 

Commercial paper

   40,796          40,796       

 

 

56,951

 

 

 

 

 

 

56,951

 

 

 

 

Corporate notes

   662,545          662,545       

 

 

373,252

 

 

 

 

 

 

373,252

 

 

 

 

Municipal debt securities

   9,005          9,005       

U.S. government-sponsored enterprise securities

   64,856          64,856       

 

 

398,298

 

 

 

 

 

 

398,298

 

 

 

 

U.S. treasury securities

   5,248          5,248       

 

 

200,475

 

 

 

 

 

 

200,475

 

 

 

 

Marketable securities (Regulus equity holdings)

   94,583     94,583            
  

 

   

 

   

 

   

 

 

Restricted cash (Money market funds)

 

 

1,471

 

 

 

1,471

 

 

 

 

 

 

 

Total

  $957,536    $150,786    $806,750    $  

 

$

1,577,988

 

 

$

124,457

 

 

$

1,453,531

 

 

$

 

  

 

   

 

   

 

   

 

 

 

Description

  At
December 31,
2013
   Quoted
Prices in
Active
Markets
(Level 1)
   Significant
Observable
Inputs
(Level 2)
   Significant
Unobservable
Inputs
(Level 3)
 

 

At

December 31,

2016

 

 

Quoted

Prices in

Active

Markets

(Level 1)

 

 

Significant

Observable

Inputs

(Level 2)

 

 

Significant

Unobservable

Inputs

(Level 3)

 

Cash equivalents

  $32,571    $32,571    $    $  

Cash equivalents:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Commercial paper

 

$

17,199

 

 

$

 

 

$

17,199

 

 

$

 

Money market funds

 

 

151,479

 

 

 

151,479

 

 

 

 

 

 

 

Marketable securities (fixed income):

        

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Certificates of deposit

 

 

17,999

 

 

 

 

 

 

17,999

 

 

 

 

Commercial paper

 

 

59,340

 

 

 

 

 

 

59,340

 

 

 

 

Corporate notes

   228,462          228,462       

 

 

333,872

 

 

 

 

 

 

333,872

 

 

 

 

U.S. government-sponsored enterprise securities

   56,863          56,863       

 

 

297,773

 

 

 

 

 

 

297,773

 

 

 

 

Commercial paper

   11,978          11,978       

U.S. treasury securities

 

 

40,000

 

 

 

 

 

 

40,000

 

 

 

 

Marketable securities (Regulus equity holdings)

   45,452     45,452            

 

 

8,997

 

 

 

8,997

 

 

 

 

 

 

 

  

 

   

 

   

 

   

 

 

Restricted cash (Money market funds)

 

 

1,471

 

 

 

1,471

 

 

 

 

 

 

 

Total

  $375,326    $78,023    $297,303    $  

 

$

928,130

 

 

$

161,947

 

 

$

766,183

 

 

$

 

  

 

   

 

   

 

   

 

 

For the yearyears ended December 31, 2014,2017 and 2016, there were no transfers between Level 1 and Level 2 financial assets. For the year ended December 31, 2013, we transferred $45.5 million of marketable securities (equity holdings in Regulus) from Level 2 to Level 1 due to the increased volume in average daily trading on the NASDAQ stock market for these instruments. The carrying amounts reflected in our consolidated balance sheets for cash, billed and unbilled collaboration receivables, other current assets, accounts payable and accrued expenses approximate fair value due to their short-term maturities.

The fair value of our long-term debt at December 31, 2017, computed pursuant to a discounted cash flow technique using a market interest rate, was $30.1 million and is considered a Level 3 fair value measurement. The effective interest rate reflects the current market rate.

 

125



5.

MARKETABLE SECURITIES

The following tables summarize the fair value, accumulated other comprehensive income (loss) and intraperiod tax allocation regarding our investment in Regulus available-for-sale marketable securities at December 31, 20142017 and 2013,2016, and for the activity recorded in theeach year, in thousands:

 

Description

  At
December 31,
2013
  Sales of Regulus
Shares During
Year Ended
December 31,
2014
  All Other
Activity During
Year Ended
December 31,
2014
  Balance at
December 31,
2014
 

Carrying value

  $12,449   $(514 $   $11,935  

Accumulated other comprehensive income, before tax

   33,003    (2,081  51,726    82,648  
  

 

 

  

 

 

  

 

 

  

 

 

 

Investment in equity securities of Regulus Therapeutics Inc., as reported

  $45,452   $(2,595 $51,726   $94,583  
  

 

 

  

 

 

  

 

 

  

 

 

 

Accumulated other comprehensive income, before tax

  $33,003   $(2,081 $51,726   $82,648  

Intraperiod tax allocation recorded as a benefit from income taxes

   (13,267      (19,525  (32,792
  

 

 

  

 

 

  

 

 

  

 

 

 

Accumulated other comprehensive income, net of tax

  $19,736   $(2,081 $32,201   $49,856  
  

 

 

  

 

 

  

 

 

  

 

 

 

Description

  At
December 31,
2012
  Sales of Regulus
Shares During
year Ended
December 31,
2013
  All Other
Activity During
Year Ended
December 31,
2013
  Balance at
December 31,
2013
 

Carrying value

  $12,449   $   $   $12,449  

Accumulated other comprehensive income, before tax

   26,299        6,704    33,003  
  

 

 

  

 

 

  

 

 

  

 

 

 

Investment in equity securities of Regulus Therapeutics Inc., as reported

  $38,748   $   $6,704   $45,452  
  

 

 

  

 

 

  

 

 

  

 

 

 

Accumulated other comprehensive income, before tax

  $26,299   $   $6,704   $33,003  

Intraperiod tax allocation recorded as a benefit from income taxes

   (10,572      (2,695  (13,267
  

 

 

  

 

 

  

 

 

  

 

 

 

Accumulated other comprehensive income, net of tax

  $15,727   $   $4,009   $19,736  
  

 

 

  

 

 

  

 

 

  

 

 

 

Description

 

At

December 31,

2016

 

 

Sales of

Regulus

Shares During

Year Ended

December 31,

2017

 

 

All Other

Activity

During

Year Ended

December 31,

2017

 

 

Balance at

December 31,

2017

 

Carrying value

 

$

8,093

 

 

$

(7,485

)

 

$

(608

)

 

$

 

Accumulated other comprehensive income (loss), before tax

 

 

904

 

 

 

1,894

 

 

 

(2,798

)

 

 

 

Investment in equity securities of Regulus Therapeutics

   Inc., as reported

 

$

8,997

 

 

$

(5,591

)

 

$

(3,406

)

 

$

 

Accumulated other comprehensive income (loss), before tax

 

$

904

 

 

$

1,894

 

 

$

(2,798

)

 

$

 

Intraperiod tax allocation recorded as a benefit from

   income taxes

 

 

(32,792

)

 

 

 

 

 

 

 

 

(32,792

)

Accumulated other comprehensive income (loss), net of tax

 

$

(31,888

)

 

$

1,894

 

 

$

(2,798

)

 

$

(32,792

)

Description

 

At

December 31,

2015

 

 

Sales of

Regulus

Shares During

Year Ended

December 31,

2016

 

 

All Other

Activity

During

Year Ended

December 31,

2016

 

 

Balance at

December 31,

2016

 

Carrying value

 

$

11,935

 

 

$

(3,842

)

 

$

 

 

$

8,093

 

Accumulated other comprehensive income (loss), before tax

 

 

39,484

 

 

 

(6,977

)

 

 

(31,603

)

 

 

904

 

Investment in equity securities of Regulus Therapeutics

   Inc., as reported

 

$

51,419

 

 

$

(10,819

)

 

$

(31,603

)

 

$

8,997

 

Accumulated other comprehensive income (loss), before tax

 

$

39,484

 

 

$

(6,977

)

 

$

(31,603

)

 

$

904

 

Intraperiod tax allocation recorded as a benefit from

   income taxes

 

 

(32,792

)

 

 

 

 

 

 

 

 

(32,792

)

Accumulated other comprehensive income (loss), net of tax

 

$

6,692

 

 

$

(6,977

)

 

$

(31,603

)

 

$

(31,888

)

We obtain fair value measurement data for our marketable securities from independent pricing services. We perform validation procedures to ensure the reasonableness of this data. This includes meeting with the independent pricing services to understand the methods and data sources used. Additionally, we perform our own review of prices received from the independent pricing services by comparing these prices to other sources and confirming those securities are trading in active markets.

126


The following tables summarize our marketable securities, other than our holdings in Regulus noted above, at December 31, 20142017 and 2013,2016, in thousands:

 

  December 31, 2014 
  Amortized
Cost
  Gross
Unrealized
Gains
  Gross
Unrealized
Losses
  Fair Value 

Certificates of deposit (Due within 1 year)

 $24,300   $   $   $24,300  

Commercial paper (Due within 1 year)

  40,785    11        40,796  

Corporate notes (Due within 1 year)

  449,044    14    (293  448,765  

Corporate notes (Due after 1 year through 2 years)

  214,510        (730  213,780  

Municipal debt securities (Due after 1 year through 2 years)

  9,002    3        9,005  

U.S. government-sponsored enterprise securities (Due within 1 year)

  13,069        (1  13,068  

U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)

  51,879        (91  51,788  

U.S. treasury securities (Due after 1 year through 2 years)

  5,254        (6  5,248  
 

 

 

  

 

 

  

 

 

  

 

 

 

Total

 $807,843   $28   $(1,121 $806,750  
 

 

 

  

 

 

  

 

 

  

 

 

 

 

 

At December 31, 2017

 

 

 

Amortized

Cost

 

 

Gross

Unrealized

Gains

 

 

Gross

Unrealized

Losses

 

 

Fair Value

 

Certificates of deposit

 

$

30,200

 

 

$

 

 

$

 

 

$

30,200

 

Commercial paper

 

 

56,951

 

 

 

 

 

 

 

 

 

56,951

 

Corporate notes

 

 

373,736

 

 

 

11

 

 

 

(495

)

 

 

373,252

 

U.S. government-sponsored enterprise securities

 

 

399,281

 

 

 

 

 

 

(983

)

 

 

398,298

 

U.S. treasury securities

 

 

200,649

 

 

 

1

 

 

 

(175

)

 

 

200,475

 

Total

 

$

1,060,817

 

 

$

12

 

 

$

(1,653

)

 

$

1,059,176

 


 

 

At December 31, 2016

 

 

 

Amortized

Cost

 

 

Gross

Unrealized

Gains

 

 

Gross

Unrealized

Losses

 

 

Fair Value

 

Certificates of deposit

 

$

17,999

 

 

$

 

 

$

 

 

$

17,999

 

Commercial paper

 

 

59,340

 

 

 

 

 

 

 

 

 

59,340

 

Corporate notes

 

 

334,266

 

 

 

47

 

 

 

(441

)

 

 

333,872

 

U.S. government-sponsored enterprise securities

 

 

298,910

 

 

 

9

 

 

 

(1,146

)

 

 

297,773

 

U.S. treasury securities

 

 

40,022

 

 

 

1

 

 

 

(23

)

 

 

40,000

 

Total

 

$

750,537

 

 

$

57

 

 

$

(1,610

)

 

$

748,984

 

 

  December 31, 2013 
  Amortized
Cost
  Gross
Unrealized
Gains
  Gross
Unrealized
Losses
  Fair Value 

Commercial paper (Due within 1 year)

 $11,983   $   $(5 $11,978  

Corporate notes (Due within 1 year)

  154,175    33    (46  154,162  

Corporate notes (Due after 1 year through 2 years)

  74,312    23    (35  74,300  

U.S. government-sponsored enterprise securities (Due within 1 year)

  26,553    8        26,561  

U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)

  30,300    2        30,302  
 

 

 

  

 

 

  

 

 

  

 

 

 

Total

 $297,323   $66   $(86 $297,303  
 

 

 

  

 

 

  

 

 

  

 

 

 

We classify our debt security investments based on their contractual maturity dates. The following table summarizes our available-for-sale debt securities by contractual maturity, at December 31, 2017, in thousands:

 

 

 

At December 31, 2017

 

 

 

Amortized

Cost

 

 

Fair

Value

 

Less than one year

 

$

1,046,834

 

 

$

1,045,257

 

Greater than one year but less than two years

 

 

13,983

 

 

 

13,919

 

Total

 

$

1,060,817

 

 

$

1,059,176

 

6.

PROPERTY, PLANT AND EQUIPMENT, NET

Property, plant and equipment consist of the following at December 31, 20142017 and 2013,2016, in thousands:

 

      December 31, 

 

At December 31,

 

  Useful Life   2014 2013 

 

2017

 

 

2016

 

Laboratory equipment

   5 years    $28,559   $22,729  

 

$

40,462

 

 

$

37,303

 

Computer equipment and software

   3 years     4,440    4,261  

 

 

9,608

 

 

 

9,650

 

Furniture and fixtures

   5 years     1,999    1,793  

 

 

5,844

 

 

 

6,002

 

Leasehold improvements

   *     30,853    28,953  

 

 

50,612

 

 

 

45,362

 

Land

 

 

9,080

 

 

 

9,080

 

Construction in progress

        1,982    28  

 

 

133,645

 

 

 

68,182

 

    

 

  

 

 
     67,833    57,764  

 

 

249,251

 

 

 

175,579

 

Less: accumulated depreciation

     (46,093  (41,316

 

 

(67,351

)

 

 

(61,007

)

    

 

  

 

 

 

$

181,900

 

 

$

114,572

 

    $21,740   $16,448  
    

 

  

 

 

 

*Shorter of asset life or lease term

During the years ended December 31, 2014, 20132017, 2016 and 2012,2015, we recorded $5.0$11.9 million, $6.1$9.6 million and $4.6$6.7 million, respectively, of depreciation expense related to our property, plant and equipment.

