UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, DC 20549

Form 10-Q
(Mark One)

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

For the Quarterly Period Ended March 31, 20202021

OR

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

For the transition period from _____ to _____

Commission file number 000-19125

   

Ionis Pharmaceuticals, Inc.
(Exact name of Registrant as specified in its charter)

Delaware 33-0336973
(State or other jurisdiction of incorporation or organization) (IRS Employer Identification No.)

2855 Gazelle Court, Carlsbad, California 92010
(Address of Principal Executive Offices) (Zip Code)

760-931-9200
(Registrant’s telephone number, including area code)

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

Title of each class Trading symbolName of each exchange on which registeredTrading symbol
Common Stock, $.001 Par Value “IONS”The Nasdaq Stock Market LLC“IONS”

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

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

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

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

Large Accelerated Filer 
Accelerated Filer
  
Non-accelerated Filer
Smaller Reporting Company
 
Emerging Growth Company

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B)13(a) of the SecuritiesExchange Act.

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12(b)-2 of the Securities Exchange Act of 1934). Yes No

The number of shares of voting common stock outstanding as of April 29, 20202021 was 139,321,047.140,963,028.




IONIS PHARMACEUTICALS, INC.
FORM 10-Q
INDEX

PART IFINANCIAL INFORMATION 
   
ITEM 1:Financial Statements: 
   
 Condensed Consolidated Balance Sheets as of March 31, 2020 (unaudited)2021 and December 31, 20192020 (unaudited) (as revised)3
   
 Condensed Consolidated Statements of Operations for the three months ended March 31, 2021 and 2020 and 2019 (unaudited) (as revised)4
   
 Condensed Consolidated Statements of Comprehensive Income (Loss)Loss for the three months ended March 31, 2021 and 2020 and 2019 (unaudited) (as revised)5
   
 Condensed Consolidated Statements of Stockholders’ Equity for the three months ended March 31, 2021 and 2020 and 2019 (unaudited) (as revised)6
   
 Condensed Consolidated Statements of Cash Flows for the three months ended March 31, 2021 and 2020 and 2019 (unaudited) (as revised)7
   
 Notes to Condensed Consolidated Financial Statements (unaudited)8
   
ITEM 2:Management’s Discussion and Analysis of Financial Condition and Results of Operations: 
   
 Overview2528
   
 Results of Operations2831
   
 Liquidity and Capital Resources3436
   
ITEM 3:Quantitative and Qualitative Disclosures about Market Risk3638
   
ITEM 4:Controls and Procedures3638
   
PART IIOTHER INFORMATION3738
   
ITEM 1:Legal Proceedings3738
   
ITEM 1A:Risk Factors3739
   
ITEM 2:Unregistered Sales of Equity Securities and Use of Proceeds5156
   
ITEM 3:Default upon Senior Securities5156
   
ITEM 4:Mine Safety Disclosures5156
   
ITEM 5:Other Information5156
   
ITEM 6:Exhibits5156
   
SIGNATURES5358

TRADEMARKS

 "Ionis," the Ionis logo, and other trademarks or service marks of Ionis Pharmaceuticals, Inc. appearing in this report are the property of Ionis Pharmaceuticals, Inc. "Akcea,"“Akcea,” the Akcea logo, and other trademarks or service marks of Akcea Therapeutics, Inc. appearing in this report including TEGSEDI (inotersen) and WAYLIVRA (volanesorsen), are the property of Akcea Therapeutics, Inc., Ionis’ wholly owned subsidiary. This report contains additional trade names, trademarks and service marks of others, which are the property of their respective owners. Solely for convenience, trademarks and trade names referred to in this report may appear without the ® or TM symbols.
2


IONIS PHARMACEUTICALS, INC.
CONDENSED CONSOLIDATED BALANCE SHEETS
(in thousands, except share data)

(Unaudited)
 
March 31,
2020
  
December 31,
2019
  
March 31,
2021
  
December 31,
2020
 
 
(Unaudited)
        (as revised*) 
ASSETS            
Current assets:            
Cash and cash equivalents $486,195  $683,287  $414,155  $397,664 
Short-term investments  1,897,892   1,816,257   1,405,840   1,494,711 
Contracts receivable  28,605   63,034   23,397   76,204 
Inventories  22,885   18,180   22,199   21,965 
Other current assets  122,468   139,839   123,827   140,163 
Total current assets  2,558,045   2,720,597   1,989,418   2,130,707 
Property, plant and equipment, net  163,952   153,651   180,413   181,077 
Patents, net  26,750   25,674   28,795   27,937 
Long-term deferred tax assets  309,614   305,557 
Deposits and other assets  32,552   27,633   49,925   50,034 
Total assets $3,090,913  $3,233,112  $2,248,551  $2,389,755 
                
