UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

FORM 10-K
(Mark One)
x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the fiscal year ended December 31, 20162019
orOR
o 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 001-36289
Genocea Biosciences, Inc.genocealogosmall.jpg
GENOCEA BIOSCIENCES, INC.
(Exact name of registrant as specified in its charter)
Delaware 51-0596811
(State or other jurisdiction of
incorporation or organization)
 
(I.R.S. Employer
Identification No.)
100 Acorn Park Drive,
Cambridge, MassachusettsMA 02140
(Address of principal executive offices) (Zip Code)
(617) 876-8191
(Registrant’s telephone number, including area code: (617) 876-8191code)
Securities registered pursuant to Section 12(b) of the Act:
Title of each class 
Trading symbol
Name of each exchange on which
registered
Common Stock, $0.001 par value NASDAQ GlobalGNCANasdaq Capital Market
Securities registered pursuant to Section 12(g)Section12(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.  o Yes  x 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.  o Yes  x No
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.  x Yes  o 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 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. x
Indicate by check mark whether the registrant has submitted electronically and posted on its corporate website, 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).  x Yes  o No
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 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 filer
o 
Accelerated filer
x
Non-accelerated filer
o 
Smaller reporting companyo
x
(Do not check if a smaller reporting company)  Emerging growth companyo
If an emerging growth company, indicate by a 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. o
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).  o Yes  xNo
EXPLANATORY NOTE: Under the Jumpstart Our Business Startups Act, the registrant qualifies as an “emerging growth company.” We therefore incorporate the scaled disclosures required of an emerging growth company in this Annual Report on Form 10-K.
The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant, based on the closing price for such stock as reported on the NASDAQ GlobalNasdaq Capital Market on June 30, 2016,2019, the last business day of the registrant’s most recently completed second quarter, was: $85,898,985.$73,983,101.
The number of shares outstanding of the registrant’s common stock as of February 15, 201711, 2020 was 28,498,694.27,643,773.
DOCUMENTS INCORPORATED BY REFERENCE
Portions of the Registrant’s definitive proxy statement related to its 2020 annual meeting of stockholders to be filed subsequently are incorporated by reference into Part III of this report.
 


TABLE OF CONTENTS
  
   
  
   
  
   
  


FORWARD-LOOKING STATEMENTS
This Annual Report on Form 10-K contains forward-looking statements that involve substantial risks and uncertainties. Forward-looking statements are neither historical facts nor assurances of future performance. Instead, they are based on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, our clinical results and other future conditions. The words “anticipate”, “believe”, “contemplate”, “continue”, “could”, “estimate”, “expect”, “forecast”, “goal”, “intend”, “may”, “plan”, “potential”, “predict”, “project”, “should”, “target”, “will”, “would”, or the negative of these terms or other similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.
The forward-looking statements in this Annual Report on Form 10-K include, among other things, statements about:
the timing of results of our ongoing and planned clinical trials;
our planned clinical trials for GEN-003;
our estimates regarding the timing and amount of funds we require to complete ourconduct clinical trials for GEN-003GEN-009, to continue preclinical studies and file an investigational new drug (“IND”) for GEN-011, to continue preclinical studies for our other product candidates and to continue our investments in our immuno-oncology;
our estimate for when we will require additional funding;
our plans to commercialize GEN-003 and our other product candidates;
the timing of, and our ability to, obtain and maintain regulatory approvals for our product candidates;
the rate and degree of market acceptance and clinical utility of any approved product candidate;
the potential benefits of strategic partnership agreements and our ability to enter into strategic partnership arrangements;
our ability to quickly and efficiently identify and develop product candidates;
our commercialization, marketing and manufacturing capabilities and strategy;
our intellectual property position; and
our estimates regarding expenses, future revenues, capital requirements, the sufficiency of our current and expected cash resources and our need for additional financing.financing;

the timing of, and our ability to, obtain and maintain regulatory approvals for our product candidates;
the potential benefits of strategic partnership agreements and our ability to enter into strategic partnership arrangements;
our intellectual property position;
the rate and degree of market acceptance and clinical utility of any approved product candidate;
our ability to quickly and efficiently identify and develop product candidates; and
our commercialization, marketing and manufacturing capabilities and strategy.
We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. We have included important factors in the cautionary statements included in this Annual Report on Form 10-K, particularly in the “Risk Factors” section, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make or collaborations or strategic partnerships we may enter into.
You should read this Annual Report on Form 10-K and the documents that we have filed as exhibits to the Annual Report on Form 10-K completely and with the understanding that our actual future results may be materially different from what we expect. We do not assume any obligation to update any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by law.


PART I

Item 1.        Business

Unless the context requires otherwise, references in this Annual Report on Form 10-K to “Genocea”, “we”, “us” and “our” refer to Genocea Biosciences, Inc.

Overview

We are a biopharmaceutical company that discoversseeks to discover and developsdevelop novel vaccines andcancer immunotherapies to address diseases with significant unmet needs. We useusing our proprietary discovery platform, ATLASTM, to rapidly design vaccines proprietary discovery platform. The ATLAS platform profiles each patient's CD4+ and immunotherapies that act, in part, throughCD8+ T cell (or cellular) immune responses to every potential target or "antigen" in contrast to approved vaccines and immunotherapies, which are designed to act primarily through B cell (or antibody) immune responses.that patient's tumor. We believe that by harnessing T cells we can develop first-in-classthis approach optimizes antigen selection for immunotherapies such as cancer vaccines and immunotherapiescellular therapies by identifying the antigens to address diseases where T cells are centralwhich the patient can respond. Consequently, we believe that ATLAS could lead to the control of the disease.more immunogenic and efficacious cancer immunotherapies.

We have one product candidate in activeOur most advanced program is GEN-009, a personalized neoantigen cancer vaccine, for which we are conducting a Phase 21/2a clinical development, GEN-003, an immunotherapy for the treatment of genital herpes. We also have a pre-clinical immuno-oncology program focused on personalized cancer vaccines ("GEN-009").trial. The GEN-009 program leveragesuses ATLAS to identify patient neoantigens, or newly formed antigensimmunogenic tumor mutations unique to each patient, for inclusion in each patient's GEN-009 vaccine. We are also advancing GEN-011, a neoantigen-specific adoptive T cell therapy program that are associated with that individual's tumor.also relies on ATLAS. We have other infectious disease programs, including GEN-004, a Phase 2-ready universal vaccineexpect to file an IND application for GEN-011 in the preventionsecond quarter of pneumococcal infections, and early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria.2020.

ATLAS Platform

Vaccines represent a major healthcare success story, having eradicated or significantly reduced the global prevalence of many infectious diseases. To date, all approved vaccines have been developed primarily to elicit B cell responses. However, there remain many diseases for which no effective vaccines or only partially effective vaccines exist. A major reason, for infectious diseases, is that the organisms that cause these diseases largely evade the antibody immune response generated by B cells, which can generally only address pathogens in the bloodstream. Such organisms may reside in host cells or mucosal surfaces of the noseHarnessing and throat. To address these pathogens, vaccines targeting responses fromdirecting the T cell arm of the immune system mayto kill tumor cells is increasingly viewed as having potential in the treatment of many cancers. This approach has been effective against hematologic malignancies and, more recently, certain solid tumors. Vaccines or cellular therapies employing this approach must target specific differences from normal tissue present in a tumor, such as antigens arising from genetic mutations. However, the solution. In the casediscovery of cancers, the success of checkpoint blockade therapies, in which essentially the brakes are taken off of T cells, it is clear that the cellular arm of the immune system needs to be engaged.

We believe T cell target discoveryoptimal antigens for such immunotherapies has been particularly challenging for two reasons. First, the genetic diversity of human T cell responses contrasts with the generally uniform B cell responses in humans.means that effective antigens vary from person to person. Second, the number of candidate targetsantigens can be very large, with up to thousands of candidates per patient in some cancers. An effective antigen selection system must therefore account both for each patient's tumor and for their T cell responses can be exponentially greater than for B cell responses. These complexities represent fundamental barriers that traditional vaccine discovery tools, which rely either on computer predictions, or on empirically selecting the potential targets by iteratively testing them in animal models, have not been able to address.repertoire.

We have designed the ATLAS platform to overcome these T cell target discovery challenges. We believe ATLAS represents the most comprehensive high-throughput system for T cell vaccine and immunotherapy discovery in the biopharmaceutical industry. ATLAS is designed to mimicachieves effective antigen selection by employing components of the T cell arm of the human immune system in a laboratory setting.from each patient. Using ATLAS, we are able to measure each patient's T cell responses to the entirea comprehensive set of protein targetscandidate neoantigens, tumor-associated antigens and tumor-associated viral antigens for a specific pathogen ortheir own cancer, from patients' blood samples, allowing us to identify vaccine and immunotherapyselect those targets associated with protectivethe anti-tumor T cell responses to disease. By comparing antigens identified in individuals who naturally control their disease with those who do not, we can select the antigens that may havekill that individual's cancer. We believe that ATLAS represents the best likelihoodmost comprehensive and accurate system for antigen discovery. Further, we believe ATLAS identifies a novel candidate antigen profile, that of inducing protectiveinhibitory T cell immune responses. Previously, all candidate antigens were thought either to be targets of effective anti-tumor responses (stimulatory), or irrelevant. However, using ATLAS, we have identified inhibitory antigens we call Inhibigenstm, which are shown to promote tumor progression in preclinical studies. We have also discovered that an antigen can be stimulatory in one patient and inhibitory in another, reinforcing the importance of selecting each patient's potentially immunogenic antigens.

We believe weThe ATLAS portfolio comprises three patent families. The first two families comprise issued U.S. patents, with patent terms until at least 2031 and 2030, respectively, as well as granted foreign patents and pending U.S. and foreign applications. The third family is directed to ATLAS-based methods for cancer diagnosis, prognosis and patient selection, as well as related compositions. This patent family currently comprises pending applications in eleven foreign jurisdictions and a pending U.S. application. Patents issuing from these applications are expected to have a leader in the field of T cell vaccine and immunotherapy discovery and development. Our management and scientific teams possess considerable experience in vaccine, immunotherapy, cancer and anti-infective research, manufacturing, clinical development and regulatory matters.

GEN-003 — Phase 2 immunotherapy for genital herpespatent term until at least March 2038.
 
Our lead program is GEN-003, a Phase 2 candidate therapeutic vaccine, or immunotherapy, that we are developing to treat genital herpes infections. Data from our double-blind, placebo-controlled, dose-escalating Phase 1/2a trial for GEN-003 represented the first reported instance of a therapeutic vaccine working against an infectious disease. Our second trial was a Phase 2 dose optimization study, which confirmed the Phase 1/2a trial results and tested six combinations of proteins and adjuvant to determine the optimal dose for future trials. Our third trial utilized the top two performing doses identified from our


Phase 2 dose optimization study and is intended to test potential Phase 3 endpoints with an improved formulation of GEN-003, manufactured with commercially-scalable processes, which will be used in future Phase 3 trials. Key data from those trials is described below.

Phase 1/2a Trial - Completed
Final analysis of the data from the Phase 1/2a trial showed that, for the best performing 30µg per protein dose group, there was a sustained reduction in the viral shedding rate. After completion of dosing for this group, the viral shedding rate was reduced by 52% versus baseline and, at six months after the final dose, the shedding rate remained at 40% below baseline. The reduction in the genital lesion rate after completion of the third dose was greatest for the 30µg dose group at 48%. After six months, the reduction from baseline in genital lesion rate for this dose group was 65% and, after 12 months, the genital lesion rate was 42% lower than baseline. GEN-003 was safe and well tolerated over the 12 months of this trial.
Phase 2 Dose Optimization Trial - Completed

A 310-subject Phase 2 dose optimization trial was completed in March 2016. Subjects were randomized to one of six dosing groups of either 30μg or 60μg per protein paired with one of three adjuvant doses (25μg, 50μg, or 75μg). A seventh group received placebo. Subjects received three doses of GEN-003 or placebo at 21-day intervals. Baseline viral shedding and genital lesion rates were established for each subject in a 28-day observation period prior to the commencement of dosing by collecting 56 genital swab samples (two per day), which were analyzed for the presence of HSV-2 DNA, and by recording the days on which genital lesions were present. This 28-day observation period was repeated immediately after the completion of dosing, and at six and twelve months following dosing. No maintenance doses were given. After the 28-day observation period immediately after dosing, patients in the placebo arm were rolled over across the six active combinations of GEN-003 and Matrix-M2 under a separate protocol. The primary endpoint of the trial was the reduction in viral shedding rate versus baseline, a measure of anti-viral activity. A number of exploratory secondary endpoints were also studied, including the reduction in genital lesion rates, the percent of patients who were lesion recurrence free up to six and 12 months after dosing and time to first lesion recurrence after dosing.

The two most promising doses from this dose optimization study were 60 µg per protein combined with either 50 or 75 µg of Matrix-M2 adjuvant ("60/50 Dose" and "60/75 Dose" respectively). In October 2015, we announced positive results from the planned interim analysis of data collected six months after dosing demonstrating that patients dosed with GEN-003 showed a statistically significant 47% (p=0.0004) and 58% (p < 0.0001) reduction from baseline in the viral shedding rate for both the 60/50 Dose and 60/75 Dose, respectively. In a planned secondary analysis, the proportion of patients receiving any one of the six GEN-003 doses who were lesion-free at six months after dosing ranged from approximately 30% to 50%, similar to results reported in clinical trials with oral antiviral therapies. In addition, the time to first recurrence after completion of dosing showed a range of 152 days to greater than 180 days among dose groups. In a further secondary analysis measuring the impact on genital lesion rates, GEN-003 demonstrated sustained and statistically significant reductions from baseline in five of six dose groups ranging from 43% to 69%.

In March 2016, we announced positive results from data collected twelve months after dosing. The 60/50 Dose and 60/75 Dose continued to demonstrate statistically significant reductions of 66% (p < 0.0001) and 55% (p=0.01), respectively, from baseline in the viral shedding rate. These two doses were advanced to our Phase 2b trial evaluating a new Phase 3-ready formulation of GEN-003.
The Phase 2 dose optimization trial continued to show that GEN-003 is safe and well tolerated by patients, with no serious adverse events ("AEs") related to the vaccine.

Phase 2b Trial - Ongoing

In December 2015, we initiated a Phase 2b trial which was our first study testing potential Phase 3 endpoints with a Phase 3-ready formulation of GEN-003, manufactured with commercially-scalable processes. The trial enrolled 131 subjects that were randomized to one of three dose groups - placebo, 60/50 Dose, and 60/75 Dose. All subjects received three injections at 21-day intervals.

In September 2016, we announced positive viral shedding rate reductions from the ongoing Phase 2b study. The study achieved its primary endpoint, with GEN-003 demonstrating a statistically significant (versus placebo and baseline) 40% reduction in the viral shedding rate compared to baseline immediately after dosing in the 60/50 Dose group. This result was consistent with a statistically significant (versus placebo and baseline) viral shedding rate reduction of 41% at this same dose and time point in the previous Phase 2 dose optimization trial. In addition, the reactogenicity profile of this dose, an indication


of the strength of the immune response to GEN-003, was consistent between the trials. This same dose in the prior Phase 2 trial subsequently demonstrated virologic and clinical efficacy durable through at least one year after dosing.

The 60/75 Dose group reduced the viral shedding rate by 27%, lower than that observed in the prior trial, and also showed a less acceptable reactogenicity profile than the prior trial. We believe that the increase in reactogenicity of this dose indicates an overstimulation of the T cell immune system leading to the reduced efficacy with this dose in this trial, as would be expected with the well-known bell-shaped T cell dose response curve. The likely driver of this effect is a more potent adjuvant formulation following customary manufacturing process changes to prepare for Phase 3 trials and commercialization.

In January 2017, we announced positive clinical results from this ongoing trial. At six months after dosing, GEN-003 demonstrated statistically significant improvements versus placebo across multiple clinical endpoints. The 60/50 Dose significantly reduced the rate of genital lesions during the six months following dosing compared to placebo (41% reduction versus placebo). The genital lesion rate is an important overall measure of disease that captures both the frequency and duration of recurrences, both of which are important to both patients and their caregivers. GEN-003 also consistently demonstrated significant benefits versus placebo across several other clinical endpoints including median duration of recurrences in days (2.8 compared to 4.2 for placebo), median duration of recurrences over six months (1.0 compared to 2.0 for placebo), and estimates of percent recurrence free after first and last dose (29% and 22%, respectively, for the 60/50 Dose versus 10% and 13%, respectively, for placebo). In addition, mean duration of recurrences in days (3.3 compared to 4.8 for placebo) and mean duration of recurrences over six months (2.1 compared to 2.7 for placebo) demonstrated significant benefit versus placebo.

The clinical efficacy data versus placebo at twelve-months post dosing is expected in the middle of 2017. The viral shedding rate reduction data at six-months post dosing is expected in the first half of 2017.

GEN-003 also continues to demonstrate a safety profile appropriate for its therapeutic setting in the judgment of the trial’s independent Drug Monitoring Committee. There was no grade 4 reactogenicity or related serious AEs and discontinuations due to AEs were low and similarly distributed across active dose groups and placebo.
We intend to conduct an end-of-Phase 2 meeting with the FDA in early 2017. We also expect to commence Phase 3 trials in the fourth quarter of 2017. We plan to commence a clinical trial exploring the potential additive effects of GEN-003 on top of daily administration of valacyclovirin parallel with the Phase 3 program.We retain all rights to GEN-003 and our strategy is to execute a partnership to maximize the potential of GEN-003 and to help fund the costs of the GEN-003 Phase 3 program.

If GEN-003 successfully completes clinical development and is approved, we believe it would represent an important new treatment option for patients with genital herpes.Immuno-Oncology Programs

Our Immuno-Oncology Program
Guided by our positive clinical results on GEN-003 and our belief in the ATLAS platform, we are focused on combining our antigen selection andcancer immunotherapies include a vaccine development expertise with that of leading cancer innovators to unlock new targets in immuno-oncology. Our potential cancer vaccines will beis designed to educate T cells to recognize and attack specific cancer targets, and a cellular therapy intended to introduce T cells that have been educated to attack these targets. We believe that neoantigen vaccines could be used in combination with existing treatment approaches for cancer to potentially direct and enhance an individual’s T cell response to his or her cancer, thereby kill cancers.potentially effecting better clinical outcomes. We are developing personalized cancer vaccines by leveragingalso believe that isolating and expanding T cell populations targeting specific neoantigens through adoptive cell therapy could provide meaningful clinical benefit.

The following describes our active immuno-oncology programs in development:


immunotablea03.jpg

Our lead program, GEN-009, is an adjuvanted neoantigen peptide vaccine candidate. Using ATLAS to identify patientspecific neoantigens, or newly formed antigens unique towe then manufacture a personalized vaccine for each patient that are associated with that individual's tumor. We anticipate filing a personalized cancer vaccine Investigational New Drug ("IND") application with the FDA in 2017. We are also applying the results fromusing only those neoantigens determined by ATLAS and its utility a prognostic tool, to identify patients that could benefit from checkpoint inhibitor therapy. Our strategy in immuno-oncology combines our own internal development programs with a focus on partnering ATLAS for other immuno-oncology applications.

Refer to "Our Immuno-Oncology Program" below for additional details on this program, including our current collaborations.
In November 2015, we also commenced a new program focused on Epstein-Barr Virus (“EBV”) ("GEN-007"). EBV infection has been linked to cancers with high unmet needs such as non-Hodgkin’s lymphoma, nasopharyngeal carcinoma and gastric carcinoma. We believe the ATLAS platform is highly suited to the creation of a new immunotherapy for EBV given that T cell responses are understood to be crucial for protection against EBV. Furthermore, EBV is part of the herpesvirus family, in which we have deep experience through our development of GEN-003.stimulatory to that patient's anti-tumor immune responses. We are currently conducting ATLAS screens for EBV and plan to select antigen candidates for further study in 2017.



Other infectious disease programs

Our other infectious disease programs include GEN-004, a potential universal Streptococcus pneumoniae, or pneumococcus, vaccine to protect against a leading cause of infectious disease mortality worldwide and early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria. In October 2015, we announced that top-line results from the Phase 1/2a clinical trial for GEN-004 showed consistent reductions versus placebo in the pre-specified endpointsGEN-009 across a range of solid tumor types:

Part A of the ratetrial is assessing the safety and densityimmunogenicity of upper airway colonizationGEN-009 as monotherapy in a human challenge model, but that neithercertain cancer patients with no evidence of disease; and
Part B of the endpoints achieved statistical significance. GEN-004 was safetrial, for which we have commenced dosing patients, is designed to assess the safety, immunogenicity, and well tolerated by subjects. Althoughpreliminary antitumor activity of GEN-009 in combination with ICI therapy in patients with advanced or metastatic tumors.

Throughout 2019, we did not achieve statistical significance in this study,presented data from Part A of the consistent apparent effect gives us confidence inclinical trial. In the vaccine concept and indata from the eight dosed patients that, we believe, confirms the potential for GEN-004. In November 2016, we paused activities on our other early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria in order to focus allantigen selection advantages of our internal research and pre-clinical resources on our immuno-oncology investments. Progress made and data generated to date in these infectious disease clinical and research programs remains valuable to Genocea for the future.ATLAS:

Our Product Candidate Pipeline

The following table describes our active programs in development:
Vaccine
Candidate
ProgramStage of DevelopmentNext MilestoneAnticipated Timeline
GEN-003Genital herpes TherapeuticPhase 212-month clinical data from Phase 2b trialThird quarter of 2017
GEN-009Immuno-oncology - NeoantigenPre-clinicalFile INDFourth quarter of 2017
GEN-007Epstein-Barr VirusResearchSelect antigen candidatesSecond half of 2017

GEN-003 Market Opportunity

Genital Herpes

We are developing our lead product candidate, GEN-003, to treat patients with genital herpes infections. GEN-003 consists of two protein antigens. The first antigen is ICP4.2, a large fragment of the protein ICP4 that we discovered in ATLAS screens to be a T cell antigen associated with protection from infection or with less severe infection. The second antigen is glycoprotein D2, or gD2, a B cell antigen that is the target of antibodies that provide anti-viral activity during the time in the life cycle of the herpes virus where the pathogen is susceptible to inactivation by antibodies. gD2 was also a target of T cells in our ATLAS screens and was selected based on such ATLAS screens as ATLAS prioritized gD2 as the B cell antigen most associated with T cell responses. We pair the antigens with Matrix-M2, a novel adjuvant that we have licensed exclusively for this indication from Novavax, Inc. ("Novavax"). See “—Other Collaborations—Novavax”.

Genital herpes is a sexually transmitted disease. Genital herpes infections have become an epidemic, spreading to approximately 16% of the United States population between the ages of 14 and 49, and more than 500 million people worldwide, according to the World Health Organization.

For infected individuals, the disease can manifest in a number of ways, with so-called viral shedding as the common element. For some of the virus’ life cycle, it lies dormant within nerve cells near the spine. Although there may be no visible sign of infection, the virus lives within these nerve cells. Periodically, the virus reactivates and virus travels to skin cells of the genitalia where they are released. The release of the virus is called viral shedding and can be detected by swabbing the genital area and testing the swab for the presence of viral DNA. For reasons not completely understood, reactivation of the virus within the nerve cells may occur, resulting in a large amount of virus shedding from skin and mucus membranes. If the replication is maintained for a long enough period of time and at a high enough level, the virus destroys the cells it inhabits and causes ulcers to form on the skin. Patients experiencing such visible ulcers are considered symptomatic patients. It is generally believed that the immune system responds to episodes of genital herpes outbreaks by activating T cells that reduce viral replication and destroy infected cells, allowing healing and resolution of genital ulcers, usually after a few days, although for many patients, ulcers return at variable intervals. Patients may also experience periodic, low-frequency viral shedding. Because the shedding at these times does not lead to the development of ulcers, these episodes are called asymptomatic shedding. These asymptomatic patients continue to pose a disease transmission risk through sexual contact while shedding virus.



Some people, approximately 60% of those infected, are asymptomatic or fail to recognize or seek medical attention for an initial mild outbreak of ulcers. According to the New England Journal of Medicine, roughly 40% of persons infected with HSV-2 experience visible symptoms. It has been reported in the Annals of Internal Medicine that approximately 70% of the people with visible symptoms experience three or more outbreaks per year, which we consider to be moderate-to-severe disease. Patients with genital herpes experience significant distress because of the potential negative impact on their ability to form and maintain sexual relationships. Infection with genital herpes can involve substantial risks in addition to the infection itself. For example, persons with genital herpes infection have a threefold increased risk for human immunodeficiency virus, or HIV, acquisition. Additionally, pregnant women can transmit genital herpes to infants in childbirth, which can result in severe brain damage or death.

_________________________
*Note: Each bar represents 1 swab; 2 swabs collected per day; the absence
100% of a bar means no shedding was detected on the swab on a particular day.patients had measurable CD4+ and CD8+ T cell responses to their GEN-009 vaccine;

The total number of days during a month that the herpes virus can beResponses were detected in the genital area with or without visible ulcers is called the shedding frequency. A pattern of shedding and outbreak for one person is illustrated in the graph above. Viral shedding is measured by collecting swabsagainst 99% of the genital area, followingadministered vaccine neoantigens (N=88 administered antigens), a protocolresponse rate in excess of that which has been usedreported previously in decadesresponse to candidate neoantigen vaccines;
GEN-009 elicited CD8+ T cell responses ex vivo, which is a measure of T cell effector function, for 41% of vaccine neoantigens and CD4+ T cell responses to 51% of neoantigens;
GEN-009 elicited broad immune responses using an in vitro stimulation assay, which is a measure of central memory responses, with 87% of neoantigens eliciting a CD4+ response and 57% of neoantigens eliciting a CD8+ response;
GEN-009 was well tolerated, with no dose-limiting toxicities observed; and
Through January 31, 2020, we are not aware of studies of HSV-2 viral shedding. In the example shown above, the subject collected swabs twice daily for 28 days. HSV-2 DNA was detectableany disease recurrence in approximately 66%any of the collected swabs, meaning the patient’s shedding frequency is 66% for the period measured. Some swabs had no detectable viral DNA, meaning the subject did not shed virus at the time of sample collection (exemplified by the blank areas of the above graph). The magnitude of viral shedding varied widely from day to day and only sometimes resulted in clinical symptoms such as visible genital ulcers (represented by the dark bars of the above graph).  Ulcers generally appear after several days of asymptomatic shedding and at times when the magnitude of shedding is highest. The extent, frequency, and duration of shedding vary from person to person, but the pattern is relatively consistent for each person.vaccinated patients.

LimitationsAs with any open label study, we may slow or pause enrollment to evaluate a smaller set of Current Genital Herpes Treatment Optionspatients in an effort to assure that a preliminary clinical signal is seen. We anticipate reporting these preliminary clinical results for our GEN-009 Part B clinical trial in the second or third quarter of 2020. Based upon this evaluation, we will consider whether it is appropriate to continue the study.

There is no known cureWe also are advancing GEN-011, an adoptive T cell therapy specific for genital herpes. For patients infected with genital herpes, oral antiviral drugs areneoantigens identified by ATLAS. Adoptive T cell therapies such as tumor infiltrating lymphocyte ("TIL") therapy offers an alternative treatment in solid tumors. TIL therapy, which relies on extracting TILs from each patient's solid tumor, non-specifically expanding them ex vivo, and reinfusing them into the only treatment option. The most commonly prescribed treatment is valacyclovir including Valtrex, marketed by GlaxoSmithKline. Other medications available are acyclovir (Zovirax, marketed by GlaxoSmithKline)cancer patient, has demonstrated measurable and famciclovir (Famvir, marketed by Novartis). These drugs all work by limiting the ability of the virus to replicate when it emerges from latency. Sales for these oral antivirals totaled $1.6 billion globallysustainable tumor shrinkage in 2008, including nearly $700 million in the United States, according to IMS Health.

Based on market surveys conducted on our behalf, most patients who use oral antivirals treatfailed immune checkpoint inhibitor ("ICI") therapy in mid-stage clinical studies. GEN-011 extracts and specifically expands ATLAS-identified neoantigen-specific T cells from each patient's peripheral blood rather than their disease episodically. At the onset of outbreaks, or in the case of some patients, at the onset of prodrome, a tingling sensation that may precede an outbreak, patients take antiviral medication to reduce the duration and severity of the outbreak. According to the approved Valtrex prescribing information, episodic treatment only reduces the duration of outbreaks by up to 50% when compared to placebo. Patients treating their symptoms episodically are not protected against asymptomatic viral shedding and, therefore, have no reduced risk of transmission of infection to an uninfected sexual partner while asymptomatic.

Some patients treat their infection with daily antiviral medication. This approachtumor (as is called chronic suppressive therapy, and has been shown to reduce—but not eliminate—viral shedding, the frequency of symptomatic outbreaks of genital ulcers, and the risk of transmission of the infection to an uninfected sexual partner. Even on chronic suppressive therapy, based on the valacyclovir prescribing information, 35% of patients taking chronic suppressive therapy suffer outbreaks within six months


after initiation of treatment and 46% of patients suffer outbreaks within 12 months. Patients taking chronic suppressive therapy reduce their disease transmission risk only by as much as 52%.

A market research survey conducted on our behalf, in 2014, which included primary research with more than 300 physicians in the United States, United Kingdom, Germany, France and Brazil, and a review of secondary sources, indicated that approximately 11 million people in the U.S. are diagnosed with genital herpes. Of those diagnosed, approximately 7 million are treated with oral anti-viral medicines. This research also indicated that approximately 2.5 million patients treat their disease chronically with daily anti-viral pills, and approximately 4.5 million patients treat episodically to reduce the severity of outbreaks when they occur. Of those patients treated chronically, approximately 30% continue to suffer three or more outbreaks of genital herpes per year and of those treated episodically, approximately 50% continue to suffer three or more outbreaks per year. This market research also indicated that the prevalence of genital herpes outside the United States is similar to the United States.

Due to the limited effectiveness of oral antiviral therapy, there remains a significant unmet medical need, against both the symptoms of genital herpes and disease transmission risk from viral shedding.

GEN-003: An Immunotherapy Candidatedone for Genital Herpes

In our three clinical studies we have shown that GEN-003 is the first immunotherapy known to have demonstrated a statistically significant reduction in viral shedding rate and the signs of clinical genital herpes disease as measured by genital lesion rates (see "Clinical Development" below)TIL generation). We believe that theseGEN-011 could provide potency, efficacy, and ease of manufacturing benefits over TIL therapy. We expect to file an IND application for GEN-011 with the U.S. Food and Drug Administration ("FDA") in the second quarter of 2020, with preliminary clinical results continue to demonstrate that GEN-003 has the potential to be a first-in-class immunotherapy to treat genital herpes.

We believe that, if approved for the treatment of genital herpes infections, GEN-003 could address the unmet needs of patients in several ways. For patients taking episodic therapy, GEN-003 could offer reduced symptomatic and asymptomatic viral shedding, potentially reducing disease transmission risk. Since episodic therapy offers no protection against disease transmission during asymptomatic shedding, these patients and their sexual partners are unprotected when the infected partner is not taking anti-viral medication.

For patients on chronic suppressive therapy, we believe GEN-003 may provide both improved outcomes and increased convenience. In a 2016 market research survey conducted on our behalf in the United States of almost 300 currently treated patients, more than 80% stated a preference for GEN-003 over their current therapy. For some patients, we anticipate that physicians will prescribe GEN-003 as baseline therapy. Such patients may still take oral antivirals in case of an outbreak to further control symptoms. Replacing daily therapy may offer convenience to these patients. For other patients, we anticipate that physicians may prescribe GEN-003 alongside chronic suppressive therapy. This combination therapy approach mirrors the treatment practice of other chronic viral infections such as HIV and hepatitis C virus. We anticipate that, since the mechanisms of action for GEN-003 and oral antiviral medication should complement each other, the control against symptoms and disease transmission risk offered by the combination would exceed that of either therapy alone.

In a second market research survey conducted on our behalf with more than 400 patients with HSV-2 infections in the United States, the United Kingdom, France and Germany, and more than 300 physicians who treat patients with HSV-2 infections, 56% of patients on chronic suppressive therapy indicated an intent to use GEN-003 in combination with other therapies and 37% of such patients indicated an intent to use GEN-003 on its own, if it were approved; 30% of patients on episodic therapy indicated an intent to use GEN-003 in combination with other therapies and 60% of such patients indicated an intent to use GEN-003 on its own, if it were approved; and 15% of patients not taking any HSV-2 therapy indicated an intent to use GEN-003 in combination with other therapies and 65% of such patients indicated an intent to use GEN-003 on its own, if it were approved.

Taking together the results of the two market research surveys conducted on our behalf, we forecast a potential market share for GEN-003 in the US of approximately 3 million of the 12 million diagnosed patients. We believe that this translates into a global revenue opportunity of over $2 billion annually. These were limited surveys and may or may not be representative of how patients might ultimately use GEN-003, if at all, or how GEN-003 may be reimbursed if GEN-003 successfully completes clinical development and is approved by regulatory authorities.

Clinical Development

Our Phase 1/2a Clinical Trial



We completed a Phase 1/2a trial, testing the safety, T and B cell immunogenicity, and impact on viral shedding of GEN-003 in subjects with documented recurrent HSV-2 infection. We also measured, as an exploratory endpoint, the effect of GEN-003 on the genital lesion rate. The trial was conducted at seven sites in the United States, including some of the leading institutions for scientific and clinical research of genital herpes. The trial was double-blind, placebo-controlled and dose-escalating. We enrolled subjects between 18 and 50 years of age. An independent Data Monitoring Committee monitored the safety of subjects enrolled in the clinical trial.

This trial enrolled 143 otherwise healthy subjects with a history of three to nine genital herpes outbreaks per year when not on suppressive therapy. Subjects were randomized into one of three dose cohorts. Within each cohort, subjects were randomized in a 3:1:1 ratio, whereby for every three subjects receiving GEN-003, one would receive placebo and one would receive the ICP4.2 and gD2 proteins without the Matrix-M2 adjuvant. We included this last cohort to demonstrate that Matrix-M2 was necessary to achieve the desired biological responses. There were three vaccine dose groups, based on the amount of protein. The lowest dose group subjects received 10µg of each protein; in the middle dose group, the protein doses increased to 30µg, and in the high dose group the protein dose was 100µg. For all subjects receiving GEN-003 (proteins plus adjuvant), the Matrix-M2 dose was 50µg. Subjects received three vaccinations, on days zero, 21 and 42.

The primary objective of this trial was to monitor the safety profile of the proposed vaccine. Overall, GEN-003 was well-tolerated. During the seven days following each injection, side-effects were generally those considered typically associated with vaccines, such as fatigue, site injection pain, tenderness and swelling. Among all vaccine dose groups, the frequency of AEs appeared greater among those subjects given the 10µg dose. In the 30µg and 100µg dose cohorts, the AE rate was lower than that of the 10µg cohort. In addition, the frequency of AEs appeared to diminish with subsequent doses. Beyond the week following vaccination with the GEN-003 immunotherapy, the AE types and frequencies appeared similar to those following vaccination with placebo. The AEs have been transient, resolved over a few days and resulted in only two subjects discontinuing further vaccinations: one for a combination of symptoms (myalgia and fatigue; and pain and tenderness at the injection site) and one for injection site pain.

Additionally, we measured the immunotherapy-induced T cell and B cell immune responses. We structured and statistically powered the trial to measure the proposed immunotherapy’s impact on the viral shedding rate, an important marker of virus activity. We selected this endpoint because of the connection between shedding, symptomatic outbreaks, and risk of transmission of virus by sexual contact. Every subject in the study swabbed their genitalia twice per day for 28 days before receiving the first assigned treatment injection, and after treatment, using the standard protocol that has been used for many clinical trials of HSV-2 shedding.

We measured immunotherapy activity in two ways: the impact on viral shedding and the impact on signs of clinical genital herpes disease as measured by genital lesion rates, defined as the total days in which a patient reported the presence of a visible genital lesion during swabbing days, divided by the total number of swabbing days. The impact on viral shedding was determined by viral DNA present in swabs from subjects over the 28-day measurement period before receiving the assigned treatment and immediately after completing the three-dose regimen and again at six months and 12 months after the final dose. The genital lesion rate was measured at the same time points.

Final analysis of the data showed that for the best performing 30µg dose group, there was a sustained and statistically significant reduction in the viral shedding and genital lesion rates. After completion of dosing for this dose group, the viral shedding rate fell by 52% versus baseline (p<0.001) and, at six months after the final dose, the shedding rate remained at 40% below baseline (p<0.001). At 12 months, the viral shedding rate returned to baseline for this dose group. The reduction in the genital lesion rate after completion of the third dose was greatest for the 30µg dose group, at 48% (p<0.001). After six months, the reduction from baseline in genital lesion rate for this dose group was 65% (p<0.001) and after 12 months the genital lesion rate was 42% lower than baseline.

Our data have also demonstrated that GEN-003 induced a broad immune response in vaccinated subjects at all dose levels. T cell responses increased from baseline 21-fold to ICP4.2 and 10-fold to gD2. Subjects also experienced strong increases in antibody response to ICP4.2 and gD2, as measured by immunoglobulin G, or IgG, a standard measure of antibody response. The antibodies generated in response to the vaccine are able to prevent the virus from infecting new cells, as measured by a standard assay for evaluating the ability of the virus to infect cells in vitro.

Phase 2 Dose Optimization Trial

The objective of our Phase 2 dose optimization trial was to confirm the results of the best performing dose in the Phase 1/2a trial, and to test other combinations of protein and adjuvant to determine the optimal dose for future trials and potentially improve on the current profile of GEN-003. The Phase 2 study enrolled 310 subjects from 17 institutions in the


United States. Subjects were randomized to one of six dosing groups of either 30 µg or 60 µg per protein paired with one of three Matrix-M2 adjuvant doses (25 µg, 50 µg, or 75 µg). A seventh group received placebo. Subjects received three doses of GEN-003 or placebo at 21-day intervals. Baseline viral shedding and genital lesion rates were established for each subject in a 28-day observation period prior to the commencement of dosing by collecting 56 genital swab samples (two per day), which were analyzed for the presence of HSV-2 DNA, and by recording the days on which genital lesions were present. This 28-day observation period was repeated immediately after the completion of dosing, was repeated at six months following dosing and will be repeated at twelve months following dosing. No maintenance doses were given.

In May 2015, we announced that, at the 28-day observation period immediately after completion of dosing, both the 60/50 Dose and 60/75 Dose demonstrated a highly statistically significant 41% (p=0.01) and 55% (p=0.006) reductions, respectively, from baseline in the viral shedding rate, the primary endpoint of the trial and a measure of anti-viral activity. All dose combinations tested, including the successful 30 µg per protein / 50 µg of adjuvant dose from the prior Phase 1/2a trial, demonstrated a statistically significant viral shedding rate reduction versus baseline and only the lowest dose combination did not demonstrate a statistically significant reduction versus placebo. In a planned secondary analysis to assess impact on patient reported genital lesion rates, all dose groups, including the placebo group, demonstrated a statistically significant reduction from baseline. Furthermore, there was no difference in discontinuations in patient dosing due to AEs across the different treatment arms.

In October 2015, we announced positive results from the interim analysis of data collected six months after dosing. At its best performing dose, the 60/75 Dose, GEN-003 demonstrated a statistically significant 58% reduction from baseline in the viral shedding rate (p < 0.0001), the primary endpoint of the study. In a planned secondary analysis, the proportion of patients receiving GEN-003 who were lesion-free at six months after dosing ranged from approximately 30% to 50%, similar to results reported in clinical trials with oral antiviral therapies. In addition, the time to first recurrence after completion of dosing showed a range of 152 days to greater than 180 days among dose groups. In a further secondary analysis measuring the impact on genital lesion rates, GEN-003 demonstrated sustained and statistically significant reductions from baseline in five of six dose groups ranging from 43% to 69%. The Phase 2 trial continued to show that GEN-003 was safe and well tolerated by patients, with no serious AEs related to the vaccine. The two most promising doses from this dose optimization study were the 60/50 Dose and the 60/75 Dose. In October 2015, we announced positive results from the planned interim analysis of data collected six months after dosing demonstrating GEN-003 usage resulted in a statistically significant 47% (p=0.004) and 58% (p < 0.0001) reduction from baseline in the viral shedding rates for both the 60/50 Dose and 60/75 Dose, respectively.

In March 2016, we announced positive results from data collected twelve months after dosing. The 60/50 Dose and 60/75 Dose continued to demonstrated statistically significant reductions of 66% (p < 0.0001) and 55% (p=0.01), respectively, from baseline in the viral shedding rate. These two doses were advanced to our Phase 2b trial evaluating a new Phase 3-ready formulation of GEN-003.
The Phase 2 dose optimization trial continued to show that GEN-003 is safe and well tolerated by patients, with no serious AEs related to the vaccine.

Phase 2b Trial

In December 2015, we initiated a Phase 2b trial which was our first study testing potential Phase 3 endpoints with a Phase 3-ready formulation of GEN-003, manufactured with commercially-scalable processes. The trial enrolled 131 subjects that were randomized to one of three dose groups - placebo, 60/50 Dose, and 60/75 Dose. All subjects received three injections at 21-day intervals.

In September 2016, we announced positive viral shedding rate reductions from this study. The trial achieved its primary endpoint, with GEN-003 demonstrating a statistically significant (versus placebo and baseline) 40% reduction in the viral shedding rate compared to baseline immediately after dosing in the 60/50 Dose group. This result was consistent with a statistically significant (versus placebo and baseline) viral shedding rate reduction of 41% at this same dose and time point in the previous Phase 2 dose optimization trial. In addition, the reactogenicity profile of this dose, an indication of the strength of the immune response to GEN-003, was consistent between the trials. This same dose in the prior Phase 2 trial subsequently demonstrated virologic and clinical efficacy durable through at least one year after dosing.

The 60/75 Dose group reduced the viral shedding rate by 27%, lower than that observed in the prior trial, and also showed a less acceptable reactogenicity profile than the prior trial. We believe that the increase in reactogenicity of this dose indicates an overstimulation of the T cell immune system leading to the reduced efficacy with this dose in this trial, as would be expected with the known bell-shaped T cell dose response curve. The likely driver of this effect is a more potent adjuvant formulation following customary manufacturing process changes to prepare for Phase 3 trials and commercialization.



In January 2017, we announced positive clinical results from this ongoing trial. At six months after dosing, GEN-003 demonstrated statistically significant improvements versus placebo across multiple clinical endpoints. The 60/50 Dose significantly reduced the rate of genital lesions during the six months following dosing compared to placebo (41% reduction versus placebo). The genital lesion rate is an important overall measure of disease that captures both the frequency and duration of recurrences, both of which are important to both patients and their caregivers. GEN-003 also consistently demonstrated significant benefits versus placebo across several other clinical endpoints including median duration of recurrences in days (2.8 compared to 4.2 for placebo), median duration of recurrences over six months (1.0 compared to 2.0 for placebo), and estimates of percent recurrence free after first and last dose (29% and 22%, respectively, for the 60/50 Dose versus 10% and 13%, respectively, for placebo). In addition, mean duration of recurrences in days (3.3 compared to 4.8 for placebo) and mean duration of recurrences over six months (2.1 compared to 2.7 for placebo) demonstrated significant benefit versus placebo.

Next Steps: Phase 2b twelve-month results; End-of-Phase 2 Meeting; Antiviral Combination GEN-003 Study; Initiation of Phase 3 Pivotal Study

The clinical efficacy data versus placebo at twelve-months post dosing is expected in the middle of 2017 for the ongoing Phase 2b trial. The viral shedding rate reduction data at six-months post dosing is expectedanticipated in the first half of 2017. In the second half of 2017, we also anticipate the 24-month data from a Phase 2 trial to inform the timing of maintenance dosing. We intend to conduct an end-of-Phase 2 meeting with the FDA in early 2017. We also expect to commence Phase 3 trials in the fourth quarter of 2017. We plan to commence a clinical trial exploring the potential additive effects of GEN-003 on top of daily administration of valacyclovirin parallel with the Phase 3 program.We retain all rights to GEN-003 and our strategy is to execute a partnership to maximize the potential of GEN-003 and to help fund the costs of the GEN-003 Phase 3 program.

Potential for GEN-003 to Treat HSV-1 Infection

We anticipate that GEN-003 may also help a patient’s immune system fight herpes simplex virus type-1, or HSV-1. HSV-1 is most commonly identified with cold sores and has infected approximately 60% of Americans, according to the Center for Disease Control and Prevention ("CDC"). Increasingly, HSV-1 has been associated with outbreaks of genital ulcers, though the frequency and severity of such outbreaks generally is less than those associated with HSV-2. HSV-1 and HSV-2 are related viruses and the proteins in GEN-003 are present in, and nearly identical to, those found in HSV-1. Consequently, we believe that GEN- 003 may be active against HSV-1 and thus intend to study the potential for GEN-003 to combat HSV-1 genital disease in the Phase 3 program.

The Opportunity to Prevent HSV-2 Infections

In addition to treating HSV-2 infection with GEN-003, we believe that ATLAS may help to develop a vaccine that can prevent HSV-2 from infecting healthy persons. We believe that a vaccine that has therapeutic effect may be the foundation for a preventative vaccine. A prophylactic vaccine may be an important step in halting the epidemic, and could be used to treat uninfected partners of HSV-2 infected subjects to prevent them from acquiring the disease. The vaccine could also be used more broadly as a preventative measure. Although we have made important progress in the development of a prophylactic vaccine and we believe this is a valuable asset for us, we have paused our research and development of this product candidate in order to focus on GEN-003 and our immuno-oncology program.

OurImmuno-Oncology Program
Cancer is among the leading causes of death worldwide, with the incidence estimated to grow to 22 million over the next two decades. In 2015 in the U.S., an estimated 1.6 million new cases of cancer will be diagnosed, and approximately 600,000 people will die from the disease.

Cancer starts in the human body when the otherwise orderly process of cell growth, division and death breaks down. As a result, abnormal or damaged cells that should die instead survive, grow and spread, forming solid tumors or cancers of the blood like leukemia. Although the body’s immune system is designed to remove abnormal or damaged cells, cancerous cells are sometimes able to evade the immune system.
A recent breakthrough in treating cancer is the development of Checkpoint Blockade ("CPB") therapies. Immune CPBs function by blocking the activity of checkpoint proteins, which inhibit normal immune responses to cancers. Several CPBs have recently been approved by the FDA, including ipilimumab (Yervoy®), nivolumab (Opdivo®) and pembrolizumab (Keytruda®). Although these therapies unleash a robust T cell response, they don’t work well for all patients - demonstrating limited efficacy and toxic effects in some populations.



Guided by our positive clinical results on GEN-003 and belief in the ATLAS platform, we are focused on combining our antigen selection and vaccine development expertise with that of leading cancer innovators to unlock new targets in immuno-oncology. Our potential cancer vaccines will be designed to educate T cells to recognize and attack specific targets and thereby kill cancers. We are developing personalized cancer vaccines by leveraging ATLAS to identify patient neoantigens, or newly formed antigens unique to each patient, that are associated with that individual's tumor. We anticipate filing a personalized cancer vaccine IND application with the FDA in 2017. We are also applying the results from ATLAS, and its utility a prognostic tool, to identify patients that could benefit from checkpoint inhibitor therapy. Our strategy in immuno-oncology combines our own internal development programs with a focus on partnering ATLAS for other immuno-oncology applications.

Our current collaborations in immuno-oncology are as follows:

Dana-Farber Cancer Institute ("DFCI") - Starting in 2014, we entered into a collaboration with F. Stephen Hodi, Jr., M.D., director of the Melanoma Center at DFCI to utilize ATLAS to potentially identify patterns of T cell response in melanoma patients receiving CBP therapy. By analyzing the immune responses of both responders and non-responders to CBP therapy, ATLAS successfully identified the cancer antigens to which either (or both) CD4+ or CD8+ T cells became activated. Although this research was not powered to draw firm conclusions, the analysis of T cell responses in patients receiving CBP therapy revealed a pattern indicating a greater breadth of T cell activation for responders than non-responders. The study also revealed preliminary evidence that different characteristics of T cell responses emerge when comparing patients who respond and those who do not. Some T cell responses did not correspond with improved patient outcomes, and may be classified as “decoys,” further validating the ability of ATLAS to distinguish clinically relevant targets of T cell response. The collaboration with Dana-Farber is ongoing as we continue to analyze more tumor samples to characterize T cell response profiles that may be prognostic of CBP efficacy, and to identify T cell antigens that may be included in novel immunotherapies.

Memorial Sloan Kettering Cancer Center ("MSKCC") - In November 2015, we announced a collaboration with Timothy A. Chan, M.D., Ph.D., Vice Chair, Department of Radiation Oncology, and Jedd D. Wolchok, M.D., Ph.D., Chief of Melanoma and Immunotherapeutics Service at the MSKCC to screen the T cell responses of melanoma and non-small cell lung cancer patients treated with CBPs against the complete repertoire of patient-specific putative cancer neoantigens. The goals of the collaboration are to identify signatures of T cell response in cancer patients associated with response or non-response to CBP therapy and to discover new T cell cancer vaccine antigens. ATLAS is being used in conjunction with MSKCC’s patient-specific cancer neoantigen sequences and blood samples from the same cancer patients.

Through this collaboration, ATLAS has discovered several neoantigens as biologically relevant T cell targets associated with significant cytotoxic T cell responses. Importantly, many of these neoantigens were not identified by commonly used predictive computer algorithms, and the majority of neoantigens that were identified by those algorithms were not associated with meaningful T cell responses in ATLAS.

Checkmate Pharmaceuticals ("Checkmate") - In December 2016, we entered into a collaboration agreement with Checkmate. Checkmate is a clinical-phase company developing a product that seeks to activate the innate immune system to attack a tumor. Checkmate’s lead therapeutic candidate is currently in a Phase 1 clinical trial in metastatic melanoma in combination with an immune CBP. We are employing ATLAS to profile the T cell responses of approximately 20 patients enrolled in Checkmate’s ongoing Phase 1b clinical trial to a library of tumor-associated antigens common to patients with advanced melanoma. The T cell response signatures of those patients who respond to CMP-001/pembrolizumab combination therapy will be compared to the signatures of those who do not respond, thereby potentially identifying antigens associated with positive or negative patient outcomes.

US Oncology Research ("US Oncology") - In December 2016, we also announced our entry into a collaboration agreement with US Oncology, one of the largest network of community oncologists in the US. Through collaboration and shared purpose, US Oncology provides the clinical, research, technology and business resources to ensure the growth and vitality of their independent, community-based oncology practices. Pursuant to our agreement, we will screen the T cell responses of cancer patients with solid tumors who will be treated with checkpoint inhibitors against the complete repertoire of patient-specific putative cancer neoantigens. The objective of the collaboration is to use ATLAS to further Genocea's expertise in identifying signatures of T cell responses in cancer patients and to discover new T cell cancer vaccine antigens to support personalized cancer vaccine clinical trials.

Our Epstein Barr Virus Program


EBV is associated with a number of cancers, such as post-transplant lymphoproliferative disease, non-Hodgkin's lymphoma, nasopharyngeal carcinoma and gastric carcinoma. EBV is also the cause of infectious mononucleosis in adolescence and is associated with higher risk of a number of other serious diseases.
We believe that an effective immunotherapy against EBV needs to direct T cells and may have therapeutic potential against some or all of these diseases with large unmet needs. Furthermore, we believe that ATLAS is well-suited to identify the clinically important antigens which drive protective T cell responses to the virus.
Discovery research using ATLAS is ongoing to identify candidate T cell antigens to form the core of an immunotherapy that could potentially be advanced into clinical development.
Other Infectious Disease Programs

Pneumococcal Disease

The Gates Foundation has noted that pneumococcus kills more children under age five globally than any other organism. There are more than 90 serotypes, or strains, of pneumococcus known to exist. Pneumococcus is a bacterium that often resides harmlessly in the nose and throat but can cause otitis media, or middle ear infection, as well as pneumonia, an infection in the lungs. Such consequences of infection are considered non-invasive pneumococcal disease. Invasive pneumococcal disease ("IPD") arises when pneumococcus enters the bloodstream and potentially spreads to other organs. The consequences of IPD can be severe and, according to the CDC, 10% of patients with IPD die.

We believe there are significant limitations with current pneumococcal vaccines given they cover only 13 serotypes of the disease compared to the more than 90 known serotypes of pneumococcus. Incidence of invasive disease caused by the 75+ serotypes not included in that vaccine is rapidly increasing and to our knowledge, other companies’ product candidates are being developed to elicit a B cell response. Our GEN-004 program was designed to prevent infections caused by all serotypes of pneumococcus. GEN-004 consists of three whole Pneumococcal T cell protein antigens, SP0148, SP1912 and SP2108, combined with the adjuvant Alhydrogel, a form of alum that is contained in several approved vaccines.

We demonstrated proof-of-concept of GEN-004 in a mouse model of nasal colonization. We subsequently launched a Phase 1 clinical trial that was a randomized, double-blind, dose-escalation, and placebo-controlled clinical trial enrolling 90 healthy adult volunteers. In June 2014, we announced positive top-line data from a Phase 1 clinical trial in the United States to evaluate the safety of, and immune response to, GEN-004. The Phase 1 clinical trial met its safety, tolerability and immunogenicity goals.

Based on these data, a Phase 2a trial was initiated in the third quarter of 2014. Subjects in the clinical trial received either 100µg dose of GEN-004 with 350µg of adjuvant or placebo, and then was “challenged” intranasally with live pneumococcus in the nasal cavity. We enrolled approximately 90 healthy adults in this trial and it was designed to monitor AEs, antibody and T-cell immune responses as determined by IgG and IL-17A, and incidence of post-challenge nasopharyngeal colonization. In October 2015, we announced that top-line results from the Phase 2a clinical trial for GEN-004 showed consistent reductions versus placebo in the pre-specified endpoints of the rate and density of colonization, but that neither of the endpoints achieved statistical significance. GEN-004 was safe and well tolerated by subjects.

Although we did not achieve statistical significance in this study, we believe the consistent apparent effect of the Phase 2a trial supports the vaccine concept and the potential for GEN-004. We believe it is possible that future trials would require a change in some combination of dose, adjuvant or trial population to confirm any effect. GEN-004 is currently not part of any active clinical trials or development as we focus our efforts on GEN-003 and our immuno-oncology program.