Manufacturing Facility

In April 2016, we purchased 12 acres of undeveloped land in Norton, Massachusetts. We are constructing a manufacturing facility at this site for drug substance, including small interfering RNAs, or siRNAs, and siRNA conjugates, for clinical and commercial use. At December 31, 2017 and 2016, property, plant and equipment, net, on our consolidated balance sheets reflects $140.5 million and $73.2 million, respectively, of land and associated costs related to the construction of our drug substance manufacturing facility.

 

127



7.

COMMITMENTS AND CONTINGENCIES

Purchase Commitments

We have future purchase commitments totaling $104.5 million at December 31, 2014, of which $59.3 million is expected to be incurred in 2015 and $45.2 million is expected to be incurred past 2015. These commitments are related to purchase orders, clinical and pre-clinical agreements, and other purchase commitments for goods or services that we are likely to continue, regardless of the fact that they were cancelable at December 31, 2014.

Technology License and Other Commitments

We have licensed from third parties the rights to use certain technologies and information in our research processes as well as in any products that we may develop including these licensed technologies.develop. In accordance with the related license or technology agreements, we are required to make certain fixed payments to the licensor or a designee of the licensorcounterparty over various agreement terms. Many of these agreement terms are consistent with the remaining lives of the underlying intellectual property that we have licensed. At December 31, 2014,2017, we were committed to make the following fixed, estimated and cancelable payments under existing license agreements, in thousands:

 

Year Ending December 31,

    

2015

  $7,379  

2016

   724  

2017

   744  

2018

   754  

2019

   762  

Thereafter

   8,592  
  

 

 

 

Total

  $18,955  
  

 

 

 

Operating

Year Ending December 31,

 

 

 

 

2018

 

$

21,012

 

2019

 

 

12,277

 

2020

 

 

795

 

2021

 

 

795

 

2022

 

 

595

 

Thereafter

 

 

1,500

 

Total

 

$

36,974

 

At December 31, 2017, we were committed to make fixed, non-cancelable payments of $5.0 million in each of 2018 and 2019 under an agreement that will provide us access to information during this time that we can use in our future research and any products that we may develop.

We in-license technology from a number of sources, including Ionis and Merck. Pursuant to these in-license agreements, we will be required to make additional payments if and when we achieve specified development, regulatory and commercialization milestones. To the extent we are unable to reasonably predict the likelihood, timing or amount of such payments, we have excluded them from the table above.

Facility Leases

300 Third Street

We lease office and laboratory space located at 300 Third Street, Cambridge, Massachusetts, for our corporate headquarters and primary research facility under a non-cancelable real property lease agreement, or the Third Street Lease, with ARE-MA Region No. 28 LLC, or the Landlord. Under the Third Street Lease, we lease a total of approximately 129,000 square feet of office and laboratory space. The term of the Third Street Lease was set to expire in September 2016. In March 2014, we and the Landlord amended the Third Street Lease to extend the term for an additional five years, through September 30, 2021. Under the amended Third Street Lease, we have the option to extend the term for one additional five-year period. As a result of the extension of the term of the Third Street Lease, our operating lease obligations through 2021 increased by $37.8 million.

665 Concord Avenue

On February 10, 2012, we entered into a non-cancelable real property lease agreement, or the BMRBMR-665 Concord Avenue Lease, with BMR-Fresh Pond Research Park LLC or BMR, for our manufacturing facility.facility for patisiran formulated bulk drug product. Under the BMRBMR-665 Concord Avenue Lease, we lease approximately 15,000 square feet of office and laboratory space located at 665 Concord Avenue, Cambridge, Massachusetts. The term of the BMRBMR-665 Concord Avenue Lease expireswas set to expire in August 2017. In August 2016, we and BMR-Fresh Pond Research Park LLC amended the BMR-665 Concord Avenue Lease to extend the term for an additional five years, through August 31, 2017. We2022. Under the amended BMR-665 Concord Avenue Lease, we have the option to extend the term for one additional five-year period.

675 West Kendall Street

In April 2015, we entered into a non-cancelable real property lease, or the BMR-675 West Kendall Lease, with BMR-675 West Kendall Street, LLC, or BMR, for laboratory and office space located at 675 West Kendall Street, Cambridge, Massachusetts. We intend to move our corporate headquarters and research facility to this location in early 2019.

Under the terms of the BMR-675 West Kendall Lease, we will lease approximately 295,000 square feet of laboratory and office space. The term of the BMR-675 West Kendall Lease will commence on May 1, 2018 and rent payments will become due commencing upon substantial completion of the building improvements, which is currently expected to be on or around February 1,


2019, and will continue for 15 years from the rent commencement date, with options to renew for two successiveterms of five years each, subject to the terms of the BMR-675 West Kendall Lease.

Annual rent under the BMR-675 West Kendall Lease, exclusive of operating expenses and real property taxes, will be $19.8 million for the first year, with annual increases of 3 percent thereafter. Under the terms of the BMR-675 West Kendall Lease, BMR will contribute a total of $56.1 million toward the cost of base building and tenant improvements.

101 Main Street

In May 2015, we entered into a non-cancelable real property lease agreement with RREEF America REIT II CORP. PPP, or RREEF, for office space located on several floors at 101 Main Street, Cambridge, Massachusetts. This lease supplements the initial lease entered into in March 2015 between us and RREEF for office space on a separate floor at the 101 Main Street location.

Under the terms of the 101 Main Street leases, we lease approximately 72,000 square feet of office space at the 101 Main Street location. The terms of the initial 101 Main Street lease and the additional 101 Main Street lease commenced in March 2015 and January 2016, and continue for four years, with an option to renew for one five-year periods.term, and five and a half years, with an option to renew for one five-year term, respectively.

We received $1.9 million, $0.2Initial annual rent for the initial lease and the additional lease, exclusive of operating expenses and real property taxes, was $1.7 million and $1.8$3.5 million, respectively, with annual increases of $1/square foot under each lease thereafter. Rent payments commenced in May 2015 under the initial lease and rent payments commenced in May 2016 under the additional lease.

        We have $1.5 million in leasehold improvement incentives from BMR during the years endedrestricted cash that is recorded in long-term other assets as of December 31, 2014, 20132017 and 2012, respectively. These leasehold improvement incentives are being accounted for as2016 in connection with an irrevocable standby letter of credit with RREEF.

Our facility leases described above generally contain customary provisions allowing the landlords to terminate the leases if we fail to remedy a reduction in rent expense ratably over the BMR Lease term. The balance from these leasehold improvement incentives is included in current portionbreach of deferred rent and deferred rent, netany of current portion, in the consolidated balance sheets at December 31, 2014 and 2013.our obligations under any such lease within specified time periods, or upon our bankruptcy or insolvency.

Total rent expense, including operating expenses, under our real property leases was $8.9$18.7 million, $4.9$15.9 million and $6.4$10.5 million for the years ended December 31, 2014, 20132017, 2016 and 2012,2015, respectively.

In addition to the lease agreements described above, we also lease additional office space in several locations in and outside of the United States to support our operations and growth.

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Future minimum payments under our non-cancelable facility leases, including rent payments for the BMR-675 West Kendall Lease which are expected to commence in early 2019, are approximately as follows, in thousands:

 

Year Ending December 31,

    

 

 

 

 

2015

  $6,810  

2016

   6,994  

2017

   7,535  

2018

   7,387  

 

$

14,464

 

2019

   7,608  

 

 

32,446

 

2020

 

 

34,570

 

2021

 

 

30,928

 

2022

 

 

23,050

 

Thereafter

   13,845  

 

 

297,726

 

  

 

 

Total

  $50,179  

 

$

433,184

 

  

 

 

Credit Agreements

On April 29, 2016, we entered into (i) a Credit Agreement, or the BOA Credit Agreement, with Alnylam U.S., Inc., our wholly-owned subsidiary, as the borrower, us, as a guarantor, and Bank of America N.A., or BOA, as the lender and (ii) a Credit Agreement, or the Wells Credit Agreement, together with the BOA Credit Agreement, the Credit Agreements, by and among Alnylam U.S., Inc., as the borrower, us, as a guarantor, and Wells Fargo Bank, National Association, or Wells, as the lender. The Credit Agreements were entered into in connection with the planned build out of our new drug substance manufacturing facility.

The BOA Credit Agreement provided for a $120.0 million term loan facility and was scheduled to mature on April 29, 2021. On December 27, 2017, we repaid in full the $120.0 million outstanding principal amount under the BOA Credit Agreement and the BOA Credit Agreement terminated in accordance with its terms upon repayment of the outstanding indebtedness. The Wells Credit


LitigationAgreement provides for a $30.0 million term loan facility and matures on April 29, 2021. The proceeds of the borrowing under the BOA Credit Agreement were, and the Wells Credit Agreement are, to be used for working capital and general corporate purposes. Interest on borrowings under the BOA Credit Agreement was, and under the Wells Credit Agreement is calculated based on LIBOR plus 0.45 percent, except in the event of default. The borrower may prepay loans under the Wells Credit Agreement at any time, without premium or penalty, subject to certain notice requirements and LIBOR breakage costs.  

The obligations of the borrower and us under the BOA Credit Agreement were, and under the Wells Credit Agreement are secured by cash collateral in an amount equal to, at any given time, at least 100 percent of the principal amount of all term loans outstanding under such Credit Agreement at such time. At  December 31, 2017 and 2016, we have recorded $30.0 million and $150.0 million, respectively, of cash collateral in connection with the Credit Agreements as restricted investments on our consolidated balance sheets. Wells and the borrower have agreed to consider the appropriateness of a change in the type of approved collateral on a periodic basis throughout the term of the Wells Credit Agreement; provided that any such change to the type of such approved collateral shall be made only upon each of the lender’s and the borrower’s consent.

The Wells Credit Agreement contains limited representations and warranties and limited affirmative and negative covenants, including quarterly reporting obligations. The Wells Credit Agreement also contains certain customary events of default, including nonpayment of principal or interest, material inaccuracy of representations, failure to comply with covenants, cross-defaults to certain other indebtedness, invalidity of any loan document relating to such Credit Agreement, judgments having a material adverse effect, insolvency events and change of control. If an event of default occurs and is continuing under the Wells Credit Agreement, the entire outstanding balance may become immediately due and payable.

Several of the lenders under each of the Credit Agreements, as well as their affiliates, have various relationships with us and our subsidiaries involving the provision of financial services, such as investment banking, commercial banking, advisory, cash management, custody and corporate credit card services for which they receive customary fees and may do so in the future.

During the years ended December 31, 2017 and 2016, we recorded $0.8 million and $1.2 million, respectively, of interest expense related to the Credit Agreements that is reflected in other income (expense) on our consolidated statements of comprehensive loss.

Litigation

From time to time, we are a party to legal proceedings in the course of our business, including the matters described below. The claims and legal proceedings in which we could be involved include challenges to the scope, validity or enforceability of patents relating to our product candidates, and challenges by us to the scope, validity or enforceability of the patents held by others. These include claims by third parties that we infringe their patents. The outcome of any such legal proceedings, regardless of the merits, is inherently uncertain. In addition, litigation and related matters are costly and may divert the attention of our management and other resources that would otherwise be engaged in other activities.  If we were unable to prevail in any such legal proceedings, our business, results of operations, liquidity and financial condition could be adversely affected. Our accounting policy for accrual of legal costs is to recognize such expenses as incurred.

Silence Litigation

On October 17, 2017, Silence Therapeutics plc, or Silence, served its previously announced claim in the High Court of England and Wales, or the High Court, issued in the name of Silence Therapeutics GmbH against Alnylam UK Ltd., Alnylam Pharmaceuticals, Inc., and The Medicines Company UK Ltd, referred to collectively as the Defendants. The claim seeks a declaration that patisiran, fitusiran, givosiran and inclisiran, together, the Products, are protected by Silence’s European Patent No. 2 258 847, or the ‘847 patent, within the meaning of the Supplementary Protection Certificate, or SPC, Regulation of the European Union. The claim alleges that any marketing authorization for any of these Products granted to any of the Defendants is a valid authorization within the meaning of the SPC Regulation, to support an application for an SPC by Silence for each of the Products, allegedly allowing Silence to extend the expiration date of their ‘847 patent on a Product by Product basis, based on the amount of time in regulatory review for each of the Products, again on a Product by Product basis, up to a statutory maximum.  In addition, Silence is seeking costs, interest and other unspecified relief.

On October 31, 2017, the Defendants acknowledged service of the claim served by Silence contesting jurisdiction of the High Court.  On November 30, 2017, the Defendants submitted substantive defenses to the claim.  

On October 27, 2017, we, through our affiliate Alnylam UK Ltd., and The Medicines Company UK Ltd filed and served a claim against Silence Therapeutics GmbH and Silence in the High Court seeking revocation of the ‘847 patent, as well as a declaration of


non-infringement by each of the Products of the ‘847 patent, and costs and interest among other potential remedies.  On November 14, 2017, Silence filed a defense to our claim along with counterclaims alleging infringement of the ‘847 patent by our Products.  On December 11, 2017, we filed an answer and defense to the counter claims.  The High Court has set a trial date of December 3, 2018 for all claims between Silence and the Defendants.

Although we believe the ‘847 patent is invalid and not infringed by our Products and that, therefore, Silence would not be entitled to obtain an SPC based on any of our Products, litigation is subject to inherent uncertainty, as noted above, and a court could ultimately rule against us.

Dicerna Litigation

On June 10, 2015, we filed a trade secret misappropriation lawsuit against Dicerna Pharmaceuticals, Inc., or Dicerna, in the Superior Court of Middlesex County, Massachusetts, or the Court, seeking to stop misappropriation by Dicerna of our confidential, proprietary and trade secret information related to the RNAi assets we purchased from Merck, including certain N-acetylgalactosamine, or GalNAc, conjugate technology. In addition to permanent injunctive relief, we are also seeking monetary damages from Dicerna. On July 10, 2015, Dicerna filed its answer to our complaint, in which it denied our claims, following which discovery proceeded.  Fact discovery on our claims against Dicerna ended on August 16, 2017, and expert discovery on those claims is underway.  In August 2017, Dicerna successfully added counterclaims against us in the trade secret lawsuit alleging that our lawsuit represented abuse of process and claiming tortious interference with its business. On September 27, 2017, we filed a motion to dismiss Dicerna’s counterclaims.  The motion was denied on October 24, 2017, and we intend to vigorously defend against those claims. The trial for this lawsuit now is scheduled for April 23, 2018.