LIABILITIES AND STOCKHOLDERS’ EQUITY                
Current liabilities:                
Accounts payable $21,174  $16,067  $9,506  $17,199 
Accrued compensation  16,437   37,357   29,263   65,728 
Accrued liabilities  62,507   66,769   78,766   90,161 
Income taxes payable  32,946   32,514   1,326   1,324 
Current portion of long-term obligations and other current liabilities  4,150   2,026 
Current portion of 1 percent convertible senior notes, net  61,816   308,809 
Current portion of long-term obligations  7,688   7,301 
Current portion of deferred contract revenue  120,811   118,272   106,740   108,376 
Total current liabilities  258,025   273,005   295,105   598,898 
Long-term deferred contract revenue  467,842   490,060   401,966   424,046 
0.125 percent convertible senior notes  439,996   434,711 
1 percent convertible senior notes  279,666   275,333 
0.125 percent convertible senior notes, net  540,679   540,136 
1 percent convertible senior notes, net  247,292   0 
Long-term obligations, less current portion  15,043   15,543   22,943   23,409 
Long-term mortgage debt  59,930   59,913   60,002   59,984 
Total liabilities  1,520,502   1,548,565   1,567,987   1,646,473 
Stockholders’ equity:                
Common stock, $0.001 par value; 300,000,000 shares authorized, 139,282,168 and 140,339,615 shares issued and outstanding at March 31, 2020 (unaudited) and December 31, 2019, respectively  139   140 
Common stock, $0.001 par value; 300,000,000 shares authorized, 140,924,356 and 140,365,594 shares issued and outstanding at March 31, 2021 (unaudited) and December 31, 2020, respectively  141   140 
Additional paid-in capital  2,233,644   2,203,778   1,925,801   1,895,519 
Accumulated other comprehensive loss  (27,235)  (25,290)  (24,203)  (21,071)
Accumulated deficit  (846,309)  (707,534)  (1,221,175)  (1,131,306)
Total Ionis stockholders’ equity  1,360,239   1,471,094 
Noncontrolling interest in Akcea Therapeutics, Inc.  210,172   213,453 
Total stockholders’ equity  1,570,411   1,684,547   680,564   743,282 
Total liabilities and stockholders’ equity $3,090,913  $3,233,112  $2,248,551  $2,389,755 


*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

See accompanying notes.

3


IONIS PHARMACEUTICALS, INC.
CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
(in thousands, except for per share amounts)
(Unaudited)

 
Three Months Ended
March 31,
 
 
Three Months Ended
March 31,
  2021  2020 
 2020  2019     (as revised*) 
Revenue:            
Commercial revenue:            
SPINRAZA royalties $66,008  $59,711  $59,986  $66,008 
Product sales, net  15,159   6,754 
TEGSEDI and WAYLIVRA revenue, net  19,838   15,159 
Licensing and other royalty revenue  2,794   1,623   4,624   2,794 
Total commercial revenue  83,961   68,088   84,448   83,961 
Research and development revenue under collaborative agreements  49,406   229,126   27,159   49,406 
Total revenue  133,367   297,214   111,607   133,367 
                
Expenses:                
Cost of products sold  2,548   1,041 
Cost of sales  2,578   2,548 
Research, development and patent  116,952   106,417   139,801   116,952 
Selling, general and administrative  74,994   68,221   61,199   74,994 
Total operating expenses  194,494   175,679   203,578   194,494 
                
Income (loss) from operations  (61,127)  121,535 
Loss from operations  (91,971)  (61,127)
                
Other income (expense):                
Investment income  10,479   12,142   4,643   10,479 
Interest expense  (10,990)  (11,599)  (2,414)  (2,207)
Other expenses  (99)  (147)
Other income (expenses)  3   (99)
                
Income (loss) before income tax benefit (expense)  (61,737)  121,931 
Loss before income tax (expense) benefit  (89,739)  (52,954)
                
Income tax benefit (expense)  3,257   (31,047)
Income tax (expense) benefit  (130)  3,072 
                
Net income (loss)  (58,480)  90,884 
Net loss  (89,869)  (49,882)
                
Net (income) loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.  10,254   (6,441)
Net loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.  0   10,254 
                
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders $(48,226) $84,443 
Net loss attributable to Ionis Pharmaceuticals, Inc. common stockholders $(89,869) $(39,628)
                
Basic net income (loss) per share $(0.35) $0.63 
Shares used in computing basic net income (loss) per share  139,429   138,582 
Diluted net income (loss) per share $(0.35) $0.62 
Shares used in computing diluted net income (loss) per share  139,429   141,537 
Basic and diluted net loss per share $(0.64) $(0.28)
Shares used in computing basic and diluted net loss per share  140,770   139,429 


*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

See accompanying notes.

4


IONIS PHARMACEUTICALS, INC.
CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS)LOSS
(in thousands)
(Unaudited)

  
Three Months Ended
March 31,
 
  2020  2019 
       
Net income (loss) $(58,480) $90,884 
Unrealized gains (losses) on debt securities, net of tax  (1,954)  4,324 
Currency translation adjustment  9   84 
         
Comprehensive income (loss)  (60,425)  95,292 
         
Comprehensive (income) loss attributable to noncontrolling interests  (10,254)  6,441 
         
Comprehensive income (loss) attributable to Ionis Pharmaceuticals, Inc. stockholders $(50,171) $88,851 
  
Three Months Ended
March 31,
 
  2021  2020 
     (as revised*) 
       
Net loss $(89,869) $(49,882)
Unrealized losses on debt securities, net of tax  (3,006)  (1,954)
Currency translation adjustment  (126)  9 
         
Comprehensive loss  (93,001)  (51,827)
         
Comprehensive loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.  0   (10,254)
         
Comprehensive loss attributable to Ionis Pharmaceuticals, Inc. common stockholders $(93,001) $(41,573)


*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

See accompanying notes.