Our Chlamydia Program

Chlamydia is the most commonly reported bacterial sexually transmitted disease in the United States. According to the CDC, an estimated 2.9 million infections occur annually in the United States. Despite the widespread availability of antibiotics that are effective against Chlamydia trachomatis, the pathogen that causes chlamydia infections, incidence has increased at greater than 5% per year over the past decade, according to the CDC. A key reason for this is that chlamydia is often an asymptomatic infection, so infected individuals do not seek treatment, which can result in severe consequences, particularly in women, such as pelvic inflammatory disease, infertility and serious neonatal infections. Antibodies appear to be unlikely to protect against infection as the pathogen is intracellular for much of its life cycle. Additionally, as a large genome pathogen, Chlamydia trachomatis represents a large T cell antigen discovery challenge and, we believe, a pathogen for use of ATLAS to identify a vaccine candidate.2021.



We have achieved promising preclinical resultsalso continue to explore additional program opportunities. We continue to evaluate GEN-010, our vaccine candidate employing next-generation antigen delivery technology, which we may advance to provide an opportunity for better immunogenicity and/or efficiency of vaccine production. In addition, we are using chlamydia antigens identified using ATLAS. The ATLAS screening, comprising 144 subjects, identified chlamydia antigen targets that elicit T cell responses preferentially in patients with positive clinical outcomes (spontaneous clearance) versus patients with infertility or pelvic inflammatory disease. Based on our screening analysis, we prioritized 25 Chlamydia trachomatisto pursue discovery of novel candidate antigens for pre-clinical testing.  Allnon-personalized cancer immunotherapies. Such programs could target shared neoantigens, non-mutated tumor-associated antigens, have been clonedcancers of viral origin such as cancers driven by Epstein-Barr virus infection and expressed and twelve have been successfully purified. These proteins were paired with Matrix-M2 adjuvant and evaluated as potential vaccine candidates in an animal efficacy model of chlamydia infection. From these studies we have identified three antigen targets that confer protection against chlamydia challenge based on bacterial burden analysis in the genital tract measured over time. Immunogenicity studies done coincident with the challenge model suggest that these antigens may be protecting mice by different mechanisms of action. Research under this program was paused in the fourth quarter of 2016 to focus on GEN-003 and our immuno-oncology program.Inhibigens

Our Malaria Program

Malaria is one of the deadliest infectious diseases in the world. Approximately 400 thousand to 800 thousand people died in 2013 due to malaria, primarily in the developing world. There is no vaccine to prevent malaria, an infection caused by the plasmodium parasites transmitted by mosquitoes. We previously collaborated with the Naval Medical Research Center "NMRC") and initiated a second collaboration with the Gates Foundation for which malaria is a priority infectious disease. When the parasite is injected into the blood through the bite of an infected mosquito, it rapidly travels to the liver where it replicates exponentially, is released into the bloodstream, and causes sickness. T cells in the liver could potentially be used to kill the cells in which the parasite is hiding, before the parasite is able to replicate itself, and could therefore protect against blood infection. Both the Gates Foundation and NMRC have sponsored several studies investigating killed or attenuated whole organism vaccines, which induce immunity, but are impractical to manufacture because the vaccines are based on irradiated parasites grown within the salivary glands of mosquitoes.

In September 2014, we announced the receipt of a $1.2 million grant from the Gates Foundation for the identification of protective T cell antigens for malaria vaccines, which extended our collaboration through 2016 and supports comprehensive screening of the malaria proteome to identify targets of protective T cell responses. We completed this grant work early in 2016 and presented our results to the Gates Foundation.tm.

Competition

The biotechnology and pharmaceutical industries are characterized by intense and rapidly changing competition to develop new technologies and proprietary products. Although we believe that our proprietary patent portfolio and T cell vaccine and cellular therapy expertise provide us with competitive advantages, we face potential competition from many different sources, including larger and better-funded pharmaceutical companies. Not only must we compete with other vaccineimmuno-oncology companies but any products that we may commercialize will have to compete with existing therapies and new therapies that may become available in the future.

There are other organizations working to improve existing therapies or to develop new vaccines or therapies for our initially selected indications. Depending on how successful these efforts are, it is possible they may increase the barriers to adoption and success of our GEN-003 product candidate, if approved.

The current standard of care for the treatment of HSV-2 is valacyclovir, an oral antiviral medicine. Other currently approved oral antiviral medications include acyclovir and famciclovir. AiCuris, a private company based in Germany, is developing a new oral antiviral, pritelivir, for which an existing clinical hold has been partially lifted for certain patient populations. We believe that GEN-003 may offer advantages in terms of improved symptom control, reduced disease transmission risk and improved compliance when compared to oral antivirals.

There are also several companies attempting to develop new therapeuticneoantigen cancer vaccines, against genital herpes, including AgenusBioNTech SE, CureVac AG, Genentech, Inc., Admedus Ltd, Sanofi PasteurGritstone Oncology Inc., Merck & Co., Inc., Moderna Inc., Nouscom, and Vical Incorporated. GEN-003 is in more advanced clinical development than these product candidates being developed by these companies. Furthermore, weVaccibody AS. We believe that GEN-003GEN-009 has advantages against each of these product candidates based on the screenspotential power of human protectionthe ATLAS platform to comprehensively identify for each cancer patient the neoantigens to which such patient has a pre-existing immune response. We believe that we have conductedselecting neoantigens for personal cancer vaccines using ATLAS that include these competitors’ antigens, published reports of non-clinical vaccine efficacy, announced clinical results in the case of Agenus, Inc. and Vical, Inc. and our own clinical resultswill lead to date.more effective vaccines. However, there can be no assurance that one or more of these companies or other companies will not achieve similar or superior clinical results in the future as compared to GEN-003GEN-009 or that our future clinical trials will be successful.


Similarly, there are other companies attempting to develop cellular therapies targeted towards neoantigens, either through transferring T cells that have been transduced with T cell Receptors ("TCR") that recognize tumor antigens, or T cells that have been enriched from tumors in a non-specific way (tumor infiltrating lymphocytes), or T cells from the peripheral blood that have been expanded on multiple tumor-specific antigens. These include Achilles Therapeutics Ltd., Adaptive Biotechnologies Corp., BioNTech SE, Cellular Biomedicine Group Inc., Eutilex Co., Ltd., Gilead Sciences, Inc., Iovance Biotherapeutics Inc., Marker Therapeutics, Inc., Oncotherapy Science Inc., PACT Pharma Inc., and Ziopharm Oncology Inc. We believe that Genocea’s ATLAS true neoantigen selection will lead to better targeted and more effective cell therapy; however, there can be no assurance that one or more of these companies, or other companies, will not achieve similar or superior clinical results in the future as compared to GEN-011, or that our future clinical trials will be successful.
Many of our competitors, either alone or with their strategic partners, have substantially greater financial, technical and human resources than we do and significantly greater experience in the discovery and development of product candidates, obtaining FDA, and other regulatory approvals of vaccines and the commercialization of those vaccines.vaccines or cell therapies. Accordingly, our competitors may be more successful than us in obtaining approval for vaccines and cell therapies and achieving widespread market acceptance. Our competitors’ vaccines or cell therapies may be more effective, or more effectively marketed and sold, than any vaccine we may commercialize and may render our vaccinesproducts obsolete or non-competitive.

Mergers and acquisitions in the biotechnology and pharmaceutical industries may result in even more resources being concentrated among a smaller number of our competitors. These competitors also compete with us in recruiting and retaining qualified scientific and management personnel and establishing clinical trial sites and patient registration for clinical trials, as well as in acquiring technologies complementary to, or necessary for, our programs. Smaller or early-stage companies may also prove to be significant competitors, particularly through collaborative arrangements with large and established companies.

We anticipate that we will face intense and increasing competition as new drugs enter the market and advanced technologies become available. We expect any vaccines or cell therapies that we develop and commercialize to compete based on, the basis of, among other things, efficacy, safety, convenience of administration and delivery, price, the level of generic competition, and the availability of reimbursement from government and other third-party payors.

Our commercial opportunity could be reduced or eliminated if our competitors develop and commercialize products that are safer, more effective, have fewer or less severe side effects, are more convenient, or are less expensive than any products that we may develop. Our competitors also may obtain FDA or other regulatory approval for their products more rapidly than we may obtain approval for our products, which could result in our competitors establishing a strong market position before we are able to enter the market. In addition, our ability to compete may be affected in many cases by insurers or other third-party payors seeking to encourage the use of generic products.

Intellectual Property



We strive to protect and enhance the proprietary technology, inventions, and improvements that are commercially important to our business, including seeking, maintaining, and defending patent rights, whether developed internally or licensed from third parties. We also rely on trade secrets relating to our proprietary technology platform and on know-how, continuing technological innovation and in-licensing opportunities to develop, strengthen and maintain our proprietary position in the vaccine field.and cell therapy fields. We additionally rely on regulatory protection afforded through data exclusivity, market exclusivity, and patent term extensions where available. Still further, we utilize trademark protection for our company name, and expect to do so for products and/or services as they are marketed.

Our commercial success may depend in part on our ability to obtain and maintain patent and other proprietary protection for commercially important technology, inventions and know-how related to our business; defend and enforce our patents; preserve the confidentiality of our trade secrets; and operate without infringing the valid enforceable patents and proprietary rights of third parties. Our ability to stop third parties from making, using, selling, offering to sell or importing our products may depend on the extent to which we have rights under valid and enforceable patents or trade secrets that cover these activities. With respect to both licensed and company-owned intellectual property, we cannot be sure that patents will be granted with respect to any of our pending patent applications or with respect to any patent applications filed by us in the future, nor can we be sure that any of our existing patents or any patents that may be granted to us in the future will be commercially useful in protecting our commercial products and methods of manufacturing the same.

We have developed or in-licensed numerous patents and patent applications and possess substantial know-how and trade secrets relating to the development and commercialization of vaccine and cell therapy products. The term of individual patents depends upon the legal term of the patents in the countries in which they are obtained. In most countries in which we file, the patent term is 20 years from the date of filing the non-provisional application. In the United States, a patent’s term may be lengthened by patent term adjustment ("Patent Term Adjustment"), which compensates a patentee for administrative delays by the United States Patent and Trademark Office ("U.S. PTO") in granting a patent, or may be shortened, if a patent is terminally disclaimed over an earlier-filed patent.

The term of a patent that covers an FDA-approved drug may also be eligible for patent term extension, which permits patent term restoration of a United States patent as compensation for the patent term lost during the FDA regulatory review process. The Hatch-Waxman Act permits a patent term extension of up to five years beyond the expiration of the patent. The length of the patent term extension is related to the length of time the drug is under regulatory review. A patent term extension cannot extend the remaining term of a patent beyond a total of 14 years from the date of product approval and only one patent applicable to an approved drug may be extended. Moreover, a patent can only be extended once, and thus, if a single patent is applicable to multiple products, it can only be extended based on one product. Similar provisions are available in Europe and


other foreign jurisdictions to extend the term of a patent that covers an approved drug. When possible, depending upon the length of clinical trials and other factors involved in the filing of a biologics license application ("BLA"), we expect to apply for patent term extensions for patents covering our product candidates and their methods of use.

As of the date of this Annual Report on Form 10-K, our patent portfolio includes the following:

ATLAS

Our discovery platform patent portfolio includes three patent families, currently comprising sixfive issued U.S. patents. We hold an exclusive license from The Regents of the University of California ("UC") to the first patent family, including U.S. Patent 6,004,815 and the related U.S. Patents 6,287,556 and 6,599,502. This first family includes claims to fundamental aspects of the ATLAS platform, developed by our scientific founder, Darren Higgins, Ph.D. while he was employed at the University of California, Berkeley. Patents in this family have a patent term until August 2018. We hold a further exclusive license from President and Fellows of Harvard College ("Harvard") to the secondfirst patent family, which covers methods related to the ATLAS discovery platform.platform, including discovery of antigens expressed in neoplastic cells. This secondfirst patent family includes U.S. PatentPatents 9,051,564 issued patents in Europe and Australia, a pending9,920,314, an allowed U.S. application, and pending applicationspatents granted in Europe, Canada, and Canada. Patents issuing from these applicationsAustralia. The granted foreign patents in this family are expected to expire in 2027 with the exception of2027. U.S. PatentPatents 9,051,564 which includes aand 9,920,314 include Patent Term AdjustmentAdjustments and extendsextend until December 2031.2031 and June 2028, respectively. We wholly own the thirda second patent family, which is specifically directed to the ATLAS platform as utilized by us.us, including for discovery of cancer- or tumor-related antigens. This thirdsecond patent family includes U.S. Patents 8,313,894, 9,045,791, and 9,045,791,9,873,870, an allowed U.S. patent application, a pending U.S. patent application, an issued patent in Australia, and pending applicationspatents in Europe, Canada, and Australia. Patents issuing from applicationsAustralia, and a pending application in Europe. The granted foreign patents in this family are expected to have a patent term until at least July 2029. U.S. Patents 8,313,894 and 9,045,791 have terms that include Patent Term Adjustments and extend until August 2030 and August 2029, respectively.

GEN-003 (Genital Herpes)

We wholly own a portfolio of patent applications directed to HSV-2 vaccines, including GEN-003. This portfolio includes two patent families covering HSV-2 vaccine compositions and methods for inhibiting or treating HSV-2 infections. The first patent family includes U.S. Patent 8,617,564, and patents granted in Australia, China, Indonesia, Israel, Japan, Mexico, New Zealand, Russia, and Singapore. A U.S. application and applications in Europe, Canada, Japan, Brazil, India, China and four additional foreign jurisdictions are pending in the first patent family. The second family includes a pending U.S. application, a patent granted in Japan, and pending applications in Europe, Canada, and Australia. Patents that issue from applications in these families are expected to expire in 2030 and 2031. The term for the issued U.S. Patent 8,617,564 includes Patent Term Adjustment and extends until at least January 2031. We own a further patent family covering follow-on HSV-2 vaccine compositions, with applications pending in the U.S., Europe, Canada, Australia and Japan. Patents issuing from this family are expected to expire in 2032.

We hold a license from Isconova AB (now Novavax, Inc.) to two patent families covering Matrix-M2, the adjuvant used in GEN-003. Both patent families include a pending U.S. application and issued patents in Europe, Canada, Australia, Japan, Brazil, New Zealand and South Africa. These issued patents have patent terms until at least July 2023 and July 2024. The second patent family also includes issued U.S. Patent 8,821,881, which9,873,870 has a term that extends until August 2026 inclusive of a Patent Term Adjustment.

GEN-004 (Pneumococcus)

July 2029. We co-own with Children’s Medical Center Corporation ("Children's"), a portfolio ofwholly own the third patent applicationsfamily, which is directed to pneumococcus vaccines, including GEN-004. This portfolio includes two patent families covering pneumococcal vaccine compositions and methods for inhibiting or treating pneumococcal infections. A U.S. applicationcancer diagnosis, prognosis, and patient selection, as well as related compositions. This third family currently comprises pending applications in Europe, Canada, Brazil, India, China and eight additionaleleven foreign jurisdictions are pending in the first patent family. The first family also includes granted patents in Australia, Japan, New Zealand and Russia. The second patent family includes U.S. Patent 9,393,294, a pending U.S. application, granted patents in Australia, Indonesia, Mexico and New Zealand, and pending applications in Europe, Canada, Japan, Brazil, Russia, India, China and six additional foreign jurisdictions. Patents that issue from applications in theseapplication. We wholly own three further patent families, each comprising a pending PCT application, claiming first priority to provisional applications filed in late 2018. These PCT applications are expecteddirected to have patent terms until at least 2030ATLAS-based methods for further selection of cancer- or tumor-related antigens, and 2032, respectively. We hold an exclusive license to Children's interest in these patent rights. We co-own with Children's one further patent family covering follow-on pneumococcal vaccine compositions, with pending applications in the U.S., Europe, Canada, Australia,for redirecting immune responses and Japan. Children's interest in these patent rights is also exclusively licensed to us.

GEN-001 (Chlamydia)re-educating T cells.



Our chlamydia patent portfolio previously included four patent families (one of which overlaps with the ATLAS portfolio). We held an exclusive license from Harvard to the first three patent families. We notified Harvard of our partial termination of the license agreement with regard to chlamydia antigens covered by these patent families on December 8th 2014. Effective March 8th 2015, the license agreement with Harvard with regard to chlamydia antigens covered by these patent families was terminated and we no longer hold an exclusive license to two of the three patent families, or to a chlamydia antigen covered by the remaining family. The remaining family covers certain aspects of the ATLAS platform, as well as one chlamydia antigen, and we maintain exclusive rights to aspects of the ATLAS platform covered by this family. We determined that the chlamydia antigens covered by these patent families were not relevant to the continued development of GEN-001. We wholly own the fourth patent family, which covers chlamydia vaccine and immunogenic compositions and methods for inhibiting or treating chlamydia infections. A U.S. application and applications in Europe, Canada, Australia and Japan are pending in this patent family. Patents issuing therefrom are expected to expire in 2031.

In addition to the above, we have established expertise and development capabilities focused in the areas of preclinical research and development, manufacturing and manufacturing process scale-up, quality control, quality assurance, regulatory affairs and clinical trial design and implementation. We believe that our focus and expertise will help us develop products based on our proprietary intellectual property.

In-LicenseLicense Agreements

University of California

In August 2006, we entered into an exclusive license agreement with UC granting us an exclusive, royalty-bearing sublicensable license to a patent family that includes claims to fundamental aspects of the ATLAS platform, to make, use, offer for sale, import and sell licensed products and services, and to practice licensed methods in all fields of use in the United States. This patent family consists entirely of issued United States patents with a patent term until August 2018. UC retains the right to practice and to allow other educational and non-profit institutions to practice, the licensed intellectual property licensed under the agreement for educational and research purposes.

Until first commercial sale of a licensed product or service, we are obligated to pay UC an annual license maintenance fee in the low five figures. Upon commercialization of our products and services covered by the licensed patents, we are obligated to pay UC royalties in the low single digits, subject to a minimum annual royalty in the low five figures, on the net sales of such products and services sold by us or our affiliates for the life of any licensed patents covering the products or services. The royalties payable to UC are subject to reduction for any third party payments required to be made, with a minimum floor in the low single digits. In addition, we agreed to pay UC a flat royalty in the low single digits on net sales of products sold by us or our affiliates which include a polypeptide, nucleotide sequence, biological organism or chemical entity identified in the practice of a licensed method or service, but not otherwise covered, by the licensed patent for the life of the licensed patents. If we receive any revenue (cash or non-cash) from any sublicensees, we must pay UC a percentage of such revenue, excluding certain categories of payments but including royalties on net sales by sublicensees, varying in the low-double digits for any sublicense depending on the scope of the license. Under the terms of the agreement, we are obligated to pay UC a specified development milestone payment and a specified commercial milestone payment up to $500 thousand in the aggregate for the first licensed product covered by the licensed patents, plus up to an additional $250 thousand if specified development and commercial milestones are met for each subsequent licensed product covered by the licensed patents. As of December 31, 2016, we have not made any milestone payments.

We are required to diligently develop and market licensed products, services and methods. If we are unable to meet our diligence obligations, even after any extension thereof, UC has the right, depending on the number of years the agreement has been effective, to either terminate the agreement or convert our exclusive license to a non-exclusive license.

Unless earlier terminated, the agreement with UC will remain in effect until the expiration of the last-to-expire patent under the licensed patent rights. We may terminate the agreement at any time by giving UC advance written notice. The agreement may also be terminated by UC in the event of a material breach by us that remains uncured after a specified period of time.

Harvard University

In November 2007, we entered intoWe have an exclusive license agreement with Harvard University (“Harvard”), granting us an exclusive, worldwide, royalty-bearing, sublicensable license to three patent families, to develop, make, have made, use, market, offer for sale, sell, have sold and import licensed products and to perform licensed services. This agreement was amended and restated in November 2012. The Harvard intellectual property covers methodsservices related to the ATLAS discovery platform, as well as certain


chlamydia immunogenic compositions and methods for inhibiting or treating chlamydia infections. Any patents within this portfolio that have issued or may be issued will expire normally in 2027 and 2028. Harvard retains the right to make and use, and to grant licenses to other not-for-profit research organizations to make and use, the licensed intellectual property for internal research, teaching and other educational purposes. We notified Harvard of our partial termination of the license agreement with regard to intellectual property covering chlamydia antigens on December 8, 2014. Effective March 8, 2015, the license agreement with Harvard with regard to intellectual property covering chlamydia antigens was terminated and we no longer hold a license to two of the three in-licensed Harvard patent families, or to a chlamydia antigen covered by the remaining family. The remaining family covers certain aspects of the ATLAS platform, as well as one chlamydia antigen, and we continue to maintain exclusive rights to aspects of the ATLAS platform covered by this family.

platform. We are obligated to pay Harvard an annual license maintenance fee ranging from the low five figures to the mid-five figures depending on the type of product and the number of years after the effective date of the agreement.  For products covered by the licensed patent rights, we arealso obligated to pay Harvard milestone payments up to $1.8$1.6 million in the aggregate upon the achievement of certain development and regulatory milestones. ForAs of December 31, 2019, we have paid $0.3 million in aggregate milestone payments. We are obligated under this license agreement to use commercially reasonable efforts to develop, market and sell licensed products discovered using the licensed methods,in compliance with an agreed upon development plan. In addition, we are obligated to pay Harvard milestone payments up to $600 thousandachieve specified development milestones and in the aggregateevent we are unable to meet our development milestones for eachany type of product or service, absent any reasonable proposed extension or amendment thereof, Harvard has the first threeright, depending on the type of product or service, to terminate this agreement with respect to such products or to convert the license to a non-exclusive, non-sublicensable license with respect to such products and up to $300 thousand in the aggregate for each additional product under the agreement upon the achievement of certain development and regulatory milestones. As of December 31, 2016, we paid $198 thousand in aggregate milestone payments. services.

Upon commercialization of our products covered by the licensed patent rights or discovered using the licensed methods, we are obligated to pay Harvard royalties on the net sales of such products and services sold by us, our affiliates, and our sublicensees. This royalty varies depending on the type of product or service but is in the low single digits. The sales-based royalty based on salesdue by our sublicensees is the greater of the applicable royalty rate or a percentage in the high single digits or the low double digits of the royalties we receive from such sublicensee, depending on the type of product. DependingBased on the type of commercialized product or service, royalties are payable until the expiration of the last-to-expire valid claim under the licensed patent rights or for a period of 10 years from first commercial sale of such product or service. The royalties payable to Harvard are subject to reduction, capped at a specified percentage, for any third partythird-party payments required to be made. In addition to the royalty payments, if we receive any additional revenue (cash or non-cash) under any sublicense, we must pay Harvard a percentage of such revenue, excluding certain categories of payments, varying from the low single digits to up to the low double digits depending on the scope of the license that includes the sublicense.

We are required to use commercially reasonable efforts to develop licensed products, introduce them into the commercial market and market them, in compliance with an agreed upon development plan. We are also obligated to achieve specified development milestones. If we are unable to meet our development milestones for any type of product or service, absent any reasonable proposed extension or amendment thereof, Harvard has the right, depending on the type of product or service, to terminate this agreement with respect to such products or to convert the              This license to a non-exclusive, non-sublicensable license with respect to such products and services.

Our agreement with Harvard will expire on a product-by-product or service-by-service and country-by-country basis until the expiration of the last-to-expire valid claim under the licensed patent rights. We may terminate the agreement at any time by giving Harvard advance written notice. Harvard may also terminate the agreement in the event of a material breach by us that remains uncured; in the event of our insolvency, bankruptcy, or similar circumstances; or if we challenge the validity of any patents licensed to us.
Other Collaborations

Children’s Medical Center CorporationOncovir License and Supply Agreement

In September 2008,January 2018, we entered into a collaborative research agreementLicense and Supply Agreement with Children’s, that was funded by PATH Vaccine Solutions ("PATH"Oncovir, Inc. (“Oncovir”). The collaborativeagreement provides the terms and conditions under which Oncovir will manufacture and supply an immunomodulator and vaccine adjuvant, Hiltonol® (poly-ICLC) (“Hiltonol”), to us for use in connection with the research, project led todevelopment, use, sale, manufacture, commercialization and marketing of products combining Hiltonol with our technology (the “Combination Product”). Hiltonol is the identificationadjuvant component of certain highly conserved pneumococcal antigens that are able to protect against colonization. The intellectual property covering these antigens is co-owned byGEN-009, which will consist of synthetic long peptides or neoantigens identified using our proprietary ATLAS platform, formulated with Hiltonol. 

              Oncovir granted us and Children's and covers pneumococcal vaccine compositions and methods for inhibiting or treating pneumococcus infections. In February 2010, we entered into an exclusivea non-exclusive, assignable, royalty-bearing worldwide license, agreement with Children's, which was amended and restated in March 2012. This agreement grants us an exclusive, worldwide, sublicensable license under Children's rights to the jointly-owned intellectual property to make, have made, use, sell, offer for sale, import and export licensed products and to practice licensed processes for the prevention and treatment of Streptococcus pneumoniae. Children's retains the right to practice and use, andgrant sublicenses through one tier, to allow academic non-profit research organizations to practice and use, the licensedcertain of Oncovir’s intellectual property forin connection with the research, educational, clinical and charitable purposes. Under the terms of the agreement, our license from Children's is subject to PATH’s separate non-exclusive, royalty-free license from Children's to develop pneumococcal T cell-based protein vaccines worldwide and to market and sell such vaccines in developing countries.



For products covered by the licensed patent rights, we are obligated to pay Children's milestone payments up to $390 thousand in the aggregate upon the achievement of certain development, and commercial milestones. As of December 31, 2016, we paid $140 thousand in aggregate milestone payments. Uponor commercialization of our products, we are obligated to pay Children's royalties inCombination Products, including the low single digitsuse of Hiltonol, but not the use of Hiltonol for manufacturing or the use or sale of Hiltonol alone. The license will become perpetual, fully paid-up, and royalty-free on the net sales of licensed products sold by us, our affiliates and our sublicensees. The royalties payable to Children's are subject to reduction for any third-party payments required to be made, with a minimum floor in the low single digits. Royalties are payable for the term of the license agreement, which is 15 years from the effective date of the amended and restated agreement or until expiration of the last-to-expire patent under the licensed patent rights, whichever period is longer. If we receive any additional revenue (cash or non-cash) under any sublicense, we must pay Children's a percentage of such income varying from the mid-single digits to low double digits depending on the clinical stage of development of the product, provided that such percentage may increase to match our financial obligations to third parties.

We are required to use commercially reasonable efforts to bring at least one licensed product to market as soon as reasonably practical, consistent with sound and legal business practices and judgment and to accomplish the objectives set forth in an agreed upon development plan. If we are unable to meet our diligence obligations, even after any extensions thereof, Children's has the right to terminate in this agreement in whole or in part.
Unless earlier terminated, the agreement with Children's will remain in effect until the later of 15 years from the effective date of the amended and restated agreementJanuary 25, 2028 or the expiration ofdate on which the last valid claim of any patent licensed to expire patentus under the licensed patent rights. We may terminate the agreement in its entirety or on a country-by-country and licensed product-by-licensed product basis. Children's may terminate the agreement in the event of our bankruptcy, insolvency or similar circumstances; if we use confidential information to formally challenge Children's joint ownership of the licensed patent rights; or if we materially breach the agreement and do not cure such breach within a specified time period.expires.

Novavax

In August 2009, we entered into an exclusive license and collaboration agreement with Isconova AB, a Swedish company which has subsequently been acquired by Novavax. The agreement grants us a worldwide, sublicensable, exclusive license to two patent families, to import, make, have made, use, sell, offer for sale and otherwise exploit licensed vaccine products containing an adjuvant which incorporates or is developed from Matrix-A, Matrix-C and/or Matrix-M technology, in the fields of HSV and chlamydia, and the time-limited exclusive fields of Neisseria gonorrhoeae, cytomegalovirus and Mycobacterium tuberculosis. In July 2015, upon expiration of the five-year exclusivity term included in the agreement, the license granted to us converted to a non-exclusive license with respect to all licensed intellectual property rights that were not jointly invented by us and Novavax under the collaboration. Under the terms of this agreement, Novavax also grants us a worldwide, sublicensable, non-exclusive license under such licensed intellectual property rights to import, make, have made, use, sell, offer for sale and otherwise exploit licensed products in the field of Streptococcus pneumoniae. Our rights in the field of Streptococcus pneumoniae are exclusive with respect to all intellectual property rights jointly invented by us and Novavax under the collaboration. The agreement further grants us certain limited rights to use Novavax trademarks.

For licensed products in each unique disease field under the agreement, we are obligated to pay NovavaxOncovir low to mid six figure milestone payments up to approximately $3.0 million in the aggregate upon the achievement of certain developmentclinical trial milestones for each Combination Product and commercial milestones. As of December 31, 2016, we paid $275 thousandthe first marketing approval for each Combination Product in aggregate milestone payments. Upon commercialization of our products, we are obligated to pay Novavaxcertain territories as well as tiered royalties in the low-single digits on a product-by-product basis based on the net sales of licensed products sold by us, our affiliates and our sublicensees. The royalties payable to Novavax are in the low single digits and vary on a country-by-country and licensed product-by-licensed product basis based on the amount of net sales and the nature and timing of the licensed product’s development. The royalties payable to Novavax are subject to reduction if the licensed product is not covered by one or more valid claims of the licensed patent rights, or if we are required to make any third-party payments. Royalties are payable for 10 years from first commercial sale in any particular country or until the date on which offer for sale of a licensed product is no longer covered by a valid claim of the licensed patent rights in such country, whichever period is longer. In addition to the royalty payments, if we receive any additional revenue (cash or non-cash) under any sublicenses, we must pay Novavax a percentage of such revenue, up to the low double digits.Combination Products.

We are required to use commercially reasonable efforts to perform specified research activities in accordance with an agreed-upon research plan. We are also obligated to use commercially reasonable efforts consistent with prudent business judgment and business and market conditions to research, develop and carry out the commercialization of licensed products in HSV and chlamydia.

Our agreement with Novavax will expire on a country-by-country and licensed product-by-licensed product basis on the date of the expiration of the royalty term with respect to such licensed product in such country.              We may terminate the


agreement onupon a country-by-country and licensed product-by-licensed product basisdecision to discontinue the development of the Combination Product or in its entirety at any timeupon a determination by giving Novavax advance written notice. Both parties may also terminate the agreement in the event ofus or an applicable regulatory authority that Hiltonol or a material breach by the other party that remains uncuredCombination Product is not clinically safe or for bankruptcy, insolvency or similar circumstances. Novavax may terminate this agreement if we challenge the validity of any patents licensed to us.

The agreement also contained a research funding clause for which we made monthly payments to Novavax between August 2009 and March 2012 of approximately $1.6 million. All amounts of research funding provided were to be refunded by Novavax. After December 31, 2015, any amounts remaining due from Novavax, including accrued interest, could be received in cash upon 30-day written notice provided by us. We provided this notice in January 2016 and received the $1.6 million refund in February 2016.

Manufacture Contracts

Fujifilm

In February 2014, we entered into a supply agreement with FUJIFILM Diosynth Biotechnologies U.S.A., Inc. ("Fujifilm") for the manufacture and supply of antigens for future GEN-003 clinical trials. In June and September 2016, the Company entered into new statements of work under the agreement with Fujifilm for the manufacture and supply of antigens for the Company's Phase 3 clinical trials. Under these agreement, we are obligated to pay Fujifilm milestone payments up to the low-eight figures upon the achievement of certain manufacturing milestones. As of December 31, 2016, we paid approximately $7.0 million in aggregate manufacturing milestone payments. Additionally, raw materials, resins and consumables purchased for the vaccine production are invoiced separately as such costs are incurred by Fujifilm. We pay Fujifilm’s actual costs plus a percentage fee in the mid-single digits for these raw materials, resins and consumables. We also are required to pay reservation fees, which equal a percentage of production fees in the low-double digits, to reserve manufacturing slots in the production timeframe as agreed upon under the agreement. We are required to use commercially reasonable efforts to timely provide Fujifilm with the technology, materials and resources needed to produce and supply the recombinant protein antigen.
Our agreement with Fujifilm will expire on February 25, 2024. Subject to termination fees under applicable circumstances, we may terminate the agreement at any time by giving Fujifilm advance written notice.effective. The agreement may also be terminated by either party due to a material uncured breach by the other party.

Baxter

In October 2014, we entered a product development and clinical supply agreement with Baxter Pharmaceutical Solutions LLC ("Baxter"). The product development and clinical supply agreement provides the terms and conditions under which Baxter will formulate, fill, inspect, package, label and test our lead product, GEN-003 for clinical supply. Under this agreement, we are obligated to pay Baxter amounts upparty, or due to the low six digits for each batch of GEN-003 manufactured. Additionally, certain set-up fees and equipment purchased for the purposes of batch production will be invoiced separately by Baxter. We will pay set-up fees and equipment costs in the low six digits upon commencement of batch production. We also pay a monthly service fee in the low five digits for project management services for the duration of the arrangement. As of December 31, 2016, we paid approximately $657 thousand under this agreement.

Our agreement with Baxter expires on October 23, 2021. Subject to termination fees under applicable circumstances, we may terminate the agreement at any time by giving Baxter advance written notice. The agreement may also be terminated by either party due to a material uncured breach by the other party.party’s bankruptcy, insolvency, or dissolution.

Trade Secrets



We may rely, in some circumstances, on trade secrets to protect our technology. However, trade secrets can be difficult to protect. We seek to protect our proprietary technology and processes, in part, by entering into confidentiality agreements with our employees, consultants, scientific advisors and contractors. We also seek to preserve the integrity and confidentiality of our data and trade secrets by maintaining physical security of our premises and physical and electronic security of our information technology systems. While we have confidence in these individuals, organizations, and systems, agreements or security measures may be breached, and we may not have adequate remedies for any breach. In addition, our trade secrets may otherwise become known or be independently discovered by competitors. To the extent that our consultants, contractors, or collaborators use intellectual property owned by others in their work for us, disputes may arise as to the rights in related or resulting know-how and inventions.



United States Government Regulation

Biological products such as vaccines and adoptive cell therapies are subject to regulation under the Federal Food, Drug, and Cosmetic Act ("FD&C Act") and the Public Health Service Act ("PHS Act"), and other federal, state, local and foreign statutes and regulations. Both the FD&C and PHS Acts and their corresponding regulations govern, among other things, the testing, manufacturing, safety, efficacy, labeling, packaging, storage, record keeping, distribution, reporting, advertising and other promotional practices involving biological products. Clinical testing of biological products is subject to FDA review before initiation. In addition, FDA approval must be obtained before marketing of biological products. The process of obtaining regulatory review and approval and the subsequent compliance with appropriate federal, state, local and foreign statutes and regulations require the expenditure of substantial time and financial resources and we may not be able to obtain the required regulatory approvals.

United States Biological Products Development Process

The process required by the FDA before a biological product may be marketed in the United States generally involves the following:following process:

completion of nonclinical laboratory tests and animal studies according to good laboratory practices ("GLP") and applicable requirements for the humane use of laboratory animals or other applicable regulations;
submission to the FDA of an application for an IND which must become effective before human clinical trials may begin;
performance of adequate and well-controlled human clinical trials according to the FDA’s regulations commonly referred to as good clinical practices ("GCP") and any additional requirements for the protection of human research subjects and their health information, to establish the safety and efficacy of the proposed biological product for its intended use, including approval by an independent Institutional Review Board (“IRB”), representing each clinical site before each clinical trial may be initiated;
submission to the FDA of a BLA for marketing approval that includes substantive evidence of safety, purity, and potency from results of nonclinical testing and clinical trials;
satisfactory completion of an FDA inspection of the manufacturing facility or facilities where the biological product is produced to assess compliance with good manufacturing practices ("GMPs")GMPs to assure that the facilities, methods and controls are adequate to preserve the biological product’s identity, strength, quality and purity and, if applicable, the FDA’s current good tissue practices ("GTP") for the use of human cellular and tissue products;
potential FDA audit of the nonclinical and clinical trial sites that generated the data in support of the BLA; and
FDA review and approval, or licensure, of the BLA.

Before testing any biological product candidate in humans, the product candidate enters the preclinical study stage. Preclinical studies, also referred to as nonclinical studies, include laboratory evaluations of product chemistry, toxicity and formulation, as well as animal studies to assess the potential safety and activity of the product candidate. The conduct of the preclinical studies must comply with federal regulations and requirements including GLPs.

The clinical trial sponsor must submit the results of the preclinical tests, together with manufacturing information, analytical data, any available clinical data or literature and a proposed clinical protocol, to the FDA as part of the IND. Some preclinical studies may continue even after the IND is submitted. The IND automatically becomes effective 30 days after receipt by the FDA, unless the FDA places the clinical trial on a clinical hold within that 30-day time period. In such a case, the IND sponsor and the FDA must resolve any outstanding concerns before the clinical trial can begin. The FDA also may impose clinical


holds on a biological product candidate at any time before or during clinical trials due to safety concerns or non-compliance. If the FDA imposes a clinical hold, studies may not recommence without FDA authorization and then only under terms authorized by the FDA. Accordingly, we cannot be sure that submission of an IND will result in the FDA allowing clinical trials to begin, or that, once begun, issues will not arise that suspend or terminate such studies.

Clinical trials involve the administration of the biological product candidate to healthy volunteers or patients under the supervision of qualified investigators, generally physicians not employed by or under the trial sponsor’s control. Clinical trials


are conducted under protocols detailing, among other things, the objectives of the clinical trial, dosing procedures, subject selection and exclusion criteria, and the parameters to be used to monitor subject safety, including stopping rules that assure a clinical trial will be stopped if certain AEsadverse events ("AEs") should occur. Each protocol and any amendments to the protocol must be submitted to the FDA as part of the IND. Clinical trials must be conducted and monitored in accordance with the FDA’s regulations comprising the GCP requirements, including the requirement that all research subjects provide informed consent. Further, each clinical trial must be reviewed and approved by an IRB, at or servicing each institution at which the clinical trial will be conducted. An IRB is charged with protecting the welfare and rights of trial participants and considers such items as whether the risks to individuals participating in the clinical studies are minimized and are reasonable in relation to anticipated benefits. The IRB also approves the form and content of the informed consent that must be signed by each clinical trial subject or his or her legal representative and must monitor the clinical trial until completed.

Human clinical trials are typically conducted in three sequential phases that may overlap or be combined:

Phase 1. The biological product is initially introduced into healthy human subjects and tested for safety, dosage tolerance, absorption, metabolism, distribution and excretion. In the case of some products for severe or life-threatening diseases, especially when the product may be too inherently toxic to ethically administer to healthy volunteers, the initial human testing is often conducted in patients.
Phase 2. The biological product is evaluated in a limited patient population to identify possible AEs and safety risks, to preliminarily evaluate the efficacy of the product for specific targeted diseases and to determine dosage tolerance, optimal dosage and dosing schedule.
Phase 3. Clinical studies are undertaken to further evaluate safety, purity, and potential of biological product in an expanded patient population at geographically dispersed clinical trial sites. These clinical studies are intended to establish the overall risk/benefit ratio of the product and provide an adequate basis for product approval and product labeling.
Post-approval clinical studies, sometimes referred to as Phase 4 clinical studies, may be conducted after initial marketing approval. These clinical studies are used to gain additional experience from the treatment of patients in the intended therapeutic indication, particularly for long-term safety follow-up.

During all phases of clinical development, regulatory agencies require extensive monitoring and auditing of all clinical activities, clinical data and clinical trial investigators. Annual progress reports detailing the results of the clinical studies must be submitted to the FDA. Written IND safety reports must be promptly submitted to the FDA and the investigators for serious and unexpected AEs, any findings from other studies, tests in laboratory animals or in vitro testing that suggest a significant risk for human subjects, or any clinically important increase in the rate of a serious suspected adverse reaction over that listed in the protocol or investigator brochure. The sponsor must submit an IND safety report within 15 calendar days after the sponsor determines that the information qualifies for reporting. The sponsor also must notify the FDA of any unexpected fatal or life-threatening suspected adverse reaction within seven calendar days after the sponsor’s initial receipt of the information. Phase 1, Phase 2 and Phase 3 clinical studies may not be completed successfully within any specified period, if at all. The FDA or the sponsor or its data safety monitoring board may suspend or terminate a clinical trial at any time on various grounds, including a finding that the research subjects or patients are being exposed to an unacceptable health risk. Similarly, an IRB can suspend or terminate approval of a clinical trial at its institution if the clinical trial is not being conducted in accordance with the IRB’s requirements or if the biological product has been associated with unexpected serious harm to patients. Sponsors of all controlled clinical trials, except for Phase 1 trials, are required to submit certain clinical trial information for inclusion in the public clinical trial registry and results data bank maintained by the National Institutes of Health, which are publicly available at http://clinicaltrials.gov.

Concurrent with clinical studies, companies usually complete additional animal studies and must also develop additional information about the physical characteristics of the biological product as well as finalize a process for manufacturing the product in commercial quantities in accordance with GMP requirements. To help reduce the risk of the introduction of adventitious agents with use of biological products, the PHS Act emphasizes the importance of manufacturing control for products whose attributes


cannot be precisely defined. The manufacturing process must be capable of consistently producing quality batches of the product candidate and, among other things, the sponsor must develop methods for testing the identity, strength, quality, potency and purity of the final biological product. Additionally, appropriate packaging must be selected and tested, and stability studies must be conducted to demonstrate that the biological product candidate does not undergo unacceptable deterioration over its shelf life.

United States Review and Approval Processes



After the completion of clinical trials of a biological product, FDA approval of a BLA must be obtained before commercial marketing of the biological product. The BLA must include results of product development, laboratory and animal studies, human studies, information on the manufacture and composition of the product, proposed labeling and other relevant information. In addition, under the Pediatric Research Equity Act, a BLA or supplement to a BLA must contain data to assess the safety and effectiveness of the biological product for the claimed indications in all relevant pediatric subpopulations and to support dosing and administration for each pediatric subpopulation for which the product is safe and effective. The FDA may grant deferrals for submission of data or full or partial waivers. The testing and approval processes require substantial time and effort and there can be no assurance that the FDA will accept the BLA for filing and, even if filed, that any approval will be granted on a timely basis, if at all, and for what indications will be approved, if any.

Under the Prescription Drug User Fee Act ("PDUFA"), as amended,re-authorized for an additional five years in 2017, each BLA must be accompanied by a significant user fee. PDFUAPDUFA also imposes an annual product fee for biologics and an annual establishment feeprogram fees based on facilities used to manufacture prescription biologics.each approved biologic. 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.

Within 60 days following submission of the application, the FDA reviews the BLA to determine if it is substantially complete before the agency accepts it for filing. The FDA may refuse to file any BLA that it deems incomplete or not properly reviewable at the time of submission and may request additional information. In this event, the BLA must be resubmitted with the additional information. The resubmitted application also is subject to review before the FDA accepts it for filing. Once the submission is accepted for filing, the FDA begins an in-depth substantive review of the BLA. The FDA reviews the BLA to determine, among other things, whether the proposed product is safe and potent, or effective, for its intended use, and has an acceptable purity profile, and whether the product is being manufactured in accordance with GMP regulations to assure and preserve the product’s identity, safety, strength, quality, potency and purity. The FDA may refer applications for novel biological products or biological products that present difficult questions of safety or efficacy to an advisory committee, typically a panel that includes clinicians and other experts, for review, evaluation and a recommendation as to whether the application should be approved and under what conditions. The FDA is not bound by the recommendations of an advisory committee, but it considers such recommendations carefully when making decisions. During the biological product approval process, the FDA also will determine whether a Risk Evaluation and Mitigation Strategy ("REMS"), is necessary to assure the safe use of the biological product. If the FDA concludes a REMS is needed, the sponsor of the BLA must submit a proposed REMS; the FDA will not approve the BLA without a REMS, if required.

Before approving a BLA, the FDA will inspect the facilities at which the product is manufactured. The FDA will not approve the product unless it determines that the manufacturing processes and facilities are in compliance with GMP requirements and adequate to assure consistent production of the product within required specifications. Additionally, before approving a BLA, the FDA will typically inspect one or more clinical sites to assure that the clinical trials were conducted in compliance with IND study requirements and GCP requirements. To assure GMP, GTP and GCP compliance, an applicant must incur significant expenditure of time, money and effort in the areas of training, record keeping, production, and quality control.

Notwithstanding the submission of relevant data and information, the FDA may ultimately decide that the BLA does not satisfy its regulatory criteria for approval and deny approval. Data obtained from clinical trials are not always conclusive and the FDA may interpret data differently than we interpret the same data. If the agency decides not to approve the BLA in its present form, the FDA will issue a complete response letter that usually describes all of the specific deficiencies in the BLA identified by the FDA. The deficiencies identified may be minor, for example, requiring labeling changes, or major, for example, requiring additional clinical trials. Additionally, the complete response letter may include recommended actions that the applicant might take to place the application in a condition for approval. If a complete response letter is issued, the applicant may either resubmit the BLA, addressing all of the deficiencies identified in the letter, or withdraw the application.

If a product receives regulatory approval, the approval may be significantly limited to specific diseases and dosages or the indications for use may otherwise be limited, which could restrict the commercial value of the product. Further, the FDA may require that certain contraindications, warnings or precautions be included in the product labeling. The FDA may impose restrictions and conditions on product distribution, prescribing, or dispensing in the form of a risk management plan,REMS, or otherwise limit the scope of any approval. In addition, the FDA may require post marketing clinical trials, sometimes referred to as Phase 4 clinical trials, designed


to further assess a biological product’s safety and effectiveness, and testing and surveillance programs to monitor the safety of approved products that have been commercialized.

One of the performance goals agreed to by the FDA under the PDUFA is to review 90% of standard BLAs in 10 months from filing and 90% of priority BLAs in six months from filing, whereupon a review decision is to be made. The FDA does not always meet its PDUFA goal dates for standard and priority BLAs and its review goals are subject to change


from time to time. The review process and the PDUFA goal date may be extended by three months if the FDA requests or the BLA sponsor otherwise provides additional information or clarification regarding information already provided in the submission within the last three months before the PDUFA goal date.

Federal and StateUnited States Fraud and Abuse, Transparency and Privacy Laws

In the United States, our business activities are subject to numerous other federal, state and local laws by federaldesigned to, for example, prevent fraud and state authorities,abuse; promote transparency in addition tointeractions with others in the FDA, including but not limited to,healthcare industry; protect the United States Departmentprivacy of Health and Human Services ("HHS"), and its various divisions, including but not limited to, the Centers for Medicare & Medicaid Services ("CMS").individual information; ensure integrity of research or protect human subjects involved in research. These laws are enforced by various federal and state enforcement authorities, including but not limited to, the United States Department of Justice, and individual United States Attorney offices within the Department of Justice, the United States Department of Health and Human Services ("HHS"), HHS’ various enforcement divisions, including but not limited to, the Centers for Medicare & Medicaid Services ("CMS"), the Office of Inspector General, the Office for Human Research Protections, and the Office of Research Integrity, and other state and local government agencies.

TheAlthough we currently have no products approved for commercial sale, we may be subject to various federal Anti-Kickback Statute prohibits, among other things, knowingly and willfullystate laws pertaining to health care “fraud and abuse,” including anti-kickback laws and false claims laws, for activities related to future sales of any of our product candidates that may in the future receive regulatory and marketing approval. Anti-kickback laws generally prohibit a pharmaceutical manufacturer from soliciting, offering, paying, soliciting,receiving, or receivingpaying any remuneration (including any kickback, bribe or rebate), directly or indirectly, overtly or covertly, in cash or in kind, to induce, or in return for, purchasing, leasing, ordering, or arranging for or recommending,generate business, including the purchase, lease,prescription or order of any good, facility, service or item for which payment is made, in whole or in part, under a federal health care program, such as Medicare. The federal Anti-Kickback Statute has been interpreted to apply to arrangements between manufacturers on one hand and prescribers, purchasers and formulary managers on the other. There are a number of statutory exceptions and regulatory safe harbors protecting certain common activities from prosecution. Failure to meet all of the requirementsuse of a particular applicable statutory exception or regulatory safe harbor does not make the conduct per se illegal under the federal Anti-Kickback Statute. Instead, the legality of the arrangement will be evaluated on a case-by-case basis based on a cumulative review of all of its factsdrug. False claims laws generally prohibit anyone from knowingly and circumstances.

The federal civil False Claims Act prohibits, among other things, any person or entity from knowinglywillingly presenting, or causing to be presented, aany claims for payment for reimbursed drugs or services to third party payors (including Medicare and Medicaid) that are false or fraudulent claim for paymentfraudulent. Although the specific provisions of these laws vary, their scope is generally broad and there may not be regulations, guidance or court decisions that apply the laws to or approvalparticular industry practices. There is therefore a possibility that our practices might be challenged under such laws.

Laws and regulations have been enacted by the federal government and various states to regulate the sales and marketing practices of pharmaceutical manufacturers with marketed products. The laws and regulations generally limit financial interactions between manufacturers and health care providers; require manufacturers to adopt certain compliance standards and/or knowingly making, using, or causing to be made or used, a false record or statement material to a false or fraudulent claimrequire disclosure to the government and public of such interactions. Many of these laws and regulations contain ambiguous requirements or require administrative guidance for implementation. Given the lack of clarity in laws and their implementation, any future activities (if we obtain approval and/or reimbursement from federal government. Recently, the civil False Claims Act has been usedhealthcare programs for our product candidates) could be subject to assert liability on the basis of kickbacks and improper referrals, improperly reported government pricing metrics such as Medicaid Best Price or Average Manufacturer Price, improper use of supplier or provider Medicare numbers when detailing a provider of services, improper promotion of drugs or off-label uses not expressly approved by the FDA in a drug’s label, and misrepresentations with respect to the services rendered or items provided.challenge.

Additionally, the civil monetary penalties statute, among other things, imposes fines against any person who is determined to have presented, or caused to be presented, claims to a federal health care program that the person knows, or should know, is for an item or service that was not provided as claimed or is false or fraudulent.

The federal Health Insurance Portability and Accountability Act of 1996 created new federal criminal statutes that prohibit knowingly and willfully executing, or attempting to execute, a scheme to defraud or to 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 health care benefit program and knowingly and willfully falsifying, concealing or covering up by trick, scheme or device a material fact or making any materially false, fictitious or fraudulent statement in connection with the delivery of, or payment for, health care benefits, items or services relating to health care matters.

Many states have similar fraud and abuse statutes and regulations that apply to items and services reimbursed under Medicaid and other state programs, or, in several states, private payors.

Additionally, the federal Physician Payments Sunshine Act within the Health Care and Education Reconciliation Act, or Health Care Reform Law, and its implementing regulations, require that certain manufacturers of drugs, devices, biological and medical supplies for which payment is available under Medicare, Medicaid or the Children’s Health Insurance Program (with certain exceptions) to report to CMS, information related to certain payments or other transfers of value made or distributed to physicians and teaching hospitals, or to entities or individuals at the request of, or designated on behalf of, the physicians and teaching hospitals and to report annually to CMS certain ownership and investment interests held by physicians and their immediate family members.

In addition, weWe may be subject to or our marketing activities may be limited by, data privacy and security regulation by bothlaws in the federal government and the statesvarious jurisdictions in which we conductoperate, obtain or store personally identifiable information. Numerous U.S. federal and state laws govern the collection, use, disclosure and storage of personal information. Various foreign countries also have, or are developing, laws governing the collection, use, disclosure and storage of personal information. Globally, there has been an increasing focus on privacy and data protection issues that may affect our business.


See “Risk Factors - Risks Related to Our Business and Industry”.

If our operations are found to be in violation of any of the health regulatory laws described above, or any other laws that apply to us, we may be subject to penalties, including, without limitation, civil, criminal, and administrative penalties, damages, monetary fines, disgorgement, possible exclusion from participation in Medicare, Medicaid and other federal health care programs, contractual damages, reputational harm, diminished profits and future earnings, and curtailment or restructuring of our operations.

Reimbursement

In both domestic and foreign markets, the commercial success of any approved products will depend, in part, on the availability of coverage and adequate reimbursement offor such products from third-party payors, such as government health care programs, commercial insuranceprivate health insurers, and managed care organizations. Patients who are provided vaccinations, and providers providing vaccinations, generally rely on third-party payors to reimburse all or part of the associated health care costs. Sales of any approved vaccines will therefore depend substantially, both domestically and abroad, on the extent to which the costs of our approved vaccines will be paid by third-party payors. These third-party payors are increasingly challenging the prices charged for medical products and services and imposing controls to manage costs. The containment of health care costs has become a priority of federal and state governments and the prices of drugs have been a focus in this effort. Governments have shown significant interest in implementing cost-containment programs, including price controls, restrictions on reimbursement and requirements for substitution of generic products. Adoption of price controls and cost-containment measures, and adoption of more restrictive policies in jurisdictions with existing controls and measures, could further limit our net revenue and results. Third-party payors may limit coverage to specific products on an approved list or formulary, which might not include all of the FDA-approved products for a particular indication. In addition, there is significant uncertainty regarding the reimbursement status of newly approved health care products. Third-party payors are increasingly examining the medical necessity and cost-effectiveness of medical products


and services, in addition to their safety and efficacy. We may need to conduct expensive pharmacoeconomic studies in order to demonstrate the cost-effectiveness of our products. If third-party payors do not consider our products to be cost-effective compared to other therapies, the payors may not cover our products after approvedapproval as a benefit under their plans or, if they do, the level of payment may not be sufficient to allow us to sell our products on a profitable basis.

Within the United States, if we obtain appropriate approval in the future to market any of our current product candidates, we may seek approval and coverage for those products under Medicaid, Medicare, and the PHS Act, pharmaceutical340B drug pricing program and also seek to sell the products to federal agencies.programs. These programs are administered by various federal and state agencies and provide prescription drug benefits to allow for individuals who are age 65 and over, low income, andor disabled beneficiaries accessor allow healthcare providers that serve vulnerable populations to purchase prescription drugs at discounted prices. In the future, we may also seek to sell any approved medicines and treatments. Under theseproduct candidates to government purchasers. In order to obtain coverage for our products under government benefit programs, manufacturers areor to sell products to government purchasers, we may be required to track and report prices for our products, offer discounts to certain purchasers, or pay rebates and the pricing of an approved treatment may be subject to various forms of price modifications.on certain utilization.