In addition, on August 8, 2017, Dicerna filed a lawsuit against us in the United States District Court of Massachusetts alleging attempted monopolization by us under the Sherman Antitrust Act.  Dicerna’s allegations related to its new claim largely overlap with its counterclaims in the state court action.  We do not believe the claim is meritorious and on October 23, 2017, we filed a motion to dismiss the antitrust lawsuit.  On November 20, 2017, Dicerna filed an amended complaint adding the fact that the motion to dismiss Dicerna’s counterclaims had been denied.  On December 4, 2017, we filed a renewed motion to dismiss Dicerna’s complaint, which Dicerna has opposed.  

Although we believe we have meritorious claims against Dicerna and meritorious defenses and responses to the counterclaims and federal claim now being asserted by Dicerna, as noted above, litigation is subject to inherent uncertainty, we will incur significant costs in defending against such claims, and a court could ultimately rule against us.

University of Utah Litigation

On March 22, 2011, The University of Utah, or Utah, filed a civil complaint in the United States District Court for the District of Massachusetts, or the MA District Court, against us, Max Planck Gesellschaft Zur Foerderung Der Wissenschaften e.V. and Max Planck Innovation GmbH, together, Max Planck, the Whitehead Institute for Biomedical Research, or Whitehead, the Massachusetts Institute of Technology, or MIT, and the University of Massachusetts, or UMass, claiming a professor at Utah is the sole inventor or, in the alternative, a joint inventor, of the Tuschl patents. Utah was seeking changes to the inventorship of the Tuschl patents, unspecified damages and other relief. After several years of court proceedings and discovery, on September 28, 2015, the MA District Court granted both of our motions for summary judgment, finding that there was no collaboration between Dr. Bass and Dr. Tuschl, which is a pre-requisite for co-inventorship, and dismissing Utah’s state law damages claims as well.

On October 31, 2011, we, Max Planck, Whitehead, MIT and UMass filed a motion to dismiss. Also on October 31, 2011, UMass filed a motion to dismiss on separate grounds, which we, Max Planck, Whitehead and MIT have joined. On December 31, 2011,28, 2015, Utah filed a second amended complaint dropping UMass as a defendant and adding as defendants several UMass officials. In June 2012, the Court denied both motionsnotice of appeal to dismiss. We, Max Planck, Whitehead, MIT and UMass filed an appeal of the Court’s ruling on the motion to dismiss for lack of jurisdiction and a motion requesting that the Court stay the case pending the outcome of the appeal. In July 2012, the Court stayed discovery in the case pending the outcome of the defendants’ appeal. In August 2013, the United States Court of Appeals for the Federal Circuit, or the CAFC. On December 18, 2015, the CAFC affirmedentered an order dismissing Utah’s appeal following a joint motion filed by us and Utah seeking dismissal of the lower Court’s ruling, in a split decision. In September 2013,appeal with prejudice. This disposed of Utah’s inventorship claims and its state law claims for damages. On October 14, 2015, we filed a petitionmotion with the MA District Court seeking reimbursement of costs and fees associated with defending this action in the amount of approximately $8.0 million. On November 30, 2015, the MA District Court denied our motion and on December 15, 2015, we filed a notice of appeal of this ruling with the CAFC. Oral arguments on our appeal were heard at the CAFC for rehearing or rehearing en banc. In November 2013,on January 12, 2017. On March 23, 2017, the CAFC denied our petition for rehearing or rehearing en bancappeal and remanded the case back to the lower Court. In February 2014, we filed a petition for writ of certiorari from the Supreme Court and a motion to stay the lower Court proceedings pending a decision from the Supreme Court on our petition. The lower Court granted our motion to stay the proceedings, however, in June 2014 the Supreme Court denied our petition for certiorari and remanded the case back to the United States District Court for the District of Massachusetts for trial, which is now scheduled to begin on November 2, 2015.

Although we believe we have meritorious defenses and intend to vigorously defend ourselves in this matter, litigation is subject to inherent uncertainty and a court could ultimately rule against us. In addition, the defense of litigation and related matters are costly and may divert the attention of our management and other resources that would otherwise be engaged in other activities. We have not recorded an estimate of the possible loss associated with this legal proceeding due to the uncertainties related to both the likelihood and the amount of any possible loss or range of loss.

Our accounting policy for accrual of legal costs is to recognize such expenses as incurred.

Tekmira Settlement Agreement

On November 12, 2012, we, Tekmira Pharmaceuticals Corporation, or TPC, Protiva Biotherapeutics, Inc., a wholly owned subsidiary of TPC, or Protiva, and together with TPC, Tekmira, and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.), or Acuitas, entered into a settlement agreement and general release resolving all ongoing litigation, as well as a patent interference proceeding between us and Protiva. The terms of the settlement agreement include mutual releases and dismissal with prejudice of all claims and counterclaims between the parties. In addition, as part of the settlement agreement, the parties agreed to a covenantdecided not to sue one anotherappeal this ruling any further.  Final judgment in our favor on the future on matters released under the settlement agreement, as well as substantial liquidated

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damages to be paid by any party that breaches such covenant. The parties also agreed to resolve any future disputes that may arise over the three years following the settlement through binding arbitration.

Pursuant to the settlement agreement, we and Tekmira also agreed to resolve the interference proceeding declaredmerits has been entered by the United States Board of Patent Appeals and Interferences between us and Protiva, captionedProtiva Biotherapeutics, Inc. v. Alnylam Pharmaceuticals, Inc., Patent Interference No. 105792.MA District Court.

Contemporaneously with the execution of the settlement agreement, we and Tekmira restructured our contractual relationship and entered into a cross-license agreement that superseded the prior license and manufacturing agreements among us, TPC and Protiva. In connection with this restructuring, we incurred a $65.0 million charge to operating expenses for the year ended December 31, 2012. Specifically, we made aone-time payment of $30.0 million to Tekmira for the termination of, and our release from, all of our obligations under the manufacturing agreement with TPC, including without limitation the obligations to obtain materials and/or services from TPC. Further, we elected to buy-down certain future potential milestone and royalty payments due to Tekmira for certain of our RNAi therapeutics, formulated using lipid nanoparticle, or LNP, technology. Specifically, pursuant to the cross-license agreement, we made a one-time payment of $35.0 million to Tekmira, which amount constituted payment for the termination of the 2008 license agreements with TPC and Protiva and the parties’ rights and obligations thereunder, as well as the buy-down of certain milestone payments and the significant reduction of royalty rates for ALN-VSP, ALN-PCS02 and patisiran. In addition, under the 2012 cross-license agreement, we were obligated to pay TPC an aggregate of $10.0 million in contingent milestone payments related to advancement of ALN-VSP and patisiran, which now represent the only potential milestones due to Tekmira for ALN-VSP, ALN-PCS02 and patisiran LNP-based RNAi therapeutics. In the fourth quarter of 2013, we paid TPC $5.0 million in connection with the initiation of the patisiran Phase 3 clinical trial. With respect to the second $5.0 million milestone, in August 2013, we initiated binding arbitration proceedings to resolve a disagreement with TPC regarding the achievement by TPC of this milestone under the parties cross-license agreement relating to the manufacture of ALN-VSP clinical trial material for use in China. We currently expect that the Tekmira arbitration hearing will be held in the second quarter of 2015. Our policy is to expense these potential milestones when incurred and record them as research and development expense. A description of our cross-license agreement with Tekmira is included in Part I, Item 1, “— Delivery-Related Licenses and Collaborations — Tekmira,” of this annual report on Form 10-K.Indemnifications

Indemnifications

Licensor indemnification — In connection with our license agreements with Max Planck relating to the Tuschl I and Tuschl II patent applications, we are required to indemnify Max Planck for certain damages arising in connection with the intellectual property rights licensed under the agreements. Under the Max Planck indemnification agreement, we are responsible for paying the costs of any litigation relating to the


license agreements or the underlying intellectual property rights, including the costs associated with certain litigation regarding the Tuschl patents, which was settled during 2011, as well as certain costs associated with defending the University of Utah litigation described above. In connection with the settlement of the litigation regarding the Tuschl patents, we also agreed to indemnify Whitehead, MIT and UMass for certain costs associated with defending the University of Utah litigation. In connection with our research agreement with Acuitas Therapeutics Inc., or Acuitas (formerly AlCana Technologies, Inc.), we agreed to indemnify Acuitas for certain legal costs, subject to certain exceptions and limitations, associated with thecertain litigation with Arbutus Biopharma Corporation, or ABC (formerly Tekmira litigation described above.Pharmaceuticals Corporation), and Protiva Biotherapeutics, Inc., a wholly owned subsidiary of ABC, and together with ABC, Arbutus, which has been settled. These indemnification costs were charged to general and administrative expense. We are also a party to a number of agreements entered into in the ordinary course of business, which contain typical provisions that obligate us to indemnify the other parties to such agreements upon the occurrence of certain events. Such indemnification obligations are usually in effect from the date of execution of the applicable agreement for a period equal to the applicable statute of limitations.

Our maximum potential future liability under any such indemnification provisions is uncertain. However, to date, other than certain costs associated with certain previously settled litigation related to the Tuschl patents and the Tekmira litigation describedwith Arbutus referenced above, and certain ongoing defense costs related to the University of Utah litigation also described above, we have not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. We have determined that the estimated aggregate fair value of our potential liabilities under all such indemnification provisions is minimal and have not recorded any liability related to such indemnification provisions at December 31, 20142017 or 2013.

2016.

 

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8.

STOCKHOLDERS’ EQUITY

Preferred Stock

We have authorized up to 5,000,000 shares of preferred stock, $0.01 par value per share, for issuance. The preferred stock will have such rights, preferences, privileges and restrictions, including voting rights, dividend rights, conversion rights, redemption privileges and liquidation preferences, as shall be determined by our Boardboard of Directorsdirectors upon its issuance. At December 31, 20142017 and 2013,2016, there were no shares of preferred stock outstanding.

Stockholder Rights Agreement

On July 13, 2005, our Board of Directors declared a dividend of one right, or collectively, the Rights, to buy one one-thousandth of a share of newly designated Series A Junior Participating Preferred Stock, or Series A Junior Preferred Stock, for each outstanding share of our common stock to stockholders of record at the close of business on July 26, 2005. Initially, the Rights are not exercisable and will be attached to all certificates representing outstanding shares of common stock. The Rights will expire at the close of business on July 13, 2015 unless earlier redeemed or exchanged. Until a Right is exercised, the holder thereof will have no rights as a stockholder of Alnylam, including the right to vote or to receive dividends. Subject to the terms and conditions of the rights agreement, or the Rights Agreement, the Rights will become exercisable upon the earlier of (1) ten business days following the later of (a) the first date of a public announcement that a person or group (an “Acquiring Person”) acquires, or obtained the right to acquire, beneficial ownership of 20% or more of our outstanding shares of common stock or (b) the first date on which an executive officer of Alnylam has actual knowledge that an Acquiring Person has become such or (2) ten business days following the commencement of a tender offer or exchange offer that would result in a person or group beneficially owning more than 20% of our outstanding shares of common stock. Each Right entitles the holder to purchase one one-thousandth of a share of Series A Junior Preferred Stock at an initial purchase price of $80.00 in cash, subject to adjustment. In the event that any person or group becomes an Acquiring Person, unless the event causing the 20% threshold to be crossed is a Permitted Offer (as defined in the Rights Agreement), each Right not owned by the Acquiring Person will entitle its holder to receive, upon exercise, that number of shares of common stock of the Company (or in certain circumstances, cash, property or our other securities) which equals the exercise price of the Right divided by 50% of the current market price (as defined in the Rights Agreement) per share of such common stock at the date of the occurrence of the event. In the event that, at any time after any person or group becomes an Acquiring Person, (i) Alnylam is consolidated with, or merged with and into, another entity and we are not the surviving entity of such consolidation or merger (other than a consolidation or merger which follows a Permitted Offer) or if we are the surviving entity, but shares of our outstanding common stock are changed or exchanged for stock or securities (of any other person) or cash or any other property, or (ii) more than 50% of our assets or earning power is sold or transferred, each holder of a Right (except Rights which previously have been voided as set forth in the Rights Agreement) shall thereafter have the right to receive, upon exercise, that number of shares of common stock of the acquiring company which equals the exercise price of the Right divided by 50% of the current market price of such common stock at the date of the occurrence of the event.

Public Offerings

In February 2012,November 2017, we sold an aggregate of 8,625,0006,440,000 shares of our common stock through an underwritten public offering at a price to the public of $10.75$125.00 per share. As a result of thisthe offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $86.8$784.5 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $5.9$20.5 million.

In January 2013,May 2017, we sold an aggregate of 9,200,0005,000,000 shares of our common stock through an underwritten public offering at a price to the public of $20.13$71.87 per share. As a result of thisthe offering, we received aggregate net proceeds of approximately $173.6$355.2 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $11.6$4.2 million.

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In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $496.4 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $21.1 million.

 


9.

STOCK INCENTIVE PLANSSTOCK-BASED COMPENSATION

Stock Plans

In June 2009, our stockholders approved an amendment and restatement of our 2004 Stock Incentive Plan, or the Amended and Restated 2004 Plan, which replaced our 2004 Stock Incentive Plan, as amended, or the 2004 Plan.amended. At December 31, 2014,2017, the Amended and Restated 2004 Plan provided for the granting of stock options to purchase up to 12,366,485 shares of common stock. Prior to the adoption of the Amended and Restated 2004 Plan, we were authorized to grant both stock options and restricted stock awards under the 2004 Plan. As of the effective date of the Amended and Restated 2004 Plan, we may only grant stock options under the Amended and Restated 2004 Plan, provided that the terms and conditions of any restricted stock awards outstanding under the 2004 Plan will continue to be governed by the Amended and Restated 2004 Plan.