5


IONIS PHARMACEUTICALS, INC.
CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS EQUITY
Three Months Ended March 31, 20192020 and 20202021
(In thousands)
(Unaudited)

 Common Stock  Additional  Accumulated Other  Accumulated  
Total Ionis
Stockholders
  
Noncontrolling
Interest in Akcea
  
Total
Stockholders
  Common Stock  Additional  Accumulated Other  Accumulated  
Total Ionis
Stockholders
  
Noncontrolling
Interest in Akcea
  
Total
Stockholders
 
Description Shares  Amount  Paid in Capital  Comprehensive Loss  Deficit  Equity  Therapeutics, Inc.  Equity  Shares  Amount  Paid in Capital  Comprehensive Loss  Deficit  Equity  Therapeutics, Inc.  Equity 
Balance at December 31, 2018  137,929  $138  $2,047,250  $(32,016) $(967,293) $1,048,079  $139,081  $1,187,160 
Net income              84,443   84,443      84,443 
Change in unrealized gains, net of tax           4,324      4,324      4,324 
Foreign currency translation           84      84      84 
Issuance of common stock in connection with employee stock plans  1,825   2   67,057         67,059      67,059 
Stock-based compensation expense        45,505         45,505      45,505 
Payments of tax withholdings related to vesting of employee stock awards and exercise of employee stock options  (130)     (7,597)        (7,597)     (7,597)
Noncontrolling interest in Akcea Therapeutics, Inc        (34,246)        (34,246)  40,688   6,442 
Balance at March 31, 2019  139,624  $140  $2,117,969  $(27,608) $(882,850) $1,207,651  $179,769  $1,387,420 
                                
Balance at December 31, 2019  140,340  $140  $2,203,778  $(25,290) $(707,534) $1,471,094  $213,453  $1,684,547 
Balance at December 31, 2019 (as revised*)  140,340  $140  $1,985,650  $(25,290) $(596,495) $1,364,005  $213,453  $1,577,458 
Net loss              (48,226)  (48,226)     (48,226)     0   0   0   (39,628)  (39,628)  0   (39,628)
Change in unrealized gains, net of tax           (1,954)     (1,954)     (1,954)
Change in unrealized losses, net of tax     0   0   (1,954)  0   (1,954)  0   (1,954)
Foreign currency translation           9      9      9      0   0   9   0   9   0   9 
Issuance of common stock in connection with employee stock plans  606      7,652         7,652      7,652   606   0   7,652   0   0   7,652   0   7,652 
Repurchases and retirements of common stock  (1,478)  (1)        (90,549)  (90,550)     (90,550)  (1,478)  (1)  0   0   (90,549)  (90,550)  0   (90,550)
Stock-based compensation expense        40,790         40,790      40,790      0   40,790   0   0   40,790   0   40,790 
Payments of tax withholdings related to vesting of employee stock awards and exercise of employee stock options  (186)     (11,603)        (11,603)     (11,603)  (186)  0   (11,603)  0   0   (11,603)  0   (11,603)
Noncontrolling interest in Akcea Therapeutics, Inc.        (6,973)        (6,973)  (3,281)  (10,254)
Balance at March 31, 2020  139,282  $139  $2,233,644  $(27,235) $(846,309) $1,360,239  $210,172  $1,570,411 
Noncontrolling interest in Akcea Therapeutics, Inc     0   (6,973)  0   0   (6,973)  (3,281)  (10,254)
Balance at March 31, 2020 (as revised*)  139,282  $139  $2,015,516  $(27,235) $(726,672) $1,261,748  $210,172  $1,471,920 
                                
Balance at December 31, 2020 (as revised*)  140,366  $140  $1,895,519  $(21,071) $(1,131,306) $743,282  $0  $743,282 
Net loss     0   0   0   (89,869)  (89,869)  0   (89,869)
Change in unrealized loss, net of tax     0   0   (3,006)  0   (3,006)  0   (3,006)
Foreign currency translation     0   0   (126)  0   (126)  0   (126)
Issuance of common stock in connection with employee stock plans  809   1   7,758   0   0   7,759   0   7,759 
Stock-based compensation expense     0   37,861   0   0   37,861   0   37,861 
Payments of tax withholdings related to vesting of employee stock awards and exercise of employee stock options  (251)  0   (15,337)  0   0   (15,337)  0   (15,337)
Balance at March 31, 2021  140,924  $141  $1,925,801  $(24,203) $(1,221,175) $680,564  $0  $680,564 


*
We revised our 2019 and 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

See accompanying notes.