RecentIn the United States, federal and state governments continue to propose and pass legislation including the American Recovery and Reinvestment Actdesigned to reform delivery of, 2009 (the "2009 Act"), the Affordable Care Act enacted in March 2010 (the "2010 Act"), as well as the pending proposals to eliminate or significantly modify the 2010 Act may impactpayment for, health care, financing by both governmental and private payors. The 2009 Act provides funding for the federal government to compare the effectiveness of different treatments for the same illness. Although the results of the comparative effectiveness studies are not intended to mandate coverage policies for public or private payors, it is not clear what effect, if any, the research will have on the sales of any product, if any such product or the condition that it is intended to treat is the subject of a trial. It is also possible that comparative effectiveness research demonstrating benefits in a competitor’s product could adversely affect the sales of any of our approved products. The 2010 Act was designedwhich include initiatives to reduce the cost of healthcare. For example, in March 2010, the United States Congress enacted the Patient Protection and Affordable Care Act and the Health Care and Education Reconciliation Act (the "Healthcare Reform Act") which expanded health care coverage through Medicaid expansion and the implementation of the individual mandate for health insurance coverage and which could limitincluded changes to the prices we are ablecoverage and reimbursement of drug products under government healthcare programs. Under the Trump administration, there have been ongoing efforts to charge or the amounts of reimbursement available for our vaccine candidates once they are approved.

Modifications tomodify or repeal of all or certain provisions of the 2010 Act are expected asHealthcare Reform Act. For example, tax reform legislation was enacted at the end of 2017 that eliminates the tax penalty for individuals who do not maintain sufficient health insurance coverage beginning in 2019 (the so-called “individual mandate”). In a resultMay 2018 report, the Congressional Budget Office estimated that, compared to 2018, the number of uninsured will increase by 3 million in 2019 and 6 million in 2028, in part due to the elimination of the outcomeindividual mandate. The Healthcare Reform Act has also been subject to judicial challenge. In December 2018, a federal district court judge, in a challenge brought by a number of state attorneys general, found the Healthcare Reform Act unconstitutional in its entirety because, once Congress repealed the individual mandate provision, there was no longer a basis to rely on Congressional taxing authority to support enactment of the recent presidential electionslaw. In December 2019, a federal appeals court agreed that the individual mandate provision was unconstitutional, but remanded the case back to the district court to assess more carefully whether any provisions of the Healthcare Reform Act were severable and Republications maintaining controlcould survive. Pending action by the district court and resolution of Congress, consistent with statements made by Donaldany appeals, which could take some time, the Healthcare Reform Act is still operational in all respects.

There have been other reform initiatives under the Trump Administration, including initiatives focused on drug pricing. For example, in May of 2018, President Trump and membersthe Secretary of Congress during the presidential campaignDepartment of Health and followingHuman Services released a “blueprint” to lower prescription drug prices and out-of-pocket costs. Certain proposals in the election.blueprint, and related drug pricing measures proposed since the blueprint, could cause significant operational and reimbursement changes for the pharmaceutical industry. As another example, legislation passed in 2019 revised how certain prices reported by manufacturers under the Medicaid Drug Rebate Program are calculated, a revision that the Congressional Budget Office has estimated will save the federal government approximately $3 billion in the next ten years.

There have also been other efforts by government officials or legislators to implement measures to regulate prices or payment for pharmaceutical products, including legislation on drug importation. Recently, there has been considerable public and government scrutiny of pharmaceutical pricing and proposals to address the perceived high cost of pharmaceuticals. There have been recent state legislative efforts to address drug costs, which generally have focused on increasing transparency around drug costs or limiting drug prices.

Adoption of new legislation at the federal or state level could affect demand for, or pricing of, our product candidates if approved for sale. We cannot, however, predict the ultimate content, timing, or effect of any changes to the 2010Healthcare Reform Act or other federal and state reform efforts. There is no assurance that federal or state health care reform will not adversely affect our future business and financial results, and we cannot predict how future federal or state legislative, judicial or administrative changes relating to healthcare reform will affect our business.results.

Outside the United States, ensuring adequate coverage and payment for our products will face challenges. In international markets, reimbursement and health care payment systems vary significantly by country, and many countries have instituted price ceilings on specific products and therapies. Pricing of prescription pharmaceuticals is subject to governmental control in many countries. Pricing negotiations with governmental authorities can extend well beyond the receipt of regulatory marketing approval for a product and may require us to conduct a clinical trial that compares the cost effectiveness of our product candidates or products to other available therapies. The conduct of such a clinical trial could be expensive and result in delays in our commercialization efforts. Third-party payors are challenging the prices charged for medical products and


services, and many third-party payors limit reimbursement for newly-approved health care products. Recent budgetary pressures in many European Union countries are also causing governments to consider or implement various cost-containment measures, such as price freezes, increased price cuts and


rebates. If budget pressures continue, governments may implement additional cost-containment measures. Cost-control initiatives could decrease the price we might establish for products that we may develop or sell, which would result in lower product revenues or royalties payable to us. There can be no assurance that any country that has price controls or reimbursement limitations for pharmaceutical products will allow favorable reimbursement and pricing arrangements for any of our products.

Foreign Regulation

In addition to regulations in the United States, we will be subject to a variety of foreign regulations governing clinical trials and commercial sales and distribution of our product candidates. Whether or not we obtain FDA approval for a product candidate, we must obtain approval from the comparable regulatory authorities of foreign countries or economic areas, such as the European Union, before we may commence clinical trials or market products in those countries or areas. The approval process and requirements governing the conduct of clinical trials, product licensing, pricing and reimbursement vary greatly from place to place, and the time may be longer or shorter than that required for FDA approval.

Certain countries outside of the United States have a process that requires the submission of a clinical trial application ("CTA") much like an IND prior to the commencement of human clinical trials. In Europe, for example, a CTA must be submitted to the competent national health authority and to independent ethics committees in each country in which a company intends to conduct clinical trials. Once the CTA is approved in accordance with a country’s requirements, clinical trial development may proceed in that country. In all cases, the clinical trials must be conducted in accordance with GCPs and other applicable regulatory requirements.

Under European Union regulatory systems, a company may submit marketing authorization applications either under a centralized or decentralized procedure. The centralized procedure is compulsory for medicinal products produced by biotechnology or those medicinal products containing new active substances for specific indications such as the treatment of AIDS, cancer, neurodegenerative disorders, diabetes, viral diseases and designated orphan medicines, and optional for other medicines which are highly innovative. Under the centralized procedure, a marketing application is submitted to the European Medicines Agency where it will be evaluated by the Committee for Medicinal Products for Human Use and a favorable opinion typically results in the grant by the European Commission of a single marketing authorization that is valid for all European Union member states within 67 days of receipt of the opinion. The initial marketing authorization is valid for five years, but once renewed is usually valid for an unlimited period. The decentralized procedure provides for approval by one or more “concerned” member states based on an assessment of an application performed by one memberone-member state, known as the “reference” member state. Under the decentralized approval procedure, an applicant submits an application, or dossier, and related materials to the reference member state and concerned member states. The reference member state prepares a draft assessment and drafts of the related materials within 120 days after receipt of a valid application. Within 90 days of receiving the reference member state’s assessment report, each concerned member state must decide whether to approve the assessment report and related materials. If a member state does not recognize the marketing authorization, the disputed points are eventually referred to the European Commission, whose decision is binding on all member states. In light of the United Kingdom’s vote in 2016 to leave the European Union, the so-called Brexit vote, there may be changes forthcoming in the scope of the centralized approval procedure as the terms of that exit are negotiated between the United Kingdom and the European Union.

Manufacturing

We do not have any manufacturing facilities. We currently rely, and expect to continue to rely, on third parties for the manufacture of our product candidates for non-clinical studies and clinical trials, as well as for commercial manufacture if our product candidates receive marketing approval. To date, we have obtained materials for GEN-003 from third-party manufacturers who are sole source suppliers to us. We intend to identify and qualify contract manufacturers to provide the protein process development, protein production, adjuvant production, and fill-and-finish services prior to submission of a BLA to the FDA.


Information about our Executive Officers

Executive Officers of the Registrant

The following table sets forth the name, age and position of each of our executive officers as of February 17, 2017.13, 2020.
Name Age Position
William Clark 4851 President and Chief Executive Officer
Seth Hetherington,Girish Aakalu, Ph.D.45Chief Business Officer
Thomas Davis, M.D. 6456 Chief Medical Officer
Jonathan PooleDiantha Duvall 4248 Chief Financial Officer
Eric Hoffman, Ph.D.47Chief Business Officer
Jessica Baker Flechtner, Ph.D. 4548 Chief Scientific Officer
Narinder Singh48Senior Vice President, Pharmaceutical Sciences and Manufacturing



William Clark"Chip" Clark. Chip has served as our President and Chief Executive Officer since February 2011. Previously he served2011 after serving as our Chief Business Officer from August 2010 to February 2011. Mr. ClarkChip has also served on our board of directors since February 2011. Prior to joining our Company,Genocea, he served as Chief Business Officer at Vanda Pharmaceuticals, Inc. ("Vanda"), a biopharmaceutical company he co-founded in 2004. While at Vanda, he leadled the company’s strategic and business development activities and played a central role in raising more than $220$400 million in multiple publicthrough business development deals and privateequity financings. Prior to Vanda, Mr. ClarkChip was a principal at Care Capital, LLC, a venture capital firm investing in biopharmaceutical companies, after serving in a variety of commercial and strategic roles at SmithKline Beecham (now GlaxoSmithKline). Mr. ClarkChip holds a B.A. from Harvard University and an M.B.A. from The Wharton School at the University of Pennsylvania.

Seth Hetherington, M.D.Girish Aakalu, Ph.D. Girish joined Genocea in December 2018 as Chief Business Officer. In this role, he leads Genocea’s business development efforts. His broad skill set spans business development, corporate and R&D strategy, product portfolio management, commercial planning, and alliance management. Prior to joining Genocea, Girish was employed by the Ipsen Group, from May 2015 until December 2018, where he was most recently Vice President: Global Head of External Innovation, and Pfizer, Inc., from October 2007 until May 2015, where he held the title of Executive Director: Head of Strategy, Innovation & Operations for Pfizer’s External R&D Innovation team prior to his departure. His previous roles also include business development and oncology pipeline market planning positions at Genentech, Inc. and life science consulting experience at L.E.K Consulting. He received a B.A. in Biophysics with General and Departmental Honors from Johns Hopkins University, a Ph.D. in Cellular and Molecular Neurobiology following an M.S. in Biology from the California Institute of Technology and has servedcompleted executive education in Corporate Governance at Northwestern University - Kellogg School of Management.

Thomas Davis, M.D. Tom joined Genocea in October 2018 as our Chief Medical Officer since joining our Companywith over 20 years of academic and industry experience in January 2011.immuno-oncology and cancer drug development. Most recently, he served as Chief Medical Officer of Gadeta B.V., a Dutch cell therapy company pursuing novel cancer targets from October 2017 to April 2018, where he steered a novel cell therapy technology into first-in human clinical studies. Prior to joining our Company, Dr. HetheringtonGadeta B.V., he served as Senior Vice PresidentChief Medical Officer of Celldex from 2006 to 2017, where he led all aspects of clinical and regulatory development including strategy, tactics, and execution. While at Celldex, Tom actively built and oversaw Clinical andScience, Medical Affairs, Safety, Clinical Operations, Statistics, Regulatory Affairs, at Icagen, Inc. ("Icagen"), from May 2006 through December 2010. Prior to Icagen, Dr. Hetheringtonand Project Management, managed collaborations with large global pharmaceutical partners, and participated in investor relations activities. He also served as Vice President, Clinical Development and Chief Medical Officer at Inhibitex Inc. from June 2002 through April 2005GenVec and held various positionsas Senior Director of increasing responsibility inClinical Science at Medarex.Prior to joining the industry, Tom supervised clinical drug development at GlaxoSmithKline from 1995 through June 2002. Dr. Hetherington has also served as a faculty memberefforts at the UniversityCancer Therapy Evaluation Program (CTEP) of North Carolina Schoolthe National Cancer Institute (NCI), and worked on the development of Medicinerituximab and held appointmentsidiotype vaccines at several leading academic medical centers, including the University of Tennessee, St. Jude Children’s Research HospitalStanford University. Dr. Davis received his B.A. in Memphis and Albany Medical College. Dr. Hetherington earnedBiophysics from Johns Hopkins, his B.S. at Yale UniversityM.S. in Physiology and his M.D. at thefrom Georgetown University, of North Carolina, Chapel Hill and he completed his postgraduate training in pediatrics and pediatric infectious diseases at the University of North Carolina and the University of Minnesota, respectively. Dr. Hetherington has published extensivelya fellowship in medical and scientific literature, and is board certified in both pediatrics and pediatric infectious diseases. He has served as the industry representative to the Vaccines and Related Blood Products Advisory Committee of the FDA and the National Vaccine Advisory Committee of the U.S. Department of Health and Human Services.oncology at Stanford University.

Jonathan PooleDiantha Duvall has served. Diantha joined Genocea in March 2019 as ourthe Chief Financial Officer since joining our Company in April 2014.Officer. Prior to joining our Company, Mr. Poole served as Seniorher appointment with Genocea, Ms. Duvall was Vice President, of Finance for PipelineController and Technical OperationChief Accounting Officer at Shire plc (“Shire”)Bioverativ, Inc. from June 2013 through March 2014, leading finance support for Shire’s global business development, research and development and technical operations activities. Mr. Poole previously served as divisional Chief Financial Officer of Shire HGT, Shire’s rare disease division, from May 2010 through June 2013 and held various positions of increasing responsibility in finance at Shire from 2006 through May 2010. He began his career in the United Kingdom in investment banking at UBS Warburg and ING Barings and also worked as an investment manager for Avanti Capital plc, a United Kingdom private equity investment firm. Mr. Poole holds an M.B.A. from London Business School and a BSc in biological sciences from Durham University in the United Kingdom.

Eric Hoffman, Ph.D.  has served as our Chief Business Officer since joining our Company in December 2014.February 2017 to January 2019. Prior to joining our Company, Dr. Hoffman servedthat, she worked at Biogen Inc., serving as Vice President of CorporateGlobal Commercial Controller from February 2016 to January 2017, and Business Development, and also oversaw Program Management andU.S. Commercial Operations, at Idenix Pharmaceuticals, Inc. ("Idenix")Controller from February 2015 to January 2012 until its acquisition by Merck & Co. in August 2014. Dr. Hoffman2016. She also held a role overseeing Investor Relationsnumber of positions at Merck and Corporate Communications whileCo. from May 2009 to January 2015. Her experiences at Idenix from January 2011 to December 2011. Prior to Idenix, Dr. Hoffman spent nearly five years, from 2006 to 2011, at Biogen IdecMerck spanned roles in investor relations andventure investment, business development, rolesjoint ventures, and spent more than five yearsalliances, as well as operational controls and technical accounting. She also has extensive experience in SEC reporting, Sarbanes Oxley compliance, transaction support and risk management, having held multiple health industries positions within PricewaterhouseCoopers from 20011996 to 2006 on Wall Street as an equity research analyst at J.P. Morgan, Schwab Soundview Capital Markets2009. Ms. Duvall has a Master of Science in Accounting and Bear Stearns. Before starting on Wall Street in 2001, he was a post-doctoral research scientist in the DepartmentMaster of Immunobiology at King's College London School of Medicine at Guy’s Hospital, studying T-cell developmentBusiness Administration from 1999 to 2000. He has authored several book chapters and peer-reviewed articles, including in Cell, Immunity, and Genes & Development. Dr. Hoffman holds a Ph.D. in Immunobiology from YaleNortheastern University and a B.S. in BiologyBachelor of Arts from Trinity University.Colby College.



Jessica Baker Flechtner, Ph.D.Ph.D. Jess joined Genocea in 2007, soon after the company was founded, and has held multiple scientific roles since joining our Company in March 2007 andGenocea. She has served as our Chief Scientific Officer since February 2016, Senior Vice President of Research from February 2014 to January 2016, and Vice President of Research from January 2010 to February 2014, and Senior Director, Research and Development from2014. From 2007 to 2010.February 2014, she held various roles of increasing seniority at Genocea. Prior to joining our Company,Genocea, Dr. Flechtner was an Immunology Consultant at BioVest International, Inc. from June 2006 to March 2007, where she guided the development of assays to evaluate the success of the company’s autologous Follicular (Non-Hodgkin’s) Lymphoma vaccine in patients. As a researcher at Mojave Therapeutics, Inc., or Mojave, and Antigenics Inc. (now Agenus), which acquired Mojave’s intellectual property, from 2001 to 2005, Dr. Flechtner developed protein and peptide-based vaccines and immunotherapies for cancer, infectious disease, autoimmunity and allergy. She is an inventor on various pending or issued patents and has multiple peer-reviewed scientific publications. Dr. Flechtner performed her post-doctoral work in the laboratory of Dr. Harvey Cantor at the Dana Farber Cancer Institute and Harvard Medical School and holds a Ph.D. in Cellular Immunology and B.S. in Animal Science from Cornell University. She is a member of the American Association of Immunologists, American Association for Cancer Research, Society for the Immunotherapy of Cancer, the American Society for Microbiology,President’s Council of Cornell Women, and Women in Bio.

Narinder Singh. Narinder joined Genocea in March 2018 as Senior Vice President, Pharmaceutical Sciences and Manufacturing. In this role, Narinder manages the manufacturing process development and manufacturing of Genocea’s products. Narinder has


extensive experience in process development, scale-up, technical operations, and manufacturing supply chain of biopharmaceuticals. Prior to joining Genocea, Narinder served as Vice President of Drug Product Development and Manufacturing at Momenta Pharmaceuticals from July 2015 to March 2018, responsible for process development and manufacturing of drug products for Momenta’s biosimilars and novel product portfolio. Prior to Momenta, Narinder served as Director, Drug Product Technology at Amgen from June 2007 to July 2015, responsible for process development, commercialization, manufacturing and new technology development for drug products development of Amgen’s biologics-based portfolio. He began his career at Amgen functioning in various junior technical roles, beginning in 1997. Narinder received an Integrated B.Tech/M.Tech. in Biochemical Engineering and Biotechnology from the Indian Institute of Technology, Delhi in 1995, an M.S. in Chemical Engineering from the University of Houston, and an M.B.A. from UCLA Anderson School of Management.

Employees

As of December 31, 2016,2019, we had 9859 full-time employees. Of these 98 employees, 80 employees areof which 46 were engaged in research and development and 18 employees are13 were engaged in finance, legal, business development, human resources, facilities, information technology or other general and business and general management. We have noadministrative functions. None of our employees is represented by a labor union or covered by a collective bargaining agreements with our employeesagreement and we have not experienced any work stoppages. We consider our relations with our employees to be good.

Our Corporate Information

We were incorporated under the laws of the State of Delaware in August 2006. Our principal executive offices are located at 100 Acorn Park Drive, 5th Floor, Cambridge, Massachusetts 02140 and our telephone number is (617) 876-8191. Genocea® and the Genocea logo are registered trademarks.

Available Information

We maintain an Internet website at http://www.genocea.com where our Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q, Current Reports on Form 8-K and other documents and all amendments to those reports and documents are available without charge, as soon as reasonably practicable following the time they are filed with, or furnished to, the Securities and Exchange Commission ("SEC"). References to our website address do not constitute incorporation by reference of the information contained on the website, and the information contained on the website is not part of this document.

The public may read and copy any materials that we file with the SEC at the SEC’s Public Reference Room at 100 F Street, NE, Washington, DC 20549. The public may obtain information on the operation of the Public Reference Room by calling the SEC at 1-800-SEC-0330. Also, the SECalso maintains an Internet website that contains reports, proxy and information statements, and other information regarding issuers, including the Company, that file electronically with the SEC. The public can obtain any documents that we file with the SEC at http://www.sec.gov. References to our website address do not constitute incorporation by reference of the information contained on the website, and the information contained on the website is not part of this document.

Item 1A.    Risk Factors

Risks Related to Our Financial Position and Need for Additional Capital

We require additional financing to execute our operating plan and continue to operate as a going concern.

Our audited financial statements for the year ended December 31, 2019 have been prepared assuming we will continue to operate as a going concern, but we believe that our continuing operating losses raise substantial doubt about our ability to continue as such. We plan to continue to fund our operations through public or private equity offerings, strategic transactions, proceeds from sales of our common stock under our at-the-market equity offering program, our equity line of credit or by other means. However, adequate additional financing may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed, or on attractive terms, we may be forced to implement further cost reduction strategies, including ceasing development of GEN-009, GEN-011, and/or other product candidates and other corporate activities.

We have incurred significant losses since our founding in 2006 and anticipate that we will continue to incur significant losses for the foreseeable future and may never achieve or maintain profitability.

We are a clinical-stage biotechnology company, and we have not yet generated significant revenues. We have incurred net losses each year since our inception, including net losses of $49.6 million, $42.5$39.0 million and $35.3$27.8 million for the years ended December 31, 2016, 2015,2019 and 2014,2018, respectively. As of December 31, 2016 and 2015,2019, we had an accumulated deficitsdeficit of approximately $207.5 million and $157.9 million, respectively.$331.0 million. To date, we have not commercialized any products or generated any revenues from the sale of products and have financed our operations primarily through private placements of our preferred stock, debt financing, our initial public offering ("IPO") completed in February 2014, and follow-on public offerings in March 2015 and August 2015 and we do not expect to generate any product revenues in the foreseeable future. We do not know whether or when we will generate product revenues or become profitable. To date, we have financed our operations primarily through multiple public equity offerings, private placements of our common and preferred stock and debt arrangements.

We have devoted most of our financial resources to research and development, including our clinical and non-clinical technology development and development activities. The amount of our future net losses will depend, in part, on the rate of our


future expenditures and our ability to obtain funding through equity offerings or debt financings, strategic collaborations or additional


grants.transactions. We have not completed pivotal clinical studies for any product candidate, and it will be several years, if ever, before we have a product candidate ready for commercialization. Even if we obtain regulatory approval to market a product candidate, our future revenues will depend upon the size of any markets in which our product candidates have received approval, our ability to achieve sufficient market acceptance, reimbursement from third-party payors and other factors.
 
We expect to continue to incur significant expenses and increasing operating losses for the foreseeable future. We anticipate that our expenses will increase significantly if and as we:

continue our Phase 2 and commence our Phase 3 programsclinical trials for GEN-003,GEN-009, our most advanced product candidate that we are developing for the treatment of genital herpes infections;
candidate;
initiate additional non-clinical, clinical or other studies for GEN-009,GEN-011 and our neoantigen cancer vaccineother product candidate;
candidates;
manufacture material for clinical trials and for commercial sale;
seek regulatory approvals for any product candidates that successfully complete clinical trials;
establish a sales, marketing and distribution infrastructure to commercialize any products for which we may obtain marketing approval;
seek to discover and develop additional product candidates;
acquire or in-license other product candidates and technologies;
make royalty, milestone or other payments under any in-license agreements;
maintain, protect and expand our intellectual property portfolio;
attract and retain skilled personnel; and
create additional infrastructure to support our operations as a public company and our product development and planned future commercialization efforts.

The net losses that we incur may fluctuate significantly from quarter to quarter and year to year, such that a period-to-period comparison of our results of operations may not be a good indication of our future performance. In any particular quarter or quarters, our operating results could be below the expectations of securities analysts or investors, which could cause our stock price to decline.
 
To become and remain profitable, we must succeed in developing and eventually commercializing products that generate significant revenue. This will require us to be successful in a range of challenging activities, including completing non-clinical studies and clinical trials of our product candidates, discovering additional product candidates, obtaining regulatory approval for these product candidates and manufacturing, marketing and selling any products for which we may obtain regulatory approval. We are only in the preliminary stages of most of these activities. We may never succeed in these activities and, even if we do, may never generate revenues that are significant enough to achieve profitability.
 
Because of the numerous risks and uncertainties associated with pharmaceutical product development, we are unable to accurately predict the timing or amount of increased expenses or when, or if, we will be able to achieve profitability. If we are required by the FDA or the European Medicines Agency to perform studies in addition to those currently expected, or if there are any delays in completing our clinical trials or the development of any of our product candidates, our expenses could increase.

Even if we do achieve profitability, we may not be able to sustain or increase profitability on a quarterly or annual basis. Our failure to become and remain profitable would depress the value of our company and could impair our ability to raise capital, expand our business, maintain our research and development efforts, diversify our product offerings or even continue our operations. A decline in the value of our company could also cause you to lose all or part of your investment.

We will require substantial additional financing to achieve our goals, and a failure to obtain this necessary capital when needed would force us to delay, limit, reduce or terminate our product development or commercialization efforts.



As of December 31, 2016,2019, our cash and cash equivalents and investments were $63.4$40.1 million. We believe that we will continue to expend substantial resources for the foreseeable future developing GEN-003GEN-009, GEN-011 and GEN-009, ourany other neoantigen cancer vaccine product candidate.candidates. These expenditures will include costs associated with research and development, potentially acquiring new technologies, potentially obtaining regulatory approvals and manufacturing products, as well as marketing and selling products approved for sale, if any. In addition, other unanticipated costs may arise. Because the outcome of our planned and anticipated clinical trials is highly uncertain, we cannot reasonably estimate the actual amounts necessary to successfully complete the


development and commercialization of our product candidates. Furthermore, because of the significant expense associated with conducting clinical trials, we cannot be certain we will have sufficient capital to complete such trials for a given product candidate.
 
Our future capital requirements depend on many factors, including:

the progress, resultstiming and costs of our ongoing Phase 2 programplanned clinical trials for GEN-003;GEN-009 and GEN-011;

the progress, timing, and costs of manufacturing GEN-009 and GEN-011 for planned clinical trials;
the outcome, timing, and costs of seeking regulatory approvals, including an IND application for GEN-011;
the initiation, progress, timing, costs, and results of preclinical studies and clinical trials for our other product candidates and potential product candidates;
the terms and timing of any future collaborations, grants, licensing, consulting, or other arrangements that we may establish;
the amount and timing of any payments we may be required to make, or that we may receive, in connection with the licensing, filing, prosecution, defense and enforcement of any patents or other intellectual property rights, including milestone payments, royalty payments and patent prosecution fees that we are obligated to pay pursuant to our license agreements;
the costs associated with initiatingof preparing, filing, and prosecuting patent applications, maintaining and protecting our planned Phase 3 program for GEN-003;

intellectual property rights, and defending against intellectual property related claims;
the numberextent to which we in-license or acquire other products and development requirementstechnologies;
the receipt of marketing approval;
the costs of commercialization activities for GEN-009 and GEN-011 and other product candidates, thatif we pursue;

the timing of, andreceive marketing approval, including the costs involved in, obtaining regulatory approvals for our product candidates if clinical trials are successful and the outcome of regulatory review of our product candidates;
the cost and timing of future commercialization activities for our products, if any of ourestablishing product candidates are approved forsales, marketing, including productdistribution, and manufacturing marketing, salescapabilities; and distribution costs;
the cost of our general and administrative functions;

the revenue if any, received from commercial sales of our product candidates for which we receive marketing approval;
the cost of manufacturing our product candidates for clinical trials in preparation for regulatory approval and in preparation for commercialization;
our ability to establish and maintain strategic partnerships, licensing or other arrangements and the financial terms of such agreements;
the costs involved in preparing, filing, prosecuting patent applications, maintaining, defending and enforcing our intellectual property rights, including litigation costs and the outcome of such litigation;candidates.

the timing, receipt, and amount of sales of, or royalties or milestone payments on, our future products, if any; and
the extent to which we acquire or in-license other products or technologies.
Based on our current operating plan, we believe that our existing cash and cash equivalents and investments are sufficient to support our operating expenses and capital expenditure requirements into the first quarter of 2018, without assuming any receipt of proceeds from potential business development partnerships, equity financings or debt drawdowns. This guidance assumes commencing Phase 3 trials for GEN-003 for genital herpes in the fourth quarter of 2017 and filing an IND for GEN-009 for cancer by the end of the year, however it is our strategy to secure additional sources of financing in advance of starting GEN-003 Phase 3 clinical trials.2021.

Our operating plan may change as a result of many factors currently unknown to us, and we may need additional funds sooner than planned. In addition, we may seek additional capital due to favorable market conditions or strategic considerations even if we believe we have sufficient funds for our current or future operating plans. Additional funds may not be available when we need them on terms that are acceptable to us, or at all. If adequate funds are not available to us when needed, we would be required to delay, limit, reduce or terminate non-clinical studies, clinical trials or other development activities for one or more of our product candidates or delay, limit, reduce or terminate our establishment of sales and marketing capabilities or other activities that may be necessary to commercialize our product candidates.

We cannot be certain that we will be successful in advancing GEN-009 or GEN-011 through clinical development, obtaining regulatory approval for either product candidate, or commercializing either product candidate or any of our future product candidates.

At this time, GEN-009 is our most advanced product candidate and our future revenues, if any, will depend highly on the successful clinical progress, approval, and commercialization of GEN-009. In addition to GEN-009, we also are advancing preclinical work on GEN-011, for which we expect to file an IND with the FDA in the second quarter of 2020. GEN-009, GEN-011 and any future product candidate will require substantial clinical development, testing and regulatory approval before we are permitted to commence commercialization. This process can take many years and will require the expenditure of substantial resources and we expect it will require that we obtain substantial additional funding.

We are currently conducting our GEN-009 Part B clinical trial. As with any open label study, we may slow or pause enrollment to evaluate a smaller set of patients in an effort to assure that a preliminary clinical signal is seen. We anticipate reporting these preliminary clinical results for our GEN-009 Part B clinical trial in the second or third quarter of 2020. Based upon this evaluation, we will consider whether it is appropriate to continue the study. A decision to stop the study would result in a delay in the clinical progress, approval and commercialization of GEN-009.



Raising additional capital may cause dilution to our existing stockholders, restrict our operations or require us to relinquish rights to our technologies or product candidates on unfavorable terms to us.



Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs through a combination of equity offerings debt financings and license and development agreements with strategic partnerships with third parties.transactions. In 2015,January 2018, we raised additional net capitalproceeds of approximately $95.2$51.7 million through follow-onconcurrent public offerings in Marchof our common stock and August alongwarrants exercisable for shares of our common stock and preferred stock and warrants exercisable for shares of our common stock (the "Concurrent Offerings"). In February 2019, we raised additional net proceeds of approximately $13.8 million through private placement. In June 2019, we raised additional net proceeds of approximately $38.4 million through an underwritten public offering of our common stock and warrants exercisable for shares of our common stock. In October 2019, we entered into an agreement (the "Purchase Agreement") with $4.7Lincoln Park Capital ("LPC") from which we raised additional net proceeds of $2.5 million, and we have the right, at our sole discretion, to sell up to an additional $27.5 million of net debt financingour common stock based on prevailing market prices of our common stock at the time of each sale. The Purchase Agreement limits our sales of shares of common stock to LPC to 5,227,323 shares of common stock, representing 19.99% of the shares of common stock outstanding on the date of the Purchase Agreement. The Purchase Agreement also prohibits us from directing LPC to purchase any shares of common stock if those shares, when aggregated with all other shares of our common stock then beneficially owned by LPC and its affiliates, would result in December. No significant capital activities occurredLPC and its affiliates having beneficial ownership, at any single point in 2016.time, of more than 9.99% of the then total outstanding shares of our common stock. We have also periodically sold shares under our at-the-market equity offering program with Cowen and Company, LLC (the "ATM"). To the extent that we raise additional capital through the sale of equity or convertible debt securities, your ownership interest will be diluted, and the terms may include liquidation or other preferences that adversely affect your rights as a stockholder. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take certain actions, such as incurring additional debt, making capital expenditures or declaring dividends. If we raise additional funds through strategic partnerships with third parties, we may have to relinquish valuable rights to our technologies or product candidates, future revenue streams, research programs or product candidates or grant licenses on terms that are not favorable to us. If we are unable to raise additional capital when needed, we would be required to delay, limit, reduce or terminate our product development or commercialization efforts for GEN-003, our immuno-oncology program,GEN-009, GEN-011, or our other product candidates,candidates.

Our stockholders will experience substantial additional dilution if shares of our preferred stock are converted into, or grant rightsoutstanding warrants are exercised for, common stock.

As of February 11, 2020 there were 1,635 shares of our Series A convertible preferred stock outstanding, which are convertible, without payment of additional consideration, into 204,375 shares of our common stock. As of February 11, 2020, there were 5,122,183 shares of common stock issuable upon the exercise of warrants, having a weighted average exercise price of $7.66 per share, and 1,310,927 shares of common stock issuable upon the exercise of stock options outstanding, having a weighted average exercise price of $11.72 per share. The conversion of the outstanding shares of our Series A convertible preferred stock into, or exercise of outstanding options or warrants for, common stock would be substantially dilutive to developexisting stockholders. Any dilution or potential dilution may cause our stockholders to sell their shares, which may contribute to a downward movement in the stock price of our common stock.

SEC regulations limit the amount of funds we may raise during any 12-month period pursuant to our shelf registration statement on Form S-3.
Our public float was less than $75 million within 60 days of filing of this Annual Report on Form 10-K. As a result, under General Instruction I.B.6 to Form S-3, the amount of funds we can raise through primary public offerings of securities, including through our ATM, in any 12-month period using our registration statement on Form S-3 is limited to one-third of the aggregate market value of the voting and market product candidates thatnon-voting common equity held by our non-affiliates. We are subject to this limitation until such time as our public float exceeds $75 million. If we would otherwise preferare required to developfile a new registration statement on another form, we may incur additional costs and market ourselves.be subject to delays due to review by the SEC.

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

We are substantially dependent on the success of the clinical development of GEN-003,GEN-009, our only product candidate currently in an active clinical trial.trials. Any failure to successfully develop or commercialize the GEN-003GEN-009 vaccine, or any significant delays in doing so, will have a material adverse effect on our business, result of operations and financial condition.
 
We have investedare now currently investing a significant portion of our efforts and financial resources in the development of the GEN-003GEN-009, a neoantigen cancer vaccine for genital herpes, the only product candidate we have thatwhich is currently in an activea Phase 1/2a clinical development.trial. Our ability to generate product revenue depends heavily on the success of clinical trials for GEN-009 and the successful development and commercialization of GEN-003.GEN-009. The successful development and commercialization of GEN-003GEN-009 will depend on several factors, including the following:

Successful

successful completion of our ongoing and additionalall required clinical studiestrials of GEN-003;GEN-009;

Obtainingobtaining marketing approvals from regulatory authorities for GEN-003;GEN-009;

Establishingestablishing manufacturing and commercialization arrangements between ourselves and third parties;

A continuedestablishing an acceptable safety and efficacy profile of GEN-003;GEN-009; and

Thethe availability of reimbursement to patients from healthcare payors for GEN-003.GEN-009.

Any failure to successfully develop or commercialize GEN-003GEN-009 or any significant delays in doing so will have a material adverse effect on our business, results of operations and financial condition.

Because our active product candidate is in an early stage of clinical development, there is a high risk of failure, and we may never succeed in developing marketable products or generating product revenue.

Our existing encouraging non-clinical andWe are currently conducting our GEN-009 Phase 1/2a clinical trial. We anticipate reporting the preliminary clinical results for GEN-003our GEN-009 Part B clinical trial in the second or third quarter of 2020. Based upon this evaluation, we will consider whether it is appropriate to continue the study. A decision to stop the study would result in a delay in the clinical progress, approval and commercialization of GEN-009. Even if the results are not necessarily predictive of the finalsuccessful, such results of our ongoing or future clinical trials. Success in non-clinical studies may not be predictive of similar results in humans during clinical trials, and successful results from early or small clinical trials of a vaccine candidate may not be replicated in later and larger clinical trials. Among other reasons for the potential failure of earlier, smaller clinical trials to be replicated in later, larger clinical trials is the fact that manufacturing scale up is necessary to prepare for Phase 3 development and commercialization. While our Phase 2b trial utilizes a formulation of GEN-003 manufactured using commercially-scalable processes, GEN-003 requiresOur product candidates may require complex manufacturing processes and scaling up these processes can cause changes in the product that may not be apparent until the product is further tested as part of our plannedduring Phase 3 trials.

If the results of our ongoing or future clinical trials are inconclusive with respect to the efficacy of our product candidates or if we do not meet our clinical endpoints with statistical significance or if there are safety concerns or AEs associated with our product candidates, we may be prevented or delayed in obtaining marketing approval for our product candidates. Alternatively, even if we obtain regulatory approval, that approval may be for indications or patient populations that are not as broad as intended or desired or may require labeling that includes significant use or distribution restrictions or safety warnings. We may also be required to perform additional or unanticipated clinical trials to obtain approval or be subject to additional post-marketing testing requirements to maintain regulatory approval. In addition, regulatory authorities may


withdraw their approval of the product or impose restrictions on its distribution in the form of a modified risk evaluation and mitigation strategy.

In addition to product candidates being developed in our non-clinical and clinical programs, we are expending resources in our immuno-oncology program. Our first program established is GEN-009, a neoantigen cancer vaccine product candidate. GEN-009 is at an early stage and our research efforts to move this candidate to clinical testing, or to identify and develop other product candidates, may not be successful. Furthermore, we need to develop the supply chain for any product candidates we identify.

If we do not obtain regulatory approval for our current and future product candidates, our business will be adversely affected.

Our product candidates are subject to extensive governmental regulations relating to, among other things, research, clinical trials, manufacturing, import, export and commercialization. In order to obtain regulatory approval for the commercial sale of any product candidate, we must demonstrate through extensive non-clinical studies and clinical trials that the product candidate is safe and effective for use in each target indication. Clinical trials are expensive, time-consuming and uncertain as to outcome. We may gain regulatory approval for GEN-003GEN-009, GEN-011 or our other current or potential future clinical and non-clinical product candidates in some but not all of the territories available or some but not all of the target indications, resulting in limited commercial opportunity for the approved vaccine or immunotherapy,our product candidates, or we may never obtain regulatory approval for these product candidates for any indication in any jurisdiction.

We may find it difficult to enroll patients in our clinical trials, which could delay or prevent clinical trials of our product candidates.

Identifying and qualifying patients to participate in clinical trials of our product candidates is critical to our success. The timing of our clinical trials depends on the speed at which we can recruit patients to participate in testing our product candidates. If patients are unwilling to participate in our studies because of negative publicity from AEs in the biotechnology industries or for other reasons, including competitive clinical trials for similar patient populations, the timeline for recruiting patients, conducting studies and obtaining regulatory approval of potential products may be delayed or prevented. These delays could result in increased costs, delays in advancing our product development, delays in testing the effectiveness of our technology or termination of the clinical trials altogether.

We may not be able to identify, recruit and enroll a sufficient number of patients, or those with required or desired characteristics to achieve diversity in a study, to complete our clinical trials in a timely manner. Patient enrollment is affected by factors including:


severity of the disease under investigation;
design of the study protocol;
size of the patient population;
eligibility criteria for the trial in question;
perceived risks and benefits of the product candidate under study;
proximity and availability of clinical trial sites for prospective patients;
availability of competing therapies and clinical trials;
efforts to facilitate timely enrollment in clinical trials;
patient referral practices of physicians; and
ability to monitor patients adequately during and after treatment.

We may not be able to initiate or continue clinical trials if we cannot enroll a sufficient number of eligible patients to participate in the clinical trials required by regulatory agencies. If we have difficulty enrolling a sufficient number of patients to conduct our clinical trials as planned, we may need to delay, limit or terminate ongoing or planned clinical trials, any of which would have an adverse effect on our business.



We may not be able to comply with requirements of foreign jurisdictions in conducting trials outside of the United States.

To date, we have not conducted any clinical trials for GEN-003 outside of the United States. Our ability to successfully initiate, enroll and complete a clinical trial in any foreign country, should we attempt to do so, is subject to numerous risks unique to conducting business in foreign countries, including:

difficulty in establishing or managing relationships with contract research organizations ("CROs") and physicians;
different standards for the conduct of clinical trials;
our inability to locate qualified local consultants, physicians and partners;
the potential burden of complying with a variety of foreign laws, medical standards and regulatory requirements, including the regulation of pharmaceutical and biotechnology products and treatment; and
the acceptability of data obtained from studies conducted outside the United States to the FDA in support of a BLA.

If we fail to successfully meet requirements for the conduct of clinical trials outside of the United States, we may be delayed in obtaining, or be unable to obtain, regulatory approval for our product candidates.

We may encounter substantial delays in our clinical trials or we may fail to demonstrate safety and efficacy to the satisfaction of applicable regulatory authorities.

Before obtaining marketing approval from regulatory authorities for the sale of our product candidates, we must conduct extensive clinical trials to demonstrate the safety and efficacy of the product candidates for the intended indications. Clinical testing is expensive, time-consuming and uncertain as to outcome. We cannot guarantee that clinical trials will be conducted as planned or completed on schedule, if at all. A failure of one or more clinical trials can occur at any stage of testing. Events that may prevent successful or timely completion of clinical development include:

delays caused by us or third parties in conducting clinical trials for GEN-009;
delays by us in reaching a consensus with regulatory agencies on trial design, including our end of Phase 2 meetingthe IND for GEN-003 expected to occur in the first quarter of 2017;GEN-011;
delays in reaching agreement on acceptable terms with prospective CROs and clinical trial sites;
delays in obtaining required IRBInstitutional Review Board ("IRB") approval at each clinical trial site;
imposition of a clinical hold by regulatory agencies or an IRB for any reason, including safety concerns raised by other clinical trials of similar vaccines that may reflect an unacceptable risk with GEN-003GEN-009 or GEN-011 or after an inspection of clinical operations or trial sites;


failure to perform in accordance with the FDA’s GCPsgood clinical practices ("GCPs") or applicable regulatory guidelines in other countries;
delays in the testing, validation, manufacturing and delivery of the product candidates to the clinical sites;
delays caused by patients not completing participation in a trial or not returning for post-treatment follow-up;
clinical trial sites or patients dropping out of a trial or failing to complete dosing;
occurrence of serious AEs in clinical trials that are associated with the product candidates that are viewed to outweigh its potential benefits; or
changes in regulatory requirements and guidance that require amending or submitting new clinical protocols.

Delays, including delays caused by the above factors, can be costly and could negatively affect our ability to complete a clinical trial. We intend to file an IND for a product candidate in our immuno-oncology program before the end of 2017, but we have experienced clinical holds on IND submissions in the past. Our IND for GEN-003 was subject to a clinical hold from January 2012 to July 2012. In our original IND submission, we described a finding of osteonecrosis (microscopic evidence of bone and bone marrow death) in a toxicity study of GEN-003 conducted in mice. Because this finding was not present in toxicity studies conducted in other species, we reasoned that this was a mouse-specific finding and did not indicate a risk to humans in clinical trials. As the FDA provided us with several options that would resolve this issue to their satisfaction, we conducted an additional toxicity study in a highly relevant species (non-human primate) that would be more representative of a risk to humans. Since no bone or bone marrow toxicity was observed in this additional study, the FDA subsequently lifted the clinical hold, allowing us to proceed with the first study in humans of GEN-003.



We cannot give any assurance that we will be able to resolve any future clinical holds imposed by the FDA or other regulatory authorities outside of the United States, or any delay caused by otherthe factors described above or any other factors, on a timely basis or at all. If we are not able to successfully initiate and complete subsequent clinical trials, we will not be able to obtain regulatory approval and will not be able to commercialize our product candidates.

Our active product candidate, GEN-003,GEN-009, GEN-011 and our current and future potential product candidates including any arising out of our immuno-oncology program, are or will be based on T cell activation, which is a novel approach for vaccines, immunotherapies and medical treatments.
We have concentrated our research and development efforts on T cell vaccine and immunotherapy technology, which is a novel approach for vaccines, immunotherapies and medical treatments, and our future success is highly dependent on the successful development of T cell immunotherapies in general, and our active development product and current and future product candidates in particular. Consequently, it may be difficult for us to predict the time and cost of product development. Unforeseen problems with the T cell approach to vaccines and immunotherapies may prevent further development or approval of our current and future product candidates. There can be no assurance that any development problems we or others researching T cell vaccines and immunotherapies may experience in the future will not cause significant delays or unanticipated costs, or that such development problems can be solved. Because of the novelty of this approach, there may be unknown safety risks associated with the vaccines and immunotherapies that we develop. Regulatory agencies such as the FDA may require us to conduct extensive safety testing prior to approval to demonstrate a low risk of rare and severe AEs caused by the vaccines and immunotherapies. If approved, the novel mechanism of action of the vaccines may adversely affect physician and patient perception and uptake of our products.

We have concentrated our research and development efforts on T cell vaccine and immunotherapy technology, and our future success is highly dependent on the successful development of T cell vaccines and immunotherapies in general, and our active development product and current and futureOur product candidates are uniquely manufactured for each patient and we may encounter difficulties in particular. There can be no assurance that any development problemsproduction, particularly with respect to scaling our manufacturing capabilities. If we or others researching T cell vaccines and immunotherapies may experience inany of the future will not cause significant delays or unanticipated costs, or that such development problems can be solved.

Public perceptionthird-party manufacturers with whom we contract encounter these types of vaccine safety issues, including adoption of novel vaccine mechanisms of action, may adversely influence willingness of subjectsdifficulties, our ability to participate inprovide our product candidates for clinical trials or our products for patients, if approved, could be delayed or stopped, or we may be unable to maintain a commercially viable cost structure. Some of physiciansour third-party manufacturers are located outside the U.S., and we may encounter disruption in clinical material supplies due to prescribe and of patients to receive novel vaccines.

Our active development product, GEN-003 includes a novel vaccine adjuvant and our other current and potential future product candidates may include one or more novel adjuvants, which may make it difficult for us to predict the time and cost of product developmentlogistics, as well as risk of adverse regulatory action due to local regulatory oversight.

We custom design and manufacture our product candidates. Manufacturing unique lots of these product candidates is susceptible to product loss or failure due to issues with:

logistics associated with the requirementscollection of a patient’s tumor or blood;
batch-specific manufacturing failures or issues that arise due to the FDAuniqueness of each patient-specific batch that may not have been foreseen;
quality control testing failures;
unexpected failures of batches placed on stability;
novel assays, cell selection or other regulatory agenciescomponents within our manufacturing processes;
significant costs associated with individualized manufacturing that may imposeadversely affect our ability to demonstratecontinue development; 
successful and timely manufacture and release of the safetypatient-specific batch;
shipment issues encountered during transport of the batch to the site of patient care; and
our reliance on single-source suppliers.


As certain of our product candidates are manufactured for each individual patient, we will be required to maintain a chain of identity with respect to each patient’s sample, sequence data derived from such sample, analyze results of such patient’s immunologic profile, and the custom manufactured product candidates.for each patient. Maintaining such a chain of identity is difficult and complex, and failure to do so could result in product mix-up, adverse patient outcomes, loss of product, or regulatory action, including withdrawal of any approved products from the market. Further, as our product candidates are developed through early-stage clinical studies to later-stage clinical trials towards approval and commercialization, we expect that multiple aspects of the complicated collection, analysis, manufacture and delivery processes will be modified in an effort to optimize processes and results. These changes may not achieve the intended objectives, and any of these changes could cause our product candidates to perform differently than we expect, potentially affecting the results of clinical trials.

Novel vaccine adjuvants, includedincluding those in some of our GEN-009 product candidates,candidate, may pose an increased safety risk to patients.
Adjuvants are compounds that are added to vaccine antigens to enhance the activation of the immune system and improve the immune response and efficacy of vaccines. Development of vaccines with novel adjuvants requires evaluation in larger numbers of patients prior to approval than would be typical for therapeutic drugs. Guidelines for evaluation of vaccines with novel adjuvants have been established by the FDA and other regulatory bodies and expert committees. Our product candidates, including GEN-003,GEN-009, may include one or more novel vaccine adjuvants. Any neoantigen cancer vaccine, because of the presence of an adjuvant, may have side effects considered to pose too great a risk to patients to warrant approval of the vaccine. Traditionally, regulatory authorities have required extensive study of novel adjuvants because vaccines typically get administered to healthy populations, in particular infants, children and the elderly, rather than in people with disease. Such extensive study has often included long-term monitoring of safety in large general populations that has at times exceeded 10,000 subjects. This contrasts with the few thousand subjects typically necessary for approval of novel therapeutics. Although GEN-003 is being developed as a treatment, and therefore is not expected to be administered to uninfected subjects, regulators nonetheless may require us to amass a prophylactic vaccine-like safety database. To date, the FDA and other major regulatory agencies have only approved vaccines containing five adjuvants, which makes it difficult to determine how long it will take or how much it will cost to obtain regulatory approvals for our product candidates in the United States or elsewhere.

If we fail to obtain regulatory approval in jurisdictions outside the United States, we will not be able to market our products in those jurisdictions.

We intend to market our product candidates, if approved, in international markets. Such marketing will require separate regulatory approvals in each market and compliance with numerous and varying regulatory requirements. The approval procedures vary among countries and may involve requirements for additional testing, and the time required to obtain approval may differ from that required to obtain FDA approval. In addition, in many countries outside the United States, a vaccine must be approved for reimbursement before it can be approved for sale in that country. In some cases, the price that we intend to charge for our vaccine is also subject to approval. Approval by the FDA does not ensure approval by regulatory authorities in other countries or jurisdictions, and approval by one foreign regulatory authority does not ensure approval by regulatory authorities in other foreign countries or by the FDA. The foreign regulatory approval process may include all of the risks associated with obtaining FDA approval. We may not obtain foreign regulatory approvals on a timely basis, if at all. We


may not be able to file for regulatory approvals and may not receive necessary approvals to commercialize our vaccines in any market.

Even if we receive regulatory approval for our product candidates, such vaccines and immunotherapies will be subject to ongoing regulatory review, which may result in significant additional expense. Additionally, our product candidates, including our active development product, GEN-003,GEN-009, GEN-011 and any other current or potential future vaccine or immunotherapy product candidates, if approved, could be subject to labeling and other restrictions, and we may be subject to penalties if we fail to comply with regulatory requirements or experience unanticipated problems with our products.

Any regulatory approvals that we receive for our product candidates may also be subject to limitations on the approved indications for which the product may be marketed or to conditions of approval, or contain requirements for potentially costly post-marketing testing, including Phase 4 clinical trials, and surveillance to monitor the safety and efficacy of the vaccine or immunotherapy potentially over many years. In addition, if the FDA approves any of our product candidates, the manufacturing processes, labeling, packaging, distribution, AE reporting, storage, advertising, promotion and recordkeeping for the product will be subject to extensive and ongoing regulatory requirements. These requirements include submissions of safety and other post-marketing information and reports, registration, as well as continued compliance with current good manufacturing practice ("cGMP"),(cGMP) and GCP, for any clinical trials that we conduct post-approval.

Later discovery of previously unknown problems with an approved product, including AEs of unanticipated severity or frequency, or with manufacturing operations or processes, or failure to comply with regulatory requirements, may result in, among other things:

restrictions on the marketing or manufacturing of the product, withdrawal of the product from the market, or voluntary or mandatory product recalls;
fines, warning letters, or holds on clinical trials;
refusal by the FDA to approve pending applications or supplements to approved applications filed by us, or suspension or revocation of product license approvals;


product seizure or detention, or refusal to permit the import or export of products; and
injunctions or the imposition of civil, criminal and/or administrative penalties, damages, monetary fines, disgorgement, exclusion from participation in Medicare, Medicaid and other federal health care programs, and curtailment or restructuring of our operations.

The FDA’s policies may change and additional government regulations may be enacted that could affect regulatory approval that we have received for our product candidates. We cannot predict the likelihood, nature or extent of government regulation that may arise from future legislation or administrative action, either in the United States or abroad. If we are slow or unable to adapt to changes in existing requirements or the adoption of new requirements or policies, or not able to maintain regulatory compliance, we may lose any marketing approval that may have been obtained and we may not achieve or sustain profitability, which would adversely affect our business.

Risks Related to Our Reliance on Third Parties

We rely on third parties to conduct technical development, non-clinical studies and clinical trials for our product candidates, including our active clinical development product, GEN-003,GEN-009, GEN-011 and any other current or future product candidates, and if they do not properly and successfully perform their obligations to us, we may not be able to obtain regulatory approvals for our product candidates.

We rely, and intend to continue to rely on, on third party CROs and other third parties to assist in managing, monitoring and otherwise carrying out our GEN-003GEN-009 and GEN-011 clinical trials. We expect to continue to rely on third parties, such as CROs, clinical data management organizations, medical institutions and clinical investigators, to conduct our clinical trials. We compete with many other companies for the resources of these third parties. The third parties on whom we rely generally may terminate their engagements at any time and having to enter into alternative arrangements would delay development and commercialization of our product candidates.

Our reliance on these third parties for research and development activities will reduce our control over these activities but will not relieve us of our responsibilities. For example, the FDA and foreign regulatory authorities require compliance with regulations and standards, including GCP, for designing, conducting, monitoring, recording, analyzing, and reporting the results of clinical trials to assure that the data and results are credible and accurate and that the rights, integrity and confidentiality of


trial participants are protected. Although we rely on third parties to conduct our clinical trials, we are responsible for ensuring that each of these clinical trials is conducted in accordance with its general investigational plan and protocol.

Furthermore, these third parties may also have relationships with other entities, some of which may be our competitors. If these third parties do not successfully carry out their duties under their agreements, if the quality or accuracy of the data they obtain is compromised due to their failure to adhere to clinical trial protocols or to regulatory requirements, or if they otherwise fail to comply with clinical trial protocols or meet expected deadlines, the clinical trials of our product candidates may not meet regulatory requirements. If clinical trials do not meet regulatory requirements or if these third parties need to be replaced, non-clinical development activities or clinical trials may be extended, delayed, suspended or terminated. If any of these events occur, we may not be able to obtain regulatory approval of our product candidates on a timely basis or at all.

We also expect to rely on other third parties to store and distribute drug supplies for our clinical trials. Any performance failure on the part of our distributors could delay clinical development or marketing approval of our product candidates or commercialization of our products, producing additional losses and depriving us of potential product revenue.

We rely on third parties to conduct some or all aspects of our product manufacturing, and these third parties may not perform satisfactorily.