In June 2009, our stockholders also approved our 2009 Stock Incentive Plan, or the 2009 Plan. The 2009 Plan provides for the granting of stock options, restricted stock awards and units, stock appreciation rights and other stock-based awards. In June 2013,May 2015, our stockholders approved an amendment and restatement of the 2009 Stock Incentive Plan, which increased the number of shares of common stock authorized for issuance from 5,900,000 to 11,700,000. In May 2017, our stockholders approved a second amendment and restatement of the 2009 Stock Incentive Plan, or the Second Amended and Restated 2009 Plan, which increased the number of shares of common stock authorized for issuance from 2,200,00011,700,000 to 5,900,000.15,480,000. The Second Amended and Restated 2009 Plan provides for the granting of stock options, restricted stock and restricted stock units (together, restricted stock awards), stock appreciation rights and other stock-based awards. The Second Amended and Restated 2009 Plan has a fungible share pool. Any award that is not a full value award is counted against the authorized share limits specified in the Second Amended and Restated 2009 Plan as one share for each share of common stock subject to the award, and all full value awards, defined in the Second Amended and Restated 2009 Plan as restricted stock awards or other stock-based awards, are counted as one and a half shares for each one share of common stock subject to such full value award. In addition, the 2009 Plan includes a non-employee director stock option program under which each eligible non-employee director is entitled to (1) a grant of an option to purchase 30,000 shares of common stock upon his or her initial appointment to the Board of Directors, or such other amount as the Board of Directors deems appropriate, and (2) a subsequent annual grant of an option to purchase 15,000 shares of common stock based on continued service, provided the non-employee director has served as a director for at least six months and is serving as a director immediately prior to and following such annual grant. Stock options granted by us to non-employee directors upon their appointment to the Board of Directors vest as to one-third of such shares on each of the first, second and third anniversaries of the date of grant, and those granted annually thereafter vest in full on the first anniversary of the date of grant. During 2014, the Compensation Committee of our Board of Directors approved an amendment to the 2009 Plan to provide that upon retirement or resignation, non-employee Directors would have three months to exercise any outstanding stock option awards, unless such non-employee Director has five or more years of service, in which case such non-employee Director will have the lesser of five years or the remainder of the stock option term post-retirement or resignation to exercise such awards.

At December 31, 2014,2017, an aggregate of 9,317,14715,556,526 shares of common stock were reserved for issuance under our stock plans, including outstanding stock options to purchase 8,168,53311,239,128 shares of common stock, 941,583148,670 outstanding restricted stock units, 3,641,501 of common stock available for additional equity awards and 207,031527,227 shares available for future grant under our Amended and Restated 2004 Employee Stock Purchase Plan, or the 2004 ESPP, excluding 612,085 shares of commonAmended and Restated ESPP. Each stock granted in December 2014 that are subject to and contingent upon receiving stockholder approval of an amendment and restatement of our 2009 Plan in connection with our 2015 annual stockholder meeting. Each option shall expire within ten years of issuance. StockTime-based stock options granted by us to employees generally vest as to 25%25 percent of the shares on the first anniversary of the grant date and 6.25%6.25 percent of the shares at the end of each successive three-month period thereafter until fully vested. Performance-based stock options granted to employees in 2015 and 2016 vest, with respect to each year, as to one-fourth of the shares upon the later of the one-year anniversary of the grant date and the achievement of each of four specific clinical development, regulatory or commercial events, as approved by our compensation committee. Performance-based stock options granted to employees in 2013 and 2014 vest, with respect to each year, as to one-third of the shares upon the achievement of each of three specific clinical development andor regulatory events, as approved by our compensation committee. Historically, stock option awards to employees for annual performance, including performance-based stock option awards beginning in 2013, were approved for grant by the compensation committee of our board of directors at year-end.  However, with respect to 2017 annual awards as well as future annual awards, our compensation committee intends to approve the grant of any such awards in the first quarter of the following year.

Change in Control Agreements

 

132On November 7, 2017, we entered into a Change in Control, or CIC, Agreement with each member of our management board. If a member of our management board is terminated by us without Cause (as defined in the CIC Agreement) or if a management board member terminates his or her employment for Good Reason (as defined in the CIC Agreement), in either case, within 12 months following a CIC, such management board member will be entitled to receive certain benefits, including the immediate acceleration of all outstanding unvested stock options and other stock-based awards. In accordance with accounting guidance for stock-based compensation expense, we expect to record the modification date fair value for any equity grants that were not considered probable of vesting as of November 7, 2017 that ultimately vest.


Inducement Equity Grants

Effective as of each of May 8, 2017 and September 19, 2016, respectively, our compensation committee approved a grant to a newly hired executive of non-qualified stock options to purchase an aggregate of 150,000 shares of common stock. For each executive, time-vested options to purchase 125,000 shares of common stock will vest as to 25 percent of the shares on the first anniversary of the respective grant date and 6.25 percent of the shares at the end of each successive three-month period thereafter until fully vested. For each executive, performance-based stock options to purchase 25,000 shares of common stock will vest upon the later of the one-year anniversary of the respective grant date and the launch of our first internally developed product. In addition, effective as of February 6, 2017, our compensation committee approved a grant to a newly hired vice president level employee, of non-qualified stock options to purchase an aggregate of 50,000 shares of common stock. This time-vested option grant will vest as to 25 percent of the shares on the first anniversary of the grant date and 6.25 percent of the shares at the end of each successive three-month period thereafter until fully vested. Each of the May 8, 2017, February 6, 2017 and September 19, 2016 option grants was granted as an inducement grant outside of our stockholder approved stock plans in accordance with NASDAQ Listing Rule 5635(c)(4). These stock options have a ten-year term and an exercise price equal to the closing price of our common stock on the respective grant date.


Stock-Based Compensation

The following table summarizes stock-based compensation expense by type of award during the three years ended December 31, 2014,2017, in thousands:

 

  2014   2013   2012 

 

2017

 

 

2016

 

 

2015

 

Stock-based compensation expense by type of award:

    

 

 

 

 

 

 

 

 

 

 

 

 

Stock options

  $24,603    $13,839    $8,739  

Time-based stock options

 

$

61,802

 

 

$

62,800

 

 

$

43,078

 

Performance-based stock options

   4,960            

 

 

23,260

 

 

 

8,337

 

 

 

 

Restricted stock awards

   1,068     3,420     2,436  

 

 

541

 

 

 

497

 

 

 

555

 

ESPP share issuances

   392     261     241  

 

 

2,155

 

 

 

1,360

 

 

 

694

 

Other equity programs

 

 

1,946

 

 

 

1,846

 

 

 

 

Non-employee stock options

   2,038     3,183     944  

 

 

3,115

 

 

 

688

 

 

 

1,456

 

  

 

   

 

   

 

 

 

$

92,819

 

 

$

75,528

 

 

$

45,783

 

  $33,061    $20,703    $12,360  
  

 

   

 

   

 

 

The following table summarizes our unrecognized stock-based compensation expense, net of estimated forfeitures, at December 31, 20142017 by type of awards, excluding performance-based stock options, and the weighted-average period over which that expense is expected to be recognized:

 

  At December 31, 2014 

 

At December 31, 2017

 

  Unrecognized Expense,
Net of
Estimated Forfeitures
   Weighted-average
Recognition
Period
 

 

Unrecognized

Expense,

Net of

Estimated

Forfeitures

 

 

Weighted-

average

Recognition

Period

 

  (in thousands)   (in years) 

 

(in thousands)

 

 

(in years)

 

Type of award:

    

 

 

 

 

 

 

 

 

Stock options

  $59,854     2.62  

Restricted stock awards

   1,571     3.46  

Time-based stock options

 

$

124,295

 

 

 

2.60

 

Performance-based stock options

 

 

59,416

 

 

*

 

Performance-based restricted stock units

 

 

14,649

 

 

*

 

ESPP share issuances

   197     0.33  

 

 

970

 

 

0.33

 

*

Performance-based stock options and performance-based restricted stock units are recorded as expense beginning when vesting events are determined to be probable. 

Valuation Assumptions for Stock Options

The fair value of stock options, at date of grant, based on the following assumptions, was estimated using the Black-Scholes option-pricing model. Our expected stock-price volatility assumption is based on the historical volatility of our publicly traded stock. The expected life assumption is based on our historical data. The dividend yield assumption is based on the fact that we have never paid cash dividends and have no present intention to pay cash dividends. The risk-free interest rate used for each grant is equal to the zero coupon rate for instruments with a similar expected life.

 

   2014  2013  2012 

Risk-free interest rate

   1.7-2.3  1.0-2.0  0.8-1.0

Expected dividend yield

             

Expected option life

   5.5-7.5 years    5.6 years    5.6-5.9 years  

Expected volatility

   53-57  55-56  57

 

 

2017

 

 

2016

 

 

2015

 

Risk-free interest rate

 

1.9-2.3%

 

 

0.9-2.2%

 

 

1.0-2.0%

 

Expected dividend yield

 

 

 

 

 

 

 

 

 

Expected option life

 

5.7-7.2 years

 

 

3.5-7.5 years

 

 

3.5-7.5 years

 

Expected volatility

 

61-67%

 

 

55-65%

 

 

53-60%

 

 


133


Stock Option Activity

The following table summarizes the activity of our stock option plans excluding stock options granted in December 2014, subject to and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan, andthe inducement grants described above, excluding performance-based stock options:

 

   Number of
Options

(in thousands)
  Weighted-
average
Exercise
Price
   Weighted-
average
Remaining
Contractual
Term (in years)
   Aggregate
Intrinsic
Value
(in thousands)
 

Outstanding, December 31, 2013

   8,245   $22.06      

Granted

   1,352    75.77      

Exercised

   (1,982  14.83      

Cancelled

   (85  35.32      
  

 

 

    

 

 

   

Outstanding, December 31, 2014

   7,530   $33.46     6.32    $478,506  
  

 

 

    

 

 

   

Exercisable at December 31, 2014

   4,736   $21.44     4.86    $357,891  

Vested or expected to vest at December 31, 2014

   7,292   $32.53     6.23    $470,149  

 

 

Number of

Options

(in thousands)

 

 

Weighted-

average

Exercise

Price

 

 

Weighted-

average

Remaining

Contractual

Term (in years)

 

Aggregate

Intrinsic

Value

(in thousands)

 

Outstanding, December 31, 2016

 

 

9,913

 

 

$

56.05

 

 

 

 

 

 

 

Granted

 

 

1,664

 

 

 

75.66

 

 

 

 

 

 

 

Exercised

 

 

(1,796

)

 

 

42.81

 

 

 

 

 

 

 

Cancelled

 

 

(680

)

 

 

83.70

 

 

 

 

 

 

 

Outstanding, December 31, 2017

 

 

9,101

 

 

$

60.18

 

 

6.92

 

$

609,620

 

Exercisable at December 31, 2017

 

 

5,294

 

 

$

51.54

 

 

5.59

 

$

400,390

 

Vested or expected to vest at December 31, 2017

 

 

8,670

 

 

$

59.64

 

 

6.82

 

$

587,480

 

The weighted-average fair value of stock options granted was $39.08, $26.33$44.76, $31.66 and $8.68$51.28 per share for the years ended December 31, 2014, 20132017, 2016 and 2012,2015, respectively. The intrinsic value of stock options exercised was $126.5$111.3 million, $57.9$22.0 million and $4.8$130.0 million for the years ended December 31, 2014, 20132017, 2016 and 2012,2015, respectively. We satisfy stock option exercises with newly issued shares of our common stock.

Performance-Based Stock Options

During 2013, we began grantingWe granted performance-based stock options to employees that vest as to one-fourth of the shares upon the later of the one-year anniversary of the grant date and the achievement of each of four specific clinical development, regulatory or commercial events, as approved by our compensation committee, with respect to 2015 and 2016 grants, and that vest as to one-third of the shares upon the later of the one-year anniversary of the grant date and the achievement of each of three specific clinical development andor regulatory events, as approved by our Compensation Committee. compensation committee, with respect to 2013 and 2014 grants. During each of the years ended December 31, 2017 and 2016, we also granted an option to purchase 25,000 shares of common stock to a newly hired executive that vests upon the later of the one-year anniversary of the grant date and the achievement of a commercial event.  