6


IONIS PHARMACEUTICALS, INC.
CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
(in thousands)
(Unaudited)

 
Three Months Ended
March 31,
 
 
Three Months Ended
March 31,
  2021  2020 
 2020  2019     (as revised*) 
Operating activities:            
Net income (loss) $(58,480) $90,884 
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:        
Net loss $(89,869) $(49,882)
Adjustments to reconcile net loss to net cash used in operating activities:        
Depreciation  3,233   3,073   3,917   3,233 
Amortization of right-of-use operating lease assets  393   476   394   393 
Amortization of patents  486   470   544   486 
Amortization of premium (discount) on investments, net  1,062   (2,433)  4,023   1,062 
Amortization of debt issuance costs  595   474   860   647 
Amortization of convertible senior notes discount  8,834   8,726 
Stock-based compensation expense  40,790   45,505   37,861   40,790 
Non-cash losses related to patents, licensing and property, plant and equipment and investments  (87)  14 
Gain on investments  (13)  (246)
Non-cash losses related to patents  221   159 
Provision for deferred income taxes  (3,437)  13,549   0   (2,288)
Changes in operating assets and liabilities:                
Contracts receivable  34,429   4,908   52,807   34,429 
Inventories  (2,181)  (2,475)  (234)  (2,181)
Other current and long-term assets  9,532   1,326   16,481   9,532 
Income taxes payable  2   (532)
Accounts payable  411   (17,191)  (9,569)  411 
Accrued compensation  (20,920)  (13,004)  (36,465)  (20,920)
Other current liabilities  (2,565)  13,756 
Accrued liabilities and other current liabilities  (11,905)  (3,006)
Deferred contract revenue  (19,679)  (40,353)  (23,717)  (19,679)
Net cash provided by (used in) operating activities  (7,584)  107,705 
Net cash used in operating activities  (54,662)  (7,592)
                
Investing activities:                
Purchases of short-term investments  (544,375)  (492,781)  (330,051)  (544,375)
Proceeds from sale of short-term investments  459,352   426,868   411,907   459,352 
Purchases of property, plant and equipment  (9,080)  (3,229)  (1,772)  (9,080)
Acquisition of licenses and other assets, net  (904)  (1,032)  (1,228)  (904)
Net cash used in investing activities  (95,007)  (70,174)
Net cash provided by (used in) investing activities  78,856   (95,007)
                
Financing activities:                
Proceeds from issuance of equity, net  7,652   67,057 
Proceeds from equity, net  7,760   7,652 
Payments of tax withholdings related to vesting of employee stock awards and exercise of
employee stock options
  (11,603)  (7,597)  (15,337)  (11,603)
Repurchases and retirements of common stock  (90,550)     0   (90,550)
Net cash provided by financing activities  (94,501)  59,460 
Net cash used in financing activities  (7,577)  (94,501)
                
Net increase in cash and cash equivalents  (197,092)  96,991 
Effects of exchange rates on cash  (126)  8 
        
Net increase (decrease) in cash and cash equivalents  16,491   (197,092)
Cash and cash equivalents at beginning of period  683,287   278,820   397,664   683,287 
Cash and cash equivalents at end of period $486,195  $375,811  $414,155  $486,195 
                
Supplemental disclosures of cash flow information:                
Interest paid $601  $667  $594  $601 
Income taxes paid $3  $  $2  $3 
                
Supplemental disclosures of non-cash investing and financing activities:                
Right-of-use assets obtained in exchange for lease liabilities $  $13,557 
Amounts accrued for capital and patent expenditures $4,903  $1,864  $1,876  $4,903 


*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

See accompanying notes.

7


IONIS PHARMACEUTICALS, INC.
NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
March 31, 20202021
(Unaudited)

1.  Basis of Presentation


We prepared the unaudited interim condensed consolidated financial statements for the three months endedMarch 31, 20202021 and 20192020 on the same basis as the audited financial statements for the year ended December 31, 2019.2020, with the exception of our retrospective adoption of Accounting Standards Update, or ASU, 2020-06, which simplifies the accounting for convertible debt instruments. See Note 2, Significant Accounting Polices, Convertible Debt, for details of our adoption of this guidance. We included all normal recurring adjustments in the financial statements, which we considered necessary for a fair presentation of our financial position at such dates and our operating results and cash flows for those periods. Our operating results for the interim periods may not be indicative of what our operating results will be for the entire year. For more complete financial information, these financial statements, and notes thereto, should be read in conjunction with the audited financial statements for the year ended December 31, 20192020 included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission, or SEC.


In theour condensed consolidated financial statements, we included the accounts of Ionis Pharmaceuticals, Inc. and the consolidated results of our majority-owned affiliate,wholly owned subsidiary, Akcea Therapeutics, Inc. and its wholly owned subsidiaries.subsidiaries (“we”, “us” or “our”). We formed Akcea in December 2014. In July 2017, Akcea completed an initial public offering, or IPO. Since Akcea’s IPO, our ownership has ranged from 68 percent to 77 percent. At March 31, 2020,which reduced our ownership of Akcea’s common stock below 100 percent. In October 2020, we acquired the shares of Akcea’s common stock we did not own. We will refer to this transaction as the Akcea was approximately 76 percent. Acquisition throughout the remainder of this document. We reflectreflected changes in our ownership of Akceapercentage in our financial statements as an adjustment to noncontrolling interest in the period the change occurs. For example, we reflected an increase in our ownership when we received 6.9 million shares of Akcea common stock as payment for the sublicense fee Akcea owed us for Pfizer’s license of vupanorsen (formerly AKCEA-ANGPTL3-LRx)in the fourth quarter of 2019. Refer to the section titled “Noncontrolling Interest in Akcea” in Note 2, Significant Accounting Policies, for further information related to our accounting for our investment in Akcea.