We do not have any manufacturing facilities or personnel. We do not expect to independently conduct all aspects of our product manufacturing. We currently rely, and expectintend to rely on third parties with respect to manufacturing including under our agreements with FujifilmGEN-009 and Novavax. For example, we relyGEN-011.We have also relied on third party suppliers and manufacturers to manufacture and supply vaccines for our GEN-003other clinical trials. This reliance on third parties increases the risk that we will not have sufficient quantities of our product candidates or products or such quantities at an acceptable cost or quality, which could delay, prevent or impair our development or commercialization efforts.

Any of these third parties may terminate their engagement with us at any time. If we need to enter into alternative arrangements, it could delay our product development activities. Our reliance on these third parties for manufacturing activities will reduce our control over these activities but will not relieve us of our responsibility to ensure compliance with all required regulations regarding manufacturing.


Reliance on third party manufacturers entails risks to which we would not be subject if we manufactured the product candidates ourselves, including:

the inability to negotiate manufacturing agreements with third parties under commercially reasonable terms;
reduced control as a result of using third party manufacturers for all aspects of manufacturing activities, including regulatory compliance and quality assurance;
termination or nonrenewal of manufacturing agreements with third parties in a manner or at a time that is costly or damaging to us;
the unavailability of a manufacturer that is capable of, or that has the capacity to, manufacture our clinical supply that results in delays or additional manufacturing costs;
the possible misappropriation of our proprietary information, including our trade secrets and know-how or infringement of third partythird-party intellectual property rights by our contract manufacturers; and
disruptions to the operations of our third partythird-party manufacturers or suppliers caused by conditions unrelated to our business or operations, including the bankruptcy of the manufacturer or supplier.

Any of these events could lead to clinical trial delays or failure to obtain regulatory approval or affect our ability to successfully commercialize future products. Some of these events could be the basis for FDA action, including injunction, recall, seizure or total or partial suspension of production.

Third partyThird-party manufacturers may not be able to comply with cGMP regulations or similar regulatory requirements outside the United States. Our failure, or the failure of our third partythird-party manufacturers, to comply with applicable regulations could result in sanctions being imposed on us, including clinical holds, fines, injunctions, civil penalties, delays, suspension or withdrawal of approvals, license revocation, seizures or recalls of product candidates or products, operating restrictions and criminal prosecutions, any of which could significantly and adversely affect supplies of our products.



Our product candidates and any products that we may develop may compete with other product candidates and products for access to manufacturing facilities. There are a limited number of manufacturers that operate under cGMP regulations and that might be capable of manufacturing for us.

Any performance failure on the part of our existing or future manufacturers could delay clinical development or marketing approval. We do not currently have arrangements in place for redundant supply or a second source for bulk drug substance.GEN-009 and GEN-011. If our current contract manufacturers cannot perform as agreed, we may be required to replace such manufacturers. Although we believe that there are several potential alternative manufacturers who could manufacture our product candidates, we may incur added costs and delays in identifying and qualifying any such replacement.

Our current and anticipated future dependence upon others for the manufacture of our product candidates or products may adversely affect our future profit margins and our ability to commercialize any products that receive marketing approval on a timely and competitive basis.

If we are unable to manufacture our products in sufficient quantities, or at sufficient yields, or are unable to obtain regulatory approvals for a manufacturing facility for our products, we may experience delays in product development, clinical trials, regulatory approval and commercial distribution.

Completion of our clinical trials and commercialization of our product candidates require access to, or development of, facilities to manufacture our product candidates at sufficient yields and at commercial-scale. We have no experience manufacturing, or managing third parties in manufacturing, any of our product candidates in the volumes that will be necessary to support large-scale clinical trials or commercial sales. Efforts to establish these capabilities may not meet initial expectations as to scheduling, scale-up, reproducibility, yield, purity, cost, potency or quality.

We expect to rely on third-parties for the manufacture of clinical and, if necessary, commercial quantities of our product candidates. These third-party manufacturers must also receive FDA approval before they can produce clinical material or commercial products. Our products may be in competition with other products for access to these facilities and may be subject to delays in manufacture if third-parties give other products greater priority. We may not be able to enter into any necessary third-party manufacturing arrangements on acceptable terms, or on a timely basis. In addition, we may have to enter into technical


transfer agreements and share our know-how with the third-party manufacturers, which can be time-consuming and may result in delays.

Our reliance on contract manufacturers may adversely affect our operations or result in unforeseen delays or other problems beyond our control. Because of contractual restraints and the limited number of third-party manufacturers with the expertise, required regulatory approvals and facilities to manufacture our bulk vaccines on a commercial-scale, replacement of a manufacturer may be expensive and time-consuming and may cause interruptions in the production of our vaccine. A third-party manufacturer may also encounter difficulties in production. These problems may include:

difficulties with production costs, scale-up and yields;
unavailability of raw materials and supplies;
insufficient quality control and assurance;
shortages of qualified personnel;
failure to comply with strictly enforced federal, state and foreign regulations that vary in each country where product might be sold; and
lack of capital funding.

As a result, any delay or interruption could have a material adverse effect on our business, financial condition, results of operations and cash flows.



We may not be successful in establishing and maintaining strategic partnerships, which could adversely affect our ability to develop and commercialize products.

A part of our strategy is to evaluate and, as deemed appropriate, enter into partnerships in the future when strategically attractive, including potentially with major biotechnology or pharmaceutical companies. We face significant competition in seeking appropriate partners for our product candidates, and the negotiation process is time-consuming and complex. In order for us to successfully partner our product candidates, potential partners must view these product candidates as economically valuable in markets they determine to be attractive in light of the terms that we are seeking and other available products for licensing by other companies. Even if we are successful in our efforts to establish strategic partnerships, the terms that we agree upon may not be favorable to us, and we may not be able to maintain such strategic partnerships if, for example, development or approval of a product is delayed or sales of an approved product are disappointing. Any delay in entering into strategic partnership agreements related to our product candidates could delay the development and commercialization of our product candidates and reduce their competitiveness even if they reach the market.

In addition, our strategic partners may breach their agreements with us, and we may not be able to adequately protect our rights under these agreements. Furthermore, our strategic partners will likely negotiate for certain rights to control decisions regarding the development and commercialization of our product candidates, if approved, and may not conduct those activities in the same manner as we would do so.

If we fail to establish and maintain strategic partnerships related to our product candidates, we will bear all of the risk and costs related to the development of any such product candidate, and we may need to seek additional financing, hire additional employees and otherwise develop expertise which we do not have and for which we have not budgeted. This could negatively affect the development of any unpartnered product candidate.

In addition, we are currently seeking to establish strategic partnerships with companies with adjuvant and delivery technologies for our neoantigen cancer vaccine candidates. If we are unable to successfully enter into these partnerships, our ability to develop our neoantigen cancer vaccine candidates may be adversely affected.
Risks Related to Our Intellectual Property

If we are unable to obtain or protect intellectual property rights related to our product candidates, we may not be able to compete effectively in our markets.

We rely upon a combination of patents, patent applications, know-how and confidentiality agreements to protect the intellectual property related to our platform technology and product candidates. The patent position of biotechnology companies is generally uncertain because it involves complex legal and factual considerations. The standards applied by the United States


Patent and Trademark Office ("U.S. PTOPTO") and foreign patent offices in granting patents are not always applied uniformly or predictably. For example, there is no uniform worldwide policy regarding patentable subject matter or the scope of claims allowable in biotechnology patents. The patent applications that we own or in-license may fail to result in issued patents with claims that cover our discovery platform or product candidates in the United States or in other countries. There is no assurance that all potentially relevant prior art relating to our patents and patent applications or those of our licensors has been found, and prior art that we have not disclosed could be used by a third party to invalidate a patent or prevent a patent from issuing from a pending patent application. Even if patents do successfully issue and even if such patents cover our discovery platform or product candidates, third parties may challenge their validity, enforceability or scope, which may result in such patents being narrowed or invalidated. Furthermore, even if they are unchallenged, our patents and patent applications, or those of our licensors, may not adequately protect our platform technology, provide exclusivity for our product candidates, prevent others from designing around our patents with similar products, or prevent others from operating in jurisdictions in which we did not pursue patent protection. Any of these outcomes could impair our ability to prevent competition from third parties, which may have an adverse impact on our business.

If patent applications we hold or have in-licensed with respect to our platform or product candidates fail to issue, if their breadth or strength of protection is threatened, or if they fail to provide meaningful exclusivity for our product candidates or ATLAS discovery platform, it could dissuade companies from collaborating with us.us and could limit or destroy our ability to develop or commercialize one or more of our products, or even any product. We or our licensors have filed several patent applications covering aspects of our product candidates. We cannot offer any assurances about which, if any, patents will be issued, the breadth of any such patents or whether any issued patents will be found invalid and unenforceable or will be challenged by third parties. Any successful opposition to these patent applications, or patents that may issue from them, or to any other patent applications or patents owned by or licensed to us, could deprive us of rights necessary for the successful commercialization of any product candidate that we may develop. Since patent applications in the United States and most other countries are confidential for a period of time after filing, and some remain so until issued, we cannot be certain that we or our licensors were the first to file a patent application relating to any particular aspect of a product candidate. Furthermore, if third parties have filed such patent applications, an interference proceeding in the United States can be initiated by such third party, or by the U.S. PTO itself, to determine who was the first to invent any of the subject matter covered by the patent claims of our applications.



In the United States, for patent applications filed prior to March 16, 2013, assuming the other requirements for patentability are met, the first to invent is entitled to the patent, while outside the United States, the first to file a patent application is entitled to the patent. On March 16, 2013, the United States transitioned to a ‘first to file’ system more like that in the rest of the world in that the first inventor to file a patent application is entitled to the patent. Under either the prior system or current one, third parties are allowed to submit prior art prior to the issuance of a patent bypatent. Furthermore, both the U.S. PTO, and may become involvedforeign patent systems permit third parties or, in some cases, the patent authorities themselves, to initiate proceedings challenging the scope and / or validity of issued patents, including for example, opposition, derivation, reexamination, inter partes review or interference proceedings challenging our patent rights or the patent rights of others.proceedings. An adverse determination against our or our licensor's patent rights in any such submission, proceeding or litigation could reduce the scope of, or invalidate, our patent rights, which could adversely affect our competitive position with respect to third parties.

In addition, patents have a limited lifespan. In most countries, including the United States, the natural expiration of a patent is 20 years from the date it is filed. Various extensions of patent term may be available in particular countries, however in all circumstances the life of a patent, and the protection it affords, has a limited term. If we encounter delays in obtaining regulatory approvals, the period of time during which we could market a product under patent protection could be reduced. We expect to seek extensions of patent terms where these are available in any countries where we are prosecuting patents. Such possible extensions include those permitted under the Drug Price Competition and Patent Term Restoration Act of 1984 in the United States, which permits a patent term extension of up to five years to cover an FDA-approved product. However, the applicable authorities, including the FDA in the United States, and any equivalent regulatory authority in other countries, may not agree with our assessment of whether such extensions are available, and may refuse to grant extensions to our patents, or may grant more limited extensions than we request. If this occurs, our competitors may be able to take advantage of our investment in development and clinical trials by referencing our clinical and non-clinical data, and then may be able to launch their product earlier than might otherwise be the case.

Filing, prosecuting and enforcing patents on our platform or product candidates in all countries throughout the world would be prohibitively expensive, and our intellectual property rights in some countries outside the United States could be less extensive than those in the United States. In addition, the laws of some foreign countries do not protect intellectual property rights to the same extent as federal and state laws in the United States. Consequently, we may not be able to prevent third parties from infringing our patents in all countries outside the United States, or from selling or importing products that infringe our patents in and into the United States or other jurisdictions. Competitors may use our technologies in jurisdictions where we have not obtained patent protection to develop their own products and, further, may export otherwise infringing products to territories where we have patent protection, but enforcement is not as strong as that in the United States. These products may compete with our products and our patents or other intellectual property rights may not be effective or sufficient to prevent them from competing.


Any loss of, or failure to obtain, patent protection could have a material adverse impact on our business. We may be unable to prevent competitors from entering the market with a product that is similar to or the same as our products.

We may become involved in lawsuits to protectdefend or enforce our intellectual property, which could be expensive, time consuming and unsuccessful.

Competitors may infringe our patents or misappropriate or otherwise violate our intellectual property rights, and competitors or other third parties may challenge the validity or enforceability of those rights. To counter infringement or unauthorized use, or to defend against other challenges, litigation may be necessary to enforce or defend our intellectual property rights, to protect our trade secrets and/or to determine the validity and scope of our own intellectual property rights or the proprietary rights of others. Such litigation can be expensive and time consuming. Many of our current and potential competitors have the ability to dedicate substantially greater resources to litigate intellectual property rights than we can. Accordingly, despite our efforts, we may not be able to prevent third parties from infringing upon or misappropriating our intellectual property. Litigation could result in substantial costs and diversion of management resources, which could harm our business and financial results. In addition, in an infringement proceeding,contested proceedings, a court or agency may decide that a patent owned by or licensed to us is invalid or unenforceable or may refuse to stop the other party from using the technology at issue on the grounds that our patents do not cover the technology in question. An adverse result in any litigation proceeding could put one or more of our patents at risk of being invalidated, held unenforceable or interpreted narrowly. Furthermore, because of the substantial amount of discovery required in connection with intellectual property litigation, there is a risk that some of our confidential information could be compromised by disclosure during this type of litigation.

Third-party claims of intellectual property infringement or misappropriation may prevent or delay our development and commercialization efforts.

Our commercial success depends in part on our ability to develop, manufacture, market and sell our product candidates, and to use our or our licensors’ proprietary technologies without infringing the patents and proprietary rights of third parties. There is a substantial amount of litigation, both within and outside the United States, involving patent and other intellectual property rights in the biotechnology and pharmaceutical industries, including patent infringement lawsuits, interferences, oppositions, reexamination, and inter partes review proceedings before the U.S. PTO and corresponding foreign patent offices. Numerous U.S. and foreign issued patents and pending patent applications owned by third parties exist in the fields in which we are developing and may develop our product candidates. As the biotechnology and pharmaceutical industries expand and more patents are issued, the risk increases that our product candidates may be subject to claims of infringement of the patent rights of third parties.

Third parties may assert that we are employing their proprietary technology without authorization. There may be third-party patents or patent applications with claims for example to materials, formulations, methods of manufacture, methods of analysis, and/or methods for treatment related to the use or manufacture of our products or product candidates. In some cases,


we may have failed to identify such relevant third-party patents or patent applications. For example, applications filed before November 29, 2000 and certain applications filed after that date that will not be filed outside the United States remain confidential until patents issue. Except for the preceding exceptions, patent applications in the United States and elsewhere are generally published only after a waiting period of approximately 18 months after the earliest filing. Therefore, patent applications covering our platform technology or our products or product candidates could have been filed by others without our knowledge. Additionally, pending patent applications which have been published can, subject to certain limitations, be later amended in a manner that could cover our platform technologies, our products or product candidates and/or the use, analysis, and/or manufacture of our product candidates.

If any third-party patents were held by a court of competent jurisdiction to cover aspects of our materials, formulations, methods of manufacture, methods of analysis, and/or methods for treatment, the holders of any such patents would be able to block our ability to develop and commercialize the applicable product candidate until such patent expired or unless we obtain a license. Such licenses may not be available on acceptable terms, if at all. Even if we were able to obtain a license, the rights may be nonexclusive, which could result in our competitors gaining access to the same intellectual property. Ultimately, we could be prevented from commercializing a product, or be forced to cease some aspect of our business operations, if, as a result of actual or threatened patent infringement claims, we are unable to enter into licenses on acceptable terms.

Parties making claims against us may obtain injunctive or other equitable relief, which could effectively block our ability to further develop and commercialize one or more of our product candidates. Defending against claims of patent infringement or misappropriation of trade secrets could be costly and time consuming, regardless of the outcome. Thus, even if we were to ultimately prevail, or to settle at an early stage, such litigation could burden us with substantial unanticipated costs. In addition, litigation or threatened litigation could result in significant demands on the time and attention of our management team, distracting them from the pursuit of other company business. In the event of a successful claim of infringement against us, we may have to pay substantial


damages, including treble damages and attorneys’ fees for willful infringement, pay royalties, redesign our infringing products or obtain one or more licenses from third parties, which may be impossible or require substantial time and monetary expenditure.

We may face a claim of misappropriation if a third party believes that we inappropriately obtained and used trade secrets of such third party. If we are found to have misappropriated a third party’s trade secrets, we may be prevented from further using such trade secrets, limiting our ability to develop our product candidates, and we may be required to pay damages. During the course of any patent or other intellectual property litigation, there could be public announcements of the results of hearings, rulings on motions, and other interim proceedings in the litigation. If securities analysts or investors regard these announcements as negative, the perceived value of our products, programs, or intellectual property could be diminished. Accordingly, the market price of our common stock may decline.

We have in-licensed a portion of our intellectual property, and, if we fail to comply with our obligations under these arrangements, or our licensors fail to obtain and maintain intellectual property rights, we could lose such intellectual property rights or owe damages to the licensor of such intellectual property.

We are a party to a number of license and collaboration agreements that are important to our business, and we may enter into additional license or collaboration agreements in the future. OurFor example, our discovery platform is built, in part, around patents exclusively in-licensed from academic or research institutions. Certain of our in-licensed intellectual property also covers, or may cover GEN-003 and other current or future product candidates. See “Business — In-License- License Agreements” and “Business — Other Collaborations” for a description of our outstandingin-license agreement with Harvard and Oncovir. These and other licenses may not provide exclusive rights to use such intellectual property and technology in all relevant fields of use and in all territories in which we may wish to develop or commercialize our technology and product candidates in the future. It is possible that we may be unable to obtain additional licenses at a reasonable cost or on reasonable terms, if at all. As a result, we may not be able to prevent competitors from developing and commercializing competitive products in territories included in all of our licenses. In that event, we may be required to expend significant time and resources to redesign our product candidates or to develop or license and collaboration agreements with UC, Harvard, Children’s, Novavax, andreplacement technology, all of which may not be feasible on a technical or commercial basis. If we are unable to do so, we may be unable to develop or commercialize the DFCI.affected product candidates, which could harm our business significantly.

Our existing license agreements impose, and we expect that future license agreements will impose, various diligence, milestone payment, royalty and other obligations on us. For example, in our existing license agreements, and we expect in our future agreements, patent prosecution of our licensed technology may be controlled by the licensor, and we may be required to reimburse the licensor for their costs of patent prosecution. If our licensors fail to obtain and maintain patent or other protection for the proprietary intellectual property we license from them, we could lose our rights to the intellectual property or our exclusivity with respect to those rights, and our competitors could market competing products covered by the intellectual property. Further, in our license agreements we may be responsible for bringing any actions against any third party for infringing the patents we have licensed. If there is any conflict, dispute, disagreement or issue of non-performance between us and our licensing partners regarding our rights or obligations under the license agreements, including any such conflict, dispute or disagreement arising from our failure to satisfy payment obligations under any such agreement, we may owe damages, our licensor may have a right to terminate the affected license, and our ability to utilize the affected intellectual property in our drug discovery and development efforts, and our ability to enter into collaboration or marketing agreements for an affected product candidate, may be adversely affected.


For example, disputes may arise regarding intellectual property subject to a licensing agreement, including the scope of rights granted under the license agreement and other interpretation-related issues; the extent to which our technology infringes the intellectual property of the licensor that is not subject to the licensing agreement; the sublicensing of patent and other rights under any collaborative development relationships; our diligence obligations under the license agreement and what activities satisfy those diligence obligations; the inventorship or ownership of inventions and know-how resulting from the joint creation or use of intellectual property by our licensors and us and our partners; and the priority of invention of patented technology. If disputes over intellectual property that we have licensed prevent or impair our ability to maintain our current licensing arrangements on acceptable terms, we may be unable to successfully develop and commercialize the affected product candidates.

Confidentiality agreements with employees and third parties may not prevent unauthorized disclosure of proprietary information.

In addition to the protection afforded by patents, we rely on confidentiality agreements to protect proprietary know-how that may not be patentable or that we may elect not to patent, processes for which patents are difficult to enforce and any other elements of our platform technology and discovery and development processes that involve proprietary know-how, information or technology that is not covered by patents. We seek to protect our proprietary technology and processes, in part, by entering into confidentiality agreements with our employees, consultants, and outside scientific advisors, contractors and collaborators. Although we use reasonable efforts to protect our know-how, our employees, consultants, contractors, or outside scientific advisors might intentionally or inadvertently disclose our know-how information to competitors. In addition, competitors may otherwise gain access to our know-how or independently develop substantially equivalent information and techniques.


Enforcing a claim that a third party illegally obtained and is using any of our know-how is expensive and time consuming, and the outcome is unpredictable. In addition, courts outside the United States sometimes are less willing than U.S. courts to protect know-how. Misappropriation or unauthorized disclosure of our know-how could impair our competitive position and may have a material adverse effect on our business.

Risks Related to Commercialization of Our Product Candidates

Our future commercial success depends upon attaining significant market acceptance of our product candidates, if approved, among physicians, patients, third-party payors and others in the medical community.

Even if we obtain marketing approval for GEN-003GEN-009, GEN-011 or any other products that we may develop or acquire in the future, the product may not gain market acceptance among physicians, third-party payors, patients and others in the medical community. For example, we currently expect that the initial administration of GEN-003 will be though three injections and future maintenance doses may be required. Physicians or patients may not accept this product as a result of this anticipated dosing requirement. In addition, market acceptance of any approved products depends on a number of other factors, including:

the efficacy and safety of the product, as demonstrated in clinical trials;
the clinical indications for which the product is approved, and the label approved by regulatory authorities for use with the product, including any warnings that may be required on the label;
acceptance by physicians and patients of the product as a safe and effective treatment and the willingness of the target patient population to try new therapies and of physicians to prescribe new therapies;
the cost, safety and efficacy of treatment in relation to alternative treatments;
the availability of adequate coursecoverage and reimbursement by third-party payors and government authorities;
relative convenience and ease of administration;
the prevalence and severity of adverse side effects;
the effectiveness of our sales and marketing efforts; and
the restrictions on the use of our products together with other medications, if any.

Market acceptance is critical to our ability to generate significant revenue. Any product candidate, if approved and commercialized, may be accepted in only limited capacities or not at all. If any approved products are not accepted by the market to the extent that we expect, we may not be able to generate significant revenue and our business would suffer.

If we are unable to establish sales, marketing and distribution capabilities, we may not be successful in commercializing our product candidates if and when they are approved.

We do not have a sales or marketing infrastructure and have no experience in the sale, marketing or distribution of pharmaceutical products. To achieve commercial success for any product for which we have obtained marketing approval, we will need to establish a sales and marketing organization.



In the future, we expect to build a focused sales and marketing infrastructure to market or co-promote some of our product candidates in the United States, if and when they are approved. There are risks involved with establishing our own sales, marketing and distribution capabilities. For example, recruiting and training a sales force is expensive and time consuming and could delay any product launch. If the commercial launch of a product candidate for which we recruit a sales force and establish marketing capabilities is delayed or does not occur for any reason, we would have prematurely or unnecessarily incurred these commercialization expenses. This may be costly, and our investment would be lost if we cannot retain or reposition our sales and marketing personnel.

Factors that may inhibit our efforts to commercialize our products on our own include:

our inability to recruit, train and retain adequate numbers of effective sales and marketing personnel;
the inability of sales personnel to obtain access to physicians;
the lack of adequate numbers of physicians to prescribe any future products;
the lack of complementary products to be offered by sales personnel, which may put us at a competitive disadvantage relative to companies with more extensive product lines; and


unforeseen costs and expenses associated with creating an independent sales and marketing organization.

If we are unable to establish our own sales, marketing and distribution capabilities, and instead enter into arrangements with third parties to perform these services, our product revenues and our profitability, if any, are likely to be lower than if we were to market, sell and distribute any products that we develop ourselves. In addition, we may not be successful in entering into arrangements with third parties to sell, market and distribute our product candidates or may be unable to do so on terms that are favorable to us. We likely will have little control over such third parties, and any of them may fail to devote the necessary resources and attention to sell and market our products effectively. If we do not establish sales, marketing and distribution capabilities successfully, either on our own or in collaboration with third parties, we will not be successful in commercializing our product candidates.

Coverage and reimbursement may be limited or unavailable in certain market segments for our product candidates, which could make it difficult for us to sell our products profitably.

Market acceptance and sales of any approved products will depend significantly on the availability of adequate coverage and reimbursement from third-party payors and may be affected by existing and future health care reform measures. Third-party payors, such as government health care programs, private health insurers and health maintenancemanaged care organizations, decide for which drugs they will provide coverage for and establish reimbursement levels. Coverage and reimbursement decisions by a third-party payor may depend upon a number of factors, including the third-party payor’s determination that use of a product is:

a covered benefit under its health plan;
safe, effective and medically necessary;
appropriate for the specific patient;
cost-effective; and
neither experimental nor investigational.

Third-party payors, whether foreign or domestic, or governmental or commercial, are developing increasingly sophisticated methods of controlling health care costs. Coverage and reimbursement can vary significantly from payor to payor. As a result, obtaining coverage and reimbursement approval for a product from each government and other third-party payor willmay require us to provide supporting scientific, clinical and cost-effectiveness data for the use of our products to each payor separately, with no assurance that we will be able to provide data sufficient to gain acceptance with respect to coverage and reimbursement. We cannot be sure that coverage or adequate reimbursement will be available for any of our product candidates. Also, we cannot be sure that coverage determinations or reimbursement amounts will not reduce the demand for or require us to lower the price of or provide discounts on, our products. If reimbursement is not available or is available only to limited levels, we may not be able to commercialize certain of our products. In addition, in the United States, third-party payors are increasingly attempting to contain health care costs by limiting both coverage and the level of reimbursement of new drugs. As a result, significant uncertainty exists as to whether and how much third-party payors will reimburse patients for their use of newly approved drugs, which in turn will put pressure on the pricing of drugs.



Price controls may be imposed, which may adversely affect our future profitability.

In international markets, reimbursement and health care payment systems vary significantly by country, and many countries have instituted price ceilings on specific products and therapies. In some countries, particularly member states of the European Union, the pricing of prescription pharmaceuticals is subject to governmental control. In these countries, pricing negotiations with governmental authorities can take considerable time after receipt of marketing approval for a product. In addition, there can be considerable pressure by governments and other stakeholders on coverage, prices and reimbursement levels, including as part of cost containment measures. Political, economic and regulatory developments may further complicate pricing negotiations, and pricing negotiations may continue after coverage and reimbursement has been obtained. Reference pricing used by various European Union member states and parallel distribution, or arbitrage between low-priced and high-priced member states, can further reduce prices. In some countries, we may be required to conduct a clinical trial or other studies that compare the cost-effectiveness of our product candidates to other available vaccines in order to obtain or maintain coverage, reimbursement or pricing approval. Publication of discounts by third-party payors or authorities may lead to further pressure on the prices or reimbursement levels within the country of publication and other countries. There can be no assurance that our vaccine candidates will be considered cost-effective by third-party payors, that an adequate level of reimbursement will be available or that the third-party payors’ reimbursement policies will not adversely affect our ability to sell our products profitably. If reimbursement of our products is unavailable or limited in scope or amount, or if pricing is set at unsatisfactory levels, our business could be adversely affected.


The impact of recent health care reform legislation and other changes in the health care industry and in health care spending on us is currently unknown and may adversely affect our business model.

In the United States, and in some foreign jurisdictions, the legislative landscape continues to evolve. Our revenue prospects could be affected by changes in health care spending and policy in the United States and abroad. We operate in a highly regulated industry and new laws or judicial decisions, or new interpretations of existing laws or decisions, related to health care availability, the method of delivery or payment for health care products and services could negatively impact our business, operations and financial condition. There is significant interest in promoting health care reform, as evidenced by the enactment in the United States of the Patient Protection and Affordable CareHealthcare Reform Act, (the "ACA"), as amended by the Health Care and Education Reconciliation Act in 2010, as well as by the pending proposalsongoing efforts to eliminate or significantly modify the ACA.Healthcare Reform Act. For example, recent tax reform legislation eliminated the tax penalty for individuals who do not maintain sufficient health insurance coverage. See “Business- Government Regulation-Reimbursement”. It is likely that federal and state legislatures within the United States andas well as foreign governments will continue to consider changes to existing health care legislation.
Modifications to or repeal of all or certain provisions of the ACA are expected as a result of the outcome of the recent presidential elections and Republications maintaining control of Congress, consistent with statements made by Donald Trump and members of Congress during the presidential campaign and following the election.
We cannot predict the ultimate content, timing or effect of any changes to the ACAHealthcare Reform Act or other federal and state reform efforts.efforts within the United States or abroad. There is no assurance that federal or state health care reform will not adversely affect our business and financial results, and we cannot predict how future federal or state legislative, judicial or administrative changes relating to healthcare reform will affect our business.

The continuing efforts of the government, insurance companies, managed care organizations and other payors of health care services to contain or reduce costs of health care may adversely affect:

the demand for any drug products for which we may obtain regulatory approval;
our ability to set a price that we believe is fair for our products;
our ability to obtain coverage and reimbursement approval for a product;
our ability to generate revenues and achieve or maintain profitability; and
the level of taxes that we are required to pay.

In addition, other broader legislative changes have been adopted that could have an adverse effect upon, and could prevent, our products’ or product candidates’ commercial success. The Budget Control Act of 2011, as amended, or the Budget Control Act, includes provisions intended to reduce the federal deficit, including reductions in Medicare payments to providers through 2029. Any significant spending reductions affecting Medicare, Medicaid, or other publicly funded or subsidized health programs, or any significant taxes or fees imposed as part of any broader deficit reduction effort or legislative replacement to the Budget Control Act, or otherwise, could have an adverse impact on our anticipated product revenues.

We face substantial competition, which may result in others discovering, developing or commercializing products before, or more successfully, than we do.

The development and commercialization of new drug products is highly competitive. Our future success depends on our ability to demonstrate and maintain a competitive advantage with respect to the design, development and commercialization of our product candidates. Our objective is to design, develop and commercialize new products with superior efficacy, convenience, tolerability and safety. In many cases, the products that we commercialize will compete with existing, market-leading products.



Oral antivirals, such as valacyclovir and famciclovir, are products currently approved to treat patients with genital herpes. GEN-003, our active development product and lead product candidate, will compete with these products, if approved. In addition, one or more products not currently approved for the treatment of genital herpes, including pritelivir (AiCuris) and HerpV (Agenus) and other vaccines in development by Admedus, Ltd and Vical Incorporated may in the future be granted marketing approval for the treatment of genital herpes or other conditions for which GEN-003 might be approved.

Other companies that are seeking to identify antigens for the development of vaccines and T cell receptor therapies using predictive tools include Foundation Medicine, NeonAchilles Therapeutics Ltd., Adaptive Biotechnologies Corp., BioNTech SE, Cellular Biomedicine Group Inc., Eutilex Co., Ltd., Genentech, Inc., Gilead Sciences, Inc., Gritstone Oncology Immatics Biotechnologies GmbH, Immunocore Limited,Inc., Iovance Biotherapeutics Inc., Marker Therapeutics, Inc., Merck & Co., Inc., Moderna Inc., Oncotherapy Science Inc., PACT Pharma Inc., Vaccibody AS and Adaptive Biotechnologies.Ziopharm Oncology Inc.

Many of our potential competitors have significantly greater financial, manufacturing, marketing, drug development, technical and human resources than we do. Large pharmaceutical companies, in particular, have extensive experience in clinical testing, including recruiting patients, obtaining regulatory approvals, recruiting patients and in manufacturing pharmaceutical products. Large and established companies such as Merck & Co., Inc., GlaxoSmithKline plc, Novartis, Inc., Sanofi Pasteur, SA, Pfizer Inc. and MedImmune, LLC (a subsidiary of AstraZeneca PLC), among others, compete in the vaccine market. In particular, these companies have greater experience and expertise in securing government contracts and grants to support their research and development efforts, conducting testing and clinical trials, obtaining regulatory approvals to market products, manufacturing such products on a broad scale and marketing approved products. These companies also have significantly greater research and marketing capabilities than we do and may also have products that have been approved or are in late stages of development and have collaborative arrangements in our target markets with leading companies and research institutions.


Established pharmaceutical companies may also invest heavily to accelerate discovery and development of novel compounds or to in-license novel compounds that could make the product that we develop obsolete. As a result of all of these factors, our competitors may succeed in obtaining patent protection and/or FDA approval or discovering, developing and commercializing products before we do. In addition, any new product that competes with an approved product must demonstrate compelling advantages in efficacy, convenience, tolerability, and safety in order to overcome price competition and to be commercially successful. If we are not able to compete effectively against potential competitors, our business will not grow and our financial condition and operations will suffer.

Our products may cause undesirable side effects or have other properties that delay or prevent their regulatory approval or limit their commercial potential.

Undesirable side effects caused by our products or even competing products in development that utilize a common mechanism of action could cause us or regulatory authorities to interrupt, delay or halt clinical trials and could result in the denial of regulatory approval by the FDA or other regulatory authorities and potential product liability claims. We are currently conducting Phase 2 clinical trials for GEN-003. Serious AEs deemed to be caused by our product candidates could have a material AE on the development of our product candidates and our business as a whole. The most commonWe do not yet have any information related to whether GEN-009 may cause AEs to date in the clinical trial evaluating the safety and tolerability of GEN-003 have been fatigue, myalgia (muscle pain), pain tenderness and induration (inflammatory hardening of the skin). Our understanding of the relationship between GEN-003 and these events, as well as our understanding of AEs in future clinical trials of other product candidates, may change as we gather more information, and additional unexpected AEs may be observed.or serious AEs.

If we or others identify undesirable side effects caused by any of our product candidates either before or after receipt of marketing approval, a number of potentially significant negative consequences could result, including:

our clinical trials may be put on hold;
we may be unable to obtain regulatory approval for our vaccine candidates;
regulatory authorities may withdraw approvals of our vaccines;
regulatory authorities may require additional warnings on the label;
a medication guide outlining the risks of such side effects for distribution to patients may be required;
we could be sued and held liable for harm caused to patients; and
our reputation may suffer.

Any of these events could prevent us from achieving or maintaining market acceptance of our products and could substantially increase commercialization costs.



Risks Related to Our Indebtedness

Our level of indebtedness and debt service obligations could adversely affect our financial condition and may make it more difficult for us to fund our operations.

In December 2015,April 2018, we entered into an amendment (the "First Amendment") to our Loan Agreement (the "2014 Term Loan")amended and restated loan and security agreement with Hercules Capital, Inc. (f/k/a Hercules Technology Growth Capital, Inc.) (“Hercules”), which was subsequently amended in November 2019 (as amended, the "2018 Term Loan"). The First Amendment required us2018 Term Loan provides up to draw an additional $5.0$14.0 million of debt financing. The 2018 Term Loan has interest only payments through December 31, 2020. Thereafter, we are obligated to make payments that will include equal installments of principal and permitted us to draw two additional $5.0 million tranches, which expired unused at December 15, 2016.interest through the maturity date of May 2021. At December 31, 2016, $17.02019, $13.4 million was outstanding under the amended 20142018 Term Loan. Principal payments are currently scheduled to begin July 1, 2017.Loan, as amended.

All obligations under our 2014the 2018 Term Loan are secured by substantially all of our existing property and assets, excluding our intellectual property and in-licensed technology. This indebtedness may create additional financing risk for us, particularly if our business or prevailing financial market conditions are not conducive to paying off or refinancing our outstanding debt obligations at maturity. This indebtedness could also have important negative consequences, including:including the fact that:

we will need to repay our indebtedness by making payments of interest and principal, which will reduce the amount of money available to finance our operations, our research and development efforts and other general corporate activities; and
our failure to comply with the restrictive covenants in our 2014the 2018 Term Loan could result in an event of default that, if not cured or waived, would accelerate our obligation to repay this indebtedness, and Hercules could seek to enforce its security interest in the assets securing such indebtedness.



To the extent that additional debt is added to our current debt levels, the risks described above could increase.

We may not have cash available to us in an amount sufficient to enable us to make interest or principal payments on our indebtedness when due. If we do not make scheduled payments when due, or otherwise materially breach or experience an event of default under the 2018 Term Loan Hercules could accelerate our total loan obligation or enforce its security interest against us.

Failure to satisfy our current and future debt obligations under our 2014the 2018 Term Loan could result in an event of default. In addition, other events, including certain events that are not entirely in our control, such as the occurrence of a material adverse event on our business, could cause an event of default and, asto occur. As a result of the occurrence of an event of default, Hercules could accelerate all of the amounts due. In the event of an acceleration of amounts due under our 2014the 2018 Term Loan as a result of an event of default, we may not have sufficient funds or may be unable to arrange for additional financing to repay our indebtedness. In addition, Hercules could seek to enforce its security interests in the assets securing such indebtedness. If we are unable to pay amounts due to Hercules upon acceleration of the 2018 Term Loan or if Hercules enforces its security interest against our assets securing our indebtedness to Hercules, our ability to continue to operate our business may be jeopardized.

We are subject to certain restrictive covenants which, if breached, could result in the acceleration of our debt under the 2018 Term Loan and have a material adverse effect on our business and prospects.

Our 2014The 2018 Term Loan imposes operating and other restrictions on us. Such restrictions will affect, and in many respects limit or prohibit, our ability and the ability of any future subsidiary to, among other things:

dispose of certain assets;
change our lines of business;
engage in mergers or consolidations;
incur additional indebtedness;
create liens on assets;
pay dividends and make distributions or repurchase our capital stock; and
engage in certain transactions with affiliates.

These restrictive covenants may prevent us from undertaking an action that we feel is in the best interests of our business. In addition, if we were to breach any of these restrictive covenants, Hercules could accelerate our indebtedness under the 2018 Term Loan or enforce its security interest against our assets, either of which would materially adversely affect our ability to continue to operate our business.

Risks Related to Our Business and Industry

If we fail to attract and keep senior management and key scientific personnel, we may be unable to successfully develop our products, conduct our clinical trials and commercialize our product candidates.



We are highly dependent on members of our senior management, including William Clark, our President and Chief Executive Officer, Seth Hetherington,Girish Aakalu, Ph.D., our Chief Business Officer, Tom Davis, M.D., our Chief Medical Officer, Jonathan Poole,Diantha Duvall, our Chief Financial Officer, and Jessica Flechtner, Ph.D., our Chief Scientific Officer.Officer, and Narinder Singh, our Senior Vice President of Pharmaceutical Sciences and Manufacturing. The loss of the services of any of these persons could impede the achievement of our research, development and commercialization objectives. We have employment agreements with each of these members of senior management.

Recruiting and retaining qualified scientific, clinical, manufacturing, sales and marketing personnel will also be critical to our success. The loss of the services of our executive officers or other key employees could impede the achievement of our research, development and commercialization objectives and seriously harm our ability to successfully implement our business strategy. Furthermore, replacing executive officers and key employees may be difficult and may take an extended period of time because of the limited number of individuals in our industry with the breadth of skills and experience required to successfully develop, gain regulatory approval of and commercialize products. Competition to hire from this limited pool is intense, and we may be unable to hire, train, retain or motivate these key personnel on acceptable terms, givenbased on the status of our clinical development programs and the competition among numerous pharmaceutical and biotechnology companies for similar personnel. We also experience competition for the hiring of scientific and clinical personnel from universities and research institutions. In


addition, we rely on consultants and advisors, including scientific and clinical advisors, to assist us in formulating our research and development and commercialization strategy. Our consultants and advisors may be employed by employers other than us and may have commitments under consulting or advisory contracts with other entities that may limit their availability to us. If we are unable to continue to attract and retain high quality personnel, our ability to pursue our growth strategy will be limited.

Our employees, independent contractors, principal investigators, consultants, commercial partners, and vendors may engage in misconduct or other improper activities, including noncompliance with regulatory standards and requirements and insider trading.

We are exposed to the risk of fraudulent or other illegal activity by our employees, independent contractors, principal investigators, consultants, commercial partners, and vendors. Misconduct by these parties could include intentional, reckless and/or negligent conduct that fails: to comply with the laws of the FDA and similar foreign regulatory bodies; to provide true, complete and accurate information to the FDA and similar foreign regulatory bodies; to comply with manufacturing standards we have established; to comply with federal, state and foreign health care fraud and abuse laws and regulations; to report financial information or data accurately; or to disclose unauthorized activities to us. In particular, the promotion, sale and marketing of health care items and services, as well as certain business arrangements in the health care industry are subject to extensive laws and regulations intended to prevent misconduct, including fraud, kickbacks, self-dealing and other abusive practices. These laws and regulations may restrict or prohibit a wide range of pricing, discounting, marketing, and, structuring and commission(s), certain customer incentive programs and other business arrangements. Activities subject to these laws also involve the improper use of information obtained in the course of patient recruitment for clinical trials. It is not always possible to identify and deter such misconduct, and the precautions we take to detect and prevent this activity may not be effective in controlling unknown or unmanaged risks or losses or in protecting us from governmental investigations or other actions or lawsuits stemming from a failure to be in compliance with such laws or regulations. If any such actions are instituted against us, and we are not successful in defending ourselves or asserting our rights, those actions could have a significant impact on our business, including the imposition of civil, criminal and administrative penalties, damages, monetary fines, disgorgement, possible exclusion from participation in Medicare, Medicaid and other federal health care programs, contractual damages, reputational harm, diminished profits and future earnings, and curtailment or restructuring of our operations, any of which could adversely affect our ability to operate our business and our results of operations.

We may encounter difficulties in managing our growth and expanding our operations successfully.

As we seek to advance our product candidates through clinical trials and commercialization, we will need to expand our development, regulatory, manufacturing, marketing and sales capabilities or contract with third parties to provide these capabilities for us. As our operations expand, we expect that we will need to manage additional relationships with various strategic partners, suppliers and other third parties. Future growth will impose significant added responsibilities on members of management. Our future financial performance and our ability to commercialize our product candidates and to compete effectively will depend, in part, on our ability to manage any future growth effectively. To that end, we must be able to manage our development efforts and clinical trials effectively and hire, train and integrate additional management, administrative and, if necessary, sales and marketing personnel. We may not be able to accomplish these tasks, and our failure to accomplish any of them could prevent us from successfully growing our company.

If product liability lawsuits are brought against us, we may incur substantial liabilities and may be required to limit commercialization of our product candidates.



We face an inherent risk of product liability as a result of the clinical testing of our product candidates and will face an even greater risk if we commercialize any products. For example, we may be sued if any product we develop allegedly causes injury or is found to be otherwise unsuitable during product testing, manufacturing, marketing or sale. Any such product liability claims may include allegations of defects in manufacturing, defects in design, a failure to warn of dangers inherent in the product, negligence, strict liability and a breach of warranties. Claims could also be asserted under state consumer protection acts. If we cannot successfully defend ourselves against product liability claims, we may incur substantial liabilities or be required to limit commercialization of our product candidates. Even a successful defense would require significant financial and management resources. Regardless of the merits or eventual outcome, liability claims may result in:

decreased demand for any product candidates or products that we may develop;
injury to our reputation and significant negative media attention;
withdrawal of clinical trial participants;
significant costs to defend the related litigations;


a diversion of management’s time and our resources;
substantial monetary awards to trial participants or patients;
product recalls, withdrawals, or labeling, marketing or promotional restrictions;
loss of revenue;
the inability to commercialize any product candidates that we may develop; and
a decline in our stock price.

Failure to obtain and retain sufficient product liability insurance at an acceptable cost to protect against potential product liability claims could prevent or inhibit the commercialization of products we develop. We currently carry product liability insurance covering our clinical trials in the amount of $5.0 million in the aggregate. Although we maintain product liability insurance, any claim that may be brought against us could result in a court judgment or settlement in an amount that is not covered, in whole or in part, by our insurance or that is in excess of the limits of our insurance coverage. Our insurance policies also have various exclusions, and we may be subject to a product liability claim for which we have no coverage. We will have to pay any amounts awarded by a court or negotiated in a settlement that exceed our coverage limitations or that are not covered by our insurance, and we may not have, or be able to obtain, sufficient capital to pay such amounts.

We must comply with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use hazardous chemicals and radioactive and biological materials in certain aspects of our business and are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, distribution, storage, handling, treatment and disposal of these materials. We cannot eliminate the risk of accidental injury or contamination from the use, manufacture, distribution, storage, handling, treatment or disposal of hazardous materials. In the event of contamination or injury, or failure to comply with environmental, occupational health and safety and export control laws and regulations, we could be held liable for any resulting damages and any such liability could exceed our assets and resources. We are uninsured for third-party contamination injury.

We may not be ableOur failure to wincomply with data protection laws and regulations could lead to government academic institution enforcement actions, private litigation and/or non-profit contracts or grants.adverse publicity and could negatively affect our operating results and business.

From timeWe are subject to time,data protection laws and regulations that address privacy and data security. The legislative and regulatory landscape for data protection continues to evolve, and in recent years there has been an increasing focus on privacy and data security issues. In the United States, numerous federal and state laws and regulations, including state data breach notification laws, state health information privacy laws and federal and state consumer protection laws govern the collection, use, disclosure and protection of health-related and other personal information. Failure to comply with data protection laws and regulations could result in government enforcement actions, which could include civil or criminal penalties, private litigation and/or adverse publicity and could negatively affect our operating results and business. In addition, we may obtain health information from third parties (e.g., healthcare providers who prescribe our products) that are subject to privacy and security requirements under the Health Insurance Portability and Accountability Act of 1996, as amended by the Health Information Technology for Economic and Clinical Health Act (collectively, “HIPAA”). While we are not a “covered entity” or “business associate” subject directly to regulation under HIPAA, HIPAA’s criminal provisions can apply for contractsto entities other than “covered entities” or grants“business associates” in certain circumstances. Accordingly. we could be subject to criminal penalties if we knowingly obtain or disclose individually identifiable health information from government agencies, non-profit entitiesa HIPAA-covered entity in a manner that is not authorized or permitted.

The collection and academic institutions. Such grants haveuse of personal health data in the European Union is governed by the provisions of the General Data Protection Regulation (“GDPR”) which came into effect in May 2018. This regulation imposes several requirements relating to the consent of the individuals to whom the personal data relates, the information provided to the individuals, notification of data processing obligations to the competent national data protection authorities and the security and confidentiality of the personal data. The GDPR also imposes strict rules on the transfer of personal data out of the European Union to the United States. Failure to comply with the requirements of the GDPR and the related national data protection laws of the European Union Member States may result in significant fines and other administrative penalties. In the United States, several state legislatures are considering enacting new data privacy legislation. One example of such legislation that has already been our only source of revenuepassed is the California Consumer Privacy Act (“CCPA”), which takes effect on January 1, 2020. The CCPA gives California consumers (defined to date. Such contracts or grants can be highly attractive because they provide capital to fundinclude all California residents) certain rights, including the ongoing development of our technologies and product candidates without diluting our stockholders. However, there is often significant competition for these contracts or grants. Entities offering contracts or grants may have requirements to apply for or to otherwise be eligibleright to receive certain contracts or grants that our competitors may be abledetails regarding the processing of their data by covered companies, the right to satisfy that we cannot. In addition, such entities may make arbitrary decisions as to whether to offer contracts or make grants, to whom the contracts or grants will be awardedrequest deletion of their data, and the sizeright to opt out of the contracts or grantssales of their data. The CCPA additionally imposes several obligations on covered companies to each awardee. Even if we are ableprovide notice to satisfy the award requirements, there is no guarantee that we will be a successful awardee. Therefore, we may not be able to win any contracts or grants in a timely manner, if at all.California consumers regarding their data processing activities. The


CCPA provides for imposition of substantial fines on companies that violate the law and also confers a private right of action on data subjects to seek statutory or actual damages for breaches of their personal information.

Significant disruptions of information technology systems or security breaches could adversely affect our business.

We are increasingly dependent upon information technology systems, infrastructure and data to operate our business. In the ordinary course of business, we collect, store and transmit large amounts of confidential information (including, among other things, trade secrets or other intellectual property, proprietary business information and personal information). It is critical that we do so in a secure manner to maintain the confidentiality and integrity of such confidential information. We also have outsourced elements of our operations to third parties, and as a result we manage a number of third-party vendors who may or could have access to our confidential information. The size and complexity of our information technology systems, and those of third-party vendors with whom we contract, and the large amounts of confidential information stored on those systems, make such systems vulnerable to service interruptions or to security breaches from inadvertent or intentional actions by our employees, consultants, third-party vendors, and/or business partners, or from cyber-attacks by malicious third parties. Cyber-attacks are increasing in their frequency, sophistication and intensity, and have become increasingly difficult to detect. Cyber-attacks could include the deployment of harmful malware, ransomware, denial-of-service attacks, social engineering and other means to affect service reliability and threaten the confidentiality, integrity and availability of information. Cyber-attacks could also include phishing attempts or e-mail fraud to cause payments or information to be transmitted to an unintended recipient.

Significant disruptions of our information technology systems, or those of our third-party vendors, or security breaches could adversely affect our business operations and/or result in the loss, misappropriation and/or unauthorized access, use or disclosure of, or the prevention of access to, confidential information, including, among other things, trade secrets or other intellectual property, proprietary business information and personal information, and could result in financial, legal, business and reputational harm to us. For example, any such event that leads to unauthorized access, use or disclosure of personal information, including personal information regarding our patients or employees, could harm our reputation, require us to comply with federal and/or state breach notification laws and foreign law equivalents, and otherwise subject us to liability under laws and regulations that protect the privacy and security of personal information. Security breaches and other inappropriate access can be difficult to detect, and any delay in identifying them may lead to increased harm of the type described above. While we have implemented security measures to protect our information technology systems and infrastructure, there can be no assurance that such measures will prevent service interruptions or security breaches that could adversely affect our business.
Risks Related to Our Common Stock

We are eligibleOur largest stockholder, New Enterprise Associates (“NEA”), could exert significant influence over us and could limit your ability to be treated as an “emerging growth company” as definedinfluence the outcome of key transactions, including any change of control.
Our largest stockholder, NEA, beneficially owns, in the Jumpstart Our Business Startups Actaggregate, shares representing approximately 30% of 2012 ("JOBS Act"), and we cannot be certain if the reduced disclosure requirements applicable to emerging growth companies will make our outstanding common stock less attractive to investors.

We are an “emerging growth company”, as defined in the JOBS Act. For as long as we continue to be an emerging growth company, we may take advantage of exemptions from various reporting requirements that are applicable to other public companies that are not emerging growth companies. These exemptions include:
not being required to comply with the auditor attestation requirements in the assessmentJanuary 31, 2020. In addition, one member of our internal controlboard of directors is associated with NEA. As a result, we expect that NEA will be able to exert significant influence over financial reporting;
not being required to complyour business. NEA may have interests that differ from your interests, and it may vote in a way with any requirementwhich you disagree and that may be adopted byadverse to your interests. The concentration of ownership of our capital stock may have the Public Company Accounting Oversight Board providingeffect of delaying, preventing or deterring a change of control of our company, could deprive our stockholders of an opportunity to receive a premium for supplemental auditor’s reports for additional information about the audit and the financial statements;
reduced disclosure obligations regarding executive compensation; and
exemptions from the requirements of holding a nonbinding advisory vote on executive compensation and shareholder approval of any golden parachute payments not previously approved.
We have taken advantage of reduced reporting burdens in this prospectus. For example, we have not included all of the executive compensation related information that would be required if we were not an emerging growth company. We cannot predict whether investors will find ourtheir common stock less attractive if we rely on these exemptions. If some investors findas part of a sale of our common stock less attractive as a result, therecompany and may be a less active trading market for our common stock and our stock price may be more volatile. In addition, the JOBS Act provides that an emerging growth company can take advantage of an extended transition period for complying with new or revised accounting standards. This allows an emerging growth company to delay the adoption of these accounting standards until they would otherwise apply to private companies. We have irrevocably elected not to avail ourselves of this exemption and, therefore, we will be subject to the same new or revised accounting standards as other public companies that are not emerging growth companies.

We could be an emerging growth company for up to five years, until December 31, 2019, although circumstances could cause us to lose that status earlier, including ifadversely affect the market valueprice of our common stock held by non-affiliates exceeds $700.0 million as of any June 30 before that time or if we have total annual gross revenue of $1.0 billion or more during any fiscal year before that time, in which cases we would no longer be an emerging growth company as of the following December 31 or, if we issue more than $1.0 billion in non-convertible debt during any three-year period before that time, we would cease to be an emerging growth company immediately. Even after we no longer qualify as an emerging growth company, we may still qualify as a “smaller reporting company” if the market value of our common stock held by non-affiliates is below $75.0 million as of June 30 in any given year, which would allow us to take advantage of many of the same exemptions from disclosure requirements, including not being required to comply with the auditor attestation requirements of Section 404 of the Sarbanes-Oxley Act and reduced disclosure obligations regarding executive compensation in our periodic reports and proxy statements.stock.

We cannot predict what the market price of our common stock will be and, as a result, it may be difficult for you to sell your shares of our common stock.

An inactive market may impair our ability to raise capital by selling shares of our common stock and may impair our ability to enter into strategic partnerships or acquire companies or products by using our shares of common stock as consideration. We cannot predict the prices at which our common stock will trade. It is possible that in one or more future periods our results of operations may be below the expectations of public market analysts and investors and, as a result of these and other factors, the price of our common stock may fall.

If our stock price is volatile, our stockholders could incur substantial losses.losses and we may become involved in securities-related litigation, including securities class action litigation, that could divert management’s attention and harm our business and subject us to significant liabilities.

Our stock price is likely to be volatile. The stock market in general and the market for biopharmaceutical companies in particular have experienced extreme volatility that has often been unrelated to the operating performance of particular companies.