The following table summarizes the activity of our performance-based stock options excluding stock options granted in December 2014 subject tounder our equity plans and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan:

   Number of
Options

(in thousands)
  Weighted-
average
Exercise
Price
   Weighted-
average
Remaining
Contractual
Term (in years)
   Aggregate
Intrinsic
Value
(in thousands)
 

Outstanding, December 31, 2013

   468   $63.00      

Granted

   194    96.45      

Exercised

   (5  63.00      

Cancelled

   (18  63.00      
  

 

 

    

 

 

   

Outstanding, December 31, 2014

   639   $73.15     9.05    $15,237  
  

 

 

    

 

 

   

Exercisable at December 31, 2014

   150   $63.00     8.40    $5,100  

On December 12, 2014, we achieved the first performance criteria of the December 18, 2013 grant of performance-based stock options and the stock option was vested as one-third of the performance-based portion of the grant.inducement grants described above:

 

 

Number of

Options

(in thousands)

 

 

Weighted-

average

Exercise

Price

 

 

Weighted-

average

Remaining

Contractual

Term (in years)

 

Aggregate

Intrinsic

Value

(in thousands)

 

Outstanding, December 31, 2016

 

 

2,357

 

 

$

69.61

 

 

 

 

 

 

 

Granted

 

 

25

 

 

 

52.61

 

 

 

 

 

 

 

Exercised

 

 

(54

)

 

 

80.46

 

 

 

 

 

 

 

Cancelled

 

 

(190

)

 

 

69.59

 

 

 

 

 

 

 

Outstanding, December 31, 2017

 

 

2,138

 

 

$

69.14

 

 

7.79

 

$

123,795

 

Exercisable at December 31, 2017

 

 

813

 

 

$

73.66

 

 

7.23

 

$

43,416

 

During the years ended December 31, 2017 and 2016, there were 614,796 and 159,122 performance-based stock options that vested, respectively. There were no performance-based stock options that vested during the year ended December 31, 2015. The weighted-average grant dategrant-date fair value for the performance-based stock options that vested during the years ended December 31, 2017 and 2016 was $37.86 and $52.29 per share, respectively. The intrinsic value of performance-based stock options exercised was $1.8 million, $35,000 and $1.4 million for the first tranche of theyears ended December 18, 201331, 2017, 2016 and 2015, respectively. We satisfy performance-based stock option was $32.26 per share.exercises with newly issued shares of our common stock. During the fourth quarterthree years ended December 31, 2017, each performance-based stock option that vested was determined to be probable of 2014,vesting, and we determined the first performance criteria of the December 18, 2013 grant was probable and began to record expense, which was recognized in full asduring the year the performance-based stock option vested based on achievement of December 12, 2014.the respective performance-criteria. As of the grant date and December 31, 2014,2017, we havehad determined that the remaining performance criteria offor all outstanding performance-based stock options reflected in the table above areas of December 31, 2017 were not probable.probable of being achieved. As a result, we have not recorded stock-based compensation expense for these performance-based stock options. The intrinsic valueoptions as of performance-based stock options exercised was $0.1

134


million for the year ended December 31, 2014. We satisfy performance-based stock option exercises with newly issued shares of our common stock.2017.


Contingent Stock Option Awards

On December 17, 2014, the Compensation Committeecompensation committee of our Boardboard of Directorsdirectors approved the grant of stock options to purchase 612,085 shares of our common stock, at an exercise price of $96.45 per share, to members of our management team. These stock option grants were approved subject to and contingent upon approval by our stockholders at our 2015 annual meeting of an amendmentthe Amended and restatement of ourRestated 2009 Plan, to, among other things, increase the shares authorized for issuance thereunder.thereunder, which approval was obtained in May 2015. One-half of the contingent stock options granted are time-based stock options and one-half are performance-based stock options. In no event will the contingent stock options be exercised before approval of the amended and restated 2009 Plan by our stockholders; and in the event that the amended and restated 2009 Plan is not approved by the stockholders at the 2015 annual meeting, the contingent stock options shall immediately terminate and be of no further force or effect. If the stockholders approve the amended and restated 2009 Plan, the grant-dateThe grant date fair value of the contingent stock options would beis based on a Black-Scholes valuation model based on the fair market value of the stock on May 1, 2015, the date of such stockholder approval. NoWe began recording stock-based compensation expense was recorded in 2014 relating to this contingent stock option grant.grant on May 1, 2015.

Performance-Based Restricted Stock AwardsUnits

In October 2010,January 2016, we granted 113,370 shares of our restricted stock to certain employees. These restricted stock awards were valued at $1.4 million on the grant date. These restricted stock awards vested ratably over an approximate three-year period. In May 2011, we granted an aggregate of 229,806172,718 shares of performance-based restricted stock awardsunits to our employees, excluding our leadership team. These restricted stock awards were valued at $2.3 million on the grant date and had a contractual term of five years. The vesting of these awards was predicated on our achievement of certain clinical development goals. These awards have vested in full due to the achievement of these goals in 2011 and 2013.

In January 2012, as part of our post-restructuring retention program, we granted an aggregate of 508,928 shares of restricted stock to our retained employees, excluding our chief executive officer and president and chief operating officer.president. These performance-based restricted stock awardsunits were valued at $5.3$16.1 million on the grant date and vested in fulldate. The vesting of these performance-based restricted stock units is predicated on the second anniversarylaunch of our first internally developed product.   As of the grant date.

The following table summarizesdate and December 31, 2017, for accounting purposes we had determined that the activity of ourperformance criteria for these performance-based restricted stock awards, includingunits was not probable of being achieved. As a result, we have not recorded stock-based compensation expense for these performance-based restricted stock and restricted stock units:

   Number of
Restricted
Stock Awards
(in thousands)
  Weighted-
average
Grant Date
Fair Value
 

Unvested at December 31, 2013

   500   $10.69  

Granted

   29    68.28  

Vested

   (499  10.59  

Forfeited

         
  

 

 

  

Unvested at December 31, 2014

   30   $68.02  
  

 

 

  

The total fair valueunits as of restricted stock awards that vested during the years ended December 31, 2014, 2013 and 2012 (measured on the date of vesting) was $44.4 million, $5.8 million and $1.5 million, respectively.2017.

Employee Stock Purchase Plan

In 2004, we adopted the 2004 ESPPEmployee Stock Purchase Plan with 315,789 shares authorized for issuance. In June 2010, our stockholders approved an amendment to the 2004 ESPP,Employee Stock Purchase Plan, which increased the shares authorized for issuance from

135


315,789 shares to 715,789 shares. In May 2017, our stockholders approved the Amended and Restated ESPP, which further increased the shares authorized for issuance from 715,789 shares to 1,215,789 shares. Under the 2004Amended and Restated ESPP, each offering period is six months, at the end of which employees may purchase shares of common stock through payroll deductions made over the term of the offering. The per-share purchase price at the end of each offering period is equal to the lesser of 85%85 percent of the closing price of our common stock at the beginning or end of the offering period. We issued 21,938, 45,141103,666, 53,499 and 73,59022,639 shares during the years ended December 31, 2014, 20132017, 2016 and 2012,2015, respectively, and at December 31, 2014, 207,0312017, 527,227 shares were available for issuance under the 2004Amended and Restated ESPP.

The weighted-average fair value of stock purchase rights granted as part of the 2004Amended and Restated ESPP was $17.03, $11.49$17.10, $24.90 and $2.82$29.96 per share for the years ended December 31, 2014, 20132017, 2016 and 2012,2015, respectively. The fair value was estimated using the Black-Scholes option-pricing model. During the three yearsyear ended December 31, 2014,2017, we used a weighted-average stock-price volatility of 55%,91 percent, expected option life assumption of six months and a risk-free interest rate of 0.1%.0.7 percent. During the years ended  December 31, 2016 and 2015, we used a weighted-average stock-price volatility of approximately 55 percent, expected option life assumption of six months and a risk-free interest rate of approximately 0.1 percent.

 

10.

INCOME TAXES

The domestic and foreign components of loss before income taxes are as follows, in thousands:

 

  2014 2013 2012 

 

2017

 

 

2016

 

 

2015

 

Domestic

  $(372,137 $(81,109 $(116,400

 

$

(378,293

)

 

$

(350,704

)

 

$

(245,681

)

Foreign

   (28,467  (10,811  (186

 

 

(112,581

)

 

 

(59,404

)

 

 

(44,392

)

  

 

  

 

  

 

 

Loss before income taxes

  $(400,604 $(91,920 $(116,586

 

$

(490,874

)

 

$

(410,108

)

 

$

(290,073

)

  

 

  

 

  

 

 


Deferred income taxes reflect the tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting and income tax purposes. We establish a valuation allowance when uncertainty exists as to whether all or a portion of the net deferred tax assets will be realized. We have allocated the valuation allowance between current and non-current deferred tax assets and liabilities. As a result of this allocation, we have recorded a long term deferred tax asset of $31.7 million and a corresponding short term deferred tax liability of $31.7 million on the balance sheet. Components of the net deferred tax (liability) asset at December 31, 20142017 and 20132016 are as follows, in thousands:

 

   2014  2013 

Deferred tax assets:

   

Net operating loss carryforwards

  $176,789   $124,797  

Research and development credits

   38,204    23,902  

AMT credits

   788    788  

Foreign tax credits

   3,196    3,196  

Capitalized research and development and start-up costs

   19,246    16,214  

Deferred revenue

   14,273    37,273  

Deferred compensation

   24,516    21,706  

Intangible assets

   17,637    2,210  

Partnership interest

   689    689  

Other

   5,871    4,885  
  

 

 

  

 

 

 

Total deferred tax assets

   301,209    235,660  

Deferred tax liabilities:

   

Intangible assets

       (7

Unrealized gain on available-for-sale securities

   (32,793  (13,267

Deferred tax asset valuation allowance

   (268,416  (222,393
  

 

 

  

 

 

 

Net deferred tax liability

  $   $(7
  

 

 

  

 

 

 

 

 

2017

 

 

2016

 

Deferred tax assets:

 

 

 

 

 

 

 

 

Net operating loss carryforwards

 

$

405,784

 

 

$

346,965

 

Research and development credits

 

 

192,094

 

 

 

111,394

 

AMT credits

 

 

788

 

 

 

788

 

Foreign tax credits

 

 

 

 

 

3,196

 

Capitalized research and development and start-up costs

 

 

13,163

 

 

 

18,138

 

Deferred revenue

 

 

13,576

 

 

 

20,853

 

Deferred compensation

 

 

42,990

 

 

 

51,355

 

Intangible assets

 

 

9,018

 

 

 

14,725

 

Partnership interest

 

 

 

 

 

1,623

 

Other

 

 

11,608

 

 

 

7,845

 

Total deferred tax assets

 

 

689,021

 

 

 

576,882

 

Deferred tax liabilities:

 

 

 

 

 

 

 

 

Unrealized gain on available-for-sale securities

 

 

(765

)

 

 

(1,524

)

Deferred tax asset valuation allowance

 

 

(688,256

)

 

 

(575,358

)

Net deferred tax liability

 

$

 

 

$

 

   

136


The benefit from income taxes for the years ended December 31, 2014, 2013 and 2012 are as follows, in thousands:

   2014  2013  2012 

U.S.:

    

Current

  $   $34   $52  

Deferred

   (40,209  (2,695  (10,572
  

 

 

  

 

 

  

 

 

 

Total U.S.

   (40,209  (2,661  (10,520
  

 

 

  

 

 

  

 

 

 

Foreign:

    

Current

             

Deferred

       (34  (52
  

 

 

  

 

 

  

 

 

 

Total Foreign

       (34  (52
  

 

 

  

 

 

  

 

 

 

Benefit from income taxes

  $(40,209 $(2,695 $(10,572
  

 

 

  

 

 

  

 

 

 

Our effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2014, 20132017, 2016 and 2012:2015:

 

  2014 2013 2012 

 

2017

 

 

2016

 

 

2015

 

At U.S. federal statutory rate

   35.0  35.0  35.0

 

 

35.0

%

 

 

35.0

%

 

 

35.0

%

State taxes, net of federal effect

   1.8    4.3    4.9  

 

 

3.8

 

 

 

3.7

 

 

 

4.0

 

Stock-based compensation

   (0.2  0.8    (0.7

 

 

3.3

 

 

 

(1.4

)

 

 

(1.1

)

Tax credits

   3.5    8.5    4.2  

 

 

9.9

 

 

 

11.8

 

 

 

8.0

 

Orphan drug credit addback

   (0.6  (2.7    

Orphan drug credit

 

 

(3.4

)

 

 

(3.5

)

 

 

(2.0

)

Other permanent items

       (0.3  (1.6

 

 

(1.0

)

 

 

(0.4

)

 

 

(0.1

)

Foreign rate differential

   (2.5  (4.1  (0.1

 

 

(8.1

)

 

 

(5.1

)

 

 

(5.4

)

In-process research and development

   (19.4        

Tax basis in intangible assets as a result of Sirna transaction

   4.2          

Tax reform change

 

 

(46.5

)

 

 

 

 

 

 

Other

 

 

(0.9

)

 

 

 

 

 

 

Valuation allowance

   (11.8  (38.5  (32.6

 

 

7.9

 

 

 

(40.1

)

 

 

(38.4

)

  

 

  

 

  

 

 

Effective income tax rate

   10.0  3.0  9.1

 

 

%

 

 

%

 

 

%

  

 

  

 

  

 

 

We have evaluated the positive and negative evidence bearing upon the realizability of our deferred tax assets. We have concluded, in accordance with the applicable accounting standards, that it is more likely than not that we may not realize the benefit of all of our deferred tax assets. Accordingly, we have recorded a valuation allowance against the deferred tax assets that management believes will not be realized. We reevaluate the positive and negative evidence on a quarterly basis. The valuation allowance increased by $46.0$112.9 million, $29.7$177.9 million and $38.3$129.1 million for the years ended December 31, 2014, 20132017, 2016 and 20122015, respectively, due primarily to additional operating losses. Increases

On December 22, 2017, the President of the United States signed into law the Tax Cuts and Jobs Act, or TCJA, tax reform legislation. The TCJA makes significant changes in U.S. tax law including a reduction in the corporate tax rates, changes to net operating loss carryforwards and carrybacks, and a repeal of the corporate alternative minimum tax. The TCJA reduced the U.S. corporate tax rate from the current rate of 35 percent down to 21 percent starting on January 1, 2018. As a result of the TCJA, we were required to revalue deferred tax assets and liabilities at 21 percent. This revaluation resulted in a provision of $227.9 million to income tax expense in continuing operations and a corresponding reduction in the valuation allowance.  As a result, there was no impact to our consolidated statements of comprehensive loss as a result of the reduction in tax rates. The other provisions of the TCJA did not have a material impact on our consolidated financial statements.


Our preliminary estimate of the TCJA and the remeasurement of our deferred tax assets and liabilities is subject to the valuation allowance were partially offset by decreasesfinalization of management’s analysis related to certain matters, such as developing interpretations of the recognitionprovisions of the TCJA, changes to certain estimates and the filing of our tax returns. U.S. Treasury regulations, administrative interpretations or court decisions interpreting the TJCA may require further adjustments and changes in our estimates. The final determination of the TCJA and the remeasurement of our deferred revenue.assets and liabilities will be completed as additional information becomes available, but no later than one year from the enactment of the TCJA.