Unless the context requires otherwise, “Ionis”, “Company,” “we,” “our,” and “us” refers to Ionis Pharmaceuticals, Inc. and its majority owned affiliate, Akcea Therapeutics, Inc. and its wholly owned subsidiaries.occurred.

2.  Significant Accounting Policies


Revenue Recognition


Our Revenue Sources


We generally recognize revenue when we have satisfied all contractual obligations and are reasonably assured of collecting the resulting receivable. We are often entitled to bill our customers and receive payment from our customers in advance of recognizing the revenue. In the instances in which we have received payment from our customers in advance of recognizing revenue, we include the amounts in deferred revenue on our condensed consolidated balance sheet.


Commercial Revenue: SPINRAZA royalties and Licensing and other royalty revenue



We earn commercial revenue primarily in the form of royalty payments on net sales of SPINRAZA. We will also recognize as commercial revenue future sales milestone payments and royalties we earn under our other partnerships.



Commercial Revenue: Product sales,TEGSEDI and WAYLIVRA revenue, net



We added product sales from TEGSEDI to our commercial revenue inIn the fourthUnited States, or U.S., through the first quarter of 2018 and2021, we added product sales from WAYLIVRA to our commercial revenue in the third quarter of 2019. In the U.S., we distributesold TEGSEDI through an exclusive distribution agreement with a third-party logistics company, or 3PL, that takestook title to TEGSEDI. The 3PL iswas our sole customer in the U.S. The 3PL then distributesdistributed TEGSEDI to a specialty pharmacy and a specialty distributor, which we collectively refer to as wholesalers, who then distributedistributed TEGSEDI to health care providers and patients. In Europe, prior to the third quarter of 2019through 2020, we distributed TEGSEDI through a non-exclusive distribution model with a 3PL that took title to TEGSEDI. The 3PL was our sole customer in Europe. The 3PL in Europe then distributed TEGSEDI to hospitals and pharmacies. In the third quarter of 2019, we entered into a distribution arrangement with a 3PL and began to sell bothsold TEGSEDI and WAYLIVRA directly to hospitals and pharmacies, which were our customers, using 3PLs as distributors. In January 2021, we began commercializing TEGSEDI and WAYLIVRA in Europe.Europe through a distribution agreement with Swedish Orphan Biovitrum AB, or Sobi. In April 2021, we expanded our distribution agreement with Sobi to also include commercializing TEGSEDI in North America. Under our agreements, we are responsible for supplying finished goods inventory to Sobi and Sobi is responsible for selling each medicine to the end customer. As a result of these agreements, we earn a distribution fee on net sales from Sobi for each medicine.


Under our collaboration agreement with PTC, PTC is responsible for commercializing TEGSEDI and WAYLIVRA in Latin America and Caribbean countries.

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Research and development revenue under collaborative agreements


We often enter into collaboration agreements to license and sell our technology on an exclusive or non-exclusive basis. Our collaboration agreements typically contain multiple elements, or performance obligations, including technology licenses or options to obtain technology licenses, research and development, or R&D, services, and manufacturing services.


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In See Note 5, Collaborative Arrangements and Licensing Agreements, for collaborations with substantive changes that occurred in 2021. Additionally, see Note 6, Collaborative Arrangements and Licensing Agreements, we have included our collaborations with substantive changes during the first three months of 2020 from those included in Note 6 of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2019.2020 for a summary of each of our material collaborative agreements.



Steps to Recognize Revenue



We use a five-step process to determine the amount of revenue we should recognize and when we should recognize it. The five-step process is as follows:

1.Identify the contract



First weAccounting rules require us to first determine if we have a contract with our partner, including confirming that we have met each of the following criteria:


We and our partner approved the contract and we are both committed to perform our obligations;
We have identified our rights, our partner’s rights and the payment terms;
We have concluded that the contract has commercial substance, meaning that the risk, timing, or amount of our future cash flows is expected to change as a result of the contract; and
We believe collectability of the consideration is probable.


2.Identify the performance obligations



We next identify our performance obligations, which represent the distinct goods and services we are required to provide under the contract. We typically have only 1 performance obligation at the inception of a contract, which is to perform R&D services.



Often times we enter into a collaboration agreement in which we provide our partner with an option to license a medicine in the future. We may also provide our partner with an option to request that we provide additional goods or services in the future, such as active pharmaceutical ingredient, or API. We evaluate whether these options are material rights at the inception of the agreement. If we determine an option is a material right, we will consider the option a separate performance obligation. Historically, we have concluded that the options we grant to license a medicine in the future or to provide additional goods and services as requested by our partner are not material rights because these items are contingent upon future events that may not occur.occur and are not priced at a significant discount. When a partner exercises its option to license a medicine or requests additional goods or services, then we identify a new performance obligation for that item.


In some cases, we deliver a license at the start of an agreement. If we determine that our partner has full use of the license and we do not have any additional material performance obligations related to the license after delivery, then we consider the license to be a separate performance obligation.