As a result of this volatility, our stockholders could incur substantial losses. The market price for our common stock may be influenced by many factors, including:


the success of competitive products or technologies;
results of clinical trials of our product candidates;
the timing of the release of results of our clinical trials;
results of clinical trials of our competitors’ products;
regulatory actions or legal developments with respect to our products or our competitors’ products;
developments or disputes concerning patent applications, issued patents or other proprietary rights;
the results of our efforts to discover, develop, acquire or in-license additional product candidates or products;
actual or anticipated fluctuations in our financial condition and operating results;
publication of research reports by securities analysts about us or our competitors or our industry;
our failure or the failure of our competitors to meet analysts’ projections or guidance that we or our competitors may give to the market;
additions and departures of key personnel;
strategic decisions by us or our competitors, such as acquisitions, divestitures, spin-offs, joint ventures, strategic investments or changes in business strategy;
the passage of legislation or other regulatory developments affecting us or our industry;
fluctuations in the valuation of companies perceived by investors to be comparable to us;
sales of our common stock by us, our insiders or our other stockholders;
speculation in the press or investment community;
announcement or expectation of additional financing efforts;
changes in accounting principles;
terrorist acts, acts of war or periods of widespread civil unrest;
natural disasters and other calamities;
changes in market conditions for biopharmaceutical stocks; and
changes in general market and economic conditions.

In addition, the stock market has recently experienced significant volatility, particularly with respect to pharmaceutical, biotechnology and other life sciences company stocks. The volatility of pharmaceutical, biotechnology and other life sciences company stocks often does not relate to the operating performance of the companies represented by the stock. As we operate in a single industry, we are especially vulnerable to these factors to the extent that they affect our industry or our products, or to a lesser extent our markets. In the past, securities class action litigation has often been initiated against companies following periods of volatility in their stock price. This type of

Further, any future lawsuits or litigation could result in substantial costs and divert our management’smanagement's attention and resources and could also require us to make substantial payments to satisfy judgments or to settle litigation.

Failure to comply with The Nasdaq Capital Market continued listing requirements may result in our common stock being delisted from The Nasdaq Capital Market.

If our stock price falls below $1.00 per share, we may not continue to qualify for continued listing on The Nasdaq Capital Market or The Nasdaq Global Market. To maintain listing, we are required, among other things, to maintain a minimum closing bid price of $1.00 per share. If the closing bid price of our common stock is below $1.00 per share for 30 consecutive business days, we will receive a deficiency notice from Nasdaq advising us that we have a certain period of time, typically 180 days, to regain compliance by maintaining a minimum closing bid price of at least $1.00 for at least ten consecutive business days, although Nasdaq could require a longer period.



On June 15, 2018, we received a written notification from Nasdaq's Listing Qualifications Department that we had failed to comply with Nasdaq Listing Rule 5450(a)(1) because the bid price for our common stock over a period of 30 consecutive business days prior to such date had closed below the minimum $1.00 per share requirement for continued listing. In accordance with Nasdaq Listing Rule 5810(c)(3)(A), we were afforded an initial period of 180 calendar days, or until December 12, 2018, to regain compliance with Rule 5450(a)(1). We determined that we would not be in compliance with Rule 5450(a)(1) by December 12, 2018, and on November 19, 2018, submitted an application to transfer our common stock from listing on the Nasdaq Global Market to the Nasdaq Capital Market. Doing so allowed us to become eligible for an additional 180 day compliance period provided for companies listed on the Nasdaq Capital Market, provided that we met the continued listing requirements for market value of publicly held shares and all other initial listing standards for the Nasdaq Capital Market, with the exception of the minimum bid price requirement, and provided written notice of our intention to cure the deficiency during the second compliance period by effecting a reverse stock split, if necessary. In accordance with the original notification, we indicated in our transfer application that we met all of the other continuing listing requirements for the Nasdaq Capital Market, with the exception of the bid price requirement, and provided written notice of our intention to cure the deficiency during the second compliance period by effecting a reverse stock split, if necessary. On December 13, 2018, we received notice from Nasdaq that we were granted an additional 180 calendar days, or until June 11, 2019, to regain compliance with the minimum $1.00 bid price per share requirement of the Nasdaq listing rules. Accordingly, at the opening of business on December 17, 2018, the listing of the shares of our common stock was transferred from the Nasdaq Global Market to the Nasdaq Capital Market. Our common stock continues to trade under the symbol "GNCA."

On May 22, 2019, we effected a reverse stock split of our issued and outstanding common stock, par value $0.001, at a ratio of one-for-eight. As such, prior to June 10, 2019 the bid price of our common stock closed at or above $1.00 per share for a minimum of 10 consecutive business days, and Nasdaq provided written notice that we achieved compliance with the Nasdaq listing rules. Even though we did regain compliance with minimum closing bid price of $1.00 per share by June 10, 2019, there is no guarantee that we will remain in compliance thereafter. The delisting of our common stock would significantly affect the ability of investors to trade our common stock and negatively impact the liquidity and price of our common stock. In addition, the delisting of our common stock could materially adversely impact our ability to raise capital on acceptable terms or at all. Delisting from Nasdaq could also have other negative results, including the potential loss of confidence by our current or prospective third-party providers and collaboration partners, the loss of institutional investor interest, and fewer licensing and partnering opportunities.

Our failure to implement and maintain effective internal control over financial reporting could result in material misstatements in our financial statements which could require us to restate financial statements, cause investors to lose confidence in our reported financial information and have a negative effect on our stock price.

As reported in our Quarterly Report on Form 10-Q filed with the SEC on May 9, 2014, during the quarter ended March 31, 2014, management and our independent registered public accounting firm identified a material weakness in our internal control over financial reporting (as defined in the Public Company Accounting Oversight Board’s Auditing Standard No. 5) related to the accounting for a non-cash stock compensation expense for a milestone-based stock option award. We


remediated this material weakness by implementing corrective measures as described in our Quarterly Report on Form 10-Q for the quarter ended March 31, 2014.

We cannot assure you that additionalany material weaknesses or significant deficiencies in our internal control over financial reporting will not be identified in the future. Any failure to maintain or implement required new or improved controls, or any difficulties we encounter in their implementation, could result in additional material weaknesses or significant deficiencies, cause us to fail to meet our periodic reporting obligations or result in material misstatements in our financial statements. Any such failure could also adversely affect the results of periodic management evaluations regarding the effectiveness of our internal control over financial reporting. The existence of a material weakness or significant deficiency could result in errors in our financial statements that could result in a restatement of financial statements, cause us to fail to meet our reporting obligations and cause investors to lose confidence in our reported financial information, leading to a decline in our stock price.

We incur significant costs as a result of being a public company and our management expects to devote substantial time to public company compliance programs.

As a public company, we incur significant legal, insurance, accounting and other expenses that we did not incur as a private company.expenses. In addition, our administrative staff are required to perform additional tasks. We invest resources to comply with evolving laws, regulations and standards, and this investment could result in increased general and administrative expenses and may divert management’s time and attention from product development activities. If our efforts to comply with new laws, regulations and standards differ from the activities intended by regulatory or governing bodies due to ambiguities related to practice, regulatory authorities may initiate legal proceedings against us and our business may be harmed. InDue to the future, it may be more expensive for us to obtainrecent changes in the shareholder class action landscape, director and officer liability insurance andhas been more expensive. If this trend continues we may be required to accept reduced coverage or incur substantially higher costs to obtain coverage. These factors could also make it more difficult for us to attract and retain qualified members of our board of directors, particularly to serve on our audit committee and compensation committee, and qualified executive officers.

The Sarbanes-Oxley Act requires that we maintain effective disclosure controls and procedures and internal control over financial reporting. Any failure to develop or maintain effective controls could adversely affect the results of periodic management evaluations. In the event that we are not able to demonstrate compliance with the Sarbanes-Oxley Act, that our internal control


over financial reporting is perceived as inadequate, or that we are unable to produce timely or accurate financial statements, investors may lose confidence in our operating results and the price of our ordinary shares could decline. In addition, if we are unable to continue to meet these requirements, we may not be able to remain listed on the NASDAQ Global Market.Nasdaq.

We are required to comply with certain of the SEC’s rules that implement Section 404 of the Sarbanes-Oxley Act, which require management to certify financial and other information in our quarterly and annual reports and provide an annual management report on the effectiveness of our internal control over financial reporting commencing with our second annual report. This assessment must include the disclosure of any material weaknesses in our internal control over financial reporting identified by our management or our independent registered public accounting firm. To achieve compliance with Section 404 within the prescribed period, we engage in a process to document and evaluate our internal control over financial reporting, which is both costly and challenging. In this regard, we will need to continue to dedicate internal resources, potentially engage outside consultants and adopt a detailed work plan to assess and document the adequacy of internal control over financial reporting, continue steps to improve control processes as appropriate, validate through testing that controls are functioning as documented and implement a continuous reporting and improvement process for internal control over financial reporting. Despite our efforts, there is a risk that we will not be able to conclude, within the prescribed timeframe or at all, that our internal control over financial reporting is effective as required by Section 404. If we identify one or more material weaknesses, it could result in an adverse reaction in the financial markets due to a loss of confidence in the reliability of our financial statement.

Our independent registered public accounting firm will not be required to formally attest to the effectiveness of our internal control over financial reporting until the later of our second annual report or the first annual report required to be filed with the SEC following the date we are no longer an “emerging growth company” as defined in the JOBS Act. We cannot assure you that there will not be material weaknesses or significant deficiencies in our internal controls in the future.

Provisions in our charter documents and under Delaware law have anti-takeover effects that could discourage an acquisition of us by others, even if an acquisition would be beneficial to our stockholders and prevent attempts by our stockholders to replace or remove our current management.



Provisions in our amended and restated certificate of incorporation and amended and restated by-laws contain provisions that may have the effect of discouraging, delaying or preventing a change in control of us or changes in our management. These provisions could also limit the price that investors might be willing to pay in the future for shares of our common stock, thereby depressing the market price of our common stock. In addition, because our board of directors is responsible for appointing the members of our management team, 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. Among other things, these provisions:

authorize “blank check” preferred stock, which could be issued by our board of directors without stockholder approval and may contain voting, liquidation, dividend and other rights superior to our common stock;
create a classified board of directors whose members serve staggered three-year terms;
specify that special meetings of our stockholders can be called only by our board of directors, the chairperson of our board of directors, our chief executive officer or our president;
prohibit stockholder action by written consent;
establish an advance notice procedure for stockholder approvals to be brought before an annual meeting of our stockholders, including proposed nominations of persons for election to our board of directors;
provide that our directors may be removed only for cause;
provide that vacancies on our board of directors may be filled only by a majority of directors then in office, even though less than a quorumquorum;
specify that no stockholder is permitted to cumulate votes at any election of directors;
expressly authorize our board of directors to modify, alter or repeal our by-laws; and
require supermajority votes of the holders of our common stock to amend specified provisions of our by-laws.

These provisions, alone or together, could delay or prevent hostile takeovers and changes in control or changes in our management.

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% 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% of our outstanding voting stock, unless the merger or combination is approved in a prescribed manner.


Any provision of our amended and restated certificate of incorporation, our amended and restated by-laws or Delaware law that has the effect of delaying or deterring a change in control could limit the opportunity for our stockholders to receive a premium for their shares of our common stock and could also affect the price that some investors are willing to pay for our common stock.

Our ability to use net operating losses to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code of 1986, as amended (the "Code"), a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-change net operating losses ("NOLs"), to offset future taxable income. Our existing NOLs are subject to limitations arising from previous ownership changes, and if we undergo an ownership change in connection any follow-on offerings of our common or preferred stock, our ability to utilize NOLs could be further limited by Section 382 of the Code. Our NOLs may also be impaired under state law. Accordingly, we may not be able to utilize a material portion of our NOLs. Furthermore, our ability to utilize our NOLs is conditioned upon our attaining profitability and generating U.S. federal taxable income. We have incurred net losses since our inception and anticipate that we will continue to incur significant losses for the foreseeable future; thus, we do not know whether or when we will generate the U.S. federal taxable income necessary to utilize our NOLs.



Our amended and restated certificate of incorporation designates the state or federal courts located in the State of Delaware as the sole and exclusive forum for certain types of actions and proceedings that may be initiated by our stockholders, which could limit our stockholders’ ability to obtain a favorable judicial forum for disputes with us or our directors, officers or employees.

Our amended and restated certificate of incorporation provides that, subject to limited exceptions, the state and federal courts located in the State of Delaware will be the sole and exclusive forum for (1) any derivative action or proceeding brought on our behalf, (2) any action asserting a claim of breach of a fiduciary duty owed by any of our directors, officers or other employees to us or our stockholders, (3) any action asserting a claim against us arising pursuant to any provision of the Delaware General Corporation Law, our amended and restated certificate of incorporation or our amended and restated by-laws or (4) any other action asserting a claim against us that is governed by the internal affairs doctrine. Any person or entity purchasing or otherwise acquiring any interest in shares of our capital stock shall be deemed to have notice of and to have consented to the provisions of our amended and restated certificate of incorporation described above. This choice of forum provision may limit a stockholder’s ability to bring a claim in a judicial forum that it finds favorable for disputes with us or our directors, officers or other employees, which may discourage such lawsuits against us and our directors, officers and employees. Alternatively, if a court were to find these provisions of our amended and restated certificate of incorporation inapplicable to, or unenforceable in respect of, one or more of the specified types of actions or proceedings, we may incur additional costs associated with resolving such matters in other jurisdictions, which could adversely affect our business and financial condition.

Because we do not anticipate paying any cash dividends on our capital stock in the foreseeable future, capital appreciation, if any, will be the source of gain for our stockholders.

You should not rely on an investment in our common stock to provide dividend income. We do not anticipate that we will pay any cash dividends to holders of our common stock in the foreseeable future. Instead, we plan to retain any earnings to maintain and expand our operations. In addition, our ability to pay cash dividends is currently prohibited by the terms of our debt financing arrangement, and any future debt financing arrangement may contain terms prohibiting or limiting the amount of dividends that may be declared or paid on our common stock. Accordingly, investors must rely on sales of their common stock after price appreciation, which may never occur, as the only way to realize any return on their investment. As a result, investors seeking cash dividends should not purchase our common stock.

Item 1B.     Unresolved Staff Comments

None.

Item 2.        Properties

Our principal executive offices areoffice is located at 100 Acorn Park Drive, 5th floor, Cambridge, Massachusetts 02140. We have two leases at this address, and in aggregate, we occupy approximately 34,200 square feet of laboratory and office space. Both leases were extended in 2016In March 2020, we will occupy an additional 22,440 square feet of laboratory and have terms that expireoffice space. The lease for just office space expires in February 2020.2020, while the lease for laboratory and office space expires in February 2025. We believe that our existing facilities are sufficient for our present operations, but that over time,in the near future our existing facility space will need to be expanded to meet the demands of our future lab operations.operations or we will have to move into a new facility.

Item 3.        Legal Proceedings

From time to time we are subject to various legal proceedings and claims that arise inIn the ordinary course of our business, activities. Although the resultswe are from time to time involved in lawsuits, claims, investigations, proceedings, and threats of litigation relating to intellectual property, commercial arrangements and claims cannot be predicted with certainty, as of the date of this Annual Report on Form 10-K, weother matters. We do not believe we are currently party to any claimpending legal action, arbitration proceeding or litigation,governmental proceeding, the outcome of which, if determined adversely to us, would individually or in the aggregate be reasonably expected to have a material adverse effect on our business. Regardlessbusiness or operating results. We are not a party to any material proceedings in which any director, member of the outcome, litigation can have ansenior management or affiliate of ours is either a party adverse impact onto us because of defense and settlement costs, diversion of management resources and other factors.or our subsidiaries or has a material interest adverse to us or our subsidiaries.

Item 4.         Mine Safety Disclosures

Not applicable.



PART II

Item 5.         Market for Registrant’s Common Equity, Related Stockholder Matters, and Issuers Purchases of Equity Securities

Market Information

Our common stock has been publicly traded on the NASDAQ GlobalThe Nasdaq Capital Market under the symbol “GNCA” since February 5, 2014.December 17, 2018. Prior to that, time, there was no public market for our common stock. The following table sets forth, for the periods indicated, the high and low sales prices for our common stock as reportedhad been publicly traded on the NASDAQThe Nasdaq Global Market.

  Year ended December 31, 2016 Year ended December 31, 2015
  HighLow HighLow
First quarter $8.07
$2.56
 $12.50
$6.15
Second quarter $7.74
$3.35
 $14.29
$9.00
Third quarter $6.39
$3.86
 $16.18
$6.63
Fourth quarter $5.22
$3.28
 $8.20
$4.27
Market since February 5, 2014.

Holders

As of February 14, 2017,11, 2020, there were approximately 2414 holders of record of our common stock. This number does not include beneficial owners whose shares are held by nominees in street name.

Dividends

We have never declared or paid cash dividends on our common stock, and we do not expect to pay any cash dividends on our common stock in the foreseeable future.

Performance Graph

The following performance graph and related information shall not be deemed to be “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, except to the extent that we specifically incorporate it by reference into such filing.

The following graph compares the performance of our common stock to the NASDAQ Composite Index and to the NASDAQ Biotechnology Index from February 5, 2014 (the first date that shares of our common stock were publicly traded) through December 31, 2016. The comparison assumes $100 was invested after the market closed on February 5, 2014 in our common stock and in each of the foregoing indices, and it assumes reinvestment of dividends, if any.



_________________________
*$100 invested on 2/5/2014 in stock or index, including reinvestment of dividends. Fiscal year ending December 31, 2016.

Cumulative Total Return Comparison
 2/5/2014 Mar-14 Jun-14 Sep-14 Dec-14 Mar-15 Jun-15 Sep-15 Dec-15 Mar-16 Jun-16 Sep-16 Dec-16
Genocea Biosciences, Inc.100.00
 165.36
 170.45
 82.27
 63.64
 107.82
 124.82
 62.27
 47.91
 70.36
 37.27
 46.55
 37.45
NASDAQ Composite100.00
 104.67
 109.89
 112.01
 118.06
 122.17
 124.31
 115.17
 124.82
 121.40
 120.72
 132.42
 134.19
NASDAQ Biotechnology100.00
 99.66
 108.44
 115.41
 128.26
 145.21
 156.00
 127.93
 142.91
 110.08
 108.73
 122.20
 111.93

Recent Sales of Unregistered Securities

None.

Purchase of Equity Securities

We did not purchase any of our registered equity securities during the period covered by this Annual Report on Form 10-K.

Securities Authorized for Issuance under Equity Compensation Plans

The following table contains information about our equity compensation plans as of December 31, 2016.2019.
Plan category    Number of securities to be issued upon exercise of outstanding stock options and warrants    Weighted-average exercise price of outstanding options and warrants    Number of securities remaining available for future issuance under equity compensation plans     Number of securities to be issued upon exercise of outstanding stock options and warrants    Weighted-average exercise price of outstanding options and warrants    Number of securities remaining available for future issuance under equity compensation plans 
Equity compensation plans approved by security holders (1)
 3,807,061
 $5.94
 485,483
(2) 6,445,288
 $8.48
 245,430
(2)

(1) Includes information regarding our Amended and Restated 2014 Equity Incentive PlanPlan.
(2) Does not include 1,137,7811,098,116 shares added to the Amended and Restated 2014 Equity Incentive Plan under the evergreen provision on January 1, 2017.2020.







Item 6.        Selected Financial Data

The selected statements of operations data for each of the three years in the period ended December 31, 2016 and the balance sheet data at December 31, 2016 and 2015 have been derived from our audited financial statements included elsewhere in this Annual Report on Form 10-K. The selected statements of operations data for the period ended December 31, 2013 and 2012 and the balance sheet data at December 31, 2013 and 2012 have been derived from our audited financial statements not included in this Annual Report on Form 10-K. Our historical results for any prior period are not necessarily indicative of results to be expected in any future period.Not applicable.

The information set forth below should be read in conjunction with the “Management’s Discussion and Analysis of Financial Condition and Results of Operations” section of this Annual Report on Form 10-K and with our consolidated financial statements and notes thereto included elsewhere in this Annual Report on Form 10-K. The selected financial data in this section are not intended to replace the consolidated financial statements and are qualified in their entirety by the consolidated financial statements and related notes included elsewhere in this Annual Report on Form 10-K.
  Years Ended December 31
(In thousands, except per share data) 2016 2015 2014 2013 2012
Grant revenue $235
 $670
 $308
 $731
 $1,977
           
Operating expenses:          
Research and development 34,645
 28,049
 23,727
 15,695
 11,240
General and administrative 15,427
 13,987
 9,747
 4,961
 3,690
Refund of research and development expense (1,592) 
 
 

 

Total operating expenses 48,480
 42,036
 33,474
 20,656
 14,930
Loss from operations (48,245) (41,366) (33,166) (19,925) (12,953)
Other expense, net:          
Interest income 410
 163
 55
 6
 13
Interest expense (1,738) (1,280) (1,025) (465) (520)
Change in fair value of warrants 
 
 (725) (222) 93
Loss on debt extinguishment 
 
 (435) (200) 
Total other expense, net (1,328) (1,117) (2,130) (881) (414)
Net loss $(49,573) $(42,483) $(35,296) $(20,806) $(13,367)
Comprehensive loss $(49,573) $(42,490) $(35,303) $(20,806) $(13,367)
           
Reconciliation of net loss to net loss attributable to common stockholders          
Net loss $(49,573) $(42,483) $(35,296) $(20,806) $(13,367)
Accretion of redeemable convertible preferred stock to redemption value 
 
 (180) (1,605) (1,781)
Net loss attributable to common stockholders $(49,573) $(42,483) $(35,476) $(22,411) $(15,148)
Net loss per share attributable to common stockholders - basic and diluted (1) $(1.75) $(1.74) $(2.27) $(75.46) $(51.35)
Weighted-average number of common shares used in net loss per share attributable to common stockholders - basic and diluted 28,299
 24,460
 15,618
 297
 295



  As of December 31,
(in thousands) 2016 2015 2014 2013 2012
Balance Sheet Data:          
Cash, cash equivalents and investments $63,362
 $106,432
 $47,079
 $12,208
 $11,516
Working capital 53,918
 89,226
 42,173
 8,382
 7,932
Total assets 69,896
 112,142
 50,332
 15,761
 13,531
Preferred stock warrant liability 
 
 
 656
 246
Preferred stock 
 
 
 81,562
 64,707
Common stock and additional paid-in capital 253,024
 247,578
 147,941
 
 
Total stockholders’ equity (deficit) 45,541
 89,661
 32,507
 (80,131) (58,402)
_________________________
(1)See Note 2 within the notes to our consolidated financial statements appearing elsewhere in this Annual Report on Form 10-K for a description of the method used to calculate basic and diluted net loss per common share.

Item 7.         Management’s Discussion and Analysis of Financial Condition and Results of Operations

You should read the following discussion and analysis of our financial condition and results of operations together with the section entitled “Selected Financial Data” and our financial statements and related notes appearing in this Annual Report on Form 10-K. Some of the information contained in this discussion and analysis or set forth elsewhere in this Annual Report on Form 10-K, including information with respect to our plans and strategy for our business and related financing, includes forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the “Risk Factors” section of this Annual Report on Form 10-K, our actual results could differ materially from the results described in or implied by the forward-looking statements contained in the following discussion and analysis.


Overview

We are a biopharmaceutical company that discoversseeks to discover and developsdevelop novel vaccines andcancer immunotherapies to address diseases with significant unmet needs. We useusing our proprietary discovery platform, ATLASTM, to rapidly design vaccines proprietary discovery platform. The ATLAS platform profiles each patient's CD4+ and immunotherapies that act, in part, throughCD8+ T cell (or cellular) immune responses to every potential target or "antigen" in contrast to approved vaccines and immunotherapies, which are designed to act primarily through B cell (or antibody) immune responses.that patient's tumor. We believe that by harnessing T cells we can develop first-in-classthis approach optimizes antigen selection for immunotherapies such as cancer vaccines and immunotherapiescellular therapies by identifying the antigens to address diseases where T cellswhich the patient can respond. Consequently, we believe that ATLAS could lead to more immunogenic and efficacious cancer immunotherapies.

Our most advanced program is GEN-009, a personalized neoantigen cancer vaccine, for which we are central to the control of the disease.
We have one product candidate in activeconducting a Phase 21/2a clinical development, GEN-003, an immunotherapy for the treatment of genital herpes. We also had a pre-clinical immuno-oncology program focused on personalized cancer vaccines ("GEN-009").trial. The GEN-009 program leveragesuses ATLAS to identify patient neoantigens, or newly formed antigensimmunogenic tumor mutations unique to each patient, that are associated with that individual's tumor. We have other non-active infectious disease programs, including GEN-004, a Phase 2-ready universal vaccine for the prevention of pneumococcal infections, and early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria.
GEN-003 — Phase 2 immunotherapy for genital herpes
Our lead program is GEN-003, a Phase 2 candidate therapeutic vaccine, or immunotherapy, that we are developing to treat genital herpes infections. We have completed two positive clinical trials and have a third trial currently underway which has also demonstrated positive interim efficacy results. Key data from those trials is described below.

Phase 1/2 Trial
Final analysis of the data from the Phase 1/2a trial showed that, for the best performing 30µg dose group, there was a sustained reductioninclusion in the viral shedding rate. After completion of dosing for this group, the viral shedding rate was reduced by 52% versus baseline and, at six months after the final dose, the shedding rate remained at 40% below baseline. The reduction in the genital lesion rate after completion of the third dose was greatest for the 30 µg dose group at 48%. After six months, the reduction from baseline in genital lesion rate for this dose group was 65% and, after 12 months, the genital lesion rate was 42% lower than baseline. GEN-003 was safe and well tolerated over the 12 months of this trial.
Phase 2 Dose Optimization Trial



A 310-subject Phase 2 dose optimization trial was completed in March 2016. The objective of this trial was to confirm the results of the Phase 1/2a trial and to test six combinations of proteins and adjuvant to determine the optimal dose for future trials and potentially improve on the profile of GEN-003. Subjects were randomized to one of six dosing groups of either 30μg or 60μg per protein paired with one of three adjuvant doses (25 μg, 50 μg, or 75 μg). A seventh group received placebo. Subjects received three doses of GEN-003 or placebo at 21-day intervals. Baseline viral shedding and genital lesion rates were established for each subject in a 28-day observation period prior to the commencement of dosing by collecting 56 genital swab samples (two per day), which were analyzed for the presence of HSV-2 DNA, and by recording the days on which genital lesions were present. This 28-day observation period was repeated immediately after the completion of dosing, and at six and twelve months following dosing. No maintenance doses were given. After the 28-day observation period immediately after dosing, patients in the placebo arm were rolled over across the 6 active combinations of GEN-003 and Matrix-M2 under a separate protocol.
The primary endpoint of the trial was the reduction in viral shedding rate versus baseline, a measure of anti-viral activity. A number of exploratory secondary endpoints were also studied, including the percent of patients who were recurrence free from lesions up to six and 12 months after dosing, the time to first recurrence of lesions after dosing and the reduction in genital lesion rates. The two most promising doses from this dose optimization study were 60 µg per protein combined with either 50 or 75 µg of Matrix-M2 adjuvant ("60/50 Dose" and "60/75 Dose" respectively). The efficacy of GEN-003 at these two dose levels over the course of the Phase 2 dose optimization trial is as follows:
 Placebo60/50 Dose60/75 Dose
EndpointPost dose 3Post dose 36 months12 monthsPost dose 36 months12 months
Viral shedding rate reduction(1)
-4%41%47%66%55%58%55%
Poisson mixed effect model (Old Model)(2)
       
   p-value vs baseline0.48<0.0001<0.0001<0.0001<0.0001<0.0001<0.0001
   p-value vs placeboNA<0.0001NANA<0.0001NANA
Poisson mixed effect model with Empirical Variance
(New Model)(3)
       
   p-value vs baseline0.880.010.0004<0.00010.006<0.00010.01
   p-value vs placeboNA0.04NANA0.01NANA
% patients lesion freeNA68%36%30%68%30%21%
Genital lesion rate reduction(1)
60%69%50%65%60%43%47%
Poisson mixed effect model (Old Model)(2)
       
   p-value vs baseline<0.0001<0.0001<0.0001<0.0001<0.0001<0.0001<0.0001
   p-value vs placeboNA0.3NANA0.79NANA
Poisson mixed effect model with Empirical Variance
(New Model)
(3)
       
   p-value vs baseline0.00020.00050.010.0030.020.030.02
   p-value vs placeboNA0.59NANA0.85NANA
(1) Rate reduction vs. pre-dosing levels.
(2) Generalized Linear Model with “Standard” Poisson distribution as pre-specified in the Phase 2 trial statistical analysis plan, formerly a widely adopted model developed by the University of Washington (“UW”) and which was used in both the GEN-003 Phase 1/2 and Phase 2 trials (the “Old Model”).
(3)Statistical analysis performed using a modified Poisson model (the “New Model”) reflecting advances in the field since the start of the Phase 2 dose optimization trial: Magaret, Amalia, "Models for HSV shedding must account for two levels of overdispersion" ((January 2016). UW Biostatistics Working Paper Series. Working Paper 410). UW developed the New Model as clinical trial data which accumulated over the years indicated that the Old Model assumptions around the distribution of data did not fit this actual genital herpes clinical trial data. The New Model corrects the assumption of data distribution by an empiric variance method which better reflects this clinical trial experience.


Critically, the results of the GEN-003 clinical trials analyzed with the New Model remain statistically significant and the estimated magnitude of the effect, confidence intervals around that effect and durability of effect are unchanged.
Genocea considers it important to reflect advances in the field of genital herpes research in its approach to the conduct of clinical trials and the analysis of clinical trial data and adopted the New Model as the primary statistical model for the viral shedding rate and genital lesion rate data in its ongoing Phase 2b trial. Results shown above from the Phase 2 trial using the New Model are provided for comparative purposes, but were not part of the original pre-specified statistical analysis plan for this trial.

Phase 2b Trial

In December 2015, a Phase 2b trial was initiated as our first study testing potential Phase 3 endpoints with a Phase 3-ready formulation of GEN-003, manufactured with commercially-scalable processes. The trial enrolled 131 subjects that were randomized to one of three dose groups - placebo, 60/50 Dose, and 60/75 Dose. All subjects received three injections at 21-day intervals.

In September 2016, we announced positive viral shedding rate reductions from the ongoing Phase 2b study. The study achieved its primary endpoint, with GEN-003 demonstrating a statistically significant (versus placebo and baseline) 40% reduction in the viral shedding rate compared to baseline immediately after dosing in the 60/50 Dose group, using a new Phase 3-ready formulation. This result was consistent with a statistically significant (versus placebo and baseline) viral shedding rate reduction of 41% at this same dose and time point in a prior Phase 2 trial. In addition, the reactogenicity profile of this dose, an indication of the strength of the immune response to GEN-003, was consistent between the trials. This same dose in the prior Phase 2 trial subsequently demonstrated virologic and clinical efficacy durable through at least one year after dosing.

The 60/75 Dose group reduced the viral shedding rate by 27%, lower than that observed in the prior trial, and also showed a less acceptable reactogenicity profile than the prior trial. We believe that the increase in reactogenicity of this dose indicates an overstimulation of the T cell immune system leading to the reduced efficacy with this dose in this trial, as would be expected with the known bell-shaped T cell dose response curve. The likely driver of this effect is a more potent adjuvant formulation following customary manufacturing process changes to prepare for Phase 3 trials and commercialization.

The top-line viral shedding rate reductions for all of the dose groups in the trial are summarized in the following table:

 Placebo60/50 Dose60/75 Dose
Viral shedding rate reduction(1)
6%-40%-27%
Poisson mixed effect model with Empirical Variance
(New Model)
(2)(3)
   
   p-value vs. baseline0.760.030.16
   p-value vs. placeboNA0.050.20
(1) Rate reduction vs. pre-dosing levels.
(2) The New Model (see note above under “Phase 2 Dose Optimization Trial”), as pre-specified in the Phase 2b statistical analysis plan.
(3) Under the Old Model (see note above under “Phase 2 Dose Optimization Trial”), p-values for the 60/50 Dose were <0.0001 vs. both baseline and placebo and for the 60/75 Dose were 0.001 vs. baseline and 0.004 vs. placebo.

In January 2017, we announced positive clinical results from this ongoing trial. At six months after dosing, GEN-003 demonstrated statistically significant improvements versus placebo across multiple clinical endpoints. The 60/50 Dose significantly reduced the rate of genital lesions during the six months following dosing compared to placebo (41% reduction versus placebo). The genital lesion rate is an important overall measure of disease that captures both the frequency and duration of recurrences, both of which are important to both patients and their caregivers. GEN-003 also consistently demonstrated significant benefits versus placebo across several other clinical endpoints across the dose groups as summarized in the following table:



Secondary clinical endpointPlacebo
(n=44)
60/50
(n=43)
60/75
(n=44)
Mean genital lesion rate (percent of days with lesions over six months)7.9%4.5%4.6%
Median genital lesion rate5.6%2.7%1.9%
  p-value versus placebo(1)
NA0.030.03
Mean duration of recurrences (days)4.83.34.3
Median duration of recurrences4.22.84.0
  p-value versus placebo(1)
NA0.010.64
Mean number of recurrences over six months2.72.11.9
Median number of recurrences over six months2.01.01.5
  p-value versus placebo(1)
NA0.080.02
Kaplan-Meier estimate of percent recurrence free after first dose10%29%31%
  p-value versus placebo(2)
NA0.030.03
Kaplan-Meier estimate of percent recurrence free after last dose13%22%36%
  p-value versus placebo(2)
NA0.170.02

Statistical tests pre-specified in Phase 2b trial protocol as follows:
(1) Wilcoxon Rank Sum test
(2) Log rank test

The clinical efficacy data versus placebo at twelve-months post dosing is expected in the middle of 2017. The viral shedding rate reduction data at six-months post dosing is expected in the first half of 2017.

GEN-003 also continues to demonstrate a safety profile appropriate for its therapeutic setting in the judgment of the trial’s independent Drug Monitoring Committee. There was no grade 4 reactogenicity or related serious adverse events and discontinuations due to adverse events were low and similarly distributed across active dose groups and placebo.

We intend to conduct an end-of-Phase 2 meeting with the FDA in early 2017. We also expect to commence Phase 3 trials in the fourth quarter of 2017. We plan to commence a clinical trial exploring the potential additive effects of GEN-003 on top of daily administration of valacyclovirin parallel with the Phase 3 program.We retain all rights to GEN-003 and our strategy is to execute a partnership to maximize the potential of GEN-003 and to help fund the costs of the GEN-003 Phase 3 program.

If GEN-003 successfully completes clinical development and is approved, we believe it would represent an important new treatment option for patients with genital herpes.

Our Immuno-Oncology Program
Guided by our positive clinical results on GEN-003 and belief in the ATLAS platform, we are focused on combining our antigen selection and vaccine development expertise with that of leading cancer innovators to unlock new targets in immuno-oncology. Our potential cancer vaccines will be designed to educate T cells to recognize and attack specific targets and thereby kill cancers. We are developing personalized cancer vaccines by leveraging ATLAS to identify patient neoantigens, or newly formed antigens unique to each patient, that are associated with that individual's tumor. We anticipate filing a personalized cancer vaccine IND application with the FDA in 2017.patient's GEN-009 vaccine. We are also applying the results from ATLAS, and its utilityadvancing GEN-011, a prognostic tool, to identify patients that could benefit from checkpoint inhibitor therapy. Our strategy in immuno-oncology combines our own internal development programs with a focus on partnering ATLAS for other immuno-oncology applications.

Refer to Part I of this report under the heading "Business - Our Immuno-Oncology Program" for additional details on this program, including our current collaborations.
In November 2015, we also commenced a new program focused on Epstein-Barr Virus (“EBV”), ("GEN-009"). EBV infection has been linked to cancers with high unmet needs such as non-Hodgkin’s lymphoma, nasopharyngeal carcinoma and gastric carcinoma. We believe the ATLAS platform is highly suited to the creation of a new immunotherapy for EBV given thatneoantigen-specific adoptive T cell responses are understoodtherapy program that also relies on ATLAS. We expect to be crucialfile an IND application for protection against EBV. Furthermore, EBV is part of the herpesvirus family, in


which we have deep experience through our development of GEN-003. We are currently conducting ATLAS screens for EBV and plan to select antigen candidates for further study in 2017.

Other infectious disease programs

Our other infectious disease programs include GEN-004, a potential universal Streptococcus pneumoniae, or pneumococcus, vaccine to protect against a leading cause of infectious disease mortality worldwide and early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria. In October 2015, we announced that top-line results from the Phase 2a clinical trial for GEN-004 showed consistent reductions versus placeboGEN-011 in the pre-specified endpointssecond quarter of the rate and density of upper airway colonization in a human challenge model, but that neither of the endpoints achieved statistical significance. GEN-004 was safe and well tolerated by subjects. Although we did not achieve statistical significance in this study, the consistent apparent effect gives us confidence in the vaccine concept and in the potential for GEN-004. In November 2016, we paused activities on our other early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria in order to focus all of our internal research and pre-clinical resources on our immuno-oncology investments. Progress made and data generated to date in these infectious disease clinical and research programs remains valuable to Genocea for the future.2020.

Financing and business operations

We commenced business operations in August 2006. To date, our operations have been limited to organizing and staffing our company, acquiring and developing our proprietary ATLAS technology, identifying potential product candidates, and undertaking preclinical studies and clinical trials for our product candidates. All of our revenue to date has been grant revenue. We have not generated any product revenue and do not expect to do so for the foreseeable future. We have primarily financed our operations primarily through the issuance of our equity securities, debt financings, and amounts received through grants. As of December 31, 2016,2019, we had received an aggregate of $279.6$399.3 million in gross proceeds from the issuance of equity securities and gross proceeds from debt facilities and an aggregate of $7.9 million from grants. At December 31, 2016,2019, our cash and cash equivalents and investments were $63.4$40.1 million.
 
Since inception, we have incurred significant operating losses. Our net losses were $49.6$39.0 million and $42.5$27.8 million for the years ended December 31, 20162019 and 2015,2018, respectively, and our accumulated deficit was $207.5$331.0 million as of December 31, 2016.2019. We expect to incur significant expenses and increasing operating losses for the foreseeable future. Our net losses may fluctuate significantly from quarter to quarterquarter-to-quarter and year to year.year-to-year. We will need to generate significant revenue to achieve profitability, and we may never do so.

In March 2015,October 2019, we entered into a purchase agreement with LPC pursuant to which LPC purchased $2.5 million of our common stock at a purchase price of $2.587 per share. In addition, for a period of 30 months, we have the right, at our sole discretion, to sell up to an additional $27.5 million of our common stock (subject to certain ownership limitations) based on prevailing market prices of our common stock at the time of each sale. In consideration for entering into the purchase agreement, we issued 289,966 shares of our common stock to LPC as a commitment fee.

In June 2019, we completed an underwritten public offering of 6.3in which we sold 10.5 million shares of our common stock at a public offering price of $8.25$3.50 per share, for an aggregate offering pricegross proceeds of $51.7approximately $36.8 million. In August 2015, we completed anotherThis underwritten public offering also included an overallotment option for the underwriters for 1.6 million shares, which they exercised in full on June 26, 2019. This generated additional gross proceeds of 3.9$5.5 million. We incurred approximately $3.9 million of offering-related expenses, resulting in total net proceeds of $38.4 million.
In February 2019, we completed a private placement financing transaction in which we issued shares of our common stock, at a public offering pricepre-funded warrant to purchase shares of $13.00 per shareour common stock, and warrants to purchase shares of our common stock for an aggregate offering pricegross cash proceeds of $50.1approximately $15.0 million. We receivedincurred $1.2 million of offering-related expenses, resulting in total net proceeds from theseof $13.8 million.



In January 2018, we completed two underwritten public offerings in which we issued common stock, warrants, and preferred shares for net proceeds of approximately $95.7$51.7 million.

As reflected in our consolidated financial statements, we used cash to fund operating activities of $37.7 million after deducting approximately $6.1for the year ended December 31, 2019 and had $40.1 million available in underwriting discountscash and commissions, excludingcash equivalents at December 31, 2019. In addition, we had an accumulated deficit of $331.0 million and anticipate that we will continue to incur significant operating losses for the foreseeable future as we continue to develop our product candidates. Until such time, if ever, as we attempt to generate substantial product revenue and achieve profitability, we expect to finance our cash needs through a combination of equity offerings, strategic transactions, proceeds from sale of our common stock under our at-the-market equity offering costs payable by us.program, and other sources of funding. If we are unable to raise additional funds when needed, we may be required to implement further cost reduction strategies, including ceasing development of GEN-009, GEN-011, and other corporate programs and activities. These factors, combined with our forecast of cash required to fund operations for a period of at least one year from the date of issuance of these consolidated financial statements, raise substantial doubt about our ability to continue as a going concern.

We believe that our cash and cash equivalents and investments at December 31, 20162019 are sufficient to support our operating expenses and capital expenditure requirements into the first quarter of 2018, without assuming any receipt of proceeds from potential business development partnerships, equity financings or debt drawdowns. This guidance assumes commencing Phase 3 trials for GEN-003 for genital herpes in the fourth quarter of 2017 and filing an IND for GEN-009 for cancer by the end of the year, however it is our strategy to secure additional sources of financing in advance of starting GEN-003 Phase 3 clinical trials.2021.

Costs related to clinical trials can be unpredictable and therefore there can be no guarantee that our current balances of cash and cash equivalents and investments, and anycombined with proceeds received from other sources, will be sufficient to fund our studiestrials or operations through this period. These funds will not be sufficient to enable us to conduct pivotal clinical trials for, seek marketing approval for, or commercially launch GEN-003GEN-009, GEN-011 or any other product candidate. Accordingly, to obtain marketing approval for and to commercialize these or any other product candidates, we will be required to obtain further funding through public or private equity offerings, debt financings, collaboration and licensing arrangements, or other sources. Adequate additional financing may not be available to us on acceptable terms, or at all. Our failureall, which could result in a decision to raise capital when needed would have a negative effect onpause or delay development or advancement of clinical trials for one or more of our financial condition andproduct candidates. Similarly, we may decide to pause or delay development or advancement of clinical trials for one or more of our ability to pursue our business strategy.product candidates if we believe that such development or advancement is imprudent or impractical.

Financial Overview

Grant revenue


Grant revenue consists of revenue earned to conduct vaccine development research. We have received grants from private not-for-profit organizations and federal agencies. These grants have related to the discovery and development of several of our product candidates, including product candidates for the prevention of pneumococcus, chlamydia, and malaria. Revenue under these grants is recognized as research services are performed. Funds received in advance of research services being performed are recorded as deferred revenue. We plan to continue to pursue grant funding, but there can be no assurance we will be successful in obtaining such grants in the future.
We have no products approved for sale. We will not receive any revenue from any product candidates that we develop until we obtain regulatory approval and commercialize such products or until we potentially enter into agreements with third parties for the development and commercialization of product candidates. If our development efforts for any of our product candidates result in regulatory approval or we enter into collaboration agreements with third parties, we may generate revenue from product sales or from such third parties.
We expect that our revenue will be less than our expenses for the foreseeable future and that we will experience increasing losses as we continue our development of, and seek regulatory approvals for, our product candidates and begin to commercialize any approved products. Our ability to generate revenue for each product candidate for which we receive regulatory approval will depend on numerous factors, including competition, commercial manufacturing capability and market acceptance of our products.

Research and development expenses
 
Research and development expenses consist primarily of costs incurred to advance our preclinical and clinical candidates, which include:

personnel-related expenses, including salaries benefits, stock-based compensation expense and travel;related expenses;
expenses incurred under agreements with contract research organizations ("CROs"), contract manufacturing organizations ("CMOs"), consultants, and other vendors that conduct our clinical trials and preclinical activities;
costs of acquiring, developing, and manufacturing clinical trial materials and lab supplies; and
facility costs, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, insurance, and other supplies.
 
We expense internal research and development costs to operations as incurred. We expense third party costsNonrefundable advance payments for goods and services that will be used in future research and development activities such as conducting clinical trials, based on an evaluation ofare expensed when the progress to completion of specific performanceactivity has been performed or tasks such as patient enrollment, clinical site activations or information, whichwhen the goods have been received rather than when the payment is provided to us by our vendors.made.
 
The following table identifies research and development expenses on a program-specific basis for our product candidates as follows (in thousands):
  Years ended December 31,
  2016 2015 2014
Genital herpes (GEN-003) (1) $19,641
 $15,555
 $15,147
Other research and development (2) 15,004
 12,494
 8,580
Total research and development $34,645
 $28,049
 $23,727
  Years ended December 31, Increase
  2019 2018 (Decrease)
Phase 1/2a programs $16,462
 $6,234
 $10,228
Discovery and pre-IND 7,141
 14,888
 (7,747)
Other research and development 3,349
 4,087
 (738)
Total research and development $26,952
 $25,209
 $1,743
_________________________
(1)Includes directPhase 1/2a programs are Phase 1 or Phase 2 development activities. Discovery and indirect internalpre-IND includes costs incurred to support our discovery research and external costs such as CMOtranslational science efforts up to the initiation of Phase 1 development. Other research and CRO costs.
(2)Includes costs related to all other product candidates and certain technology platform

development costs related to ATLAS. Additionally,includes costs that are not specifically allocated by projectto active product candidates, including facilities costs, depreciation expense, and non-project specific costs incurred by R&D personnel, are included in this line item.
We expect our research and development expenses will increase as we continue the manufacture of pre-clinical and clinical materials and manage the clinical trials of, and seek regulatory approval for, GEN-003.other costs.
 
General and administrative expenses
 


General and administrative expenses consist principallyprimarily of salaries and related costsexpenses for personnel including stock-based compensation and travel expenses, in executive and other administrative functions. Other general and administrative expenses include facility-relatedfacility costs, communication expenses and professional fees associated with consulting, corporate and intellectual property legal expenses, consulting and accounting services.
 
We anticipate that our general and administrative expenses will increase in the future to support the continued research and development of our product candidates and to operate as a public company. These increases will likely include higher costs for insurance, hiring activities, and professional services, such as outside consultants, lawyers and accountants, among other expenses. Additionally, if and when we believe a regulatory approval of our first product candidate appears likely, we anticipate that we will increase our salary and personnel costs and other expenses as a result of our preparation for commercial operations.
Refund of research and development expenses
The refund of research and development expenses recorded in year ended December 31, 2016 related to a one-time payment received from Novavax pursuant to contractual obligations under the Novavax Agreement that existed to refund research and development expenses paid to Novavax between 2009 and 2011.Other income (expense)

Other expense, net

Other expenseincome (expense) consists of fair value adjustments on warrants to purchase preferred stock, loss on debt extinguishment,the change in warrant liability, interest expense, net of interest income, and interest expense. Upon completion of our IPO on February 10, 2014, warrants to purchase preferred stock were converted to warrants to purchase common stock andother expense for miscellaneous items, such as a result, the Company no longer recorded fair value adjustments for its warrants. Losses on debt extinguishment were recorded on the retirement of outstanding borrowings due to the refinancing of existing debt with a new lender.

Interest income
Interest income consists of interest earned on our cash, cash equivalent and investment portfolio.

Interest expense

Interest expense consists of interest expense on our long-term debt facilities and non-cash interest related to the amortization of debt discount and issuance costs

Accretion of redeemable convertible preferred stock
Certain classes of our preferred stock were redeemable beginning in 2017 at the original issuance price plus any declared or accrued but unpaid dividends upon written election of the preferred stockholders in accordance with the terms of our articles of incorporation. Accretion of preferred stock reflects the accretion of issuance costs and, for Series B preferred stock, cumulative dividends based on their respective redemption values. On February 10, 2014, we completed our IPO and all shares of preferred stock were converted into 11,466,479 shares of our Common Stock. No accretion of preferred stock is recorded after this date as no shares of preferred stock are outstanding.transaction expenses.

Critical Accounting Policies and Significant Judgments and Estimates

Our management’s discussion and analysis of our financial position and results of operations is based on our consolidated financial statements, which have been prepared in accordance with U.S. generally accepted accounting principles ("GAAP"). The preparation of consolidated financial statements in conformity with GAAP requires us to make estimates and assumptionsjudgments that affect the amounts of assets, liabilities and expenses reported in the consolidated financial statements and accompanying notes. On an ongoing basis, we evaluate these estimates which include, but are not limited to, estimates related to clinical trial accruals, prepaid and accrued research and development expenses, stock-based compensation expense, common stock warrants, warrants to purchase redeemable securities, and reported amounts of revenues and expenses during the reported period.judgments, including those described below. We base our estimates on historical experience and other market-specific or other relevant assumptions that we believe to be reasonable under the circumstances. These estimates and assumptions form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from those estimates or assumptions.

While our significant accounting policies are described in more detail in the notes to our financial statements Note 2. Summary of significant accounting policies appearing elsewherein Item 8 in this Annual Report on Form 10-K, we believe the following accounting policies to beare the most critical to aid you in fully understanding and evaluating our reported financial results and affect the more significant judgments and estimates usedthat we use in the preparation of our consolidated financial statements.



Prepaid and Accrued Research and Development Expenses

As part of the process of preparing our consolidated financial statements, we are required to estimate our prepaid and accrued research and development expenses. This process involves reviewinga thorough review of open contracts and purchase orders communicating with ourand an evaluation by internal personnel to identify services received that have been performed for us and estimating the level of service performed and the associated cost incurred for the service whenthese services for which we have not yet been invoiced or otherwise notified of the actual cost. The majority of our service providers invoice us monthly in arrears for services performed or when contractual milestones are met. We make estimates of our prepaid and accrued research and development expenses as of each balance sheet date in our consolidated financial statements based on facts and circumstances known to us at that time. We periodically confirm the accuracy of our estimates with the service providers and make adjustments, if necessary. Examples of estimated prepaid and accrued research and development expenses include fees paid to CROs in connection with clinical trials, CMOs with respect to pre-clinicalpreclinical and clinical materials and intermediaries, and vendors in connection with preclinical development activities.

We base our expenses related to clinical trials on our estimates of the services performed pursuant to contracts with clinical sites that conduct clinical trials on our behalf. The financial terms of these agreements are subject to negotiation, vary from contract to contract and may result in uneven payment flows. Payments under some of these contracts depend on factors such as the successful enrollment of subjectspatients and the completion of required data submission. In recording service fees, we make estimates based upon the time period over which services will be performed or other observable and measureablemeasurable progress points as defined in the contracts, such as number of subjectspatients enrolled, number of sites, or quantityextent of services performed in each period. The calculated amount of service fee expense is compared to the actual payments made pursuant to the contract's billing schedule to determine the resulting prepaid or accrual position. Additionally, for each clinical site, we accrue 10% of the earned amounts which is payable upon completion of the required data submission for the clinical trial. If our estimates of the status and timing of services performed differs from the actual status and timing of services performed, we may report amounts that are too high or too low in any particular period. To date, there has been no material differences from our estimates to the amount actually incurred.

Stock-Based CompensationWarrants to Purchase Redeemable Securities

We have appliedrecorded the warrants issued in a 2018 public offering to purchase redeemable securities (the "2018 Public Offering Warrants") as a liability on our balance sheets. As the 2018 Public Offering Warrants are liability-classified, we remeasure the fair value recognition provisions of Financial Accounting Standards Board Accounting Standards Codification ("FASB ASC"), Topic 718, Compensation — Stock Compensation ("ASC 718"), to account for stock-based compensation for employees and ASC 718 and FASB ASC Topic 505, Equity ("ASC 505"), for non-employees.the 2018 Public Offering Warrants at each reporting date. We recognize compensation costs related to stock options granted to employees based oncalculated the estimated fair value of the awards on the date of grant. Stock compensation related to non-employee awards is re-measured at each reporting period until the awards are vested.2018 Public

Determining
Offering Warrants using a Monte Carlo simulation. The Monte Carlo simulation requires the amountinput of stock-based compensationassumptions, including our stock price, the volatility of our stock price, remaining term in years, expected dividend yield, and risk-free rate. In addition, the valuation model considers our probability of being acquired during each annual period within the 2018 Public Offering Warrant term, as an acquisition event can potentially impact the settlement of the 2018 Public Offering Warrants. Changes to be recorded requires us to develop estimates ofthe assumptions used in determining the fair value of stock-based awards as of their measurement date. We recognize stock-based compensation expense over the requisite service period, which is the vesting period2018 Public Offering Warrants could result in materially different fair values of the award. Calculating the fair value of stock-based awards requires that we make highly subjective assumptions. We use the Black-Scholes option pricing model to value our stock option awards. Use of this valuation methodology requires that we make assumptions as to the volatility of our common stock, the fair value of our common stock on the measurement date, the expected term of our stock options, the risk free interest rate for a period that approximates the expected term of our stock options and our expected dividend yield. Because of our limited operating history as a publicly traded entity, we utilize data from a representative group of publicly traded companies to estimate expected stock price volatility. We selected representative companies from the biopharmaceutical industry with characteristics similar to us. We use the simplified method as prescribed by the SEC Staff Accounting Bulletin No. 107, Share-Based Payment as we do not have sufficient historical stock option activity data to provide a reasonable basis upon which to estimate the expected term of stock options granted to employees. For non-employee grants, we use an expected term equal to the remaining contractual term of the award. We utilize a dividend yield of zero based on the fact that we have never paid cash dividends and have no current intention of paying 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.

Under ASC 718, we are also required to estimate forfeitures at the time of grant, and revise those estimates in subsequent periods if actual forfeitures differ from our estimates. In March 2016, the FASB issued ASU 2016-09, Compensation — Stock Compensation (Topic 718), which provides for improvements to employee share-based payment accounting.  The Company early adopted ASU 2016-09 as of June 30, 2016. In connection with the early adoption, the Company elected an accounting policy to record forfeitures as they occur. There was no financial statement impact upon adoption as the Company had estimated a forfeiture rate of zero given that most options awards vest on a monthly basis. Stock-based compensation expense recognized in the financial statements is based on awards that ultimately vest.



Stock-based compensation expense includes options granted to employees and non-employees and has been reported in our statements of operations and comprehensive loss as follows (in thousands):
  Years ended December 31,
  2016 2015 2014
Research and development $1,568
 $1,690
 $1,511
General and administrative 2,579
 2,158
 1,394
Total $4,147
 $3,848
 $2,905

We estimated the fair value of stock options of each employee stock award at the grant date using the following assumptions:
  Years ended December 31,
  2016 2015 2014
Expected Volatility 67.4% - 77.9% 68.5% - 85.3% 86.2% - 103.6%
Risk-free interest rate 1.14% - 2.09% 1.56% - 1.94% 1.75% - 2.00%
Expected term (in years) 5.50 - 6.08 5.50 - 6.08 6.25
Expected dividend yield 0% 0% 0%

At December 31, 2016, we had approximately $6.6 million of total unrecognized compensation expense, which we expect to recognize over a weighted-average remaining vesting period of approximately three years. Our stock-based compensation expense for stock options has increased primarily based upon headcount growth and the related number of stock option awards granted to new and existing employees.2018 Public Offering Warrants.