ForThere was no benefit from income taxes recorded during the years ended December 31, 2014, 20132017, 2016, and 2012,2015.   

On January 1, 2017, we recorded a tax benefitadopted new accounting guidance released in March 2016 that updates the accounting for certain aspects of $40.2 million, $2.7 million and $10.6 million, respectively. Forshare-based payments to employees, including the years ended December 31, 2014, 2013 and 2012, we recorded unrealized gains on our investments in available-for-sale securities in other comprehensive income and additional paid-in capital. The benefit of $19.5 million, $2.7 million and $10.6 million for the years ended December 31, 2014, 2013 and 2012, respectively, is due to the recognition of corresponding income tax expense associated withconsequences, classification of awards as either equity or liabilities and classification on the increase inconsolidated statement of cash flows. On January 1, 2017, the value of our investment in Regulus that we carried at fair market value during the same period. In addition, for the year ended December 31, 2014, we recorded a benefit of $20.7 million due to the difference between the fair value of stock and the cash proceeds received from Genzyme for the issuance of our common stock calculated at the closing date of the transaction. The corresponding income tax expense has

137


been recorded in other comprehensive income and additional paid-in capital, respectively. Intraperiod tax allocation rules require us to allocate our provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income and additional paid-in capital. In periods in which we have a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income and additional paid-in capital, we must allocate the tax provision to the other categories of earnings. We then record a related tax benefit in continuing operations.

The deferred tax assets above exclude $83.5 million ofassociated with net operating losses increased by $122.2 million and $0.4 million ofthe deferred tax asset associated with federal and state research and development credits related to tax deductions fromcredit increased by $30.8 million.  These amounts were offset by a corresponding increase in the exercise of stock options subsequent to thevaluation allowance.  The adoption of the 2006 accountingthis standard on stock-based compensation. This amount represents an excess tax benefit and hasdid not been included in the gross deferred tax assets.impact our consolidated financial statements.

At December 31, 2014,2017, we had federal and state net operating loss carryforwards of $639.3 million$1.47 billion and $701.8 million, respectively. These amounts will$1.55 billion, respectively, to reduce future taxable income that will expire at various dates through 2034.2037. At December 31, 2014,2017, we had federal and state research and development and investment tax credit carryforwards were $32.3of $180.0 million and $10.1$15.3 million, respectively, available to reduce future tax liabilities that expire at various dates through 2034.2037. At December 31, 2014, foreign tax credit carryforwards were $3.2 million available to reduce future tax liabilities that expire in 2017. At December 31, 2014,2017, we had alternative minimum tax credits of $0.8 million arethat will either be available to reduce future regular tax liabilities toor be fully refundable in 2021. We have a valuation allowance against the extent such regularnet operating loss and credit deferred tax less other non-refundable credits exceeds the tentative minimum tax.assets as it is unlikely that we will realize these assets. Ownership changes, as defined in the Internal Revenue Code, including those resulting from the issuance of common stock in connection with our public offerings, may limit the amount of net operating loss and tax credit carryforwards that can be utilized to offset future taxable income or tax liability. The amount of the limitation is determined in accordance with Section 382 of the Internal Revenue Code. We have determinedperformed an analysis of ownership changes through December 31, 2017.  Based on this analysis, we do not believe that based on the valueany of Alnylam, in the event there was an annual limitation underour tax attributes will expire unutilized due to Section 382 all net operating loss and tax credit carryforwards would still be available to offset taxable income.limitations.    

At December 31, 2014, 20132017, 2016 and 2012,2015, we had no unrecognized tax benefits that, if recognized, would favorably impact our effective income tax rate in future periods.benefits.

The tax years 20102014 through 20142017 remain open to examination by major taxing jurisdictions to which we are subject, which are primarily in the United States, as carryforward attributes generated in years past may still be adjusted upon examination by the Internal Revenue Service or state tax authorities if they have or will be used in a future period. However, the statute of limitations remains open to the extent we utilize net operating losses or credits from earlier years. We have not recorded any interest and penalties on any unrecognized tax benefits since its inception.

 

11.

REGULUS

ACCRUED EXPENSES

In September 2007, we and Isis established Regulus, a company focused on the discovery, development and commercialization of microRNA therapeutics, a potential new class of drugs to treat the pathways of human disease. Regulus, which initially was established as a limited liability company, converted to a C corporation in January 2009 and changed its name to Regulus Therapeutics Inc. Regulus operates as an independent company with a separate board of directors, scientific advisory board and management team. We currently own approximately 12% of Regulus’ outstanding common stock.

In consideration for our and Isis’ initial interests in Regulus, each party granted Regulus exclusive licenses to its intellectual property for certain microRNA therapeutic applications as well as certain patents in the microRNA field. In addition, we made an initial cash contribution to Regulus of $10.0 million, resulting in us and Isis making approximately equal aggregate initial capital contributions to Regulus. In March 2009, we and Isis each purchased $10.0 million of Series A preferred stock of Regulus.

From the formation of Regulus in September 2007 to October 2012, we accounted for our interest in Regulus using the equity method of accounting. We reviewed the consolidation guidance that defines a variable interest entity, or VIE, and concluded that Regulus qualified as a VIE during such time period. We did not consolidate Regulus as we lacked the power to direct the activities that could significantly impact the economic success of this entity.

138


Summary results of Regulus’ statements of comprehensive loss for the nine months ended September 30, 2012 are presented in the tables below, in thousands:

   Nine months ended
September 30,
 
   2012 

Statements of Comprehensive Loss Data:

  

Net revenues

  $9,462  

Operating expenses

   17,733  
  

 

 

 

Loss from operations

   (8,271

Other expense

   (2,289

Income tax benefit

   28  
  

 

 

 

Net loss

  $(10,532
  

 

 

 

Under the equity method of accounting, we were required to recognize losses up to the amount of Regulus’ debt, which was guaranteed by us. This resulted in a negative carrying amount. In October 2012, Regulus completed an initial public offering, resulting in our ownership percentage decreasing from approximately 44% to 17% of Regulus’ outstanding common stock. Upon the completion of the Regulus’ initial public offering, our debt guarantee was terminated.

Based upon our ownership percentage of 17% after the initial public offering, as well as a review of qualitative factors, we did not believe that we had the ability to exercise significant influence over the operating decisions and financial policies of Regulus and therefore discontinued the equity method of accounting for Regulus at September 30, 2012. We determined that the period between September 30, 2012 and the date on which Regulus’ closed its initial public offering was immaterial for additional equity method accounting. Accordingly, beginning in October 2012, we accounted for our investment in Regulus as an available-for-sale marketable security due to its readily determinable fair value. As a result of the issuance of additional common stock by Regulus, we recognized a gain of $16.1 million. This amount was recorded as other income in our consolidated statements of comprehensive loss for the year ended December 31, 2012. Our carrying amount in Regulus increased to $12.4 million following the initial public offering, which became the initial basis of our investment in Regulus under the accounting standard for marketable securities. In addition, we recorded $15.7 million as an unrealized gain in other comprehensive income, net of an intraperiod tax benefit of $10.6 million during the year ended December 31, 2012. After sales of our investment in Regulus during 2014, our carrying amount in Regulus decreased to $11.9 million at December 31, 2014.

12.ACCRUED EXPENSES

Accrued expenses consist of the following at December 31, 20142017 and 2013,2016, in thousands:

 

  At December 31, 

 

At December 31,

 

  2014   2013 

 

2017

 

 

2016

 

Compensation and related

  $7,357    $4,822  

 

$

33,826

 

 

$

13,689

 

Clinical trial and manufacturing

   5,548     2,933  

 

 

20,004

 

 

 

11,756

 

Consulting and professional services

   3,886     2,135  

 

 

7,276

 

 

 

2,788

 

Pre-clinical

   3,081     1,004  

 

 

239

 

 

 

1,257

 

Other

   3,808     3,266  

 

 

10,858

 

 

 

12,628

 

  

 

   

 

 

 

$

72,203

 

 

$

42,118

 

  $23,680    $14,160  
  

 

   

 

 

 

13.RESTRUCTURING

In January 2012, our Board of Directors approved, and we implemented, a strategic corporate restructuring pursuant to which we reduced our overall workforce by approximately 33%, to approximately 115 employees.

 

139


During the three months ended March 31, 2012, we substantially completed the implementation of the strategic corporate restructuring and recorded $3.9 million of restructuring-related costs in operating expenses, including employee severance, benefits and related costs. We paid substantially all of these restructuring costs during 2012. We did not incur any additional significant costs associated with this restructuring and do not expect to incur any additional significant costs in the future.


12.

14. QUARTERLY FINANCIAL DATA (UNAUDITED)

The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.

 

  Three Months Ended 

 

Three Months Ended

 

  March 31,
2014
 June 30,
2014
 September 30,
2014
 December 31,
2014
 

 

March 31,

2017

 

 

June 30,

2017

 

 

September 30,

2017

 

 

December 31,

2017

 

  (In thousands, except per share data) 

 

(In thousands, except per share data)

 

Revenues

  $8,275   $7,295   $10,972   $24,019  

 

$

18,960

 

 

$

15,932

 

 

$

17,096

 

 

$

37,924

 

Operating expenses

   277,339    52,300    56,171    69,731  

 

 

125,471

 

 

 

136,406

 

 

 

142,896

 

 

$

185,227

 

Net loss

   (250,943  (44,074  (43,989  (21,389

 

$

(107,290

)

 

$

(118,420

)

 

$

(122,937

)

 

$

(142,227

)

Net loss per common share — basic and diluted

  $(3.70 $(0.58 $(0.58 $(0.28

 

$

(1.25

)

 

$

(1.34

)

 

$

(1.34

)

 

$

(1.48

)

Weighted-average common shares — basic and diluted

   67,786    75,835    76,408    76,957  

 

 

86,027

 

 

 

88,098

 

 

 

91,828

 

 

 

96,139

 

 

  Three Months Ended 

 

Three Months Ended

 

  March 31,
2013
 June 30,
2013
 September 30,
2013
 December 31,
2013
 

 

March 31,

2016

 

 

June 30,

2016

 

 

September 30,

2016

 

 

December 31,

2016

 

  (In thousands, except per share data) 

 

(In thousands, except per share data)

 

Revenues

  $18,642   $8,687   $8,991   $10,847  

 

$

7,345

 

 

$

8,709

 

 

$

13,651

 

 

$

17,454

 

Operating expenses

   28,446    29,999    41,225    40,439  

 

 

117,373

 

 

 

101,159

 

 

 

120,327

 

 

 

132,887

 

Net loss

   (9,013  (18,169  (29,686  (32,357

 

$

(102,974

)

 

$

(90,129

)

 

$

(104,071

)

 

$

(112,934

)

Net loss per common share — basic and diluted

  $(0.15 $(0.29 $(0.48 $(0.51

 

$

(1.21

)

 

$

(1.05

)

 

$

(1.21

)

 

$

(1.32

)

Weighted-average common shares — basic and diluted

   59,173    61,661    62,416    62,909  

 

 

85,277

 

 

 

85,545

 

 

 

85,716

 

 

 

85,843

 

The increase in operating expenses for the three months ended March 31, 2014 resulted from a $224.7 million charge to in-process research and development expense in connection with the purchase of the Sirna RNAi assets from Merck. During the three months ended June 30, 2014, we recorded a credit of $3.9 million to in-process research and development expense, resulting in $220.8 million in-process research and development expense recorded for the year ended December 31, 2014 as a result of this asset acquisition. See Note 3, “Significant Agreements,” for further information.

 

140



ITEM 9.

CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTSACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

None.

 

ITEM  9A.

CONTROLS AND PROCEDURES

Our management, with the participation of our chief executive officer (principal executive officer) and senior vice president, of finance and treasurer,chief financial officer (principal financial officer), evaluated the effectiveness of our disclosure controls and procedures as of December 31, 2014.2017. The term “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of December 31, 2014,2017, our chief executive officer and senior vice president, of finance and treasurerchief financial officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

Management’s report on our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) and the independent registered public accounting firm’s report on the effectiveness of our internal control over financial reporting are included in Item 8, “Financial Statements and Supplementary Data” of this annual report on Form 10-K and are incorporated herein by reference.

No change in our internal control over financial reporting occurred during the fiscal quarter ended December 31, 20142017 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

 

ITEM 9B.

OTHER INFORMATION

None.


PART III

 

ITEM  10.

DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

The information required by this item is incorporated hereinIncorporated by reference tofrom the information contained underin our Proxy Statement for our 2018 Annual Meeting of Stockholders, which we will file with the sections captioned “Proposal One — Election of Class II Directors,” “Section 16(a) Beneficial Ownership Reporting Compliance” and “Corporate Governance”SEC within 120 days of the Proxy Statement. The information required by this item relating to executive officers is included in Part I, Item 1, “— Business-Executive Officersend of the Registrant,” offiscal year to which this annual reportAnnual Report on Form 10-K.10-K relates.

ITEM  11.

EXECUTIVE COMPENSATION

The information required by this item is incorporated hereinIncorporated by reference tofrom the information contained underin our Proxy Statement for our 2018 Annual Meeting of Stockholders, which we will file with the sections captioned “Information about Executive Officer and Director Compensation,” “Compensation Committee Interlocks and Insider Participation,” “Employment Arrangements” and “Compensation Committee Report”SEC within 120 days of the Proxy Statement.end of the fiscal year to which this Annual Report on Form 10-K relates.

141


ITEM 12.

SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

The information required by this item is incorporated hereinIncorporated by reference tofrom the information contained underin our Proxy Statement for our 2018 Annual Meeting of Stockholders, which we will file with the sections captioned “Security Ownership of Certain Beneficial Owners and Management,” “Information about Executive Officer and Director Compensation” and “Securities Authorized for Issuance Under Equity Compensation Plans”SEC within 120 days of the Proxy Statement.end of the fiscal year to which this Annual Report on Form 10-K relates.

ITEM 13.

CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information required by this item is incorporated hereinIncorporated by reference tofrom the information contained underin our Proxy Statement for our 2018 Annual Meeting of Stockholders, which we will file with the sections captioned “Corporate Governance,” “Employment Arrangements” and “Certain Relationships and Related Transactions”SEC within 120 days of the Proxy Statement.end of the fiscal year to which this Annual Report on Form 10-K relates.

ITEM  14.

PRINCIPAL ACCOUNTANT FEES AND SERVICES

The information required by this item is incorporated hereinIncorporated by reference tofrom the information contained underin our Proxy Statement for our 2018 Annual Meeting of Stockholders, which we will file with the sections captioned “Corporate Governance,” “Principal Accountant Fees and Services” and “Pre-Approval Policies and Procedures”SEC within 120 days of the Proxy Statement.end of the fiscal year to which this Annual Report on Form 10-K relates.


PART IV

 

ITEM  15.

EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

(a) (1) Financial Statements

The following consolidated financial statements are filed as part of this report under “Item 8 — Financial Statements and Supplementary Data”:

 

Page

Management’s Annual Report on Internal Control Over Financial Reporting

101

87

Report of Independent Registered Public Accounting Firm

102

88

Consolidated Balance Sheets at December 31, 20142017 and 20132016

103

90

Consolidated Statements of Comprehensive Loss for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

104

91

Consolidated Statements of Stockholders’ Equity for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

105

92

Consolidated Statements of Cash Flows for the Years Ended December 31, 2014, 20132017, 2016 and 20122015

106

93

Notes to Consolidated Financial Statements

107

94

(a) (2) List of Schedules

All schedules to the consolidated financial statements are omitted as the required information is either inapplicable or presented in the consolidated financial statements.

(a) (3) List of Exhibits

The exhibits which are filed with this report or which are incorporated herein by reference are set forth in the Exhibit Index hereto.

142


SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized, on February 13, 2015.

 

Exhibit No.

ALNYLAM PHARMACEUTICALS, INC.

Exhibit

By:

/s/ John M. Maraganore, Ph.D.
John M. Maraganore, Ph.D.
Chief Executive Officer

Pursuant to the requirements of the Securities Exchange Act of 1934, the Report has been signed below by the following persons on behalf of the Registrant and in the capacities indicated as of February 13, 2015.

 

Name  2.1†*

Title

/s/    John M. Maraganore, Ph.D.

John M. Maraganore, Ph.D.

Director and Chief Executive Officer

(Principal Executive Officer)

/s/    Michael P. Mason

Michael P. Mason

Vice President of Finance and Treasurer

(Principal Financial and Accounting Officer)

/s/    Dennis A. Ausiello, M.D.

Dennis A. Ausiello, M.D.

Director

/s/    Michael W. Bonney

Michael W. Bonney

Director

/s/    John K. Clarke

John K. Clarke

Director

/s/    Marsha H. Fanucci

Marsha H. Fanucci

Director

/s/    Steven M. Paul, M.D.

Steven M. Paul, M.D.

Director

/s/    Paul R. Schimmel, Ph.D.

Paul R. Schimmel, Ph.D.

Director

/s/    Amy W. Schulman

Amy W. Schulman

Director

/s/    Phillip A. Sharp, Ph.D.

Phillip A. Sharp, Ph.D.

Director

/s/    Kevin P. Starr

Kevin P. Starr

Director

143


EXHIBIT INDEX

Exhibit No.

Exhibit

  2.1†*Stock Purchase Agreement dated as of January 10, 2014 by and among the Registrant, Sirna Therapeutics, Inc., Merck Sharp & Dohme Corp., and solely for the purposes of certain specified provisions, Merck & Co., Inc. (filed as Exhibit 2.1 to the Registrant’s Quarterly Report on Form 10-Q filed on May 9, 2014 (File No. 001-36407) for the quarterly period ended March 31, 2014 and incorporated herein by reference)

  3.1

Restated Certificate of Incorporation of the Registrant (filed as Exhibit 3.1 to the Registrant’s QuarterlyAnnual Report on Form 10-Q10-K filed on August 11, 2005February 12, 2016 (File No. 000-50743)001-36407) for the quarterly periodyear ended June 30, 2005December 31, 2015 and incorporated herein by reference)

  3.2

Amended and Restated Bylaws of the Registrant, as amended (filed as Exhibit 3.43.2 to the Registrant’s Registration StatementAnnual Report on Form S-110-K filed on February 12, 2016 (File No. 333-113162)001-36407) for the year ended December 31, 2015 and incorporated herein by reference)

  4.1

Specimen certificate evidencing shares of common stock (filed as Exhibit 4.1 to the Registrant’s Registration Statement on Form S-1 (File No. 333-113162) and incorporated herein by reference)

  4.2

Rights Agreement dated as of July 13, 2005 between the Registrant and EquiServe Trust Company, N.A., as Rights Agent, which includes as Exhibit A the Form of Certificate of Designations of Series A Junior Participating Preferred Stock, as Exhibit B the Form of Rights Certificate and as Exhibit C the Summary of Rights to Purchase Preferred Stock (filed as Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on July 14, 2005(File No. 000-50743) and incorporated herein by reference)

10.1**

2002 Employee, Director and Consultant Stock Plan, as amended, together with forms of Incentive Stock Option Agreement, Non-qualified Stock Option Agreement and Restricted Stock Agreement (filed as Exhibit 10.1 to the Registrant’s Registration Statement on Form S-1(File (File No. 333-113162) and incorporated herein by reference)

10.2**

2003 Employee, Director and Consultant Stock Plan, as amended, together with forms of Incentive Stock Option Agreement, Non-qualified Stock Option Agreement and Restricted Stock Agreement (filed as Exhibit 10.2 to the Registrant’s Registration Statement on Form S-1(File (File No. 333-113162) and incorporated herein by reference)

10.3**

Amended and Restated 2004 Stock Incentive Plan (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 2014 (File No. 001-36407) for the quarterly period ended June 30, 2014 and incorporated herein by reference)

10.4**

Forms of Incentive Stock Option Agreement and Nonstatutory Stock Option Agreement under 2004 Stock Incentive Plan, as amended (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 2014 (File No. 001-36407) for the quarterly period ended June 30, 2014 and incorporated herein by reference)

10.5**

Second Amended and Restated 2009 Stock Incentive Plan (filed as amendedExhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on August 9, 2017 (File No. 001-36407) for the quarterly period ended June 30, 2017 and incorporated herein by reference)


Exhibit No.

Exhibit

10.6**

Forms of Incentive Stock Option Agreement, Nonstatutory Stock Option Agreements, Restricted Stock Agreement and Restricted Stock Unit Award Agreement under Second Amended and Restated 2009 Stock Incentive Plan (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on August 9, 2017 (File No. 001-36407) for the quarterly period ended June 30, 2017 and incorporated herein by reference)

10.7**

Form of Nonstatutory Stock Option Agreement for Non-Plan Inducement Grant (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 3, 2016 (File No. 001-36407) for the quarterly period ended September 30, 2016 and incorporated herein by reference)

10.8**

Amended and Restated 2004 Employee Stock Purchase Plan (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 20149, 2017 (File No. 001-36407) for the quarterly period ended June 30, 20142017 and incorporated herein by reference)

10.6**Forms of Incentive Stock Option Agreement and Nonstatutory Stock Option Agreement under 2009 Stock Incentive Plan (filed as Exhibit 10.4 to the Registrant’s Quarterly Report onForm 10-Q filed on August 8, 2014 (File No. 001-36407) for the quarterly period ended June 30, 2014 and incorporated herein by reference)
10.7**Form of Restricted Stock Agreement under 2009 Stock Incentive Plan (filed as Exhibit 10.5 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 2014 (File No. 001-36407) for the quarterly period ended June 30, 2014 and incorporated herein by reference)
10.8**Form of Director Nonstatutory Stock Option Agreement under 2009 Stock Incentive Plan (filed as Exhibit 10.6 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 2014 (File No. 001-36407) for the quarterly period ended June 30, 2014 and incorporated herein by reference)

144


Exhibit No.

Exhibit

10.9**

2004 Employee Stock Purchase Plan, as amended (filed as Appendix A to the Registrant’s Definitive Proxy Statement on Schedule 14A filed on April 20, 2010 (File No. 000-50743) and incorporated herein by reference)
10.10**

Letter Agreement between the Registrant and John M. Maraganore, Ph.D. dated October 30, 2002 (filed as Exhibit 10.7 to the Registrant’s Registration Statement on Form S-1(File (File No. 333-113162) and incorporated herein by reference)

10.11**

10.10**

Letter Agreement between the Registrant and Barry E. Greene dated September 29, 2003 (filed as Exhibit 10.10 to the Registrant’s Registration Statement on Form S-1 (File No. 333-113162) and incorporated herein by reference)

10.11**

Letter Agreement between the Registrant and Yvonne L. Greenstreet, MBChB dated August 12, 2016 (filed as Exhibit 10.14 to the Registrant’s Annual Report on Form 10-K filed on February 15, 2017 (File No. 001-36407) for the year ended December 31, 2016 and incorporated herein by reference)

10.12**

Letter Agreement between the Registrant and Manmeet S. Soni dated April 20, 2017 (filed as Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on August 9, 2017 (File No. 001-36407) for the quarterly period ended June 30, 2017 and incorporated herein by reference)

10.13**

Consulting Agreement dated as of March 1, 2006 by and between the Registrant and Phillip A. Sharp, Ph.D., as amended (filed as Exhibit 10.16 to the Registrant’s Annual Report on Form 10-K filed on February 19, 2013 (File No. 000-50743) for the year ended December 31, 2012 and incorporated herein by reference)

10.13**

10.14**

Consulting Agreement dated as of April 20, 2012 by and between the Registrant and Dennis A. Ausiello, M.D. (filed as Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on April 23, 2012 (File No. 000-50743) and incorporated herein by reference)

10.14

10.15**

Forms of Director and Officer Indemnification Agreements (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on August 4, 2016 (File No. 001-36407) for the quarterly period ended June 30, 2016 and incorporated herein by reference)

10.16**

Form of Change in Control Agreement (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 7, 2017 (File No. 001-36407) for the quarterly period ended September 30, 2017 and incorporated herein by reference)

10.17

Lease, dated as of September 26, 2003 by and between the Registrant and Three Hundred Third Street LLC (filed as Exhibit 10.15 to the Registrant’s Registration Statement on Form S-1 (File No. 333-113162) and incorporated herein by reference)

10.15

10.18

First Amendment to Lease, dated March 16, 2006, by and between the Registrant and ARE-MA Region No. 28, LLC (filed as Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on March 17, 2006 (File No. 000-50743) and incorporated herein by reference)

10.16

10.19

Second Amendment to Lease, dated June 26, 2009, by and between the Registrant and ARE-MA Region No. 28, LLC (filed as Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on August 7, 2009 (File No. 000-50743) for the quarterly period ended June 30, 2009 and incorporated herein by reference)

10.17

10.20

Third Amendment to Lease, dated May 11, 2010, by and between the Registrant and ARE-MA Region No. 28, LLC (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on August 5, 2010 (File No. 000-50743) for the quarterly period ended June 30, 2010 and incorporated herein by reference)

10.18

10.21

Fourth Amendment to Lease, dated November 4, 2011, by and between the Registrant andARE-MA Region No. 28, LLC (filed as Exhibit 10.19 to the Registrant’s Annual Report on Form 10-K filed on February 13, 2012 (File No. 000-50743) for the year ended December 31, 2011 and incorporated herein by reference)

10.19


Exhibit No.

Exhibit

10.22

Fifth Amendment to Lease, dated March 27, 2014, by and between the Registrant and ARE-MA Region No. 28, LLC (filed as Exhibit 10.5 to the Registrant’s Amendment No. 1 to its Quarterly Report on Form 10-Q/A filed on January 9, 2015 (File No. 001-36407) for the quarterly period ended March 31, 2014 and incorporated herein by reference)

10.20†

10.23†

Lease entered into as of February 10, 2012 by and between BMR-Fresh Pond Research Park LLC and the Registrant (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on May 3, 2012 (File No. 000-50743) for the quarterly period ended March 31, 2012 and incorporated herein by reference)

10.21†

10.24

First Amendment to Lease entered into as of August 2, 2016 by and between BMR-Fresh Pond Research Park LLC and the Registrant (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on November 3, 2016 (File No. 001-36407) for the quarterly period ended September 30, 2016 and incorporated herein by reference)

10.25

Lease dated as of March 18, 2015 between RREEF America REIT II CORP. PPP and the Registrant, as amended by First Amendment to Lease dated as of April 16, 2015 (filed as Exhibit 10.5 to the Registrant’s Quarterly Report on Form 10-Q filed on August 7, 2015 (File No. 001-36407) for the quarterly period ended June 30, 2015 and incorporated herein by reference)

10.26

Lease dated as of May 5, 2015 between RREEF America REIT II CORP. PPP and the Registrant (filed as Exhibit 10.6 to the Registrant’s Quarterly Report on Form 10-Q filed on August 7, 2015 (File No. 001-36407) for the quarterly period ended June 30, 2015 and incorporated herein by reference)

10.27

Lease entered into as of April 3, 2015 by and between BMR-675 West Kendall Street LLC and the Registrant (filed as Exhibit 10.7 to the Registrant’s Quarterly Report on Form 10-Q filed on August 7, 2015 (File No. 001-36407) for the quarterly period ended June 30, 2015 and incorporated herein by reference)

10.28

Purchase and Sale Agreement entered into as of February 10, 2016 by and between 20 Commerce LLC and the Registrant (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on May 4, 2016 (File No. 001-36407) for the quarterly period ended March 31, 2016 and incorporated herein by reference)

10.29†

Co-exclusive License Agreement between Garching Innovation GmbH (now known as Max Planck Innovation GmbH) and Alnylam U.S., Inc. dated December 20, 2002, as amended by Amendment dated July 8, 2003 together with Indemnification Agreement by and between Garching Innovation GmbH (now known as Max Planck Innovation GmbH) and Alnylam Pharmaceuticals, Inc. effective April 1, 2004 (filed as Exhibit 10.19 to the Registrant’s Registration Statement on Form S-1 (File No. 333-113162) and incorporated herein by reference)

145


Exhibit No.