3.Determine the transaction price



We then determine the transaction price by reviewing the amount of consideration we are eligible to earn under the collaboration agreement, including any variable consideration. Under our collaboration agreements, consideration typically includes fixed consideration in the form of an upfront payment and variable consideration in the form of potential milestone payments, license fees and royalties. At the start of an agreement, our transaction price usually consists of only the upfront payment. We do not typically include any payments we may receive in the future in our initial transaction price because the payments are not probable and are contingent on certain future events. We reassess the total transaction price at each reporting period to determine if we should include additional payments in the transaction price.

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Milestone payments are our most common type of variable consideration. We recognize milestone payments using the most likely amount method because we will either receive the milestone payment or we will not, which makes the potential milestone payment a binary event. The most likely amount method requires us to determine the likelihood of earning the milestone payment. We include a milestone payment in the transaction price once it is probable we will achieve the milestone event. Most often, we do not consider our milestone payments probable until we or our partner achieve the milestone event because the majority of our milestone payments are contingent upon events that are not within our control andand/ or are usually based on scientific progress.progress which is inherently uncertain. For example, in the firstfourth quarter of 2020, we earned a $10$20 million milestone payment from AstraZeneca when AstraZeneca advanced ION532initiated a Phase 2b study for ION449, our medicine in development targeting APOL1 for the treatment of kidney disease under our cardiovascular, renal and metabolic diseases collaboration.PCSK9 to lower LDL-cholesterol. We did not consider the milestone payment probable until AstraZeneca achieved the milestone event because advancing ION532ION449 was contingent on AstraZeneca initiating a contingent event thatPhase 2b study and was not within our control. We recognized the milestone payment in full in the period the milestone event was achieved because we did not have any remaining performance obligations related to the milestone payment.


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4.Allocate the transaction price



Next, we allocate the transaction price to each of our performance obligations. When we have to allocate the transaction price to more than one performance obligation, we make estimates of the relative stand-alone selling price of each performance obligation because we do not typically sell our goods or services on a stand-alone basis. We then allocate the transaction price to each performance obligation based on the relative stand-alone selling price. We do not reallocate the transaction price after the start of an agreement to reflect subsequent changes in stand-alone selling prices.



We may engage a third party, independent valuation specialist to assist us with determining a stand-alone selling price for collaborations in which we deliver a license at the start of an agreement. We estimate the stand-alone selling price of these licenses using valuation methodologies, such as the relief from royalty method. Under this method, we estimate the amount of income, net of taxes, for the license. We then discount the projected income to present value. The significant inputs we use to determine the projected income of a license could include:


Estimated future product sales;
Estimated royalties we may receive from future product sales;
Estimated contractual milestone payments we may receive;
Expenses we expect to incur;
IncomeEstimated income taxes; and
A discount rate.


We typically estimate the selling price of R&D services by using our internal estimates of the cost to perform the specific services. The significant inputs we use to determine the selling price of our R&D services include:

The number of internal hours we estimate we will spend performing these services;
The estimated cost of work we will perform;
The estimated cost of work that we will contract with third parties to perform; and
The estimated cost of API we will use.



For purposes of determining the stand-alone selling price of the R&D services we perform and the API we will deliver, accounting guidance requires us to include a markup for a reasonable profit margin.

5.Recognize revenue



We recognize revenue in one of two ways, over time or at a point in time. We recognize revenue over time when we are executing on our performance obligation over time and our partner receives benefit over time. For example, we recognize revenue over time when we provide R&D services. We recognize revenue at a point in time when our partner receives full use of an item at a specific point in time. For example, we recognize revenue at a point in time when we deliver a license or API to a partner.



For R&D services that we recognize over time, we measure our progress using an input method. The input methods we use are based on the effort we expend or costs we incur toward the satisfaction of our performance obligation. We estimate the amount of effort we expend, including the time we estimate it will take us to complete the activities, or costs we incur in a given period, relative to the estimated total effort or costs to satisfy the performance obligation. This results in a percentage that we multiply by the transaction price to determine the amount of revenue we recognize each period. This approach requires us to make numerous estimates and use significant judgement. If our estimates or judgements change over the course of the collaboration, they may affect the timing and amount of revenue that we recognize in the current and future periods. For example, in the third quarter of 2019, we updated our estimate of the total effort we expected to expend to satisfy our performance obligation under our 2013 Strategic Neurology collaboration with Biogen. As of September 30, 2019, we had completed a significant portion of the research and development services. We expect to complete the remainder of our services in 2020. As a result of our change in estimate, in the third quarter of 2019, we recorded a cumulative catch up adjustment of $16.5 million to decrease revenue. Refer to Note 6, Collaborative Arrangements and Licensing Agreements, in our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2019 for further discussion of the cumulative catch up adjustment we made.


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The following are examples of when we typically recognize revenue based on the types of payments we receive.


Commercial Revenue: SPINRAZA royalties and Licensing and other royalty revenue



We recognize royalty revenue, including royalties from SPINRAZA sales, in the period in which the counterparty sells the related product and recognizes the related revenue, which in certain cases may require us to estimate our royalty revenue.