Results of Operations

Comparison of the Years Ended December 31, 20162019 and December 31, 20152018

 
Years Ended
December 31,
 Increase Years Ended December 31, Increase
(in thousands) 2016 2015 (Decrease) 2019 2018 (Decrease)
Grant revenue $235
 $670
 $(435)
      
Operating expenses:            
Research and development 34,645
 28,049
 6,596
 $26,952
 $25,209
 $1,743
General and administrative 15,427
 13,987
 1,440
 12,037
 14,309
 (2,272)
Refund of research and development expense (1,592) 
 1,592
Total operating expenses 48,480
 42,036
 6,444
 38,989
 39,518
 (529)
Loss from operations (48,245) (41,366) 6,879
 (38,989) (39,518) (529)
Other income and expenses:      
Interest income 410
 163
 247
Interest expense (1,738) (1,280) 458
Total other income and expense (1,328) (1,117) 211
Other income (expense):  ��   
Change in fair value of warrant 986
 14,757
 (13,771)
Interest expense, net (946) (1,021) (75)
Other expense (1) (2,029) (2,028)
Total other income 39
 11,707
 (11,668)
Net loss $(49,573) $(42,483) 7,090
 $(38,950) $(27,811) $11,139
Research and development expenses

Grant revenue
Grant revenue decreased by $0.4Research and development expenses increased $1.7 million to $27.0 million for the year ended December 31, 2016 to $0.2 million2019 from $0.7$25.2 million for the year ended December 31, 2015. We entered into a $1.22018. The increase was due largely to increased external manufacturing costs of approximately $2.2 million, grant with the Bill & Melinda Gates Foundation (the "Gates Foundation") in September 2014. Grant revenue was earned on activities that occurred throughout the twelve-month period in 2015increased headcount-related costs of approximately $0.6 million, and were largely completed in the first quarterincreased clinical costs of 2016.
Research and development expenses


Research and development ("R&D") expenses increased approximately $6.6$0.3 million, to $34.6 million for the year ended December 31, 2016 from $28.0 million for the same period ended December 31, 2015.  Increases in compensation,offset by decreased consulting and professional services (approximately $5.0 million), lab-related costs (approximately $1.4 million), facility costs (approximately $0.9 million), and depreciation expense (approximately $0.4 million), were offset by decreases in manufacturing costs (approximately $0.8 million) and clinical costs (approximately $0.4 million). The remaining increases, all insignificant by spending category, are attributable to theof approximately $1.3 million.

We expect that our overall growth of the research and development function.

On a program basis, GEN-003 costs increased $4.1 million in the year ended December 31, 2016, driven by increased headcount related costs of $2.1 million and higher clinical, consulting and professional service costs of $2.0 millionexpenses will increase due to the timing of activities in supportour continued development of our clinical trials. GEN-004 clinicaloperations and our supply chain capabilities for our GEN-009 program. We also expect to incur costs decreased by $2.6 million followingrelated to the completionpreparation and submission of an investigational new drug ("IND") application and subsequent initiation of a clinical trial in November 2015 andfor the decision to pause further developmentadvancement of this product candidate. Costs to advance our pre-clinical product candidates and develop our ATLAS platform for immuno-oncology increased by $5.1 million, driven by higher headcount and lab-related costs. Development on infectious disease research programs, all of which were paused in November 2016, increased by $2.0 million, and an increase of $3.1 million in spending in our immuno-oncology program.GEN-011.

General and administrative expenses
 
General and administrative expense increased $1.4decreased approximately $2.3 million to $15.4$12.0 million for the year ended December 31, 20162019 from $14.0$14.3 million for the year ended December 31, 2015.2018. The increasedecrease was primarily due largely to market researchreduced legal costs of $0.9 million and higher depreciation costs from facility expansion of $0.5approximately $2.2 million. In 2018, the Company incurred significant legal fees related to shareholder litigation, which was settled in 2019.

RefundWe anticipate that our general and administrative expenses will increase in the future to support the expected growth in our business, expand our operations and organizational capabilities. Additionally, if and when we believe regulatory approval of research and developmentour first product candidate appears likely, we anticipate that we will increase costs in preparation for commercial launch.

In February 2016, weChange in fair value of warrants

Change in fair value of warrants reflects the non-cash change in the fair value of the 2018 Public Offering Warrants, which were recorded at their fair value on the date of issuance and are remeasured as of any warrant exercise date and at the end of each reporting period. The decrease in income is attributed to a gain upon receipt of $1.6 million, including accrued interest, pursuant to contractual obligations undersmaller decrease in our stock price than that in the Novavax Agreement to refund research and development expenses paid to Novavax between 2009 and 2011.prior year.

Interest Income expense, net



Interest expense, net, consists primarily of interest expense on our long-term debt facilities, offset by interest earned on our cash equivalents.

Other income increased $0.2(expense)

Other income (expense) decreased $2.0 million for the year ended December 31, 2016 due to both higher levels of investing activity (full year of investing excess cash2019, as compared to beginning to invest in September 2015 in the prior year) and a higher interest rate environment.

Interest Expense

Interest expense increased $0.5 million for the year ended December 31, 2016. The increase was due primarily to the $5.0 million increase in principal borrowings under our 2014 Term Loan as a result of the First Amendment entered into in the fourth quarter of 2015.

Comparison of the Years Ended December 31, 2015 and December 31, 2014



  Years Ended December 31, Increase
(in thousands) 2015 2014 (Decrease)
Grant revenue $670
 $308
 $362
       
Operating expenses:      
Research and development 28,049
 23,727
 4,322
General and administrative 13,987
 9,747
 4,240
Total operating expenses 42,036
 33,474
 8,562
Loss from operations (41,366) (33,166) 8,200
Other expense, net:      
Change in fair value of warrants 
 (725) (725)
Loss on debt extinguishment 
 (435) (435)
Interest income 163
 55
 108
Interest expense (1,280) (1,025) 255
Total other expense, net (1,117) (2,130) (1,013)
Net loss $(42,483) $(35,296) 7,187

Grant revenue

Grant revenue increased $0.4 million to $0.7 million for2018. For the year ended December 31, 2015 from $0.32018, other expense included $2.2 million forof transaction costs allocated to the year ended December 31, 2014. The increase was due to a full year of activities performed related to a $1.2 million grant entered into with the Gates Foundation in September 2014.

Research and development expenses

R&D expense increased $4.3 million to $28.0 million for the year ended December 31, 2015 from $23.7 million for the year ended December 31, 2014.  This net increase was attributable to increases of $2.1 million in R&D personnel costs, approximately $1.8 million in lab-related and facilities costs and other general increases to support research activities offset by a $1.0 million decrease in clinical costs and licensing payments. R&D headcount increased by more than 55% to support the clinical and manufacturing activities related to our Phase 2 trials, along with hiring to support our oncology and other research programs. The decline in both clinical costs and licensing paymentswarrants related to the relative timing of major clinical activities and milestones in 2015 versus 2014.
On a program basis, GEN-003 costs increased by $0.4 million largely due to (i) the ongoing Phase 2 dose optimization that began in the second half of 2014 (ii) costs incurred to drive improvements in the manufacturing process for GEN-003 to enable production at commercial scale, and (iii) costs related to the initiation of patient screening for our 131-subject Phase 2b study in the fourth quarter of 2015. Pre-clinical R&D increased by $5.4 million as we accelerated our investment in immuno-oncology research and collaborations and increased spending on our other product candidates and the development of the ATLAStechnology platform. These increases were offset by a $1.5 million cost decrease in GEN-004 due to our fourth quarter decision to suspend investment in this program.

General and administrative expenses

G&A expense increased $4.2 million to $14.0 million for the year ended December 31, 2015 from $9.7 million for the year ended December 31, 2014. The increase was due largely to additional personnel costs of $2.3 million attributable to higher headcount, increases in depreciation costs of approximately $0.4 million due to capital additions and expansion of our offices, and a $0.4 million increase in consulting and professional services mainly due to the recruitment and hiring activities that occurred during 2015. The remaining $1.1 million increase was generally attributable to higher public company overhead costs.

Other expense

Other expense decreased $1.2 million for the year ended December 31, 2015. The decrease was due to a non-recurring adjustment recorded in the first quarter ended March 31, 2014 to the fair value of warrants to purchase preferred stock as a result of an increase in the fair value of the underlying stock both before and on the date of the completion of our IPO on February 10, 2014. Additionally, in the fourth quarter end December 31, 2014, we incurred a $0.4 million loss on our debt extinguishment of a term note.



Interest income 

Interest income increased $0.1 million in the year ended December 31, 2015 due to a higher average cash balance based upon proceeds from follow-on offerings in March and August of 2015.

Interest expense

Interest expense increased $0.3 million for the year ended December 31, 2015 due primarily to higher average principal balances on our outstanding debt for the year to date period in 2015 as compared to the same period in 2014.2018 Public Offering Warrants.

Liquidity and Capital Resources

Overview

Since our inception in 2006, we have funded operations primarily through proceeds from public issuances of common stock, our long-term debt and the private placement of our common stock.

As of December 31, 2016,2019, we have received an aggregate of $279.6 million in gross proceeds from the issuance of equity securities and gross proceeds from debt facilities and an aggregate of $7.9 million from grants. At December 31, 2016, our cash, cash equivalents and investments were $63.4 million, comprised of $27.4had approximately $40.1 million in cash and cash equivalents and $35.9 million of investments.equivalents.

In February 2014, we completed an IPO of 5.5 million shares of our common stock at a price of $12.00 per share for an aggregate offering price of $66.0 million. We received net proceeds from the offering of approximately $61.4 million, after deducting approximately $4.6 million in underwriting discounts and commission, excluding offering costs payable by us.
In March 2015, we completed an underwritten public offering of 6.3 million shares of our common stock at a public offering price of $8.25 per share for an aggregate offering price of $51.7 million. In August 2015, we completed another underwritten public offering of 3.9 million shares of our common stock at a public offering price of $13.00 per share for an aggregate offering price of $50.1 million. We received net proceeds from these offerings of approximately $95.7 million, after deducting approximately $6.1 million in underwriting discounts and commissions, excluding offering costs payable by us.

Debt Financings

On November 20, 2014 (the "Closing Date"),April 2018, we entered into aan amended and restated loan and security agreement (the “Loan Agreement”) with Hercules Technology Growth Capital, Inc. (“Hercules”("Hercules"), which provided up to $27.0 millionwas subsequently amended in debt financing in three separate tranches (“2014 Term Loan”). The first tranche of $17.0 million was available through June 30, 2015, of which $12.0 million was drawn down at loan inception for which approximately $9.8 million ofNovember 2019 (as amended, the proceeds were used to repay the previously existing $10.0 million loan agreement (the "2013"2018 Term Loan"). We recorded a $435 thousand loss on extinguishment of debt in other expense on the Statements of Operations related to deferred debt charges, the unamortized portion of the original issue discount related to the 2013The 2018 Term Loan and other fees associated with extinguishing the debt.provides a $14.0 million term loan. The option to draw down the remaining $5.0 million under the first tranche expired unused on June 30, 2015. The second tranche of $5.0 million was subject to certain eligibility requirements which were achieved as of June 30, 2015 and we had the option to draw down the second tranche on or prior to December 15, 2015. The second tranche expired unused on December 15, 2015. The third tranche of $5.0 million was not eligible to draw as we did not achieve positive results from its Phase 2a human challenge study of GEN-004.

In December 2015, we entered into an amendment to the Loan Agreement (the "First Amendment") with Hercules. The First Amendment required us to draw an additional $5.0 million and permits us to draw two additional $5.0 million tranches. One $5.0 million tranche was immediately available to draw through December 15, 2016 and a second $5.0 million tranche would become available through December 15, 2016, subject to us demonstrating sufficient evidence of continued clinical progression of our GEN-003 product and making favorable progress in applying our proprietary technology platform toward the development of novel immunotherapies with application in oncology. Both tranches expired unused at December 31, 2016, and $17.0 million was outstanding under the amended 20142018 Term Loan at December 31, 2016.

The 2014 Term Loan had an original maturity of Julywill mature on May 1, 2018. The eligibility requirements for the second tranche also contained an election for us to extend the maturity date to January 1, 2019. During the second quarter of 2015, we elected to extend the maturity date of the 2014 Term Loan. The maturity date of January 1, 2019 remained unchanged by the First Amendment.



Each advance2021 and accrues interest at a floating rate per annum equal to the greater of (i) 7.25%8.00% or (ii) the sum of 7.25%3.00% plus the prime rate minus 5.0%.rate. The 20142018 Term Loan providedprovides for interest-only payments until December 31, 2015, which was extended by us for a six-month period as the eligibility requirements for the second tranche were met during the second quarterJanuary 1, 2021. Thereafter, payments will include equal installments of 2015. The First Amendment subsequently extended the interest only period through June 30, 2017. Thereafter, beginning July 1, 2017, principal and interest payments will be made monthly for 18 months with a payoff schedule based upon a 30-month amortization schedule, the original amortization term of the 2014 Term Loan.through maturity. The remaining unpaid principal is due at January 1, 2019.

The 20142018 Term Loan may be prepaid in whole or in part upon seven business days’ prior written notice to Hercules.  Prepayments will be subject to a charge of 3.0% if an advance is prepaid within 12 months following the Closing Date, 2.0%, if an advance is prepaid between 12 and 24 months following the Closing Date, and 1.0% thereafter. Amounts outstanding at the time of an event of default shall be payable on demand and shall accrue interest at an additional rate of 5.0% per annum on any outstanding amounts past due.prepayment charge. We are also are obligated to pay Hercules an end of term charge of 4.95%$1.0 million at maturity. As of the balance drawn when the advances are repaid.

Events of default under the Loan Agreement include failure to make any payments of principal or interest as due on any outstanding indebtedness, breach of any covenant, any false or misleading representations or warranties, insolvency or bankruptcy, any attachment or judgment on the Company’s assets of at least $100 thousand, or the occurrence of any material default ofDecember 31, 2019, the Company involving indebtedness in excesshad outstanding borrowings of $100 thousand.$13.4 million.

In connectionOctober 2019, we entered into a purchase agreement with LPC pursuant to which LPC purchased $2.5 million of our common stock at a purchase price of $2.587 per share. In addition, for a period of 30 months, we have the 2014 Term Loan,right, at our sole discretion, to sell up to an additional $27.5 million of our common stock based on prevailing market prices of our common stock at the time of each sale. In consideration for entering into the purchase agreement, we issued a289,966 shares of our common stock warrant to HerculesLPC as a commitment fee. The purchase agreement limits our sales of shares of common stock to LPC to 5,227,323 shares of common stock, representing 19.99% of the shares of common stock outstanding on November 20, 2014.the date of the purchase agreement. The warrant is exercisable for 73,725purchase agreement also prohibits us from directing LPC to purchase any shares of common stock if those shares, when aggregated with all other shares of our common stock then beneficially owned by LPC and its affiliates, would result in LPC and its affiliates having beneficial ownership, at any single point in time, of more than 9.99% of the then total outstanding shares of our common stock.

In June 2019, we entered into an underwriting agreement relating to the underwritten public offering of 10,500,000 shares of our common stock, par value $0.001 per share, at a price to the public of $3.50 per share, for gross proceeds of approximately $36.8 million (the “2019 Public Offering”). We also granted the underwriters an option to purchase up to an additional 1,575,000 shares of common stock (“Overallotment Option”). In June 2019, the underwriters exercised this option in full. We received approximately $5.5 million in gross proceeds from the underwriter’s exercise of the Overallotment Option. In connection with the 2019 Public Offering, inclusive of the Overallotment Option, we incurred approximately $3.9 million of offering-related expenses, resulting in total net proceeds of $38.4 million.

In February 2019, we completed a private placement financing transaction (the “Private Placement”). We issued 3,199,998 shares (the “Shares”) of common stock, prefunded warrants (the “Pre-Funded Warrants”) to purchase 531,250 shares of common stock (the “Pre-Funded Warrant Shares”), and warrants (the “Private Placement Warrants”) to purchase up to 932,812 shares of common stock (the “Warrant Shares”). The Shares, Pre-Funded Warrants and Private Placement Warrants (collectively, the “Units”) were sold at a purchase price of $4.02 per Unit. We received net cash proceeds of approximately $13.8 million for the purchase of the Shares, Pre-Funded Warrant Shares and Warrant Shares.

Cash Flows

The following table summarizes our sources and uses of cash for the years ended December 31, 2019 and 2018 (in thousands):


  Years ended December 31, Increase
  2019 2018 (Decrease)
Net cash used in operating activities $(37,734) $(41,235) $(3,501)
Net cash used in investing activities (1,087) (131) 956
Net cash provided by financing activities 52,901
 55,455
 (2,554)
Net increase in cash and cash equivalents $14,080
 $14,089
 $(9)

Operating Activities

Net cash used in operations decreased $3.5 million to $37.7 million for the year ended December 31, 2019 from $41.2 million for the year ended December 31, 2018. The decrease in net cash used was due to favorable changes in working capital attributable to accounts payable and accrued expenses.

Investing Activities

Net cash used in investing activities increased $1.0 million to $1.1 million of cash used in investing activities for the year ended December 31, 2019 compared to $0.1 million of cash used in investing activities for the year ended December 31, 2018. The increase in cash used in investing activities was due to increased purchases of property and equipment.

Financing Activities

Net cash provided by financing activities decreased $2.6 million to $52.9 million for the year ended December 31, 2019 from $55.5 million of cash provided by financing activities for the year ended December 31, 2018. In 2018, we generated net proceeds of $51.7 million from a 2018 public offering of common stock and warrants and we generated net proceeds of $2.9 million from the sale of shares of common stock issued pursuant to our ATM facility, whereas in 2019, the Private Placement generated net proceeds of $13.8 million, the 2019 Public Offering generated net proceeds of $38.4 million, and the transactions pursuant to the purchase agreement with LPC generated net proceeds of $2.5 million. During the years ended December 31, 2019 and 2018, we made payments of $1.9 million and $0.5 million on our long term debt.

Operating Capital Requirements

Our primary uses of capital are for compensation and related expenses, manufacturing costs for pre-clinicalpreclinical and clinical materials, third party clinical trial R&D services, laboratory and related supplies, clinical costs, legal and other regulatory expenses, and general overhead costs. We expect these costs will continue to be the primary operating capital requirements for the near future.

We believeexpect that our existing cash and cash equivalents and investments at December 31, 2016 are sufficient to support our operating expenses and capital expenditure requirementsoperations into the first quarter of 2018, without assuming any receipt of proceeds from potential business development partnerships, equity financings or debt drawdowns. This guidance assumes commencing Phase 3 trials for GEN-003 for genital herpes2021. As reflected in the fourth quarterconsolidated financial statements, we had available cash and cash equivalents of 2017 and filing an IND$40.1 million at December 31, 2019. In addition, we had cash used in operating activities of $37.7 million for GEN-009 for cancer by the end of the year however it isended December 31, 2019. These factors, combined with our strategyforecast of cash required to secure additional sourcesfund operations for a period of financing in advanceat least one year from the date of starting GEN-003 Phase 3 clinical trials.
issuance of these financial statements, raise substantial doubt about our ability to continue as a going concern. We have based our projections of operating capital requirements on assumptions that may prove to be incorrect and we may use all of our available capital resources sooner than we expect. Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

the timing and costs of our ongoing and planned clinical trials for GEN-003;GEN-009;
the progress, timing, and costs of manufacturing GEN-003GEN-009 for current and planned clinical trials;
the outcome, timing, and costs of seeking regulatory approvals, including an IND application for GEN-011;
the initiation, progress, timing, costs, and results of preclinical studies and clinical trials for our other product candidates and potential product candidates;
the outcome, timing and costs of seeking regulatory approvals;
the costs of commercialization activities for GEN-003 and other product candidates if we receive marketing approval, including the costs and timing of establishing product sales, marketing, distribution and manufacturing capabilities;
the receipt of marketing approval, revenue received from commercial sales of our product candidates;
the terms and timing of any future collaborations, grants, licensing, consulting, or other arrangements that we may establish;


the amount and timing of any payments we may be required to make, or that we may receive, in connection with the licensing, filing, prosecution, defense and enforcement of any patents, or other intellectual property rights, including


milestone andpayments, royalty payments, and patent prosecution fees that we are obligated to pay pursuant to our license agreements;
the costs of preparing, filing, and prosecuting patent applications, maintaining and protecting our intellectual property rights, and defending against intellectual property related claims; and
the extent to which we in-license or acquire other products and technologies.technologies;
the receipt of marketing approval;
the costs of commercialization activities for GEN-009 and other product candidates, if we receive marketing approval, including the costs and timing of establishing product sales, marketing, distribution, and manufacturing capabilities; and
revenue received from commercial sales of our product candidates.

We expect that we will need to obtain substantial additional funding in order to commercialize GEN-003complete clinical trials and receive regulatory approval for GEN-009, GEN-011 and our other product candidates in order to receive regulatory approval.candidates. To the extent that we raise additional capital through the sale of our common stock, convertible securities, or other equity securities, the ownership interests of our existing stockholders may be materially diluted and the terms of these securities could include liquidation or other preferences that could adversely affect the rights of our existing stockholders. In addition, debt financing, if available, would result in increased fixed payment obligations and may involve agreements that include restrictive covenants that limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends, that could adversely affect our ability to conduct our business. If we are unable to raise capital when needed or on attractive terms, we could be forced to significantly delay, scale back, or discontinue the development or commercialization of GEN-003GEN-009, GEN-011 or our other product candidates, seek collaborators at an earlier stage than otherwise would be desirable or on terms that are less favorable than might otherwise be available, and relinquish or license, potentially on unfavorable terms, our rights to GEN-003GEN-009, GEN-011 or our other product candidates that we otherwise would seek to develop or commercialize ourselves.

Cash Flows

The following table summarizes our sources and uses of cash for the years ended December 31, 2016 and 2015 (in thousands):
  Years ended December 31,
  2016 2015
Net cash used in operating activities $(41,835) $(38,360)
Net cash provided by (used in) investing activities 50,711
 (64,937)
Net cash provided by financing activities 1,289
 100,498
Net increase in cash and cash equivalents $10,165
 $(2,799)

Operating Activities

Net cash used in operations increased $3.4 million to $41.8 million for the year ended December 31, 2016 from $38.4 million for the year ended December 31, 2015. The increase was due primarily to a higher net loss of approximately $7.1 million, offset by increases in depreciation and amortization of $0.8 million, accounts payable and accrued expenses of $1.9 million, stock based compensation of $0.3 million, and a decrease in deferred revenue of $0.4 million. The remaining $0.3 million relates to changes in other working capital accounts.

Investing Activities

Net cash provided by investing activities increased $115.6 million to $50.7 million for the year ended December 31, 2016 compared to $64.9 million of cash used in investing activities for the year ended December 31, 2015. The increase was primarily due to net proceeds from investment maturities and sales of $53.2 million in 2016 compared to net investments made of $62.2 million in 2015.

Financing Activities

Net cash provided by financing activities decreased $99.2 million to $1.3 million for the year ended December 31, 2016 from $100.5 million for the year ended December 31, 2015. The decrease was due largely to a reduction of $94.4 million in net proceeds from public offerings due to two follow-on offerings completed in 2015. In addition, there were no proceeds from debt financing in 2016 compared to $4.7 million of additional borrowing proceeds related to the First Amendment of our 2014 Term Loan in 2015.



The following table summarizes our sources and uses of cash for the years ended December 31, 2015 and 2014 (in thousands):
  Years Ended December 31,
  2015 2014
Net cash used in operating activities $(38,360) $(27,604)
Net cash used in investing activities (64,937) (28,573)
Net cash provided by financing activities 100,498
 64,027
Net increase in cash and cash equivalents $(2,799) $7,850

Operating Activities

Net cash used in operations increased $10.8 million to $38.4 million for the year ended December 31, 2015 from $27.6 million for the year ended December 31, 2014. The increase was due primarily to increases in (i) the net loss of approximately $7.2 million, (ii) accounts payable and accrued expenses of $2.0 million, and (iii) stock based compensation of $0.9 million, offset by decreases in deferred revenue of $1.6 million and fair value of warrant liability of $0.7 million, along with other changes in our working capital accounts.

Investing Activities

Net cash used in investing activities increased $36.4 million to $64.9 million for the year ended December 31, 2015 from $28.6 million for the year ended December 31, 2014. The increase was due largely to a net $35.1 million increase in investments and an increase in cash used to purchase property and equipment of $1.3 million.

Financing Activities

Net cash provided by financing activities increased $36.5 million to $100.5 million for the year ended December 31, 2015 from $64.0 million for the year ended December 31, 2014. The increase was due largely to $35.2 million in higher net proceeds from two follow-on public offerings in 2015 compared to the proceeds from IPO in 2014, $3.4 million of additional borrowing proceeds primarily related to the First Amendment, both offset by a decrease of $2.2 million in proceeds from other common stock issuances that occurred in 2014.


Off-Balance Sheet Arrangements

We do not have any off-balance sheet arrangements.

Net Operating Loss Carryforwards

At December 31, 2016, we had United States federal and state net operating loss carryforwards of approximately $136.6 million and $121.2 million, respectively, which may be available to offset future income tax liabilities and expire at various dates through 2036. At December 31, 2016, we had federal and state R&D tax credit carryforwards of approximately $4.8 million and $2.5 million available, respectively, to reduce future tax liabilities which expire at various dates through 2036. Net operating loss and tax credit carryforwards are subject to review and possible adjustment by the Internal Revenue Service and state tax authorities and may become subject to an annual limitation in the event of certain cumulative changes in the ownership interest of significant stockholders over a three-year period in excess of 50%, as defined under Sections 382 and 383 of the United States Internal Revenue Code of 1986, as amended, as well as similar state provisions. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of our company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation in future years. At December 31, 2016, we recorded a 100% valuation allowance against our net operating loss and R&D tax credit carryforwards, as we believe it is more likely than not that the tax benefits will not be fully realized. In the future, if we determine that a portion or all of the tax benefits associated with our tax carryforwards will be realized, net income would increase in the period of determination.

Contractual Obligations

The following table summarizes our outstanding contractual obligations as of payment due date by period at December 31, 2016 (in thousands):



  Total Less Than 1 Year 1 - 3 Years 3 - 5 Years More than 5 Years
Long-term debt(1) $17,842
 $3,149
 $14,693
 $
 $
Operating leases 5,068
 1,550
 3,518
 
 
  $22,910
 $4,699
 $18,211
 $
 $
_________________________
(1)As of December 31, 2016, we had a total of $17.0 million in long-term debt due consisting of amounts due under the 2014 Term Loan. We are obligated to pay an end of term charge of 4.95% of the balance drawn when the principal balance is repaid. We have included $0.8 million in this table for the end of term charge based upon the debt outstanding at December 31, 2016.
In February 2014, we entered into a supply agreement with FUJIFILM Diosynth Biotechnologies U.S.A., Inc. (“Fujifilm”) for the manufacture and supply of antigens for future GEN-003 clinical trials. Under the agreement, we are obligated to pay Fujifilm manufacturing milestones, in addition to reimbursement of certain material production related costs. In June and September 2016, we entered into new statements of work under the agreement with Fujifilm for the manufacture and supply of antigens for our Phase 3 clinical trials. We incurred expenses of $4.7 million and $4.2 million under this agreement for the years ended December 31, 2016 and 2015, respectively.

In October 2014, we entered a product development and clinical supply agreement with Baxter Pharmaceutical Solutions LLC ("Baxter"). The product development and clinical supply agreement provides the terms and conditions under which Baxter will formulate, fill, inspect, package, label and test our lead product, GEN-003 for clinical supply. We are obligated to pay Baxter for each batch of GEN-003 manufactured. Additionally, certain set-up fees and equipment purchased for the purposes of batch production will be invoiced separately by Baxter. We are also responsible for the payment of a monthly service fee for project management services for the duration of the arrangement. There are no minimum purchase obligations and we may cancel the agreement at any point subject to payment for services rendered through the date of cancellation. We incurred no expenses and $702 thousand under this agreement for the years ended December 31, 2016 and 2015, respectively.

We also have obligations to make future payments to third party licensors that become due and payable on the achievement of certain development, regulatory and commercial milestones. We have not included these commitments on our balance sheet or in the table above because the achievement and timing of these milestones is not fixed or determinable. These additional contractual commitments include the following:

License Agreement with The Regents of the University of California.  Under our license agreement with The Regents of the University of California ("UC"), in respect of UC patent rights covering aspects of our ATLAS discovery platform, we agreed to pay UC low single digit royalties on net sales by us of vaccine products comprising antigens identified through use of the ATLAS discovery platform covered by licensed UC patent rights. If we sublicense UC patent rights, we will owe UC a percentage of sublicensing revenue, including any royalty paid to us on net sales by sublicensees.

License Agreement with Harvard.  Under our license agreement with President and Fellows of Harvard College ("Harvard"), in respect of Harvard patent rights covering certain chlamydia antigens, we agreed to pay Harvard royalties in the high single-digits on worldwide net sales by us or our sublicensees of vaccine products comprising such chlamydia antigens. In addition, we are required to pay Harvard specified milestone payments for development of the first such chlamydia vaccine. Under the same license agreement, in respect of patent rights covering aspects of our antigen discovery platform, we agreed to pay Harvard royalties in the low single-digits on worldwide net sales by us or our sublicensees, for a period of 10 years from first commercial sale, of vaccine products comprising antigens (other than chlamydia antigens above) identified through use of the antigen discovery platform covered by licensed Harvard patent rights. In addition, we are required to pay Harvard specified milestone payments for development of such vaccines. We do not expect to make milestone payments in 2017 under this agreement. If we sublicense Harvard patent rights, we will owe Harvard a percentage of sublicensing revenue, excluding payments we receive based on the level of sales or profits. We notified Harvard of our partial termination of the license agreement with regard to the chlamydia antigens on December 8, 2014. Effective March 8, 2015, the license agreement with Harvard with regard to the chlamydia antigens was terminated and we no longer hold a license to two of the three in-licensed Harvard patent families, or to a chlamydia antigen covered by the remaining family. The remaining family covers certain aspects of the ATLAS platform, as well as one chlamydia antigen, and we continue to maintain exclusive rights to aspects of the ATLAS platform covered by this family.



License Agreement with Novavax.  Under our license agreement with Isconova AB, now Novavax, Inc., in respect of Novavax patent rights and trademarks covering adjuvant Matrix-M, we agreed to pay Novavax tranched royalties in the low single-digits on worldwide net sales by us or our sublicensees of vaccine products comprising our antigens and Matrix-M. In addition, we are required to pay Novavax specified milestone payments for development and commercialization of the first vaccine in each unique disease field. We expect to make a milestone payment in 2017 if we are successful in initiating a Phase 3 trial for GEN-003. If we sublicense Novavax patent rights, we will owe Novavax a percentage of the initial signing or upfront sublicensing fees we receive.

License Agreement with Children’s Medical Center Corporation.  Under our license agreement with Children’s Medical Center Corporation ("Children's"), in respect of Children's rights in jointly-owned patent rights covering certain Streptococcus antigens, we agreed to pay Children's low single digit royalties on worldwide net sales by us or our sublicensees of vaccine products comprising such Streptococcus antigens. In addition, we are required to pay Children's specified milestone payments for development and commercialization of such vaccines. We do not expect to make milestone payments in 2017 under this agreement. If we sublicense the jointly-owned patent rights, we will owe Children's a percentage of sublicensing revenue, excluding payments we receive based on the level of sales or profits.

We also enter into contracts in the normal course of business with CROs for clinical trials and clinical supply manufacturing and with vendors for preclinical safety and research studies, research supplies and other services and products for operating purposes. These contracts generally provide for termination on notice and do not include any minimum purchase commitments, and therefore are cancelable contracts and not included in the table above.

JOBS Act

In April 2012, the JOBS Act was enacted in the United States. Section 107 of the JOBS Act provides that an “emerging growth company” can take advantage of the extended transition period provided in Section 7(a)(2)(B) of the Securities Act for complying with new or revised accounting standards. Thus, an emerging growth company can delay the adoption of certain accounting standards until those standards would otherwise apply to private companies. We have irrevocably elected not to avail ourselves of this extended transition period and, as a result, we will adopt new or revised accounting standards on the relevant dates on which adoption of such standards is required for non-emerging growth public companies.

Item 7A.    Qualitative and Quantitative Disclosures About Market Risk

We are exposed to market risk related to changes in interest rates. Ashad cash and cash equivalents of approximately $40.1 million as of December 31, 2016 and 2015, we had cash, cash, cash equivalents and investments of $63.4 million and $106.4 million, respectively, consisting primarily of money market funds, U.S Treasury securities, and FDIC insured certificates of deposits. The investments in these financial instruments are made in accordance with an investment policy approved by our board of directors, which specifies the categories, allocations and ratings of securities we may consider for investment.2019. The primary objectiveobjectives of our investment activities isare to preserve principal, while at the same time maximizing theprovide liquidity and maximize income we receive without significantly increasing risk. Some of the financial instruments in which we invest could be subjectOur primary exposure to market risk. This meansrisk relates to fluctuations in interest rates, which are affected by changes in the general level of U.S. interest rates. Given the short-term nature of our cash and cash equivalents, we believe that a sudden change in prevailingmarket interest rates may cause the value of the instrumentswould not be expected to fluctuate. For example, if we purchasehave a security that was issued with a fixed interest rate and the prevailing interest rate later rises, the value of that security will probably decline. To minimize this risk, we intend to maintain a portfolio that may include cash, cash equivalents and investment securities available-for-sale in a variety of securities, which may include money market funds, government and non-government debt securities and commercial paper, all with various maturity dates. Basedmaterial impact on our current investment portfolio, wefinancial condition and/or results of operations. We do not own any derivative financial instruments.

We do not believe that our results of operations or our financial position would be materially affected by an immediate change of 10% in interest rates.
We do not hold or issue derivatives, derivative commodity instruments or other financial instruments for speculative trading purposes. Further, we do not believe ourcash, cash equivalents and investmentmarketable securities have significant risk of default or illiquidity. We made this determination based on discussions with our investment advisors and a review of our holdings. AlthoughWhile we believe our cash equivalents and investment securitiescash equivalents do not contain excessive risk, we cannot provide absolute assurance that in the future our investments will not be subject to adverse changes in market value. AllIn addition, we maintain significant amounts of our investments are recordedcash, cash equivalents and marketable securities at fair value.
We are also exposed to market risk related to change in foreign currency exchange rates. We contract with certain vendorsone or more financial institutions that are located in Europe which have contracts denominated in foreign currencies. We are subject to fluctuations in foreign currency rates in connection with these agreements.excess of federally insured limits.

Inflation generally affects us by increasing our cost of labor and clinical trial costs. We do not currently hedgebelieve that inflation had a material effect on our foreign exchange rate risk. Asresults of operations during the year ended December 31, 2016 and December 31, 2015, we had minimal liabilities denominated in foreign currencies.2019.



Item 8.        Financial Statements and Supplementary Data

Our consolidated financial statements, together with the report of our independent registered public accounting firm, appear beginning on page F-1 of this Annual Report on Form 10-K.

Item 9.        Changes in and Disagreements with Accountants andon Accounting and Financial Disclosure

Not applicable.

Item 9A.    Controls and Procedures

Evaluation of Disclosure Controls and Procedures

We maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Securities and Exchange Act of 1934 (the "Exchange Act") is (1) recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms, and (2) accumulated and communicated to our management, including our principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure.

Our management, with the participation of our principal executive officerChief Executive Officer and principal financial officer,Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures as of December 31, 20162019 (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act). Our 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. Our principal executive officer and principal financial officer have concluded, based upon the evaluation described above that, as of December 31, 2016,2019, our disclosure controls and procedures were effective at the reasonable assurancereasonable-assurance level.



Management’s Annual Report on Internal Controls Over Financial Reporting

Our management is responsible for establishing and maintaining adequate internal control over our financial reporting. Internal control over financial reporting is defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act as the process designed by, or under the supervision of, our Chief Executive Officer and our Chief Financial Officer, and effected by our board of directors, management, and other personnel, to provide reasonable assurance regarding the reliability of our financial reporting and the preparation of our financial statements for external purposes in accordance with generally accepted accounting principles ("GAAP"), and includes those policies and procedures that:
(1)pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of assets;
(2)provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with GAAP, and that receipts and expenditures are being made only in accordance with the authorizations of management and directors; and
(3)provide reasonable assurance regarding the prevention or timely detection of unauthorized acquisition, use or disposition of assets that could have a material effect on our financial statements.
Under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer, we conducted an evaluation of the effectiveness of our internal control over financial reporting based on the framework provided in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO)("COSO"). Based on this evaluation, our management concluded that our internal control over financial reporting was effective as of December 31, 2016.2019.

Changes in Internal Control Over Financial Reporting

During the quarter ended December 31, 2016,2019, there have been no changes in our internal control over financial reporting, as such term is defined in Rules 13a-15(f) and 15(d)-15(f) promulgated under the Exchange Act, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Item 9B.    Other Information

On February 12, 2020, our board of directors (the “Board”) elected Gisela M. Schwab, M.D., age 63, to the Board as an independent director, effective February 14, 2020. Ms. Schwab will be a Class II director of the Company and will be nominated for re-election at the annual meeting of our stockholders to be held in 2022.

Dr. Schwab has served as President, Product Development and Medical Affairs and Chief Medical Officer of Exelixis, Inc. (“Exelixis”) since February 2016. Previously she served as Executive Vice President and Chief Medical Officer of Exelixis from January 2008 to February 2016 and as Senior Vice President and Chief Medical Officer of Exelixis from September 2006 to January 2008. From 2002 to 2006, she held the position of Senior Vice President and Chief Medical Officer at Abgenix, Inc. (“Abgenix”), a human antibody-based drug development company. She also served as Vice President, Clinical Development, at Abgenix from 1999 to 2001. Prior to working at Abgenix, from 1992 to 1999, she held positions of increasing responsibility at Amgen Inc., most recently as Director of Clinical Research and Hematology/Oncology Therapeutic Area Team Leader. From August 2011 through July 2014, Dr. Schwab served as a member of the board of directors of Topotarget A/S, a publicly-held biopharmaceutical company. Since June 2012 she has served as a member of the board of directors of Cellerant Therapeutics, Inc. a privately-held biopharmaceutical company and since March 2015, she has served as a member of the board of directors of Nordic Nanovector A.S., a Norwegian biotechnology company. She received her Doctor of Medicine degree from the University of Heidelberg, trained at the University of Erlangen-Nuremberg and the National Cancer Institute and is board certified in internal medicine and hematology and oncology. We believe that Dr. Schwab’s scientific expertise, which includes advancing product candidates through development and regulatory approval to commercial launch, qualifies her to serve as a member of our Board.

Dr. Schwab will receive compensation for her service as a director in accordance with our non-employee director compensation policy, including an annual director fee of $35,000. Pursuant to our non-employee director compensation policy and our Amended and Restated 2014 Equity Incentive Plan and non-qualified stock option award agreement, Dr. Schwab will receive an award of stock options to purchase 9,375 shares of our common stock on February 14, 2020.

In accordance with our customary practice, we have entered into an indemnification agreement with Dr. Schwab, which requires us to indemnify her against certain liabilities that may arise in connection with her status or service as a director. The indemnification agreement also provides for an advancement of expenses incurred by Dr. Schwab in connection with any proceeding


None.relating to her status as a director. The foregoing description is qualified in its entirety by the full text of the form of indemnification agreement, which was filed with the Securities and Exchange Commission as Exhibit 10.1 to our Registration Statement on Form S-1 (Registration No. 333-197247), and which is incorporated herein by reference.

There is no arrangement or understanding between Dr. Schwab and any other person pursuant to which Dr. Schwab was selected as a director. Other than as described above, there are no transactions involving Dr. Schwab requiring disclosure under Item 404(a) of Regulation S-K of the Securities and Exchange Commission.



PART III

Item 10.        Directors, Executive Officers and Corporate Governance

Other than the information regarding our executive officers provided in Part I of this report under the heading
“Business— “Business—Information about our Executive Officers, of the Registrant,” the information required to be furnished pursuant to this item is
incorporated herein by reference to our definitive proxy statement for the 20172020 Annual Meeting of the Stockholders.

Item 11.        Executive and Director Compensation

The information required by this Item 11 is incorporated herein by reference from our definitive proxy statement
for the 20172020 Annual Meeting of Stockholders.

Item 12.        Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

The information required by this Item 12 is incorporated herein by reference from our definitive proxy statement
for the 20172020 Annual Meeting of Stockholders.

Item 13.        Certain Relationships and Related Party Transactions and Director Independence

The information required by this Item 13 is incorporated herein by reference from our definitive proxy statement
for the 20172020 Annual Meeting of Stockholders.

Item 14.        Principal Accountant Fees and Services

The information required by this Item 14 is incorporated herein by reference from our definitive proxy statement
for the 20172020 Annual Meeting of Stockholders.







PART IV

Item 15.        Exhibits and Financial Statement Schedules

Financial Statements

The following financial statements and supplementary data are filed as a part of this Annual Report on Form 10-K.

Report of Independent Registered Public Accounting Firm

Consolidated Balance Sheets as of December 31, 20162019 and 20152018

Consolidated Statements of Operations and Comprehensive Loss for each of the three years in the period ended December 31, 20162019 and 2018

Consolidated Statements of Convertible Preferred Stock and Stockholders’ Equity (Deficit) for each of the three years in the period ended December 31, 20162019 and 2018

Consolidated Statements of Cash Flows for each of the three years in the period ended December 31, 20162019 and 2018

Notes to Consolidated Financial Statements

Item 16.        Form 10-K Summary

None.

Financial Statement Schedules

All financial statement schedules are omitted because they are not applicable or the required information is included in the financial statements or notes thereto.

Exhibits

Those exhibits required to be filed by Item 601 of Regulation S-K are listed in the Exhibit Index immediately preceding the exhibits hereto and such listing is incorporated herein by reference.



Genocea Biosciences, Inc.
Index to Financial Statements


Report of Independent Registered Public Accounting Firm

The Board of Directors and Stockholders of
Genocea Biosciences, Inc.
Opinion on the Financial Statements

We have audited the accompanying consolidated balance sheets of Genocea Biosciences, Inc. (the Company) as of December 31, 20162019 and 2015, and2018, the related consolidated statements of operations and comprehensive loss, convertible preferred stock and stockholders’ equity (deficit) and cash flows for each of the three years in the period ended December 31, 2016. 2019 and 2018, and the related notes (collectively referred to as the “financial statements”). In our opinion, the financial statements present fairly, in all material respects, the consolidated financial position of the Company at December 31, 2019 and 2018, and the consolidated results of its operations and its cash flows for the years ended December 31, 2019 and 2018, in conformity with U.S. generally accepted accounting principles.

Adoption of New Accounting Standards

As discussed in Note 2 to the consolidated financial statements, the Company changed its method of accounting for leases as a result of the adoption of Accounting Standards Update (ASU) No. 2016-02, Leases (Topic 842), and the related amendments effective January 1, 2019.

The Company's Ability to Continue as a Going Concern

The accompanying consolidated financial statements have been prepared assuming that the Company will continue as a going concern. As discussed in Note 1 to the financial statements, the Company has suffered recurring losses from operations, has a working capital deficiency, and has stated that substantial doubt exists about the Company’s ability to continue as a going concern. Management's evaluation of the events and conditions and management’s plans regarding these matters are also described in Note 1. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

Basis for Opinion

These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on these consolidatedthe Company’s financial statements based on our 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 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 audit to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement. Wemisstatement, whether due to error or fraud. The Company is not required to have, nor were notwe engaged to perform, an audit of the Company’sits internal control over financial reporting. OurAs part of our audits included considerationwe are required to obtain an understanding of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes

Our audits included performing procedures to assess the risks of material misstatement of the 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 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 financial statement presentation.statements. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the consolidated financial position of Genocea Biosciences, Inc. at December 31, 2016 and 2015, and the consolidated results of its operations and its cash flows for each of the three years in the period ended December 31, 2016, in conformity with U.S. generally accepted accounting principles.

/s/ Ernst & Young LLP

We have served as the Company’s auditor since 2009
Boston, Massachusetts
February 17, 201713, 2020



Genocea Biosciences, Inc.
Consolidated Balance Sheets
(In thousands, except per share data)
December 31,
2016
 December 31,
2015
December 31,
2019
 December 31,
2018
Assets      
Current assets:      
Cash and cash equivalents$27,424
 $17,259
$40,127
 $26,361
Investments, current portion35,938
 77,069
Prepaid expenses and other current assets926
 865
1,457
 696
Total current assets64,288
 95,193
41,584
 27,057
Property and equipment, net4,871
 4,083
2,617
 2,582
Right of use assets6,306
 
Restricted cash316
 316
631
 316
Investments, net of current portion
 12,104
Other non-current assets421
 446
1,473
 1,160
Total assets$69,896
 $112,142
$52,611
 $31,115
      
Liabilities and stockholders’ equity      
Current liabilities:      
Accounts payable$3,043
 $1,757
$553
 $1,659
Accrued expenses and other current liabilities4,178
 3,975
4,611
 3,816
Deferred revenue
 235
Lease liabilities1,117
 
Current portion of long-term debt3,149
 

 5,257
Total current liabilities10,370
 5,967
6,281
 10,732
Non-current liabilities:      
Long-term debt13,809
 16,477
Long-term debt, net of current portion13,407
 9,565
Warrant liability2,486
 3,472
Lease liabilities, net of current portion5,395
 
Other non-current liabilities176
 37

 11
Total liabilities24,355
 22,481
27,569
 23,780
Commitments and contingencies (Note 8)

 

Commitments and contingencies (Note 6)

 

Stockholders’ equity:      
Common stock, $0.001 par value;28
 28
Authorized – 175,000 shares; Issued – 28,446 and 28,161 shares at December 31, 2016 and December 31, 2015, respectively; outstanding – 28,445 and 28,152 at December 31, 2016 and December 31, 2015, respectively   
Additional paid-in-capital252,996
 247,550
Accumulated other comprehensive loss
 (7)
Preferred stock, $0.001 par value; (shares authorized of 25,000,000 at December 31, 2019 and 2018; 1,635 shares issued and outstanding at December 31, 2019 and 2018)701
 701
Common stock, $0.001 par value; (shares authorized of 85,000,000 and 250,000,000 at December 31, 2019 and 2018; 27,452,900 shares issued and outstanding at December 31, 2019 and 10,846,397 shares issued and outstanding at December 31, 2018)27
 11
Additional paid-in capital355,268
 298,627
Accumulated deficit(207,483) (157,910)(330,954) (292,004)
Total stockholders’ equity45,541
 89,661
25,042
 7,335
Total liabilities and stockholders’ equity$69,896
 $112,142
$52,611
 $31,115

See accompanying notes to consolidated financial statements.



Genocea Biosciences, Inc.
Consolidated Statements of Operations and Comprehensive Loss
(In thousands, except per share data)
 Years Ended December 31,
 2016 2015 2014
Grant revenue$235
 $670
 $308
      
Operating expenses:     
Research and development34,645
 28,049
 23,727
General and administrative15,427
 13,987
 9,747
Refund of research and development expense(1,592) 
 
Total operating expenses48,480
 42,036
 33,474
Loss from operations(48,245) (41,366) (33,166)
Other expense, net:     
Interest income410
 163
 55
Interest expense(1,738) (1,280) (1,025)
Change in fair value of warrants
 
 (725)
Loss on debt extinguishment
 
 (435)
Total other expense, net(1,328) (1,117) (2,130)
Net loss(49,573) (42,483) (35,296)
Other comprehensive income (loss):     
Unrealized (loss) on available-for-sale securities
 (7) (7)
Comprehensive loss$(49,573) $(42,490) $(35,303)
      
Reconciliation of net loss to net loss applicable to common stockholders     
Net loss$(49,573) $(42,483) $(35,296)
Accretion of redeemable convertible preferred stock to redemption value
 
 (180)
Net loss attributable to common stockholders$(49,573) $(42,483) $(35,476)
Net loss per share attributable to common stockholders-basic and diluted$(1.75) $(1.74) $(2.27)
Weighted-average number of common shares used in net loss per share attributable to common stockholders - basic and diluted28,299
 24,460
 15,618
      
 Years Ended December 31,
 2019 2018
Operating expenses:   
Research and development$26,952
 $25,209
General and administrative12,037
 14,309
Total operating expenses38,989
 39,518
Loss from operations(38,989) (39,518)
Other income (expense):   
Change in fair value of warrant986
 14,757
Interest expense, net(946) (1,021)
Other expense(1) (2,029)
Total other income39
 11,707
Net loss$(38,950) $(27,811)
    
Comprehensive loss$(38,950) $(27,811)
Net loss per share - basic and diluted$(1.89) $(2.69)
Weighted-average number of common shares used in computing net loss per share20,644
 10,321

See accompanying notes to consolidated financial statements.


Genocea Biosciences, Inc.
Consolidated Statements of Convertible Preferred Stock and Stockholders’ Equity (Deficit)
(In thousands)
               Total
 Convertible     Additional Other   Stockholders’
 Preferred Shares Common Shares Paid-In Comprehensive Accumulated Equity
 Shares Amount Shares Amount Capital Income Deficit 
(Deficit)
Balance at December 31, 2013127,359
 $81,562
 303
 $
 $
 $
 $(80,131) $(80,131)
Accretion of dividends on redeemable convertible preferred stock
 180
 
 
 (180) 
 
 (180)
Exercise of warrants for cash51
 33
 
 
 
 
 
 
Cashless exercise of warrants317
 98
 54
 
 
 
 
 
Conversion of redeemable convertible preferred stock into common stock(127,727) (81,873) 11,466
 11
 81,763
 
 
 81,774
Reclassification of warrants to additional paid-in capital
 
 
 
 1,381
 
 
 1,381
Issuance of common stock upon IPO, net of issuance costs of $2,403
 
 5,500
 6
 58,971
 
 
 58,977
Issuance of common Stock; ESPP purchase
 
 16
 
 93
 
 
 93
Issuance of common Stock upon private placement offering, net of issuance costs of $36
 
 223
 
 1,964
 
 
 1,964
Issuance of warrants, net of issuance costs of $6
 
 
 
 334
 
 
 334
Exercise of stock options
 
 282
 1
 682
 
 
 683
Vesting of restricted stock
 
 8
 
 10
 
 
 10
Stock-based compensation expense
 
 
 
 2,905
 
 
 2,905
Unrealized loss on investments
 
 
 
 
 (7) 
 (7)
Net loss
 
 
 
 
 
 (35,296) (35,296)
Balance at December 31, 2014
 
 17,852
 18
 147,923
 (7) (115,427) 32,507
Issuance of common stock upon secondary public offering, net of issuance costs of $509
 
 10,123
 10
 95,173
 
 
 95,183
Issuance of common Stock; ESPP purchase
 
 41
 
 213
 
 
 213
Exercise of stock options
 
 128
 
 383
 
 
 383
Vesting of restricted stock
 
 8
 
 10
 
 
 10
Stock-based compensation expense
 
 
 
 3,848
 
 
 3,848
Net loss
 
 
 
 
 
 (42,483) (42,483)
Balance at December 31, 2015
 
 28,152
 28
 247,550
 (7) (157,910) 89,661
Issuance of common stock, net of issuance costs of $3
 
 136
 
 815
 
 
 815
Issuance of common Stock; ESPP purchase
 
 71
 
 247
 
 
 247
Exercise of stock options
 
 79
 
 227
 
 
 227
Vesting of restricted stock
 
 7
 
 10
 
 
 10
Stock-based compensation expense
 
 
 
 4,147
 
 
 4,147
Unrealized gain on marketable securities
 
 
 
 
 7
 
 7
Net loss
 
 
 
 
 
 (49,573) (49,573)
Balance at December 31, 2016
 $
 28,445
 $28
 $252,996
 $
 $(207,483) $45,541
            
     Preferred Additional   Total
 Common Shares Shares Paid-In Accumulated Stockholders’
 Shares Amount Amount Capital Deficit Equity (Deficit)
Balance at December 31, 20173,592
 $3
 $
 $258,140
 $(264,193) $(6,050)
Issuance of common stock, net7,230
 8
 701
 38,077
 
 38,786
Issuance of common Stock; ESPP purchase25
 
 
 67
 
 67
Stock-based compensation expense
 
 
 2,153
 
 2,153
Issuance of warrants in connection with debt modification
 
 
 190
 
 190
Net loss
 
 
 
 (27,811) (27,811)
Balance at December 31, 201810,847
 $11
 $701
 $298,627
 $(292,004) $7,335
Issuance of common stock, net16,530
 16
 
 54,653
 
 54,669
Issuance of common stock; ESPP purchase71
 
 
 130
 
 130
Exercise of stock options5
 
 
 21
 
 21
Stock-based compensation expense
 
 
 1,837
 
 1,837
Net loss
 
 
 
 (38,950) (38,950)
Balance at December 31, 201927,453
 $27
 $701
 $355,268
 $(330,954) $25,042

See accompanying notes to consolidated financial statements.