Exhibit

10.22†

10.30†

Co-exclusive License Agreement between Garching Innovation GmbH (now known as Max Planck Innovation GmbH) and Alnylam Europe, AG dated July 30, 2003 (filed as Exhibit 10.20 to the Registrant’s Registration Statement on Form S-1 (File No. 333-113162) and incorporated herein by reference)

10.23†

10.31†

Agreement between the Registrant, Garching Innovation GmbH (now known as Max Planck Innovation GmbH), Alnylam U.S., Inc. and Alnylam Europe AG dated June 14, 2005 (filed as Exhibit 10.8 to the Registrant’s Quarterly Report on Form 10-Q filed on August 11, 2005 (File No. 000-50743) for the quarterly period ended June 30, 2005 and incorporated herein by reference)

10.24†

10.32

Confidential Settlement Agreement and Mutual Release entered into as of March 14, 2011 by and between Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V., Max-Planck-Innovation GmbH and the Registrant, on the one hand, and Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, and the University of Massachusetts, on the other hand (filed as Exhibit 10.210.1 to the Registrant’s QuarterlyCurrent Report on Form 10-Q8-K filed on May 5, 2011October 2, 2015 (File No. 000-50743) for the quarterly period ended March 31, 2011001-36407) and incorporated herein by reference)

10.25†

10.33

Exclusive License Agreement for Tuschl II United States Patents and Patent Applications dated as of March 14, 2011, by and between the Registrant and University of Massachusetts (filed as Exhibit 10.310.2 to the Registrant’s QuarterlyCurrent Report on Form 10-Q8-K filed on May 5, 2011October 2, 2015 (File No. 000-50743) for the quarterly period ended March 31, 2011001-36407) and incorporated herein by reference)

10.26

10.34

Amendment to Co-Exclusive License Agreement dated as of March 14, 2011, by and between the Registrant, on the one hand, and Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology and Max-Planck-Innovation GmbH (filed as Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on May 5, 2011 (File No. 000-50743) for the quarterly period ended March 31, 2011 and incorporated herein by reference)

10.27†

Research Collaboration and License Agreement effective as of October 12, 2005 by and between the Registrant and Novartis Institutes for BioMedical Research, Inc. (filed as Exhibit 10.23 to the Registrant’s Annual Report on Form 10-K filed on March 2, 2009 (File No. 000-50743) for the quarterly and annual period ended December 31, 2008 and incorporated herein by reference)

10.28†

10.35†

License and Collaboration Agreement, entered into as of July 8, 2007, by and among F. Hoffmann-La Roche, Ltd, Hoffmann-La Roche Inc. (which assigned its rights and obligations to Arrowhead Research Corporation), the Registrant and, for limited purposes, Alnylam Europe AG (filed as Exhibit 10.26 to the Registrant’s Annual Report on Form 10-K filed on March 2, 2009 (File No. 000-50743) for the quarterly and annual period ended December 31, 2008 and incorporated herein by reference)
10.29†

License and Collaboration Agreement entered into as of May 27, 2008 by and among Takeda Pharmaceutical Company Limited and the Registrant (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on August 8, 2008 (File No. 000-50743) for the quarterly period ended June 30, 2008 and incorporated herein by reference)

10.30†


Exhibit No.

Exhibit

10.36†

Amended and Restated License and Collaboration Agreement, entered into as of January 1, 2009, by and among the Registrant, Ionis Pharmaceuticals, Inc. (formerly Isis Pharmaceuticals, Inc.) and Regulus Therapeutics Inc. (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on May 8, 2009 (File No. 000-50743) for the quarterly period ended March 31, 2009 and incorporated herein by reference)

10.31†

10.37†

Founding Investor Rights Agreement entered into as of January 1, 2009, by and among Regulus Therapeutics Inc., Ionis Pharmaceuticals, Inc. (formerly Isis Pharmaceuticals, Inc.) and the Registrant (filed as Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on May 8, 2009 (File No. 000-50743) for the quarterly period ended March 31, 2009 and incorporated herein by reference)

146


Exhibit No.

Exhibit

10.32†

10.38†

Sublicense Agreement dated effective January 8, 2007 among the Registrant and INEX Pharmaceuticals Corporation (now Tekmira PharmaceuticalsArbutus Biopharma Corporation, as successor in interest) (filed as Exhibit 10.38 to the Registrant’s Annual Report on Form 10-K filed on February 18, 2011 (File No. 000-50743) for the year ended December 31, 2010 and incorporated herein by reference)

10.33†

10.39†

Sponsored Research Agreement dated as of July 27, 2009 by and among the Registrant, The University of British Columbia and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.) (filed as Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on June 29, 2011 (File No. 000-50743) and incorporated herein by reference)

10.34†

10.40†

Supplemental Agreement effective July 27, 2009 by and among the Registrant, Arbutus Biopharma Corporation (formerly Tekmira Pharmaceuticals Corporation,Corporation), Protiva Biotherapeutics Inc., The University of British Columbia and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.) (filed as Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on June 29, 2011 (File No. 000-50743) and incorporated herein by reference)

10.35†

10.41†

Amendment No. 1, dated as of July 27, 2011, to the Sponsored Research Agreement dated as of July 27, 2009 by and among the Registrant, The University of British Columbia and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.) (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 3, 2011 (File No. 000-50743) for the quarterly period ended September 30, 2011 and incorporated herein by reference)

10.36†

10.42†

License and Collaboration Agreement dated as of August 27, 2012 by and among Monsanto Company and the Registrant (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 5, 2012 (File No. 000-50743) for the quarterly period ended September 30, 2012 and incorporated herein by reference)

10.37†

10.43†

Letter Agreement dated September 5, 2014 by and among the Registrant and Monsanto Company (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 6, 2014 (File No. 001-36407) for the quarterly period ended September 30, 2014 and incorporated herein by reference)

10.38†

10.44†

Cross-License Agreement dated as of November 12, 2012 by and among the Registrant, Arbutus Biopharma Corporation (formerly Tekmira Pharmaceuticals CorporationCorporation) and Protiva Biotherapeutics Inc. (filed as Exhibit 10.50 to the Registrant’s Annual Report on Form 10-K filed on February 19, 2013 (File No. 000-50743) for the year ended December 31, 2012 and incorporated herein by reference)

10.39†

10.45†

Settlement Agreement and General Release entered into as of November 12, 2012 by and among Arbutus Biopharma Corporation (formerly Tekmira Pharmaceuticals Corporation,Corporation), Protiva Biotherapeutics Inc., the Registrant and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.) (filed as Exhibit 10.51 to the Registrant’s Annual Report on Form 10-K filed on February 19, 2013 (File No. 000-50743) for the year ended December 31, 2012 and incorporated herein by reference)

10.40†

10.46†

License and Collaboration Agreement dated as of February 3, 2013 by and among The Medicines Company and the Registrant (filed as Exhibit 10.2 to the Registrant’s Amendment No. 1 to its Quarterly Report on Form 10-Q/A filed on July 26, 2013 (File No. 000-50743) for the quarterly period ended March 31, 2013 and incorporated herein by reference)

10.41†

Master Services Agreement dated as of January 15, 2010 between Medpace, Inc. and the Registrant, as amended, together with Task Order No. 10 thereto, dated July 2, 2013 (filed as Exhibit 10.49 to the Registrant’s Annual Report on Form 10-K filed on February 20, 2014 (File No. 000-50743) for the year ended December 31, 2013 and incorporated herein by reference)

10.42

10.47

Stock Purchase Agreement dated as of January 11, 2014 by and between the Registrant and Sanofi Genzyme Corporation(formerly Genzyme Corporation) (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on May 9, 2014 (File No. 001-36407) for the quarterly period ended March 31, 2014 and incorporated herein by reference)

147


Exhibit No.

Exhibit

10.43†

10.48†

Investor Agreement dated as of February 27, 2014 by and between the Registrant and Sanofi Genzyme Corporation(formerly Genzyme Corporation) (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on May 9, 2014 (File No. 001-36407) for the quarterly period ended March 31, 2014 and incorporated herein by reference)

10.44†


Exhibit No.

Exhibit

10.49†

Master Collaboration Agreement dated as of January 11, 2014 by and between the Registrant and Sanofi Genzyme Corporation,(formerly Genzyme Corporation), including the Regional, Global and Co-Co License Terms Appended thereto (filed as Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on May 9, 2014 (File No. 001-36407) for the quarterly period ended March 31, 2014 and incorporated herein by reference)

12#

Computation of Consolidated Ratios of Earnings/Deficiencies to Fixed Charges

21.1#

10.50†

Amendment No. 1 effective as of July 1, 2015 to Master Collaboration Agreement dated as of January 11, 2014, including certain Regional, Global and Co-Co License Terms attached thereto, by and between the Registrant and Sanofi Genzyme (formerly Genzyme Corporation) (filed as Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 9, 2015 (File No. 001-36407) for the quarterly period ended September 30, 2015 and incorporated herein by reference)

10.51†

Second Amended and Restated Strategic Collaboration and License Agreement dated January 8, 2015 between Ionis Pharmaceuticals, Inc. (formerly Isis Pharmaceuticals, Inc.) and the Registrant (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on May 8, 2015 (File No. 001-36407) for the quarterly period ended March 31, 2015 and incorporated herein by reference)

10.52†

Amendment No. 1 dated as of July 13, 2015 to Second Amended and Restated Strategic Collaboration and License Agreement dated as of January 8, 2015 by and among the Registrant and Ionis Pharmaceuticals, Inc. (formerly Isis Pharmaceuticals, Inc.) (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on November 9, 2015 (File No. 001-36407) for the quarterly period ended September 30, 2015 and incorporated herein by reference)

10.53†

Amended and Restated Development and Manufacturing Services Agreement effective as of July 6, 2015 by and between the Registrant and Agilent Technologies, Inc. (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on November 9, 2015 (File No. 001-36407) for the quarterly period ended September 30, 2015 and incorporated herein by reference)

10.54

Credit Agreement dated as of April 29, 2016 among Alnylam U.S., Inc., the Registrant and Bank of America N.A. (filed as Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed on August 4, 2016 (File No. 001-36407) for the quarterly period ended June 30, 2016 and incorporated herein by reference)

10.55

Credit Agreement dated as of April 29, 2016 among Alnylam U.S., Inc., the Registrant and Wells Fargo Bank, National Association (filed as Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on August 4, 2016 (File No. 001-36407) for the quarterly period ended June 30, 2016 and incorporated herein by reference)

21.1#

Subsidiaries of the Registrant

23.1#

23.1#

Consent of PricewaterhouseCoopers LLP, an Independent Registered Public Accounting Firm

31.1#

31.1#

Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002, Rule 13(a)-14(a)/15d-14(a), by Principal Executive Officer

31.2#

31.2#

Certification pursuant to Section 302 of the Sarbanes-Oxley Act of 2002, Rule 13(a)-14(a)/15d-14(a), by Principal Financial Officer

32.1#

32.1#

Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, by Principal Executive Officer

32.2#

32.2#

Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, by Principal Financial Officer

101#


Exhibit No.

Exhibit

101#

The following materials from Registrant’s Annual Report on Form 10-K for the year ended December 31, 2014,2017, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Balance Sheets, (ii) the Consolidated Statements of Comprehensive Loss, (iii) the Consolidated Statements of Stockholders’ Equity, (iv) the Consolidated Statements of Cash Flows and (v) Notes to Consolidated Financial Statements.

 

*

*

Schedules, exhibits and similar supporting attachments or agreements to the Stock Purchase Agreement are omitted pursuant to Item 601(b)(2) of Regulation S-K. The Registrant agrees to furnish a supplemental copy of any omitted schedule or similar attachment to the Securities and Exchange Commission upon request.

**

 

**

Management contracts or compensatory plans or arrangements required to be filed as an exhibit hereto pursuant to Item 15(a) of Form 10-K.

 

Indicates confidential treatment requested as to certain portions, which portions were omitted and filed separately with the Securities and Exchange Commission pursuant to a Confidential Treatment Request.

#

Filed herewith.

 

#Filed herewith.

ITEM  16.FORM 10-K SUMMARY

 

148Not applicable.


SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized, on February 15, 2018.

ALNYLAM PHARMACEUTICALS, INC.

By:

/s/ John M. Maraganore, Ph.D.

John M. Maraganore, Ph.D.

Chief Executive Officer

Pursuant to the requirements of the Securities Exchange Act of 1934, the Report has been signed below by the following persons on behalf of the Registrant and in the capacities indicated as of February 15, 2018.

Name

Title

/s/    John M. Maraganore, Ph.D.

Director and Chief Executive Officer

(Principal Executive Officer)

John M. Maraganore, Ph.D.

/s/    Manmeet S. Soni

Senior Vice President, Chief Financial Officer

Manmeet S. Soni

(Principal Financial Officer)

/s/    Michael P. Mason

Vice President of Finance and Treasurer

(Principal Accounting Officer)

Michael P. Mason

/s/    Dennis A. Ausiello, M.D.

Director

Dennis A. Ausiello, M.D.

/s/    Michael W. Bonney

Director

Michael W. Bonney

/s/    John K. Clarke

Director

John K. Clarke

/s/    Marsha H. Fanucci

Director

Marsha H. Fanucci

/s/    Steven M. Paul, M.D.

Director

Steven M. Paul, M.D.

/s/    David E. I. Pyott

Director

David E. I. Pyott

/s/    Paul R. Schimmel, Ph.D.

Director

Paul R. Schimmel, Ph.D.

/s/    Amy W. Schulman

Director

Amy W. Schulman

/s/    Phillip A. Sharp, Ph.D.

Director

Phillip A. Sharp, Ph.D.

/s/    Kevin P. Starr

Director

Kevin P. Starr

134