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Commercial Revenue: TEGSEDI and WAYLIVRA revenue, net


Commercial Revenue: Product sales, net



We recognize product salesPrior to our distribution agreement with Sobi, we recognized TEGSEDI and WAYLIVRA commercial revenue in the period when our customer obtainsobtained control of our products, which occursoccurred at a point in time upon transfer of title to the customer. We classifyclassified payments to customers or other parties in the distribution channel for services that arewere distinct and priced at fair value as selling, general and administrative, or SG&A, expenses in our condensed consolidated statements of operations. Otherwise,We classified payments to customers or other parties in the distribution channel that dodid not meet those criteria are classified as a reduction of revenue, as discussed further below. We excludeexcluded from revenues taxes collected from customers relating to product salesTEGSEDI and WAYLIVRA commercial revenue and remitted these amounts to governmental authorities.



ReservesUnder our distribution agreement with Sobi we concluded that our performance obligation is to supply finished goods inventory to Sobi. This performance obligation is a series of distinct activities that are substantially the same because we transfer title using the same criteria each time we ship inventory to Sobi. Therefore, we recognize as revenue the price Sobi pays us for Productthe inventory when we deliver the finished goods inventory to Sobi. We also recognize distribution fee revenue based on Sobi’s net sales of TEGSEDI and WAYLIVRA. Additionally, Sobi does not generally have a right of return.


We record product salesReserves for TEGSEDI and WAYLIVRA commercial revenue


Prior to our distribution agreement with Sobi, we recorded TEGSEDI and WAYLIVRA commercial revenue at our net sales price, or transaction price. We includeincluded in our transaction price estimated reserves for discounts, returns, chargebacks, rebates co-pay assistance and other allowances that we offeroffered within contracts between us and our customers, wholesalers, distributors, health care providers and other indirect customers. We estimateestimated our reserves using the amounts we have earned or what we cancould claim on the associated sales. We classifyclassified our reserves as a reduction of accounts receivable when we arewere not required to make a payment or as a current liability when we arewere required to make a payment. In certain cases, our estimates includeincluded a range of possible outcomes that are probability-weightedwere probability weighted for relevant factors such as our historical experience, current contractual and statutory requirements, specific known market events and trends, industry data and forecasted customer buying and payment patterns. Overall, our reserves reflectreflected our best estimates under the terms of our respective contracts. When calculating our reserves and related product sales,TEGSEDI and WAYLIVRA commercial revenue, we only recognizerecognized amounts to the extent that we considerconsidered it probable that we would not have to reverse in a future period a significant amount of the cumulative sales we previously recognized.recognized in a future period. The actual amounts we receive may ultimately differ from our reserve estimates. If actual amounts in the future vary from our estimates, we will adjust these estimates, which would affect our net product salesTEGSEDI and WAYLIVRA revenue in the respectivecorresponding period. See our revenue recognition policy in Note 1, Organization and Significant Accounting Policies, of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2020 for additional details regarding how we accounted for the reserves related to TEDSEDI and WAYLIVIRA product sales.



The following are the components of variable consideration related to product sales:

Chargebacks: In the U.S., we estimate obligations resulting from contractual commitments with the government and other entities to sell products to qualified healthcare providers at prices lower than the list prices charged to our U.S. customer. Our U.S. customer charges us for the difference between what it pays for the product and the selling price to the qualified healthcare providers. We also estimate the amount of chargebacks related to our estimated product remaining in the distribution channel at the end of the reporting period that we expect our customer to sell to healthcare providers in future periods. We record these reserves as an accrued liability on our condensed consolidated balance sheet for the chargebacks related to product sales to our U.S. customer during the reporting period.

Government rebates: We are subject to discount obligations under government programs, including Medicaid and Medicare programs in the U.S. and we record reserves for government rebates based on statutory discount rates and estimated utilization. We estimate Medicaid and Medicare rebates based on a range of possible outcomes that are probability-weighted for the estimated payer mix. We record these reserves as an accrued liability on our condensed consolidated balance sheet with a corresponding offset reducing our product sales in the same period we recognize the related sale. For Medicare, we also estimate the number of patients in the prescription drug coverage gap for whom we will owe an additional liability under the Medicare Part D program. On a quarterly basis, we update our estimates and record any adjustments in the period that we identify the adjustments.

Managed care rebates: We are subject to rebates in connection with value-based agreements with certain of our commercial payers. We record these rebates as an accrual on our condensed consolidated balance sheet in the same period we recognize the related revenue. We estimate our managed care rebates based on our estimated payer mix and the applicable contractual rebate rate.

Trade discounts: We provide customary invoice discounts on product sales to our U.S. customer for prompt payment. We record this discount as a reduction of product sales in the period in which we recognize the related product revenue.

Distribution services: We receive and pay for various distribution services from our U.S. and EU customers and wholesalers in the U.S.. We classify the costs for services we receive that are either not distinct from the sale of the product or for which we cannot reasonably estimate the fair value as a reduction of product sales. To the extent that the services we receive are distinct from the sale of the product, we classify the costs for such services as SG&A expenses.