Genocea Biosciences, Inc.
Consolidated Statements of Cash Flows
(In thousands)
 Years Ended December 31,
 2016 2015 2014
Operating activities     
Net loss$(49,573) $(42,483) $(35,296)
Adjustments to reconcile net loss to net cash used in operating activities     
Depreciation and amortization1,813
 1,051
 469
Stock-based compensation4,147
 3,848
 2,905
Change in fair value of warrants liability
 
 725
Non-cash interest expense481
 369
 254
Loss on debt extinguishment
 
 435
Changes in operating assets and liabilities:     
Prepaid expenses and other current assets(37) 266
 (442)
Other long-term assets25
 (399) 782
Accounts payable1,190
 (1,431) 524
Deferred revenue(235) (670) 893
Accrued expenses and other liabilities354
 1,089
 1,147
Net cash used in operating activities(41,835) (38,360) (27,604)
Investing activities     
Purchases of property and equipment(2,538) (2,784) (1,520)
Proceeds from maturities of investments79,313
 27,498
 
Purchase of investments(26,064) (89,651) (27,053)
Net cash provided by (used in) investing activities50,711
 (64,937) (28,573)
Financing activities     
Proceeds from underwritten public offering, net of issuance costs815
 95,183
 61,938
Proceeds from issuance of long-term debt, net of issuance costs
 4,719
 11,681
Repayment of long-term debt
 
 (10,401)
Proceeds from issuance of common stock under ESPP247
 213
 93
Proceeds from exercise of stock options227
 383
 683
Proceeds from the exercise of warrants
 
 33
Net cash provided by financing activities1,289
 100,498
 64,027
Net increase (decrease) in cash and cash equivalents$10,165
 $(2,799) $7,850
Cash and cash equivalents at beginning of period17,259
 20,058
 12,208
Cash and cash equivalents at end of period$27,424
 $17,259
 $20,058
Supplemental cash flow information     
Cash paid for interest$1,255
 $897
 $815
Supplemental disclosure of non-cash investing and financing activities     
Conversion of preferred stock to common stock upon closing of IPO$
 $
 $81,774
Reclassification of prepaid IPO closing costs from non-current assets to additional paid-in capital$
 $
 $997
Reclassification of warrants to additional paid-in capital$
 $
 $1,381
Accretion of redeemable convertible preferred stock to redemption value$
 $
 $180
Cashless exercise of warrants$
 $
 $98
Issuance of common stock warrant$
 $
 $340
Property and equipment, net included in accounts payable and accrued expenses$63
 $394
 $
 Years Ended December 31,
 2019 2018
Operating activities   
Net loss$(38,950) $(27,811)
Adjustments to reconcile net loss to net cash used in operating activities   
Depreciation and amortization1,097
 1,088
Stock-based compensation1,837
 2,153
Allocation of proceeds to transaction expenses
 2,115
Change in fair value of warrant liability(986) (14,757)
Gain on sale of equipment(29) (78)
Write-off of deferred financing fees110
 355
Non-cash interest expense504
 643
Changes in operating assets and liabilities

 

Prepaid expenses and other current assets(803) 53
Right of use assets, net of lease liabilities206
 
Other non-current assets(423) (989)
Accounts payable(1,106) (2,103)
Accrued expenses and other liabilities809
 (1,904)
Net cash used in operating activities(37,734) (41,235)
Investing activities   
Purchases of property and equipment(1,135) (241)
Proceeds from sale of equipment48
 110
Net cash used in investing activities(1,087) (131)
Financing activities   
Proceeds from equity offerings, net of issuance costs54,669
 55,458
Payment of deferred financing costs
 (127)
Proceeds from long-term debt
 592
Repayment of long-term debt(1,919) (535)
Proceeds from exercise of stock options21
 
Proceeds from the issuance of common stock under ESPP130
 67
Net cash provided by financing activities52,901
 55,455
Net increase in cash, cash equivalents and restricted cash$14,080
 $14,089
Cash, cash equivalents and restricted cash at beginning of period26,678
 12,589
Cash, cash equivalents and restricted cash at end of period$40,758
 $26,678
Non-cash financing activities and supplemental cash flow information   
Cash paid in connection with operating lease liabilities$1,637
 $
Cash paid for interest$1,103
 $1,074
Warrants issued in connection with debt modification$
 $190

See accompanying notes to consolidated financial statements.


Genocea Biosciences, Inc.

Notes to Consolidated Financial Statements

1. Organization and operations

The Company

Genocea Biosciences, Inc. (the “Company”) is a biopharmaceutical company that was incorporated in Delaware on August 16, 2006 and has a principal place of business in Cambridge, Massachusetts. The Company seeks to discover and develop novel vaccines andcancer immunotherapies to address diseases with significant unmet needs throughusing its AnTigen Lead Acquisition System ("ATLASTM") proprietary discovery platform. The ATLAS is used to rapidly design vaccinesplatform profiles each patient's CD4+ and immunotherapies that act, in part, throughCD8+ T cell (or cellular) immune responses to every potential target or "antigen" in contrast to approved vaccines and immunotherapies, which are designed to act primarily through B cell (or antibody) immune responses.that patient's tumor. The Company believes that by harnessing T cells, first-in-classthis approach optimizes antigen selection for immunotherapies such as cancer vaccines and immunotherapies can be developedcellular therapies. Consequently, the Company believes that ATLAS could lead to address diseases where T cells are central to the control of the disease.more immunogenic and efficacious cancer immunotherapies.

The Company has one product candidate in activeCompany’s most advanced program is GEN-009, a personalized neoantigen cancer vaccine, for which it is conducting a Phase 21/2a clinical development, GEN-003, an immunotherapy for the treatment of genital herpes. The Company also has a pre-clinical immuno-oncology program focused on personalized cancer vaccines (GEN-009).trial. The GEN-009 program leveragesuses ATLAS to identify patient neoantigens, or newly formed antigensimmunogenic tumor mutations unique to each patient, for inclusion in each patient's GEN-009 vaccine. The Company is also advancing GEN-011, a neoantigen-specific adoptive T cell therapy program that are often foundalso relies on ATLAS, and is targeting an IND filing for GEN-011 in tumor cells that have not been previously recognized by the immune system. We have other non-active infectious disease programs, including GEN-004, a Phase 2-ready universal vaccine for the preventionsecond quarter of pneumococcal infections, and early stage programs focused on genital herpes prophylaxis, chlamydia, and malaria.2020.

The Company is devoting substantially all of its efforts to product research and development, initial market development, and raising capital. The Company has not generated any product revenue related to its primary business purpose to date and is subject to a number of risks similarand uncertainties common to thosecompanies in the biotech and pharmaceutical industry, including, but not limited to, the risks associated with the uncertainty of othersuccess of its preclinical and clinical stage companies, includingtrials; the challenges associated with gaining regulatory approval of product candidates; the risks associated with commercializing pharmaceutical products, if approved for marketing and sale; the potential for development by third parties of new technological innovations that may compete with the Company’s products; the dependence on key individuals, competition from other companies,personnel; the need and related uncertainty associated to the developmentchallenges of commercially viable products, andprotecting proprietary technology; the need to obtain adequate additional financing to fundcomply with government regulations; the developmenthigh costs of its product candidates. The Company is also subject to a number of risks similar to other companies in the life sciences industry, including regulatory approval of products, uncertainty of market acceptance of products, competition from substitute products and larger companies, the need to obtain additional financing,drug development; compliance with government regulations, protectioncompetition from companies with greater financial, technological and other resources; and the uncertainty of proprietary technology, dependence on third parties, product liability, and dependence on key individuals.being able to secure additional capital when needed to fund operations.

Accounting Standards Update ("ASU"), 2014-15, Presentation of Financial Statements-Going Concern (Subtopic 205-40), also referred to as Accounting Standards Codification ("ASC") 205-40 (“ASC 205-40”), requires the Company to evaluate whether conditions and/or events raise substantial doubt about its ability to meet its future financial obligations as they become due within one year after the financial statements are issued. As of December 31, 2016,2019, the Company had an accumulated deficit of approximately $207.5 million. The$331.0 million and anticipates that it will continue to incur significant operating losses for the foreseeable future as it continues to develop its product candidates. Until such time, if ever, as the Company can generate substantial product revenue and achieve profitability, the Company expects to finance its cash needs through a combination of equity offerings, strategic transactions, and other sources of funding. If the Company is unable to raise additional funds when needed, the Company may be required to implement further cost reduction strategies, including ceasing development of GEN-009, GEN-011, and other corporate programs and activities.

As reflected in the consolidated financial statements, the Company had available cash and cash equivalents and investments of $63.4$40.1 million at December 31, 2016. The Company expects that existing cash, cash equivalents and investments are sufficient to support operating expenses and capital expenditure requirements into the first quarter of 2018, without assuming any receipt of proceeds from potential business development partnerships, equity financings or debt drawdowns. This guidance assumes commencing Phase 3 trials for GEN-003 for genital herpes in the fourth quarter of 2017 and filing an IND for GEN-009 for cancer by the end of the year, however it is the Company’s strategy to secure additional sources of financing in advance of starting GEN-003 Phase 3 clinical trials.

At-the-market equity offering program
On March 2, 2015,2019. In addition, the Company entered into a Sales Agreement with Cowen and Company, LLC (the "Sales Agreement") to establish an at-the-market equity offering program (“ATM”) pursuant to which it was able to offer and sell up to $40had cash used in operating activities of $37.7 million of its Common Stock at prevailing market prices from time to time. On May 8, 2015,for the Sales Agreement was amended to increase the offering amount under the ATM to $50 million of its Common Stock. In April 2016, the Company sold 136 thousand shares and received $0.8 million in net proceeds after deducting commissions. There were no sales under this program during the fiscal year ended December 31, 2015.2019. These factors, combined with the Company’s forecast of cash required to fund operations for a period of at least one year from the date of issuance of these consolidated financial statements, raise substantial doubt about the Company’s ability to continue as a going concern.

The accompanying consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and satisfaction of liabilities in the ordinary course of business. The consolidated financial statements do not include any adjustments relating to the recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might result from the outcome of this uncertainty.

Effective May 22, 2019, the Company effected a reverse stock split of its issued and outstanding common stock, par value $0.001, at a ratio of one-for-eight, and decreased the number of authorized shares of common stock from 250,000,000 shares to 85,000,000 shares. The share and per share information presented in these financial statements and related notes have been retroactively adjusted to reflect the one-for-eight reverse stock split.



2. Summary of significant accounting policies

PrinciplesThe following is a summary of Consolidation

The consolidatedsignificant accounting policies followed in the preparation of these financial statements include the accounts of Genocea Biosciences, Inc., and a wholly-owned subsidiary. All inter-company accounts and transactions have been eliminatedstatements.    

Basis of presentation and useprinciples of consolidation

The accompanying consolidated financial statements include those accounts of the Company and a wholly-owned subsidiary after elimination of all intercompany accounts and transactions. The Company operates as one segment, which is discovering, researching, developing and commercializing novel cancer immunotherapies.

Use of estimates



The accompanying financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“GAAP”). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. On an ongoing basis, the Company’s management evaluates its estimates, which include, but are not limited to, estimates related to clinical trial accruals, estimates related to prepaid and accrued research and development expenses, stock-based compensation expense, the valuation of common stock warrants and warrants to purchase redeemable securities, and reported amounts of revenues and expenses during the reported period.securities. The Company bases its estimates on historical experience and other market-specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results may differ from those estimates or assumptions.

Segment information

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision-making group, in deciding how to allocate resourcesCash and in assessing performance. The Company and the Company’s chief operating decision maker view the Company’s operations and manage its business in one operating segment, which is the business of developing and commercializing vaccines. The Company operates in only one geographic segment.

Cash, cash equivalents and investments
    
The Company determines the appropriate classificationconsiders only those investments which are highly liquid, readily convertible to cash and that mature within three months from date of its investments at the time of purchase. All liquid investments with original maturities of 90 days or less from the purchase date are considered to be cash equivalents. The Company’s currentcarrying values of money market funds approximate fair value due to their short-term maturities.

Prepaid research and non-current investmentsdevelopment

Cash advances paid by the Company prior to receipt of preclinical or clinical material and preclinical and clinical trial services are comprised of certificates of depositrecorded as prepaid research and government securities thatdevelopment costs. The prepayments are classified as available-for-sale in accordance with FASB ASC Topic 320, Investments—Debtapplied against future research and Equity Securities.development costs. The Company classifies investments available to fund current operations as current assets on its balance sheets. Investments are classified as non-current assets on the balance sheets if (i) the Company has the intent and ability to hold the investments for a period of at least one year and (ii) the contractual maturity date of the investments is greater than one year.
Available-for-sale investments are recorded at fair value, with unrealized gains or losses included in Accumulated other comprehensive loss on the Company’s balance sheets. Realized gains and losses are determined using the specific identification method and are included as a component of Interest income. There were no realized gains or losses recognized for the years ended December 31, 2016 and 2015.
The Company reviews investments for other-than-temporary impairment whenever the fair value of an investment is less than the amortized cost and evidence indicates that an investment’s carrying amount is not recoverable within a reasonable period of time. To determine whether an impairment is other-than-temporary, the Company considers its intent to sell, or whether it is more likely than not that the Company will be required to sell the investment before recovery of the investment’s amortized cost basis. Evidence considered in this assessment includes reasons for the impairment, the severity and the duration of the impairment and changes in value subsequent to period end. As of December 31, 2016, there were no investments with a fair value that was significantly lower than the amortized cost basis or any investments that had been in an unrealized loss position for a significant period.

Concentrations of credit risk and off-balance sheet risk

Financial instruments that potentially subject the Company to concentrations of credit risk are primarily cash, cash equivalents and investments. The Company’s cash, cash equivalents and investments are held in accounts with financial institutions that management believes are creditworthy. The Company’s investment policy includes guidelines on the quality of the institutions and financial instruments and defines allowable investments that the Company believes minimizes the exposure to concentration of credit risk. These amounts at times may exceed federally insured limits. The Company has not experienced any credit losses in such accounts and does not believe it is exposed to any significant credit risk on these funds. The Company has no financial instruments with off-balance sheet risk of loss.
Deferred financing costs

Offering costs related to debt and equity financing primarily consist of direct and incremental external expenses. In accordance with ASU No. 2015-03 Interest—Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt


Issuance Costs (“ASU 2015-03”) the Company presents debt issuance costs related to a recognized debt liability in the balance sheet as a direct deduction ofexpects the carrying value of the debt liability, consistent with the accounting treatment of debt discounts. The amortization of deferred debt financingprepaid research and development costs follows the effective interest rate method.

Offering costs related to registration statements and the initiation of the ATM are recorded as an asset and are reclassified to equity on a pro-rata basis based upon the successful selling of common shares compared to the available limits in either equity program. The costs are reviewed for impairment and will be recorded to expense if and when the Company determines that future equity offerings are not probable of occurring. At December 31, 2016 and 2015, the Company had $339 thousand and $304 thousand of deferred offering costs, respectively, recorded as an Other non-current asset.

Fair value of financial instruments

The Company is required to disclose information on all assets and liabilities reported at fair value that enables an assessment of the inputs used in determining the reported fair values. FASB ASC Topic 820, Fair Value Measurement and Disclosures, (“ASC 820”) established a hierarchy of inputs used in measuring fair value that maximizes the use of observable inputs and minimizes the use of unobservable inputs by requiring that the observable inputs be used when available. Observable inputs are inputs that market participants would use in pricing the financial instrument based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the financial instrument and are developed based on the best information available in the circumstances. The fair value hierarchy applies only to the valuation inputs used in determining the reported or disclosed fair value of the financial instruments and is not a measure of the investment credit quality. Fair value measurements are classified and disclosed in one of the following three categories:
Level 1—Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the measurement date.
Level 2—Valuations based on quoted prices for similar assets or liabilities in markets that are not active or for which all significant inputs are observable, either directly or indirectly.
Level 3—Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and unobservable.
To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized in Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement.

Financial instruments measured at fair value on a recurring basis include cash equivalents and investments (Note 3) and warrants (Note 7).

An entity may elect to measure many financial instruments and certain other items at fair value at specified election dates. Subsequent unrealized gains and losses on items for which the fair value option has been elected will be reported in net loss. The Company did not elect to measure any additional financial instruments or other items at fair value. The Company is also required to disclose the fair value of financial instruments not carried at fair value. The fair value of the Company’s long-term debt (Note 6) is determined using current applicable rates for similar instruments as of the balance sheet dates and assessment of the credit rating of the Company. The carrying value of the Company’s long-term debt approximates fair value because the Company’s interest rate yield is near current market rates. The Company’s long-term debt is considered a Level 3 liability within the fair value hierarchy.

Except for the valuation methodology utilized to value the warrants to purchase redeemable securities (Note 7), there have been no changes to the valuation methods utilized by the Company during the three years ended December 31, 2016. The Company evaluates transfers between levels at the end of each reporting period. There were no transfers of financial instruments between levels during the years ended December 31, 2016, 2015 and 2014.

Derivative Instruments

The Company occasionally issues financial instruments in which a derivative instrument is “embedded”. Upon issuing the financial instrument, the Company assesses whether the economic characteristics of the embedded derivative are clearly and closely related to the economic characteristics of the remaining component of the financial instrument (i.e., the host contract) and whether a separate, non-embedded instrument with the same terms as the embedded instrument would meet the


definition of a derivative instrument. When it is determined that (1) the embedded derivative possesses economic characteristics that are not clearly and closely related to the economic characteristics of the host contract and (2) a separate, stand-alone instrument with the same terms would qualify as a derivative instrument, the embedded derivative is separated from the host contract and carried at fair value with any changes in fair value recorded in current period earnings.

In connection with the issuance of the 2014 Term Loan and the First Amendment (Note 6), the Company evaluated all features of the agreement noting none that required bifurcation under FASB ASC Topic 815, Derivatives and Hedging (“ASC 815”).fully realized.

Property and equipment

Property and equipment is stated at cost, less accumulated depreciation. Maintenance and repairs that do not improve or extend the lives of the respective assets are expensed to operations as incurred, while costs of major additions and betterments are capitalized. Upon disposal, the related cost and accumulated depreciation is removed from the accounts and any resulting gain or loss is included in the statements of operations.operations and comprehensive loss. Depreciation is recorded using the straight-line method over the estimated useful lives of the respective assets, which are as follows:
Asset Estimated useful life
Laboratory equipment 5
Furniture and office equipment 5
Computer hardware and software 3-5 years
Leasehold improvements Shorter of the useful life or remaining lease term

Development of Softwaresoftware for Internal Useinternal use

The Company accounts for the costs of software developed or obtained for internal use in accordance with ASC 350-40, Internal-Use Software(“ASC 350-40”). Costs of materials, consultants, payroll, and payroll-related costs for employees incurred in developing internal-use software are capitalized as incurred. These costs are included in Propertyproperty and equipment, net.net on the consolidated balance sheet. Costs incurred during the preliminary project and post-implementation stages are charged to expense. Amortization is recorded using the straight-line method over the estimated useful lives of the respective asset which is three to five years.

Impairment of long-lived assets



The Company evaluates long-lived assets for potential impairment when events or changes in circumstances indicate the carrying value of the assets may not be recoverable. RecoverabilityDetermination of recoverability is measured by comparingbased on an estimate of undiscounted future cash flows resulting from the book valuesuse of the assets toasset and its eventual disposition. In the expected future net undiscountedevent that such cash flows thatare not expected to be sufficient to recover the carrying amount of the asset, the assets are expectedwritten down to generate. If suchtheir estimated fair values. Long-lived assets are considered to be impaired,disposed are reported at the lower of the carrying amount or fair value less cost to sell. The Company recognized no asset impairment losses in the years ended December 31, 2019 and 2018.

Deferred financing costs

Offering costs primarily consist of direct and incremental expenses incurred related to bedebt and equity financing in accordance with ASU 2015-03, Interest-Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs (“ASU 2015-03”). The Company presents debt issuance costs related to a recognized is measured bydebt liability in the amount by whichbalance sheet as a direct deduction of the bookcarrying value of the assets exceed their fair value.debt liability, consistent with the accounting treatment of debt discounts in accordance with ASU 2015-03. The Company has not recognized any impairment losses in any reporting periods through December 31, 2016.amortization of deferred debt financing costs follows the effective interest rate method.

Revenue recognitionFair value of financial instruments

The Company has generated revenue solely through researchcertain financial assets and development grants with private not-for-profit organizationsliabilities recorded at fair value which have been classified as Level 1, 2 or 3 within the fair value hierarchy as described in the accounting standards for fair value measurements.
Level 1—Fair values are determined by utilizing quoted prices (unadjusted) in active markets for identical assets or liabilities that the Company has the ability to access;
Level 2—Fair values are determined by utilizing quoted prices for similar assets and federal agencies forliabilities in active markets or other market observable inputs such as interest rates, yield curves and foreign currency spot rates; and
Level 3—Prices or valuations that require inputs that are both significant to the developmentfair value measurement and commercializationunobservable.
The Company's financial assets consist of product candidates.cash equivalents and the Company's financial liabilities consist of a warrant liability.

The fair value of the Company’s cash equivalents is determined using quoted prices in active markets. The Company's cash equivalents consist of money market funds that are classified as Level 1.

The fair value of the Company’s warrant liability is determined using a Monte Carlo simulation. See Note 9. Warrants for assumptions used and methodologies utilized in calculating the estimated fair value. The Company’s warrant liability is classified as Level 3.

Leases

At the inception of the contract, the Company recognizes revenue in accordance with FASB ASC Topic 605, Revenue Recognition (“ASC 605”). Accordingly, revenuedetermines if an arrangement is recognized for each unit of accounting when alla lease and has a lease term greater than 12 months. A lease qualifies as a finance lease if any of the following criteria are met:
persuasive evidencemet at the inception of the lease: (i) there is a transfer of ownership of the leased asset to the Company by the end of the lease term, (ii) the Company holds an arrangement exists
delivery has occurred or services have been rendered
option to purchase the fee is fixed or determinable
collectabilityleased asset that it is reasonably assured
Amounts received priorcertain to satisfyingexercise, (iii) the revenue recognition criterialease term is for a major part of the remaining economic life of the leased asset, (iv) the present value of the sum of lease payments equals or exceeds substantially all of the fair value of the leased asset, or (v) the nature of the leased asset is specialized to the point that it is expected to provide the lessor no alternative use at the end of the lease term. All other leases are recorded as deferred revenueoperating leases. All leases that are concluded to be in accordance with ASU No. 2018-11, Leases (Topic 842): Targeted Improvements are included in lease right-of-use (“ROU”) assets and lease liabilities in the Company’sconsolidated balance sheets. Amounts

ROU assets represent the Company's right to use an underlying asset for the lease term and lease liabilities represent the Company's obligation to make lease payments arising from the lease. Lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments over the lease term. As most of the Company's leases do not provide an implicit rate, the Company uses an estimate of its incremental borrowing rate based on the information available at the lease commencement date in determining the present value of lease payments. The Company uses the implicit rate when readily determinable. The operating lease ROU asset is reduced by deferred lease payments and unamortized lease incentives. The Company's lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Lease expense for fixed lease payments on operating leases are recognized over the expected to beterm on a straight-line basis, while lease expense for fixed lease payments on financing leases are recognized as revenue withinusing the 12 months following the balance sheet date are classified as a current liability. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as a non-current liability.effective interest



Grant revenue

Periodically,method over the Company receives grants from private not-for-profit organizations and federal agencies to conduct vaccine development research. Funds received in advance of services being performed are recorded as deferred revenue. Revenue under these grants is recognized as research services are performed.

Multiple-element arrangements

lease term. The Company analyzes multiple-element arrangements based on the guidance in FASB ASC Topic 605-25, Revenue Recognition—Multiple-Element Arrangements (“ASC 605-25”).has lease agreements with lease and non-lease components, which are generally accounted for separately. The Company applies this guidance to new arrangementsnon-lease components generally consist of common area maintenance that is expensed as well as existing arrangements that contain multiple deliverables. The Company determines the elements, or deliverables, included in the arrangement and allocates consideration under the arrangement to the various elements based on each element’s relative selling price. The identification of individual elements in a multiple-element arrangement and the estimation of the selling price of each element involves significant judgment, including consideration as to whether each delivered element has stand-alone value to the collaborator.

The Company determines the estimated selling price for deliverables within the arrangement using vendor-specific objective evidence (“VSOE”) of selling price, if available, or third-party evidence of selling price if VSOE was not available or the Company’s best estimate of selling price, if neither VSOE nor third-party evidence was available. The Company uses its best estimate of a selling price if it does not have VSOE or third-party evidence of selling price for these deliverables. In order to determine the best estimate of selling price, the Company considers market conditions, as well as entity- specific factors, including those factors contemplated in negotiating the agreements, as well as internally developed estimates that include assumptions related to the market opportunity, estimated development costs, probability of success, and the time needed to commercialize assays. In validating its best estimate of selling price, the Company evaluates whether changes in the key assumptions used to determine best estimate of selling price would have a significant effect on the allocation of arrangement consideration between deliverables. The Company recognizes consideration allocated to an individual element when all other revenue recognition criteria are met for that element, which generally occurs upon delivery or over the period in which services are provided.incurred.

Research and development expenses

Research and development costs are charged to expenseexpensed as incurred in performingincurred. The Company has entered into various research and development activities. The costs include employee compensation costs, facilities and overhead, clinical study and related clinical manufacturing costs, regulatorycontracts with research institutions and other related costs.
companies. Nonrefundable advanced payments for goods or services to be received in the future for use in research and development activities are deferred and capitalized. The capitalized amounts are expensed as the related goods are delivered or the services are performed.performed or when the goods have been received rather than when the payment is made. When evaluating the adequacy of the related accrued liabilities, the Company analyzes progress of the studies and/or services performed, including the phase or completion of events, invoices received and contracted costs.

Stock-based compensation expense

The Company accounts for its stock-based compensation awards to employees and directors in accordance with FASB ASC Topic 718, Compensation-Stock Compensation (“ASC 718”). ASC 718 requires alland adjusts the amounts recorded each period to reflect actual forfeitures.

Effective January 1, 2019, the Company recognizes stock-based payments to employees,compensation expense for stock-based awards, including grants of employee stock options and restricted stock, made to be recognized in the statements of operations and comprehensive loss based on their grant date fair values. Compensation expense related to awards to employees is recognized on a straight-line basisnon-employee consultants based on the grant dateestimated fair value on the date of grant, over the associatedrequisite service periodperiod. Through December 31, 2018, the Company recognized stock-based compensation expense for stock-based awards granted to non-employee consultants based on the fair value of the award,awards on each date on which is generallythe awards vest. Stock-based compensation expense was recognized over the vesting term. Share-based payments issued to non-employees are recorded at theirperiod, provided that services were rendered by such non-employee consultants during that time. At the end of each financial reporting period, the fair values,value of unvested options was re-measured using the then-current fair value of the common stock of the Company and are periodically revalued asupdated assumptions in the equity instrumentsBlack-Scholes option-pricing model.

For awards that vest and are recognized asor begin vesting upon achievement of a performance condition, the Company recognizes stock-based compensation expense overwhen achievement of the related service period in accordance with the provisions of ASC 718 and FASB ASC Topic 505, Equity, (“ASC 505”) and are expensedperformance condition is deemed probable using an accelerated attribution model.

The Company estimatesmodel over the fair value of its stock options using the Black- Scholes option pricing model, which requires the input of subjective assumptions, including (a) the expected volatilityimplicit service period. Certain of the Company’s stock price, (b) the expected term of the award, (c) the risk-free interest rate, (d) expected dividends and (e) the estimated fair value of the Company’s common stock on the measurement date. Due to the limited operating history ofawards that contain performance conditions also require the Company as a public entity and a lackto estimate the number of company specific historical and implied volatility data,awards that will vest, which the Company has based its estimateestimates when the performance condition is deemed probable of expected volatility on the historical volatility of a group of similar companies that are publicly traded. When selecting these public companies on which it has based its expected stock price volatility, the Company selected companies with comparable characteristics to it, including enterprise value, risk profiles, position within the industry, and with historical share price information sufficient to


meet the expected term of the stock-based awards. The Company computes historical volatility data using the daily closing prices for the selected companies’ shares during the equivalent period of the calculated expected term of the stock-based awards. The Company will continue to apply this process until a sufficient amount of historical information regarding the volatility of its own stock price becomes available. Due to the lack of Company specific historical option activity, the Company has estimated the expected term of its employee stock options using the “simplified” method, whereby, the expected term equals the arithmetic average of the vesting term and the original contractual term of the option. The expected term for non-employee awards is the remaining contractual term of the option. The risk-free interest rates are based on the U.S. Treasury securities with a maturity date commensurate with the expected term of the associated award. The Company has never paid, and does not expect to pay dividends in the foreseeable future. Following the closing of the Company’s IPO, the fair value of common stock is determined based on the quoted market price of the common stock.

The Company early adopted ASU 2016-09 Compensation — Stock Compensation (Topic 718) as of June 30, 2016. In connection with the early adoption, the Company elected an accounting policy to record forfeitures as they occur. There was no financial statement impact upon adoption as the Company had estimated a forfeiture rate of zero given that most options awards vest on a monthly basis. ASU 2016-09 also provides that companies no longer record excess tax benefits or certain tax deficiencies in additional paid-in capital (APIC). Instead, all excess tax benefits and tax deficiencies are recorded as income tax expense or benefit in the income statement. There was no financial statement impact of adopting this provision of the ASU as the Company is in a net operating loss (NOL) position and all excess tax benefits that exist from options previously exercised require a full valuation allowance. As such, the adoption of this standard did not have a material impact on the financial statements. For the year ended December 31, 2016, the Company did not record an income statement benefit for excess tax benefits as a valuation allowance is also required on these amounts.achievement.

Income taxes

IncomeThe Company accounts for income taxes are recorded in accordance with FASB ASC Topic 740, Income Taxes (“ASC 740”), which provides for deferred taxes using anunder the asset and liability approach.method. Under this method, deferred tax assets and liabilities are determined based onrecognized for the differenceestimated future tax consequences attributable to differences between the financial reporting and the tax reporting basisstatement carrying amounts of existing assets and liabilities and their respective tax basis. Deferred tax assets and liabilities are measured using the enacted tax rates and laws that are expected to be in effect whenfor the year in which these temporary differences are expected to reverse. The Company provides a valuation allowance against net deferred tax assets unless,recovered or settled. Valuation allowances are provided if, based uponon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will be realized. The Company has evaluated available evidence and concluded that the Company may not realize the benefit of its deferred tax assets; therefore, a valuation allowance has been established for the full amount of the deferred tax assets.

The Company accounts for uncertain tax positions in accordance with the provisions of ASC 740. When uncertain tax positions exist, the Company recognizes the tax benefit of tax positions to the extent that the benefit will more likely than not be realized. The determination as to whether the tax benefit will more likely than not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. As of December 31, 2016 and 2015, the Company does not have any significant uncertain tax positions. The Company’s practice is to recognize interest and/or penalties related to income tax matters in income tax expense.

Earnings per share

Basic earnings per share attributable to common stockholders is calculated by dividing net loss attributable to common stockholders by the weighted average shares outstanding during the period, without consideration for common stock equivalents. Net loss attributable to common stockholders is calculated by adjusting the net loss of the Company for cumulative preferred stock dividends and accretion of preferred stock issuance costs.

Diluted earnings per share attributable to common stockholders is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock and if-converted methods. For purposes of the diluted net loss per share attributable to common stockholders' calculation, preferred stock, stock options, unvested restricted stock, and warrants are considered to be common stock equivalents but have been excluded from the calculation of diluted net loss per share attributable to common stockholders, as their effect would be anti-dilutive for all periods presented. Therefore, basic and diluted net loss per share were

Basic net loss per share is computed by dividing the net loss by the weighted average number of common shares outstanding for the period. For periods in which the Company has reported net losses, diluted net loss per share is the same as basic net loss per share, because dilutive common shares are not assumed to have been issued if their effect is antidilutive. The Company reported a net loss for all periods presented.the years ended December 31, 2019 and 2018.

Comprehensive lossNew Accounting Pronouncements

Comprehensive loss consists of net lossThe following new accounting pronouncements were adopted by the Company on January 1, 2019:

In February 2016, the FASB issued ASU No. 2016-02, Leases, which replaced existing guidance in ASC 840, “Leases”, and changes in equity duringJuly 2018, the FASB issued ASU No. 2018-11, Leases (Topic 842): Targeted Improvements. The new standard establishes a period from transactionsROU that requires a lessee to recognize a ROU asset and other events and circumstances generated from non-owner sources. For all periods presented other comprehensive income (loss), if any, consists of unrealized gains and losseslease liability on the Company’s investments.balance sheet for all leases with a term longer than 12 months. Leases are classified as finance or operating, with classification affecting the pattern and classification of expense recognition in the income statement. The adoption of ASC 842 resulted in the Company recognizing ROU assets and related operating lease liabilities of $1.7 million and $1.8 million, respectively, in the consolidated balance sheet as of January 1, 2019. The Company used the modified retrospective method of adoption, with January 1, 2019 as the effective date of initial application.


Recent accounting pronouncements
StandardDescriptionEffect on the financial statements
ASU 2014-09, Revenue from Contracts with Customers (Topic 606)
The standard will replaceThe Company elected the short-term lease recognition exemption for all leases that qualify. The Company also elected the package of practical expedients for leases that commenced prior to January 1, 2019, allowing it not to reassess (i) whether any expired or existing contracts contain leases, (ii) the lease classification for any expired or existing leases and (iii) the initial indirect costs for any existing revenue recognition standards and significantly expand the disclosure requirements for revenue arrangements. It may be adopted either retrospectively or on a modified retrospective basis to new contracts and existing contracts with remaining performance obligations as of the effective date.

In July 2015, the FASB affirmed its proposal to defer the effective date of the new revenue standard for all entities by one year. As a result, public business entities will be required to apply the new revenue standard to annual reporting periods beginning after December 15, 2017. The standard will become effective for us on January 1, 2018 (the first quarter of the 2018 fiscal year).
At this time, the Company has not decided on which method it will use to adopt the new standard, nor has it determined the effects of the new guidelines on its results of operations and financial position as the Company does not currently have any arrangements that would be impacted by the new standard. As a result, the Company is continuing to evaluate the method of adoption and the impact of this standard on its consolidated financial statements.

ASU 2014-15, Presentation of Financial Statements — Going Concern (Subtopic 205-40)


In August 2014, the FASB issued ASU 2014-15, Disclosures of Uncertainties about an Entity’s Ability to Continue as a Going Concern. The standard requires an evaluation of whether there are conditions or events, considered in the aggregate, that raise substantial doubt about an entity’s ability to continue as a going concern. Substantial doubt about an entity’s ability to continue as a going concern exists when relevant conditions and events, considered in the aggregate, indicate that it is probable that the entity will be unable to meet its obligations as they become due within one year after the date that the financial statements are issued.

ASU 2014-15 is effective for annual periods ending after December 15, 2016 and for interim periods within annual periods beginning after December 15, 2016.
The Company adopted this standard as of December 31, 2016 and the adoption did not have a material impact. Refer to Footnote 1 for further details regarding the Company’s liquidity.


ASU 2016-02,
 Leases (Topic 842)

In February 2016, the FASB issued ASU 2016-02, which replaces the existing lease accounting standards.

The new standard requires a dual approach for lessee accounting under which a lessee would account for leases as finance (also referred to as capital) leases or operating leases. Both finance leases and operating leases will result in the lessee recognizing a right-of-use asset and corresponding lease liability. For finance leases the lessee would recognize interest expense and amortization of the right-of-use asset and for operating leases the lessee would recognize straight-line total lease expense.

ASU 2016-02 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2018.

The Company generally does not finance purchases of equipment but it does lease office and lab facilities. The Company is in the process of evaluating the effect that this ASU will have on its consolidated financial statements and related disclosures.


In June 2018, the FASB issued ASU No. 2018-07, Improvements to Nonemployee Share Based Payment Accounting. The new standard largely aligns the accounting for share-based payment awards issued to employees and nonemployees by expanding the scope of ASC 718 to apply to nonemployee share-based transactions, as long as the transaction is not effectively a form of financing. The Company adopted the provisions of ASU No. 2018-17 effective January 1, 2019, which did not have a material impact on the Company's consolidated financial statements for the year ended December 31, 2019.

ASU 2016-18, Statement of Cash Flows (Topic 230): Restricted Cash
In November 2016, the FASB issued ASU 2016-18, which requires additional disclosures related to restricted cash.

The new standard requires that amounts generally described as restricted cash and restricted cash equivalents be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows.

ASU 2016-18 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2017.


The Company does not expect the adoption of this standard to have a material effect on its consolidated financial statements.
The following new accounting pronouncements have been issued but are not yet effective as of December 31, 2019:

In June 2016, the FASB issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available-for-sale debt securities. The new standard is effective beginning January 1, 2020. Based on the composition of the Company's investment portfolio, which includes only money market funds, and the insignificance of the Company's other financial assets, current market conditions, and historical credit loss activity, the Company does not expect the adoption of this standard to have a material impact on the consolidated financial position and results of operations and related disclosures.

In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework – Changes to the Disclosure Requirements for Fair Value Measurement. The new standard requires public entities to disclose certain new information and modifies some disclosure requirements. The new standard is effective beginning January 1, 2020. The Company does not expect that the adoption of this standard will have a material impact on its disclosures.

In August 2018, the FASB issued ASU 2018-15, Intangibles-Goodwill and Other-Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract. ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. The new standard is effective beginning January 1, 2020. The Company does not expect that the adoption of this standard will have a material impact on its consolidated financial position and results of operations and related disclosures.

3. Cash, cash equivalents and investments

AsFair value of December 31, 2016 and 2015, cash, cash equivalents and investments comprised funds in depository, money market accounts, U.S treasury securities, and FDIC-insured certificates of deposit.financial instruments
    
The following table presentssets forth the cash equivalentsCompany's assets and investments carriedliabilities that are measured at fair value in accordance with the hierarchy defined in Note 2 (in thousands): 

 Total 
Quoted prices
in active
markets
(Level 1)
 
Significant
other
observable
inputs
(Level 2)
 
Significant
unobservable
inputs
(Level 3)
December 31, 2016       
Money market funds, included in cash equivalents$25,602
 $25,602
 $
 $
Certificates of deposit, included in cash equivalents992
 
 992
 
Investments - U.S treasuries16,508
 16,508
 
 
Investments - certificates of deposit19,429
 
 19,429
 
Total$62,531
 $42,110
 $20,421
 $
        
December 31, 2015       
Money market funds, included in cash equivalents$14,207
 $14,207
 $
 $
U.S treasuries, included in cash equivalents2,203
 2,203
 
 
Investments - U.S. treasuries27,924
 27,924
 
 
Investments - certificates of deposit61,249
 
 61,249
 
Total$105,583
 $44,334
 $61,249
 $

Cash equivalents and marketable securities have been initially valued at the transaction price and subsequently valued, at the end of each reporting period, utilizing third party pricing services or other market observable data. The pricing services utilize industry standard valuation models, including both income and market based approaches and observable market inputs to determine value. The Company validates the prices provided by its third party pricing services by reviewing their pricing methods and obtaining market values from other pricing sources. After completing its validation procedures, the Company did not adjust any fair value measurements provided by the pricing serviceson a recurring basis as of December 31, 20162019 and 2015.
Cash equivalents and investments at December 31, 2016 consist of the following2018 (in thousands):
 Total 
Quoted prices in active markets
(Level 1)
 
Significant other
observable inputs
(Level 2)
 
Significant
unobservable inputs
(Level 3)
December 31, 2019       
Assets       
Cash equivalents39,971
 39,971
 
 
Total assets$39,971
 $39,971
 $
 $
        
Liabilities       
Warrant liability2,486
 
 
 2,486
Total liabilities$2,486
 $
 $
 $2,486
        
December 31, 2018       
Assets       
Cash equivalents24,651
 24,651
 
 
Total assets$24,651
 $24,651
 $
 $
        
Liabilities       
Warrant liability3,472
 
 
 3,472
Total liabilities$3,472
 $
 $
 $3,472



 
Contractual
Maturity
 
Amortized
Cost
 
Unrealized
Gains
 
Unrealized
Losses
 Fair Value
Cash equivalents and investments   
  
  
  
U.S. Treasuries31-181 days $16,508
 $
 $
 $16,508
Certificates of deposit4-180 days 20,421
 
 
 20,421
Total  $36,929
 $
 $
 $36,929

Cash equivalents and investments at December 31, 2015 consist ofThe following table reflects the followingchange in the Company’s Level 3 warrant liability (in thousands):

 
Contractual
Maturity
 
Amortized
Cost
 
Unrealized
Gains
 
Unrealized
Losses
 Fair Value
Cash equivalents and investments   
  
  
  
U.S. Treasuries60-184 days $30,120
   $7
   $
   $30,127
Certificates of deposit91-365 days 49,145
 
 
 49,145
Certificates of depositgreater than 365 days 12,104
 
 
 12,104
Total  $91,369
 $7
 $
 $91,376

  Warrant liability
Balance at Issuance (January 2018) $18,231
Change in fair value (14,757)
Warrants exercised (2)
Balance at December 31, 2018 $3,472
Change in fair value (986)
Balance at December 31, 2019 $2,486

4. Property and equipment, net

Property and equipment, net consist of the following (in thousands):
December 31,December 31,
2016 20152019 2018
Laboratory equipment$4,894
 $3,943
$4,125
 $3,761
Furniture office equipment921
 610
Internally developed software2,547
 1,970
Leasehold improvements1,524
 1,524
Furniture and office equipment456
 447
Computer hardware317
 259
338
 338
Leasehold improvements1,514
 1,433
Internally developed software1,390
 338
Internally developed software in progress97
 
Total property and equipment9,036
 6,583
9,087
 8,040
Accumulated depreciation(4,165) (2,500)
Accumulated depreciation and amortization(6,470) (5,458)
Property and equipment, net$4,871
 $4,083
$2,617
 $2,582

Depreciation expense was $1.7$0.7 million $1.1 million, and $0.5 million, for both the years ended December 31, 2016, 2015, 2014,2019 and 2018, respectively. A portion ofAmortization related to the Company's internally developed computer software was placed into service during April 2016 and $0.1$0.4 million of amortization was recorded for both the yearyears ended December 31, 2016. No internally developed software was available to be placed into service2019 and no amortization was recorded for the year ended December 31, 2015.2018, respectively.





5. Accrued expenses and other current liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):
December 31,December 31,
2016 20152019 2018
Payroll and employee-related costs$2,090
 $1,736
$2,245
 $2,147
Research and development costs1,239
 1,359
1,607
 759
Other current liabilities849
 880
759
 910
Total$4,178
 $3,975
$4,611
 $3,816

6. Long-term debtCommitments and contingencies

Operating Leases

As of January 1, 2019, the Company has entered into two lease agreements for two floors of lab and office space in a multi-tenant building in Cambridge, Massachusetts. 

In March 2019, the Company entered into a sublease agreement for a portion of office space lease through February 2020. Since the Company retained its obligations under the sublease, it did not adjust the lease liability, however the sublease is being reflected as a reduction of lease expense.

In May 2019, the Company entered into a lease extension for office and lab space through February 2025. As a result of the lease term extension, the Company recognized an increase in the ROU assets of $5.4 million and associated lease liabilities of $5.3 million. The associated lease obligation for the extension is included in the Company’s ROU assets and associated lease liabilities as of December 31, 2019. The Company has the option to extend the lease terms for an additional five years, which is not included in the Company's ROU assets and associated lease liabilities as of December 31, 2019.
In July 2019, the Company exercised an option for additional office and lab space from March 2020 through February 2025. As the Company does not have the right to use or control the office space, the Company has not included the associated lease obligation in its determination of ROU assets and associated lease liabilities as of December 31, 2019. The Company's lease obligation associated with the additional lab and office space is $7.2 million and will be reflected as a lease liability upon it's right to use the office space in March 2020.

For the year ended December 31, 2019, lease expense, net of sublease income, was $1.5 million.

The weighted average remaining lease term and weighted average discount rate of the Company's operating leases are as follows:
December 31, 2019
Weighted average remaining lease term in years5.12
Weighted average discount rate8.27%

2014 Term Loan, First Amendment    Finance Lease

In December 2019, the Company entered into an agreement to lease lab equipment for a term of 15 months. The Company determined that the agreement qualifies as a finance lease based on the criteria that the Company holds the option to purchase the asset and is reasonably certain to exercise at the end of the lease term. The ROU asset and lease liability were calculated using an incremental borrowing rate of 7.95%. Lease payments on this lease begin in January 2020.



On November 20, 2014 (the "Closing Date"





The following table summarizes the presentation in the Company's consolidated balance sheets:
Leases (in thousands) Classification December 31, 2019
Assets    
Operating Lease right-of-use asset $6,156
Finance Lease right-of-use asset 150
Total leased assets   $6,306
Liabilities    
Current    
   Operating Lease liabilities $990
   Finance Lease liabilities 127
Non-current    
   Operating Lease liabilities, net of current portion 5,373
   Finance Lease liabilities, net of current portion 22
Total lease liabilities   $6,512

The minimum lease payments related to the Company's operating leases in accordance with ASC 842 as of December 31, 2019 were as follows (in thousands):

 Operating Leases Finance Leases Total
2020$1,477
 $134
 $1,611
20211,473
 23
 1,496
20221,511
 
 1,511
20231,548
 
 1,548
2024 and thereafter1,853
 
 1,853
   Total lease payments$7,862
 $157
 $8,019
Less imputed interest(1,500) (7) (1,507)
   Total$6,362
 $150
 $6,512

The following information is disclosed in accordance with ASC 840, which was applicable until the adoption of ASC 842 as of January 1, 2019. As of December 31, 2018, future minimum commitments under the Company's operating leases with initial terms of more than one year were as follows (in thousands):
  Total Lease Commitments
2019 $1,637
2020 274
Total $1,911

For the year ended December 31, 2018, under ASC 840, the Company paid $1.5 million in rent expense.

At December 31, 2019 and 2018, the Company has an outstanding letter of credit of $0.6 million and $0.3 million, respectively, with a financial institution related to a security deposit for the office and lab space lease. The amount is secured by cash on deposit and expires on February 28, 2025.

Contractual obligations
The Company has entered into certain agreements with various contract research organizations ("CROs") and contract manufacturing organizations ("CMOs"), which generally include cancellation clauses.




Harvard University License Agreement

              The Company has an exclusive license agreement with Harvard University (“Harvard”), granting the Company an exclusive, worldwide, royalty-bearing, sublicensable license to three patent families, to develop, make, have made, use, market, offer for sale, sell, have sold and import licensed products and to perform licensed services related to the ATLAS discovery platform. The Company is also obligated to pay Harvard milestone payments up to $1.6 million in the aggregate upon the achievement of certain development and regulatory milestones. As of December 31, 2019, the Company has paid $0.3 million in aggregate milestone payments. The Company is obligated under this license agreement to use commercially reasonable efforts to develop, market and sell licensed products in compliance with an agreed upon development plan. In addition, the Company is obligated to achieve specified development milestones and in the event the Company is unable to meet its development milestones for any type of product or service, absent any reasonable proposed extension or amendment thereof, Harvard has the right, depending on the type of product or service, to terminate this agreement with respect to such products or to convert the license to a non-exclusive, non-sublicensable license with respect to such products and services.

Upon commercialization of our products covered by the licensed patent rights or discovered using the licensed methods, the Company is obligated to pay Harvard royalties on the net sales of such products and services sold by the Company, the Company's affiliates, and the Company's sublicensees. This royalty varies depending on the type of product or service but is in the low single digits. The sales-based royalty due by the Company’s sublicensees is the greater of the applicable royalty rate or a percentage in the high single digits or the low double digits of the royalties the Company receives from such sublicensee, depending on the type of product. Based on the type of commercialized product or service, royalties are payable until the expiration of the last-to-expire valid claim under the licensed patent rights or for a period of 10 years from first commercial sale of such product or service. The royalties payable to Harvard are subject to reduction, capped at a specified percentage, for any third-party payments required to be made. In addition to the royalty payments, if the Company receives any additional revenue (cash or non-cash) under any sublicense, the Company must pay Harvard a percentage of such revenue, excluding certain categories of payments, varying from the low single digits to up to the low double digits depending on the scope of the license that includes the sublicense.

              This license agreement with Harvard will expire on a product-by-product or service-by-service and country-by-country basis until the expiration of the last-to-expire valid claim under the licensed patent rights. The Company may terminate the agreement at any time by giving Harvard advance written notice. Harvard may also terminate the agreement in the event of a material breach by the Company that remains uncured; in the event of our insolvency, bankruptcy, or similar circumstances; or if the Company challenges the validity of any patents licensed to us.

Oncovir License and Supply Agreement

In January 2018, the Company entered into a License and Supply Agreement with Oncovir, Inc. (“Oncovir”). The agreement provides the terms and conditions under which Oncovir will manufacture and supply an immunomodulator and vaccine adjuvant, Hiltonol® (poly-ICLC) (“Hiltonol”), to the Company for use in connection with the research, development, use, sale, manufacture, commercialization and marketing of products combining Hiltonol with the Company's technology (the “Combination Product”). Hiltonol is the adjuvant component of GEN-009, which will consist of synthetic long peptides or neoantigens identified using the Company's proprietary ATLAS platform, formulated with Hiltonol. 

              Oncovir granted the Company a non-exclusive, assignable, royalty-bearing worldwide license, with the right to grant sublicenses through one tier, to certain of Oncovir’s intellectual property in connection with the research, development, or commercialization of Combination Products, including the use of Hiltonol, but not the use of Hiltonol for manufacturing or the use or sale of Hiltonol alone. The license will become perpetual, fully paid-up, and royalty-free on the later of January 25, 2028 or the date on which the last valid claim of any patent licensed to the Company under the agreement expires.

Under this agreement, the Company is obligated to pay Oncovir low to mid six figure milestone payments upon the achievement of certain clinical trial milestones for each Combination Product and the first marketing approval for each Combination Product in certain territories, as well as tiered royalties in the low-single digits on a product-by-product basis based on the net sales of Combination Products.

              The Company may terminate the agreement upon a decision to discontinue the development of the Combination Product or upon a determination by the Company or an applicable regulatory authority that Hiltonol or a Combination Product is not clinically safe or effective. The agreement may also be terminated by either party due to a material uncured breach by the other party, or due to the other party’s bankruptcy, insolvency, or dissolution.



7. Long-term debt
In April 2018, the Company entered into an amended and restated loan and security agreement (the “Loan Agreement”) with Hercules Technology Growth Capital, Inc. (“Hercules”("Hercules"), which provided up to $27.0 millionwas subsequently amended in debt financing in three separate tranches (the “2014 Term Loan”). The first tranche of $17.0 million was available through June 30, 2015, of which $12.0 million was drawn down at loan inception for which approximately $9.8 million ofNovember 2019 (as amended, the proceeds were used to repay all outstanding indebtedness under the previously existing $10.0 million loan agreement (the "2013"2018 Term Loan"). The Company recorded a $435 thousand loss on extinguishment of debt in other expense on the Statements of Operations related to deferred debt charges, the unamortized portion of the original issue discount related to the 20132018 Term Loan and other fees associated with extinguishing the debt.provides a $14.0 million term loan. The option to draw down the remaining $5.0 million under the first tranche expired unused on June 30, 2015. The second tranche of $5.0 million was subject to certain eligibility requirements which were achieved as of June 30, 2015 and the Company had the option to draw down the second tranche on or prior to December 15, 2015. The second tranche expired unused on December 15, 2015 The third tranche of $5.0 million was not eligible to draw as the Company did not achieve positive results from its Phase 2a human challenge study of GEN-004.

In December 2015, the Company amended the Loan Agreement (the "First Amendment") with Hercules. The First Amendment required the Company to draw an additional $5.0 million and permits it to draw two additional $5.0 million tranches. One $5.0 million tranche was immediately available to draw through December 15, 2016 and a second $5.0 million tranche could have become available through December 15, 2016, subject to the Company demonstrating sufficient evidence of continued clinical progression of its GEN-003 product and making favorable progress in applying its proprietary technology platform toward the development of novel immunotherapies with application in oncology. Both tranches expired unused at December 31, 2016, and $17.0 million was outstanding under the amended 20142018 Term Loan at December 31, 2016.

2014 Term Loan

The 2014 Term Loan had an original maturity of Julymatures on May 1, 2018. The eligibility requirements for the second tranche also contained an election for the Company to extend the maturity date to January 1, 2019. During the second quarter of 2015, the Company elected to extend the maturity date of the 2014 Term Loan. The maturity date of January 1, 2019 remained unchanged by the First Amendment.

Each advance2021 and accrues interest at a floating rate per annum equal to the greater of (i) 7.25%8.00%, or (ii) the sum of 7.25%3.00% plus the prime rate minus 5.0%.rate. The 20142018 Term Loan providedprovides for interest-only payments until December 31, 2015, which was extended by the Company for a six-month period as the eligibility requirements for the second tranche were met during the second quarterJanuary 1, 2021. Thereafter, payments will include equal installments of 2015. The First Amendment subsequently extended the interest only period through June 30, 2017. Thereafter, beginning July 1, 2017, principal and interest payments will be made monthly for 18 months with a payoff schedule based upon a 30-month amortization schedule, the original amortization term of the 2014 Term Loan.through maturity. The remaining unpaid principal is due at January 1, 2019.

The 20142018 Term Loan may be prepaid in whole or in part upon seven business days’ prior written notice to Hercules.  Prepayments will be subject to a charge of 3.0% if an advance is prepaid within 12 months following the Closing Date, 2.0%, if an advance is prepaid between 12 and 24 months following the Closing Date, and 1.0% thereafter. Amounts outstanding at the time of an event of default shall be payable on demand and shall accrue interest at an additional rate of 5.0% per annum on any outstanding amounts past due.prepayment charge. The Company is also obligated to pay an end of term charge of 4.95% (the "End of$1.0 million at maturity. The Company evaluated the November 2019 amendment to the 2018 Term Charge") of the balance drawn when the advances are repaid.Loan and concluded that it was a modification pursuant to ASC 470-50, Debt (Topic 470).

The 20142018 Term Loan is secured by a lien on substantially all of the assets of the Company, other than intellectual property, provided that such lien on substantially all assets includes any rights to paymentsproperty. Hercules has a perfected first-priority security interest in certain cash, cash equivalents and proceeds from the sale, licensing or disposition of intellectual property.investment accounts. The 2018 Term Loan Agreement contains non-financial covenants, representations and representations, including a financial reporting covenant, and limitations on dividends, indebtedness, collateral, investments, distributions, transfers, mergers or acquisitions, taxes, corporate changes, deposit accounts, and subsidiaries.Material Adverse Effect provision. There are no financial covenants.

Under the provisions of the 2014 Term Loan, the Company has also entered into account control agreements ("ACAs") with Hercules and certain of the Company's financial institutions in which cash, cash equivalents, and investments are held. These ACAs grant Hercules a perfected first priority security interest in the subject accounts. The ACAs do not restrict the Company's ability to utilize cash, cash equivalents, or investments to fund operations and capital expenditures unless there is an Event of Default and Hercules activates its rights under the ACAs.

The Loan Agreement contains a Material A "Material Adverse Effect provision that requires all material adverse effects to be reported under the financial reporting covenant. Loan advances are subject to a representation that no event that has had or could reasonably be expected to have a Material Adverse Effect has occurred and is continuing. Under the Loan Agreement, a


Material Adverse EffectEffect" means a material adverse effect upon: (i) the business, operations, properties, assets or condition (financial or otherwise) of the Company; or (ii) the ability of the Company to perform the secured obligations in accordance with the terms of the Loan Agreements,loan documents, or the ability of agent or lender to enforce any of its rights or remedies with respect to the secured obligations; or (iii) the collateral or agent’s liens on the collateral or the priority of such liens. Any event that has a Material Adverse Effect or would reasonably be expected to have a Material Adverse Effect is an event of default under the Loan Agreement and repayment of amounts due under the Loan Agreement may be accelerated by Hercules under the same terms as an event of default.

Events As of default underDecember 31, 2019, the Loan Agreement include failure to make any payments of principal or interest as due on any outstanding indebtedness, breach of any covenant, any false or misleading representations or warranties, insolvency or bankruptcy, any attachment or judgment on the Company’s assets of at least $100 thousand, or the occurrence of any material defaultCompany was in compliance with all covenants of the Company involving indebtedness in excess of $100 thousand. If an event of default occurs, repayment of all amounts due under the Loan Agreement may be accelerated by Hercules, including the applicable Prepayment Charge.

2018 Term Loan. The 20142018 Term Loan is automatically redeemable upon a change in control whereas the Company must prepay the outstanding principal and any accrued and unpaid interest through the prepayment date including any unpaid agent’s and lender’s fees and expenses accrued to the date of the repayment including the End of Term Charge and the applicable Prepayment Charge. If a change in control occurs, repayment of amounts due under the Loan Agreement may be accelerated by Hercules.control. The Company believes acceleration of the repayment of amounts outstanding under the loan is remote.remote, and therefore, the debt balance is classified according to the contractual payment terms at December 31, 2019.

In connection with a previously issued term loan in 2014 the Company issued common stock warrants to Hercules which expired unexercised in November 2019. In connection with the 2018 Term Loan, the Company issued common stock warrants to Hercules (the “Hercules Warrant”). See Note 9. Warrants.

As of December 31, 2019 and 2018, the Company had outstanding borrowings of $13.4 million and $14.8 million, respectively. During the years ended December 31, 2019 and 2018, the Company made payments of $1.9 million and $0.5 million on its long term debt. Interest expense was $1.6 million and $1.7 million for the years ended December 31, 2019 and 2018, respectively.

Future principal payments, including the End of Term Charges, are as follows (in thousands):
 December 31,
 2019
2020$
202113,960
Total$13,960

8. Stockholders' equity

2019 Public Offering

In June 2019, the Company entered into an underwriting agreement relating to the public offering of 10,500,000 shares of the Company’s common stock, par value $0.001 per share, at a price of $3.50 per share, for gross proceeds of approximately $36.8 million (the “2019 Public Offering”). The Company also granted the underwriters an option to purchase up to an additional 1,575,000 shares of common stock (“Overallotment Option”). On June 26, 2019, the underwriters exercised this option in full. The Company received approximately $5.5 million in gross proceeds from the underwriter’s exercise of the Overallotment Option. In connection with the 2019 Public Offering, inclusive of the Overallotment Option, the Company received net proceeds of $38.4 million.

Private Placement

In February 2019, the Company completed a private placement financing transaction (the “Private Placement”). The Company issued 3,199,998 shares of common stock, prefunded warrants (the “Pre-Funded Warrants”) to purchase 531,250 shares of common stock (the “Pre-Funded Warrant Shares”), and warrants (the “Private Placement Warrants”) to purchase up to 932,812 shares of common stock (the “Warrant Shares”). The Shares, Pre-Funded Warrants and Private Placement Warrants (collectively, the “Units”) were sold at a purchase price of $4.02 per Unit. The Company received net cash proceeds of approximately $13.8 million for the purchase of the Shares, Pre-Funded Warrant Shares and Warrant Shares. See Note 9. Warrants.



The Company had the option to issue additional shares of common stock in a second closing (the “Second Closing”) for gross proceeds of up to $24.2 million. The occurrence of the Second Closing was conditioned on top-line results from Part A of the Company's Phase 1/2a clinical trial for GEN-009 and a decision by the Company's board of directors to proceed with the Second Closing. In June 2019, the Company announced top-line results from this trial but elected not to proceed with the Second Closing. In lieu of the Second Closing, the Company proceeded with the 2019 Public Offering.

2018 Public Offering

In January 2018, the Company entered into two underwriting agreements, the first relating to the public offering of 6,670,625 shares of the Company’s common stock, par value $0.001 per share, and accompanying warrants to purchase up to 3,335,313 shares of common stock (“2018 Public Offering Warrants”), at a combined price of $8.00 per share, for gross proceeds of approximately $53.4 million (the “2018 Common Stock Offering”) and the second relating to the public offering of 1,635 shares of the Company’s Series A convertible preferred stock ("Preferred Stock"), par value $0.001 per share, which are convertible into 204,375 shares of common stock, and accompanying warrants to purchase up to 102,188 shares of common stock for gross proceeds of approximately $1.6 million (the “Preferred Stock Offering,” and together with the 2018 Common Stock Offering, the “January 2018 Financing”). The Company received approximately $1.0 million in gross proceeds and issued 119,718 shares of common stock and warrants to purchase up to 179,757 shares of common stock from the underwriters' exercise of their overallotment option.

Preferred Stock

Each share of preferred stock is convertible into 125 shares of common stock, subject to certain adjustments upon stock dividends and stock splits. The holders of preferred stock shall be entitled to receive dividends in the same form as dividends actually paid on shares of common stock when, as and if such dividends are declared by the Board of Directors and paid on shares of the common stock, on an as-if-converted-to-common stock basis.

Issuance costs

In connection with the 2014 Term Loan,January 2018 Financing, the Company issued a common stock warrant to Hercules on November 20, 2014.incurred approximately $4.0 million of issuance costs. The warrant is exercisable for 73,725 sharesCompany allocated approximately $2.6 million of the Company’sissuance costs to the common and preferred stock (equal to $607,500 divided by the exercise price of $8.24). The exercise pricewithin additional paid-in capital and the number of shares are subject to adjustment upon a merger event, reclassificationimmediately expensed approximately $1.4 million of the shares of common stock, subdivision or combination of the shares of common stock or certain dividends payments. The warrant is exercisable until November 20, 2019 and will be exercised automatically on a net issuance basis if not exercised priorcosts allocated to the expiration date and if the then-current fair market value of one share of common stock is greater than the exercise price then in effect. The warrant has beenliability classified as equity for all periods it has been outstanding.2018 Public Offering Warrants.

ContemporaneouslyWarrants

See Note 9. Warrants.

Hercules

In connection with the 2014 Term2018 Loan Agreement with Hercules, the Company also entered into an amendment to the November 2014 equity rights letter agreement on November 20, 2014 (the “Equity“Amended Equity Rights Letter Agreement”). Pursuant to the Equity Rights Letter Agreement, the Company issued to Hercules 223,463 shares of the Company’s Common Stock for an aggregate purchase price of approximately $2.0 million at a price per share equal to the closing price of the Company’s Common Stock as reported on The NASDAQ Global Market on November 19, 2014.  The shares will be subject to resale limitations and may be resold only pursuant to an effective registration statement or an exemption from registration.

Additionally, under the Equity Rights Letter Agreement, Hercules has the right to participate in any one or more subsequent private placement equity financings of up to $2.0 million on the same terms and conditions as purchases by the other investors in each subsequent equity financing. The Amended Equity Rights Letter Agreement and all rights and obligations thereunder, will terminate upon the earlier of (1) such time when Hercules has purchased $2.0 million of subsequent equity financing securities in the aggregate, and (2) the later of (a) the repayment of all indebtedness under the 2018 Term Loan, Agreement andor (b) the expiration or termination of the exercise period for the warrantHercules Warrant. See Note 9. Warrants.

Agreement with Lincoln Park Capital

In October 2019, the Company entered into a purchase agreement with Lincoln Park Capital (“LPC”) pursuant to which LPC purchased shares of the Company's common stock at a purchase price of $2.587 per share and received net proceeds of approximately $2.5 million. In addition, for a period of thirty months, the Company has the right, at its sole discretion, to sell up to an additional $27.5 million of the Company's common stock based on prevailing market prices of its common stock at the time of each sale. In consideration for entering into the purchase agreement, the Company issued 289,966 shares of its common stock to LPC as a commitment fee. The purchase agreement limits our sales of shares of common stock to LPC to 5,227,323 shares of common stock, representing 19.99% of the shares of common stock outstanding on the date of the purchase agreement. The purchase agreement also prohibits us from directing LPC to purchase any shares of common stock if those shares, when aggregated with all other shares of our common stock then beneficially owned by LPC and its affiliates, would result in connection withLPC and its affiliates having beneficial ownership, at any single point in time, of more than 9.99% of the Loan Agreement.then total outstanding shares of our common stock. The Company allocated $36 thousand of financing costsdetermined that the right to sell additional paid-in capital for issuance feesshares represents a freestanding put option that were reimbursed to Hercules.meets the criteria

The
of a derivative pursuant to ASC 815 Derivatives and Hedging, but has a fair value of zero, and therefore no additional accounting was required.

At-the-market equity offering program

In 2015, the Company incurred $0.3entered into an agreement, as amended, with Cowen and Company, LLC to establish an at-the-market equity offering program (“ATM”) pursuant to which it was able to offer and sell shares of its common stock at prevailing market prices from time to time. Through December 31, 2019, the Company has sold an aggregate of 463,887 shares under the ATM and received approximately $4.0 million in debt financing costs related to the First Amendment which was recorded as a debt discount and will be amortized over the remaining loan term. In connection with the issuance of the 2014 Term Loan, the Company incurred $0.1 million of financing costs and also reimbursed Hercules $0.2 million for debt financing costs which has been recorded as a debt discount and will be amortized over the remaining loan term. The End of Term Charge is amortized ratably over the term loan period based upon the outstanding debt and the increase in the amount of End of Term Charge due to the additional borrowing from the First Amendment is being amortized from the First Amendment date through maturity. The debt discount is being amortized to interest expense over the life of the 2014 Term Loan using the effective interest method. At December 31, 2016, the 2015 Term Loan bears an effective interest rate of 10.2%.net proceeds.

9. Warrants

As of December 31, 2016 and 2015,2019, the Company had outstanding borrowings under the 2014 Term Loanfollowing potentially issuable shares of $17.0 million. Interest expensecommon stock related to unexercised warrants outstanding:

  Shares Exercise price Expiration date Classification
Hercules Warrant 41,177
 $6.80
 Q2 2023 Equity
2018 Public Offering Warrants 3,616,944
 $9.60
 Q1 2023 Liability
Private Placement Warrants 932,812
 $4.52
 Q1 2024 Equity
Pre-Funded Warrants 531,250
 $0.08
 Q1 2039 Equity
  5,122,183
      

Hercules Warrant

The exercise price and the 2014 Term Loan was $1.7number of shares are subject to adjustment upon a merger event, reclassification of the shares of common stock, subdivision or combination of the shares of common stock or certain dividends payments. The Company determined that the Hercules Warrant should be equity classified in accordance with ASC 480, Distinguishing Liabilities from Equity ("ASC 480") for all periods presented.

2018 Public Offering Warrants

The exercise price and the number of shares are subject to adjustment upon a merger event, reclassification of the shares of common stock, subdivision or combination of the shares of common stock or certain dividends payments. In the event of an “Acquisition,” defined generally to include a merger or consolidation resulting in the sale of 50% or more of the voting securities of the Company, the sale of all, or substantially all, of the assets or voting securities of the Company, or other change of control transaction, as defined in the 2018 Public Offering Warrants, the Company will be obligated to use its best efforts to ensure that the holders of the 2018 Public Offering Warrants receive new warrants from the surviving or acquiring entity (the “Acquirer”). The new warrants to purchase shares in the Acquirer shall have the same expiration date as the 2018 Public Offering Warrants and a strike price that is based on the proportion of the value of the Acquirer’s stock to the Company’s common stock. If the Company is unable, despite its best efforts, to cause the Acquirer to issue new warrants in the Acquisition as described above, then, if the Company’s stockholders are to receive cash in the Acquisition, the Company will settle the 2018 Public Offering Warrants in cash and if the Company’s stockholders are to receive stock in the Acquisition, the Company will issue shares of its common stock to each Warrant holder.

The Company determined that the 2018 Public Offering Warrants should be liability classified in accordance with ASC 480. As the 2018 Public Offering Warrants are liability-classified, the Company remeasures the fair value at each reporting date. The Company initially recorded the 2018 Public Offering Warrants at their estimated fair value of approximately $18.2 million. In connection with the Company's remeasurement of the 2018 Public Offering Warrants to fair value, the Company recorded income of $1.0 million and $1.3 million and $0.1$14.8 million for the years ended December 31, 2016, 2015,2019 and 2014,2018, respectively. Interest expense related to the 2013 Term Loan was $0.8 million for the year ended December 31, 2014.

Future principal payments, including the End of Term Charge, on the 2014 Term Loan are as follows (in thousands):


 December 31,
 2016
2017$3,149
20186,659
20198,034
Total$17,842

2013 Term Loan

On September 30, 2013, the Company entered into the 2013 Term Loan which provided up to $10.0 million. The Company drew down $3.5 million upon closing the 2013 Term Loan to pay off existing debt obligations and drew down the remaining facility of $6.5 million in December 2013. The Company was obligated to make interest-only payments for the first 9 months and 33 equal payments of principal, together with accrued interest thereafter for each advance. The 2013 Term Loan bore interest at a rate of 8% per annum. The Company was also obligated to pay 2% of the advance on the final repayment date of each draw which was accrued over the term of the debt.

In connection with the 2013 Term Loan, the Company issued a warrant to purchase 689,655 shares of Series C Preferred Stock at $0.58 per share. Upon the completion of the Company's IPO, these Series C preferred stock warrants automatically converted into warrants exercisable for 57,954 shares of Common Stock at an exercise price of $6.90 per share (Note 7).

7. Warrants

As of December 31, 2016 and December 31, 2015, the Company had warrants outstanding that represent the right to acquire 77,603 shares of common stock, of which 73,725 represented warrants issued to Hercules in relation to the 2014 Term Loan and 3,878 represented warrants to purchase common stock issued in periods prior to the Company's IPO.

Hercules Warrants

In accordance with ASC Topic No. 815, “Derivatives and Hedging” (Topic No. 815), the Company determined the common stock warrant issued to Hercules to be equity classified. The Company estimated the fair value of this warrant as of the issuance date using a Black-Scholes option pricing model (with a 10% discount for lack of marketability) with the following assumptions:
 November 20,
2014
Fair value of underlying instrument$9.05
 
Expected volatility70.0
%
Expected term (in years)5
 
Risk-free interest rate1.64
%
Expected dividend yield0.0
%

The Company utilized this fair value in its allocation of debt proceeds between debt and the warrants which was performed on a relative fair value basis. Ultimately, the Company allocated $334 thousand to the Hercules warrants and recognized this amount in additional paid-in capital.

As of December 31, 2016, the common stock warrants issued to Hercules remained outstanding.

Warrants to purchase redeemable securities

As of December 31, 2013, the Company had outstanding warrants to purchase 2,291,512 shares of redeemable convertible preferred stock. On January 29, 2014, 21,695 warrants to purchase Series A preferred stock were exercised for cash. On February 4, 2014, an additional 28,926 warrants to purchase Series A preferred stock were exercised for cash. Prior to the completion of the Company's IPO on February 10, 2014, warrants to purchase 987,840 shares of Series A preferred stock were exercised in a cashless exercise for 316,932 shares of Series A preferred stock, which automatically converted into 26,633 shares of Common Stock upon the completion of the Company's IPO. Also upon the completion of the Company's IPO, warrants exercisable for 1,253,051 shares of redeemable convertible preferred stock were automatically converted into warrants


exercisable for 105,297 shares of Common Stock. On February 12, 2014, 43,465 warrants were exercised in a cashless exercise for 16,593 shares of Common Stock. On April 23, 2014, 57,954 warrants were exercised in a cashless exercise for 37,250 shares of Common Stock. As of December 31, 2016, 3,878 of these warrants remain outstanding.

In connection with the completion of the Company's IPO, all the warrants exercisable for redeemable convertible preferred stock were automatically converted into warrants exercisable for Common Stock, resulting in the reclassification of the related warrant to purchase redeemable securities liability to additional paid-in capital as the warrants to purchase shares of Common Stock are accounted for as equity instruments. The warrant to purchase redeemable securities liability was re-measured to fair value prior to reclassification to additional paid-in capital.

These warrants are considered Level 3 liabilities because their fair value measurements are based, in part, on significant inputs not observed in the market and reflect the Company’s assumptions as to the expected volatility of the Company’s preferred stock. The Company determined the fair value of the warrants to purchase redeemable securities based on input from management and the board of directors, which utilized an independent valuation of the Company’s enterprise value, determined utilizing an analytical valuation model. Any reasonable changes in the assumptions used in the valuation could materially affect the financial results of the Company.

The following table sets forth a summary of changes in the fair value of the Company’s warrants to purchase redeemable securities, which represents a recurring measurement that is classified within Level 3 of the fair value hierarchy wherein fair value is estimated using significant unobservable inputs (in thousands):
  Years ended December 31,
  2016 2015 2014
Beginning balance $
 $
 $656
Change in fair value 
 
 725
Warrants exercised 
 
 (323)
Reclassification to accumulated paid-in capital 
 
 (1,058)
Ending balance $
 $
 $

At December 31, 2013, the analytical valuation model used to calculate the fair value of warrants to purchase redeemable securities was a hybrid approach based on an Option-Pricing Model (“OPM”) backsolve method and the Probability-Weighted Expected Return Model (“PWERM”). Thirty-five percent of the value was attributed to the OPM backsolve method and 65% was attributed to the PWERM. After the enterprise value was determined, the total enterprise value was then allocated to the various outstanding equity instruments, including the warrants to purchase redeemable securities, utilizing the OPM.

The fair value of warrants to purchase 21,695 shares of Series A preferred stock prior to exercise on January 29, 2014 was estimated using the Black-Scholes option pricing model with the following weighted-average assumptions:
 January 29,
2014
Fair value of underlying instrument$0.65
 
Expected Volatility55.57
%
Expected term (in years)0.04
 
Risk-free interest rate1.52
%
Expected dividend yield0.0
%

These warrants were re-measured to a fair value of $8 thousand, which resulted in an increase in fair value of $2 thousand. The fair value of the warrants was reclassified to additional paid-in capital upon exercise on January 29, 2014.

The fair valuewarrant liability is approximately $2.5 million and $3.5 million as of warrants to purchase 28,926 shares of Series A preferred stock prior to exercise on February 4, 2014 was estimated using the Black-Scholes option pricing model with the following weighted-average assumptions:


 February 4,
2014
Fair value of underlying instrument$0.65
 
Expected Volatility55.03
%
Expected term (in years)0.02
 
Risk-free interest rate1.46
%
Expected dividend yield0.0
%

These warrants were re-measured to a fair value of $10 thousand, which resulted in an increase in fair value of $3 thousand. The fair value of the warrants was reclassified to additional paid-in capital upon exercise on February 4, 2014.

The fair value of warrants to purchase 987,840 shares of Series A preferred stock prior to a cashless exercise for 316,932 shares of Series A preferred stock on February 10, 2014, which automatically converted into 26,633 shares of Common Stock upon the completion of the Company's IPO, was estimated using the Black-Scholes option pricing model with the following weighted-average assumptions:
 February 10,
2014
Fair value of underlying instrument$7.74
 
Expected Volatility50.81
%
Expected term (in years)1
 
Risk-free interest rate1.48
%
Expected dividend yield0.0
%

These warrants were re-measured to a fair value of $304 thousand, which resulted in an increase in fair value of $47 thousand. The fair value of the warrants was reclassified to additional paid-in capital upon exercise on February 10, 2014.

The fair value of warrants exercisable for 1,253,051 shares of redeemable convertible preferred stock, which were automatically converted into warrants exercisable for 105,297 shares of Common Stock, was estimated using the Black-Scholes option pricing model with the following weighted-average assumptions:
 February 10,
2014
Fair value of underlying instrument$6.96
 
Expected Volatility92.9
%
Expected term (in years)8.66
 
Risk-free interest rate2.43
%
Expected dividend yield0.0
%

The fair value of the remaining 105,297 warrants to purchase Common Stock were re-measured to a fair value of $1,058 thousand, which resulted in an increase in fair value of $673 thousand. The fair value of the warrants was reclassified to additional paid-in capital upon conversion on February 10, 2014.

8. Commitments and contingencies

Lease commitments

In February 2014, the Company signed an operating lease for office and laboratory space that commenced in March 2014 and expires in February 2017 (the "2014 Lease"). In May 2016, the Company entered into a lease amendment (the "2016 Lease") for office and laboratory space currently occupied under the 2014 Lease that was set to expire in February 2017. The 2016 Lease extends the 2014 Lease by an additional three years through February 2020.

In June 2015, the Company signed a second operating lease for office space in the same building as the 2014 Lease, which also expires in February 2017 (the "2015 Lease"). In August 2016, the Company exercised a three-year renewal option extending the 2015 Lease to February 2020. Rent expense for the years ended December 31, 2016, 2015,2019 and 2014, was $1.4 million, $1.2 million, and $0.8 million,2018, respectively.



The minimum future lease payments under both the 2016 Lease and the 2015 Lease are as follows (in thousands):

 December 31, 2016
2017$1,550
20181,607
20191,637
2020274
Total$5,068

At December 31, 2016, the Company has an outstanding letter of credit of $316 thousand with a financial institution related to a security deposit for the 2016 Lease, which is secured by cash on deposit and expires on February 29, 2020. An additional unsecured deposit was required for the 2015 Lease.

Significant Contracts and Agreements

In addition to lease commitments, the Company enters into contractual arrangements that obligate it to make payments to the contractual counterparties upon the occurrence of future events. In the normal course of operations, the Company enters into license and other agreements and intends to continue to seek additional rights relating to compounds or technologies in connection with its discovery, manufacturing and development programs. These agreements may require payments to be made by the Company upon the occurrence of certain development milestones and certain commercialization milestones for each distinct product covered by the licensed patents (in addition to certain royalties to be paid on marketed products or sublicense income) contingent upon the occurrence of future events that cannot be reasonably estimated.

In March 2014, the Company announced a joint research collaboration with Dana-Farber Cancer Institute to characterize anti-tumor T cell responses in melanoma patients. This collaboration extends the use of the Company's proprietary ATLAS platform for the rapid discovery of T cell antigens to cancer immunotherapy approaches.

In September 2014, the Company received $1.2 million in the form of a grant entered into with the Bill & Melinda Gates Foundation for the identification of protective T-cell antigens for malaria vaccines. The grant provided for the continued expansion of the Company’s malaria antigen library and aid in the identification of novel protein antigens to facilitate the development of highly efficacious anti-infection malarial vaccines. The Company recognized revenue under the agreement of$235 thousand, $640 thousand and $308 thousand for the years ended December 31, 2016, 2015, and 2014, respectively.
The Company relies on research institutions, contract research organizations, clinical investigators as well as clinical and commercial material manufacturers for its product candidates. Under the terms of these agreements, the Company is obligated to make milestone payments upon the achievement of manufacturing or clinical milestones defined in the contracts. In some cases, monthly service fee for project management services are charged over the duration of the arrangement. In addition, clinical and manufacturing contracts generally require reimbursement to suppliers for certain set-up, production, travel, and other related costs as they are incurred. In some manufacturing contracts, the Company also may be responsible for the payment of a reservation fee, which will equal a percentage of the expected production fees, to reserve manufacturing slots in the production timeframe. Generally, the Company is liable for actual effort expended by these organizations at any point in time during the contract through the notice period. To the extent amounts paid to a supplier exceed the actual efforts expended, the Company records a prepaid asset, and to the extent actual efforts expended exceed amounts billed or billable under a contract, an accrual for the estimate of services rendered is recorded.

In February 2014, the Company entered into a supply agreement with FUJIFILM Diosynth Biotechnologies U.S.A., Inc. (“Fujifilm”) for the manufacture and supply of antigens for future GEN-003 clinical trials. Under the agreement, the Company is obligated to pay Fujifilm manufacturing milestones, in addition to reimbursement of certain material production related costs. Additionally, the Company is responsible for the payment of a reservation fee, which will equal a percentage of the expected production fees, to reserve manufacturing slots in the production timeframe. In June and September 2016, the Company entered into new statements of work under the agreement with Fujifilm for the manufacture and supply of antigens for the Company's Phase 3 clinical trials.  The Company incurred expenses under this agreement of $4.7 million, $4.2 million, and $3.5 million for the years ended December 31, 2016, 2015 and 2014, respectively.

Litigation


The Company is not a party to any litigation and does not have contingency reserves established for any litigation liabilities.

Refund of research and development expense

In August 2009,following table details the Company entered into an exclusive license and collaboration agreement (the “Novavax Agreement”) with Isconova AB, a Swedish company which subsequently was acquired by Novavax, Inc. ("Novavax"). Pursuant to the agreement, Novavax granted the Company a worldwide, sublicensable, exclusive license to two patent families, to import, make, have made, use, sell, offer for sale and otherwise exploit licensed vaccine products containing an adjuvant which incorporates or is developed from Matrix-A, Matrix-C and/or Matrix-M technology,assumptions used in the fieldsMonte Carlo simulation models used to estimate the fair value of HSV and chlamydia. Matrix-M is the adjuvant used in GEN-003.

The Novavax Agreement includes a research funding clause for which the Company made monthly payments to Novavax between August 2009 and March 2012Warrant Liability as of approximately $1.6 million. All amounts of research funding provided were to be refunded by Novavax. After December 31, 2015, any amounts remaining due from Novavax, including accrued interest, could be received in cash upon 30-day written notice provided by the Company. The Company provided this notice in January 2016.

The Company provided the research funding solely to benefit the supply plan for the Matrix-M adjuvant to the point that a Phase 1 clinical trial could be initiated. Because of the benefit received from the research funding payments, an assessment of Novavax's financial ability to repay the research funding at the time of the payments, along with the duration of which amounts could be outstanding, the Company concluded the initial research funding should be recorded as research2019 and development expense at the time of payment. In February 2016, upon receipt of the $1.6 million refund including accrued interest, the Company recorded a gain within operating expenses in the Consolidated Statements of Operations and Comprehensive Loss.

9. Convertible Preferred Stock and Stockholder's Equity (Deficit)
At December 31, 2016, the Company authorized 175,000,000 shares of common stock at $0.001 par value per share, of which 28,446,461 shares of common stock were issued and 28,444,520 shares of common stock were outstanding.

The Company computes basic and diluted earnings (loss) per share using a methodology that gives effect to the impact of outstanding participating securities (the “two-class method”). For the three years ended December 31, 2016, there is no income allocation required under the two-class method or dilution attributed to weighted average shares outstanding in the calculation of diluted loss per share.

The following common stock equivalents, presented on an as converted basis, were excluded from the calculation of net loss per share for the periods presented, due to their anti-dilutive effect (in thousands):2018, respectively:

  Years ended December 31,
  2016 2015 2014
Warrants 78
 78
 78
Outstanding options 3,807
 2,723
 2,290
Total 3,885
 2,801
 2,368
  December 31, 2019 December 31, 2018
Stock Price $2.07
 $2.32
Volatility 50.0% - 116.6%
 50.0% - 111.3%
Remaining term (years) 3.1
 4.1
Expected dividend yield % %
Risk-free rate 1.6% 2.4% - 2.5%
Range of annual acquisition event probability 20.0% 0.0% - 30.0%

Restricted stockPrivate Placement and Prefunded Warrants

During 2013, a Company director exercised stock options and received 31,092 sharesThe exercise price of common stock that werethe warrants is subject to appropriate adjustment in the event of stock dividends, subdivisions, stock splits, stock combinations, reclassifications, reorganizations or a Stock Restriction and Repurchase Agreement with the Company. Under the termschange of the agreement, shares of common stock issued are subject to a vesting schedule and unvested shares are subject to repurchase by the Company. Vesting occurs periodically at specified time intervals and specified percentages. All shares of common stock become fully vested in February 2017, four years from the date of grant.

At both December 31, 2016 and December 31, 2015, the Company had issued 35,964 shares of restrictedcontrol affecting our common stock. At December 31, 2016, 1,941 shares of nonvested restricted stock were subject to repurchase byThe Company determined that the Company. At December 31, 2015, 9,717 shares of nonvested restricted stock were subject to repurchase byPrivate Placement Warrants and the Company


Conversion of Preferred Shares

In connectionPre-Funded Warrants should be equity classified in accordance with the Company's IPO, all preferred shares outstanding were converted into common shares outstanding. The table below includes the conversion detail for each class of preferred shares that is summarized as convertible preferred stock in the Consolidated Statements of Convertible Preferred Stock and Stockholders' Equity (Deficit) ASC 480for the yearperiod ended December 31, 2014.

     Series A Redeemable Series B Redeemable Series C Redeemable    
 Seed Convertible Convertible Convertible Convertible Total Convertible
 Preferred Shares Preferred Shares Preferred Shares Preferred Shares Preferred Shares
 Shares Amount Shares Amount Shares Amount Shares Amount Shares Amount
Balance at December 31, 20134,615
 $3,000
 35,577
 $23,125
 34,581
 $24,937
 52,586
 $30,500
 127,359
 $81,562
Accretion of dividends on redeemable convertible preferred stock
 
 
 
 
 180
 
 
 
 180
Exercise of warrants for cash
 
 51
 33
 
 
 
 
 51
 33
Cashless exercise of warrants
 
 317
 98
 
 
 
 
 317
 98
Conversion of redeemable convertible preferred stock into common stock at IPO date(4,615) $(3,000) (35,945) $(23,256) (34,581) $(25,117) (52,586) $(30,500) (127,727) $(81,873)
2019. The Company also determined that the Pre-Funded Warrants should be included in the determination of basic earnings per share in accordance with ASC 260,
Earnings per Share.

10. Stock and employee benefit plans

The Company’s board of directors adoptedCompany issues stock options with service conditions, which are generally the 2014 Equity Incentive Plan (the “2014 Equity Plan”), which was approved by its stockholders and became effective prior to the commencementvesting of the Company's IPO.awards. The Company has also issued stock options that vest upon the satisfaction of certain performance conditions.

The 2014 Equity Incentive Plan ("2014 Equity Plan"), which was subsequently amended and restated in June 2018, provides for the grant of incentive stock options, non-qualified stock options, restricted stock, and other awards to key employees and directors of, and consultants and advisors to, the Company. The maximum number of shares of common stock that may be delivered in satisfaction of awards under the 2014 Equity Plan, is 903,494 shares, plus 219,765 shares that were available for grant under the 2007 Equity Incentive Plan (the "2007 Equity Plan") on the date the 2014 Equity Plan was adopted. The 2014 Equity Planas amended, provides that the number of shares available for issuance will automatically increase annually on each January 1, from January 1, 2015 through January 1, 2024, in amount equal to the lesser of 4.0% of the outstanding shares of the Company’s outstanding common stock as of the close of business on the immediately preceding December 31 or the number of shares determined the Company’s board of directors. On January 1, 2017,2020, the total number of shares available for issuance under the 2014 Equity Plan, as amended. increased by 1,137,7811,098,116 for shares under this provision.

Outstanding options awards granted from the 2007 Equity Plan, at the time of the adoption of the 2014 Equity Plan, remain outstanding and effective. The shares of common stock underlying awards that are cancelled, forfeited, repurchased, expire or are otherwise terminated under the 2007 Equity Plan are added to the shares of common stock available for issuance under the 2014 Equity Plan. At December 31, 2016, 4,292,5442019, 1,568,535 option awards are permittedreserved for issuance under the Company's equity plans and 485,483245,430 awards remain available for future grants.

Determining the Fair Value of Stock options issued to non-employees are accounted for usingOptions

The Company measures the fair value method of accounting,stock options with service-based and are periodically revalued asperformance-based vesting criteria to employees, consultants and directors on the options vest, and are recognized as expense overdate of grant using the related service period. The total expense related to all nonemployee options for the years ended December 31, 2016, 2015 and 2014 was $271 thousand, $263 thousand, and $324 thousand, respectively.Black-Scholes option pricing model.

Stock Based Compensation ExpenseThe Company does not have sufficient history to support a calculation of volatility and expected term using only its historical data. As such, the Company has used a weighted-average volatility considering the Company’s own volatility since its initial public offering and the volatilities of several guideline companies. For purposes of identifying similar entities, the Company considered characteristics such as industry, length of trading history, and stage of life cycle. The assumed dividend yield was based on the Company’s expectation of not paying dividends in the foreseeable future. The average expected life was determined according to the “simplified method” as described in SAB 110, which is the mid-point between the vesting date and the end of the contractual term. The risk-free interest rate is determined by reference to implied yields available from U.S. Treasury securities with a remaining term equal to the expected life assumed at the date of grant.

Total stock-based compensation expense is recognized for stock options granted to employees and non-employees and has been reportedThe weighted-average assumptions used in the Company’s Statements of OperationsBlack-Scholes option-pricing model are as follows (in thousands):follows:
  Years ended December 31,
  2016 2015 2014
Research and development $1,568
 $1,690
 $1,511
General and administrative 2,579
 2,158
 1,394
Total $4,147
 $3,848
 $2,905
  Years ended December 31,
  2019 2018
Expected volatility 79.7% 78.6%
Risk-free interest rate 2.3% 2.8%
Expected term (in years) 6.0 6.0
Expected dividend yield 0% 0%



Stock Options

The following table summarizes stock option activity for employees and nonemployeesnon-employees (shares in thousands):

  Shares 
Weighted-
Average
Exercise
Price
 
Weighted-
Average
Remaining
Contractual
Term (years)
 
Aggregate
Intrinsic
Value
Outstanding at December 31, 2015 2,723
 $7.60
 7.61 $2,840
Granted 1,577
 $3.56
    
Exercised (79) $2.85
    
Canceled (414) $8.47
    
Outstanding at December 31, 2016 3,807
 $5.94
 7.52 $2,441
Exercisable at December 31, 2016 1,892
 $6.18
 6.32 $1,589
Vested or expected to vest at December 31, 2016 3,807
 $5.94
 7.52 $2,441
  Shares 
Weighted-Average
Exercise Price
 
Weighted-Average
Remaining
Contractual
Term (years)
 
Aggregate
Intrinsic Value
Outstanding at December 31, 2018 893
 $18.79
 
 

Granted 679
 $4.36
    
Exercised (5) $4.32
    
Canceled (244) $17.64
    
Outstanding at December 31, 2019 1,323
 $11.65
 8.0 $
Exercisable at December 31, 2019 522
 $20.09
 6.6 $

During the years ended December 31, 2016, 20152019 and 2014,2018, the Company granted stock options to purchase an aggregate of 1,576,700, 715,262,678,710 and 1,064,640657,375 shares of its common stock, respectively, with weighted-average grant date fair values of $3.56, $9.12,$4.36 and $10.11,$6.96, respectively.

The total intrinsic value of options exercised was $113 thousand, $1.0 million, and $3.1 million in the years ended December 31, 2016, 2015, and 2014, respectively. As of December 31, 2016,2019, there was $6.6$3.0 million of total unrecognized compensation cost, related to employee and non-employee stock options granted under the Company’s equity plans.

The total unrecognized compensation costs, related to non-employee stock options was $269 thousand, $255 thousand, and $55 thousand for the years ended December 31, 2016, 2015, and 2014, respectively.

Total unrecognized compensation cost for employee and non-employee will be adjusted for future forfeitures as they occur based upon the policy adopted by the Company upon early adoption of ASU 2016-09. The Company expects to recognize that cost over a remaining weighted-average period of 2.62.65 years.

The Company estimatesStock-based compensation expense

Total stock-based compensation expense is recognized for stock options and restricted stock granted to employees and non-employees and has been reported in the fair valueCompany’s consolidated statements of each employee stock award on the grant date using the Black-Scholes option-pricing model based on the following assumptions:operations as follows (in thousands):
  Years ended December 31,
  2016 2015 2014
Expected Volatility 67.4% - 77.9% 68.5% - 85.3% 86.2% - 103.6%
Risk-free interest rate 1.14% - 2.09% 1.56% - 1.94% 1.75% - 2.00%
Expected term (in years) 5.50 - 6.08 5.50 - 6.08 6.25
Expected dividend yield 0% 0% 0%

Performance-Based Stock Options

The Company granted stock options to certain employees, executive officers and consultants, which contain performance-based vesting criteria. Milestone events are specific to the Company’s corporate goals, which include, but are not limited to, certain clinical development milestones, business development agreements and capital fundraising events. Stock-based compensation expense associated with these performance-based stock options is recognized if the performance conditions are considered probable of being achieved, using management’s best estimates. During the year ended December 31, 2014, the Company determined that 96,988 options related to performance-based milestones were probable of achievement and, accordingly, recorded $453 thousand in related stock-based compensation expense. As of December 31, 2014, there were 56,336 performance-based common stock options outstanding for which the probability of achievement was not deemed probable. During the years ended December 31, 2016 and 2015, the Company recorded no stock based compensation expense related to the 56,336 performance-based common stock options that remain outstanding for which the probability of achievement was not deemed probable at both December 31, 2016 and 2015.


  Years ended December 31,
  2019 2018
Research and development $725
 $620
General and administrative 1,112
 1,533
Total $1,837
 $2,153

Employee Stock Purchase Plan

OnIn February 10, 2014, the Company’s board of directors adopted the 2014 Employee Stock Purchase Plan (the “2014 ESPP”)., which was subsequently amended in June 2018. The 2014 ESPP, as amended, authorizes the initial issuance of up to a total of 200,776337,597 shares of common stock to participating eligible employees. The 2014 ESPP, as amended, provides for six-month option periods commencing on January 1 and ending June 30, and commencing July 1 and ending December 31 of each calendar year. The first offeringCompany issued 71,118 and 23,417 shares under the 2014 ESPP, began on July 1, 2014. Foras amended, for the yearyears ended December 31, 2014, the Company incurred $43 thousand in stock-based compensation expense2019 and 15,622 shares were issued. For the year ended2018, respectively. As of December 31, 2015, the Company incurred $113 thousand in stock-based compensation expense and 40,9122019, there were 217,985 shares were issued. For the year ended December 31, 2016, the Company incurred $155 thousand in stock-based compensation expense and 70,774 shares were issued. Shares remaining for future issuance under the plan were 73,468 as of December 31, 2016.plan.

401(k) Savings plan

In 2007, the Company established a defined-contribution savings plan under Section 401(k) of the Internal Revenue Code (“401(k) Plan”). The 401(k) Plan covers all employees who meet defined minimum age and service requirements, and allows participants to defer a portion of their annual compensation on a pretax basis. Beginning January 1, 2015, the Company began making matching contributions to participants in this plan which totaled $174 thousand for the year ended December 31, 2015.plan. The Company made matching contributions to participants in this plan which totaled $243 thousand$0.2 million and $0.1 million for the yearyears ended December 31, 2016.2019 and 2018, respectively.



11. Net loss per share

Basic and diluted net loss per share was calculated as follows for the years ended December 31, 2019 and 2018:

  Years ended December 31,
  2019 2018
Basic net loss per share:    
Numerator:    
   Net loss (in thousands) $(38,950) $(27,811)
Denominator:    
   Weighted average common stock outstanding - basic (in
     thousands)
 20,644
 10,321
   Dilutive effect of shares of common stock equivalents
     resulting from common stock options and restricted stock
     units
 
 
   Weighted average common stock outstanding - diluted 20,644
 10,321
Net loss per share - basic and diluted $(1.89) $(2.69)


The following common stock equivalents outstanding as of December 31, 2019 and 2018, presented on an as converted basis, were excluded from the calculation of net loss per share for the periods presented, due to their anti-dilutive effect (in thousands):

  Years ended December 31,
  2019 2018
Stock options 1,323
 893
Warrants 4,591
 3,668
Total 5,914
 4,561

Stock options that are outstanding and contain performance-based vesting criteria for which the performance conditions have not been met are excluded from the calculation of common stock equivalents outstanding.

11.12. Income taxes

For the years ended December 31, 20162019 and 2015,2018, the Company did not record a current or deferred income tax expense or benefit. The Company’s losses before income taxes consist solely of domestic losses. The significant components of the Company’s deferred tax assets are comprised of the following:


December 31,December 31,
2016 20152019 2018
Deferred tax assets:      
U.S and state net operating loss carryforwards$52,829
 $54,570
U.S. and state net operating loss carryforwards$56,906
 $49,614
Capitalized R&D20,280
 
28,427
 25,366
Research and development credits6,422
 5,226
11,717
 10,445
Stock based compensation2,184
 1,410
Lease liability1,779
 
Stock-based compensation1,053
 1,989
Depreciation and amortization545
 640
Accrued expenses794
 603
507
 450
Depreciation and amortization784
 516
Other temporary differences365
 353
38
 85
Total deferred tax assets83,658
 62,678
100,972
 88,589
Less valuation allowance(83,658) (62,678)(99,249) (88,589)
Net deferred tax assets$
 $
Deferred tax assets less valuation allowance$1,723
 $
   
Deferred tax liabilities:   
ROU asset$(1,723) $
Total deferred tax liabilities(1,723) 
Net deferred tax assets (deferred tax liabilities)$
 $

The Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets. Based on the Company’s history of operating losses, the Company has concluded that it is more likely than not that the benefit of its deferred tax assets will not be realized. Accordingly, the Company has provided a full valuation allowance for deferred tax assets as of December 31, 20162019 and 2015.2018. The valuation allowance increased approximately $21.0$10.7 million during the year ended December 31, 2016 primarily related to the Company's election to capitalize and amortize certain research and development expenses. The valuation allowance increased approximately $17.5 million during the year ended December 31, 2015,2019 due primarily to the generation of net operating losses.

A reconciliation of income tax expense computed at the statutory federal income tax rate to income taxes as reflected in the consolidated financial statements is as follows:


 Years ended December 31, Years ended December 31,
 2016 2015 2014 2019 2018
Federal income tax expense at statutory rate 34.0 % 34.0 % 34.0 % 21.0 % 21.0 %
State income tax, net of federal benefit 5.0 % 4.6 % 5.1 % 6.3 % 8.9 %
Permanent differences (1.5)% (2.1)% (0.9)% 0.0 % 9.0 %
Research and development credit 2.5 % 1.9 % 3.6 % 3.3 % 6.7 %
Change in valuation allowance (40.0)% (38.4)% (41.8)% (27.4)% (43.1)%
Other, net (3.2)% (2.5)%
Effective tax rate 0.0 % 0.0 % 0.0 % 0.0 % 0.0 %

As of December 31, 2016, 2015,2019 and 2014,2018, the Company had U.S. federal net operating loss carryforwards of approximately $136.6 million, $143.8$211.5 million and $105.0$184.8 million, respectively, which may be available to offset future income tax liabilities and expire at various dates through 2036.2038. The federal net operating losses generated in tax years after December 31, 2017 can be carried forward indefinitely. As of December 31, 2016, 2015,2019 and 2014,2018, the Company also had U.S. state net operating loss carryforwards of approximately $121.2 million, $128.5$197.7 million and $90.5$171.1 million, respectively, which may be available to offset future income tax liabilities and expire at various dates through 2036. For the year ended December 31, 2016, deductions related to the excess tax benefit from stock option exercises are recognized in the federal and state net operating loss carryforwards as a component of the tax provision as the Company early adopted ASU 2016-09 (see Note 2). For the years ended December 31, 2015 and 2014, approximately $2.8 million and $1.9 million, respectively, of excess tax benefits related to the exercise of stock options were included in the federal and state net operating loss carryforwards.2039.

As of December 31, 20162019 and 2015,2018, the Company had federal research and development tax credit carryforwards of approximately $4.8$8.9 million and $3.7$7.8 million, respectively, available to reduce future tax liabilities which expire at various dates through 2036.2039. As of December 31, 20162019 and 2015,2018, the Company had state research and development tax credit carryforwards of approximately $2.5$3.5 million and $2.4$3.2 million, respectively, available to reduce future tax liabilities which expire at various dates through 2031.2034.

Under the provisions of the Internal Revenue Code of 1986, as amended (the "Code"), the net operating loss and tax credit carryforwards are subject to review and possible adjustment by the Internal Revenue Service and state tax authorities. Net


operating loss and tax credit carryforwards may become subject to an annual limitation in the event of certain cumulative changes in the ownership interest of significant shareholders over a three-year period in excess of 50%, as defined under Sections 382 and 383 of the Code, respectively, as well as similar state provisions. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation in future years. The Company has completed several financings since its inception which may have resulted in a change in control as defined by Sections 382 and 383 of the Code, or could result in a change in control in the future.

The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. As of December 31, 20162019 and 2015,2018, the Company had no accrued interest or penalties related to uncertain tax positions and no amounts have been recognized in the Company’s statements of operations and comprehensive loss.

For all years through December 31, 2016,2019, the Company generated research credits but has not conducted a study to document the qualified activities. This study may result in an adjustment to the Company’s research and development credit carryforwards; however,carryforwards. However, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position for these two years. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the deferred tax asset established for the research and development credit carryforwards and the valuation allowance.

The Company files income tax returns in the United States and various state jurisdictions.the Commonwealth of Massachusetts. The federal and state income tax returns are generally subject to tax examinations for the tax years ended December 31, 20132015 through December 31, 2016.2019. To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the Internal Revenue Service, state, or foreign tax authorities to the extent utilized in a future period.



12.13. Quarterly financial information (unaudited, in thousands, except share and per share data)
  Three Months Ended,
  March 31, 2016 June 30, 2016 September 30, 2016 December 31, 2016
Revenue $235
 $
 $
 $
Operating expenses 9,664
 10,704
 12,430
 15,682
Net loss (9,751) (11,023) (12,765) (16,034)
Net loss per share - basic and diluted $(0.35) $(0.39) $(0.45) $(0.56)
Weighted-average number of common shares used in net loss per share - basic and diluted 28,152
 28,276
 28,370
 28,394
  Three Months Ended,
  March 31, 2019 June 30, 2019 September 30, 2019 December 31, 2019
Operating expenses $9,477
 10,066
 9,584
 9,862
Net income (loss) (15,567) (6,495) (7,532) (9,356)
Net loss per share - basic and diluted $(1.22) $(0.42) $(0.28) $(0.34)
Weighted-average number of common shares used in computing net loss per share - basic and diluted 12,713
 15,344
 26,681
 27,620

 Three Months Ended, Three Months Ended,
 March 31, 2015 June 30, 2015 September 30, 2015 December 31, 2015 March 31, 2018 June 30, 2018 September 30, 2018 December 31, 2018
Revenue $121
 $115
 $213
 $221
Operating expenses 11,898
 10,141
 9,703
 10,294
 $10,384
 9,788
 10,460
 $8,886
Net loss (12,084) (10,314) (9,771) (10,314) (15,890) (4,438) (7,833) 350
Net loss per share - basic and diluted $(0.64) $(0.43) $(0.37) $(0.37) $(1.78) $(0.42) $(0.72) $0.03
Weighted-average number of common shares used in net loss per share - basic and diluted 18,834
 24,154
 26,610
 28,118
Weighted-average number of common shares used in computing net loss per share - basic and diluted 8,905
 10,693
 10,829
 10,847



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 17, 2017.13, 2020.
 GENOCEA BIOSCIENCES, INC.
   
 By:/s/ William Clark
   
  William Clark
  President and Chief Executive Officer

Pursuant to the requirements of the Securities Act of 1934, this report has been signed by the following persons on behalf of the registrant in the capacities and on the dates indicated.



Signature Title Date
     
/s/ William Clark President and Chief Executive Officer and Director  
William Clark (Principal Executive Officer) February 17, 201713, 2020
     
/s/ Jonathan PooleDiantha Duvall Chief Financial Officer  
Jonathan PooleDiantha Duvall (Principal Financial Officer and Principal Accounting Officer) February 17, 201713, 2020
     
/s/ Kenneth Bate    
Kenneth Bate Director February 17, 201713, 2020
     
/s/ Kevin BittermanAli Behbahani    
Kevin Bitterman, Ph.D.Ali Behbahani Director February 17, 201713, 2020
     
/s/ Katrine Bosley    
Katrine Bosley Director February 17, 201713, 2020
     
/s/ Ronald Cooper    
Ronald Cooper Director February 17, 201713, 2020
     
/s/ Michael Higgins    
Michael Higgins Director February 17, 201713, 2020
     
/s/ Stephen HoffmanHoward Mayer    
Stephen Hoffman,Howard Mayer, M.D., Ph.D. Director February 17, 201713, 2020
     
/s/ George Siber    
George Siber, M.D. Director February 17, 201713, 2020


Exhibit
Number
 Exhibit
   
3.1 
   
3.2 
3.3
3.4
   
4.1 
   
4.2 Form of Warrant to Purchase Preferred Stock, dated January 7, 2008 (incorporated by reference to Exhibit 4.2 to the Company’s Registration Statement on Form S-1, File No. 333-193043, filed on December 23, 2013)
4.3
4.3
   
4.4 
4.5
4.6
4.7
4.8*
   
10.1 
   
10.2++* Amended and Restated Exclusive License Agreement between Children’s Medical Center Corporation and Genocea Biosciences, Inc., dated March 23, 2012 (incorporated by reference to Exhibit 10.1 to the Company’s Form 10-Q, File No.001-36289, dated November 4, 2016)
10.3+
   
10.4+10.3 License and Collaboration Agreement between Genocea Biosciences, Inc. and Isconova AB, dated August 5, 2009, as amended on March 19, 2010, June 18, 2010, August 17, 2010, October 19, 2011 and February 6, 2012 (incorporated by reference to Exhibit 10.3 to the Company’s Form 10-Q, File No.001-36289
10.5+Exclusive License Agreement for Escherichia Coli K12 to Deliver Protein to the Macrophage Cytosol between Genocea Biosciences, Inc. and The Regents of the University of California, dated August 18, 2006 (incorporated by reference to Exhibit 10.5 to the Company’s Registration Statement on Form S-1, File No. 333-193043, as amended on January 13, 2014)
10.6
   
10.710.4 
   
10.810.5† 


Exhibit
Number
Exhibit
   
10.6† 
10.9†Consulting Agreement between Genocea Biosciences, Inc. and George Siber, dated May 16, 2007, as amended on June 30, 2009, December 16, 2010, June 15, 2011 and June 5, 2013 (incorporated by reference to Exhibit 10.11 to the Company’s Registration Statement on Form S-1, File No. 333-193043, filed on December 23, 2013)
10.10†


Exhibit
Number
Exhibit
   
10.11†10.7† 
10.12†Letter Agreement, dated April 7, 2014, between the Company and Jonathan Poole (incorporated by referenced to Exhibit 10.1 to the Company’sCompany's Current Report on Form 8-K, File No. 001-36289, filed on April 8, 2014)June 25, 2018)
   
10.13†10.8† Genocea Biosciences, Inc. 2014 Equity Incentive Plan (incorporated by reference to Exhibit 10.15 to the Company’s Registration Statement on Form S-1, File No. 333-193043, as amended on January 13, 2014)
10.14†
   
10.15†10.9† 
   
10.16†10.10† 
   
10.17†10.11† 
   
10.18†10.12† 
   
10.19†10.13† Restricted Stock Agreement between Genocea Biosciences, Inc. and Katrine Bosley, dated November 7, 2013 (incorporated by reference to Exhibit 10.25 to the Company’s Registration Statement on Form S-1, File No. 333-193043, as amended on January 13, 2014)
10.20†
June 25, 2018)


Exhibit
Number
Exhibit
   
10.2110.14† 
   
10.22†10.15† 
   
10.23+10.16 Bioprocessing Services Agreement between the Company and FUJIFILM Diosynth Biotechnologies U.S.A., Inc. dated February 26, 2014 (incorporated by reference to Exhibit 10.1 to the Company’s Form 10-Q, File No. 001-36289, filed on May 9, 2014)
10.24Loan and Security Agreement between the Company and Hercules Technology Growth Capital, Inc., dated November 20, 2014 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, File No. 001-36289, filed on November 21, 2014)
10.25
   
10.26+10.17 Product Development and Clinical Supply Agreement between the Company and Baxter Pharmaceutical Solutions LLC, dated October 23, 2014 (incorporated by reference to Exhibit 10.32 to the Company’s Annual Report on Form 10-K File No. 001-36289, filed on February 27, 2015)
10.27†Fifth Amendment to the Consulting Agreement between Genocea Biosciences, Inc. and George Siber, dated June 15, 2015 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, File No. 001-36289, filed on June 19, 2015)
10.28Amendment No. 1 to Loan and Security Agreement between the Company and Hercules Technology Growth Capital, Inc., dated December 17, 2015 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K File No. 001-36289, filed on December 18, 2015)
10.29
   
10.3010.18 
   
21.110.19+ List of Subsidiaries of
   
23.1*10.20+ Consent of Ernst & Young LLP
   
31.1*10.21 Certification pursuant
31.2*Certification pursuantreference to Section 302 of Sarbanes Oxley Act of 2002 by Chief Financial OfficerExhibit 10.1 to the Company's Current Report on Form 8-K, File No. 001-36289, filed on April 30, 2018)
   


Exhibit
Number
 Exhibit
   
10.22
10.23*
21.1
23.1*
31.1*
31.2*
32.1** 
   
32.2** 
   
101. INS* XBRL Instance Document
   
101. SCH* XBRL Taxonomy Extension Schema
   
101. CAL* XBRL Taxonomy Extension Calculation Linkbase
   
101. DEF* XBRL Taxonomy Extension Definition Linkbase
   
101. LAB* XBRL Taxonomy Extension Label Linkbase
   
101. PRE* XBRL Taxonomy Extension Presentation Linkbase
_________________________
*Filed herewith.
**Furnished herewith.
Indicates a management contract or compensatory plan.
+Portions of this exhibit (indicated by asterisks) have been omitted pursuant to a request for confidential treatment and this exhibit has been submitted separately to the Securities and Exchange Commission.
++Portions of this exhibit (indicated by asterisks) have been omitted because the Registrant has determined they are not material and would likely cause competitive harm to the Registrant if publicly disclosed.