Product returns: Our U.S. customer has return rights and the wholesalers have limited return rights primarily related to the product’s expiration date. We estimate the amount of product sales that our customer may return. We record our return estimate as an accrued refund liability on our condensed consolidated balance sheet with a corresponding offset reducing our product sales in the same period we recognize the related sale. Based onUnder our distribution modelagreement with Sobi, Sobi is financially responsible for product sales, contractual inventory limits with our customer and wholesalers and the price of the product, we have had minimal returns to date and we believe we will continue to have minimal returns. Our EU customers only take title to the product after they receive an order from a hospital or pharmacy and therefore they do not maintain excess inventory levels of our products. Accordingly, we have limited return risk in the EU and we do not estimate returns in the EU.

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Other incentives: In the U.S., we estimate reserves for other incentives including co-payment assistance we provide to patients with commercial insurance who have coverage and reside in states that allow co-payment assistance. We record a reserve for the amount we estimate we will pay for co-payment assistance. We base our reserve on the number of estimated claims and our estimate of the cost per claim related to product sales that we have recognized as revenue. We record our other incentive reserve estimates as an accrued liability on our condensed consolidated balance sheet with a corresponding offset reducing our product sales in the same period we recognize the related sale.any applicable reserves.



Research and development revenue under collaboration agreements:



Upfront payments



When we enter into a collaboration agreement with an upfront payment, we typically record the entire upfront payment as deferred revenue if our only performance obligation is for R&D services we will provide in the future. We amortize the upfront payment into revenue as we perform the R&D services. For example, under our collaboration agreement with Roche to develop IONIS-FB-LRx for the treatment of complement-mediated diseases,, we received a $75 million upfront payment in the fourth quarter of 2018. We allocated the upfront payment to our single performance obligation, R&D services. We are amortizing the $75 million upfront payment using an input method over the estimated period of time we are providing R&D services.

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Milestone payments



We are required to include additional consideration in the transaction price when it is probable. We typically include milestone payments for R&D services in the transaction price when they are achieved. We include these milestone payments when they are achieved because typically there is considerable uncertainty in the research and development processes that trigger these payments. Similarly, we include approval milestone payments in the transaction price once the medicine is approved by the applicable regulatory agency. We will recognize sales-based milestone payments in the period in which we achieve the milestone under the sales-based royalty exception allowed under accounting rules.



We recognize milestone payments that relate to an ongoing performance obligation over our period of performance. For example, in the firstfourth quarter of 2020, we achieved a $7.5 million milestone payment from Biogen when we advanced IONIS-MAPTRx a target under our 2012 neurology2018 strategic collaboration. We added this payment to the transaction price and allocated it to our R&D services performance obligation for IONIS-MAPTRx.obligation. We are recognizing revenue related to this milestone payment over our estimated period of performance.



Conversely, we recognize in full those milestone payments that we earn based on our partners’ activities when our partner achieves the milestone event and we do not have a performance obligation. For example, in the firstthird quarter of 2020, we recognized $18 million in milestone payments when Biogen initiated a $10 million milestone payment when AstraZeneca advanced ION532Phase 1/2 trial for ION464, our medicine in development targeting APOL1 for the treatment of kidney disease under our cardiovascular, renal and metabolic diseases collaboration agreement. alpha-synuclein to treat patients with multiple system atrophy. We concluded that the milestone payment waspayments were not related to our R&D services performance obligation. Therefore, we recognized the milestone paymentpayments in full in the firstthird quarter of 2020.



License fees



We generally recognize as revenue the total amount we determine to be the relative stand-alone selling price of a license when we deliver the license to our partner. This is because our partner has full use of the license and we do not have any additional performance obligations related to the license after delivery. For example, in the fourth quarter of 2019,2020, we earned a $45$30 million license fee from AstraZeneca when BiogenAstraZeneca licensed IONIS-MAPTRx from us. We also recognized $246 million of license fee revenue relatedION455, an investigational medicine in development to Akcea’s license of vupanorsen to Pfizer in the fourth quarter of 2019.treat nonalcoholic steatohepatitis, or NASH.


Sublicense fees



We recognize sublicense fee revenue in the period in which a party, who has already licensed our technology, further licenses the technology to another party because we do not have any performance obligations related to the sublicense.For example, in the second quarter of 2019, we earned a $20 million sublicense fee when Alnylam Pharmaceuticals sublicensed our technology to Regeneron Pharmaceuticals.


Amendments to Agreements


From time to time we amend our collaboration agreements. When this occurs, we are required to assess the following items to determine the accounting for the amendment:


1)If the additional goods and/or services are distinct from the other performance obligations in the original agreement; and
2)If the goods and/or services are sold at a stand-alone selling price.

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If we conclude the goods and/or services in the amendment are distinct from the performance obligations in the original agreement and at a stand-alone selling price, we account for the amendment as a separate agreement. If we conclude the goods and/or services are not distinct and are sold at theira stand-alone selling price, we then assess whether the remaining goods or services are distinct from those already provided. If the goods and/or services are distinct from what we have already provided, then we allocate the remaining transaction price from the original agreement and the additional transaction price from the amendment to the remaining goods and/or services. If the goods and/or services are not distinct from what we have already provided, we update the transaction price for our single performance obligation and recognize any change in our estimated revenue as a cumulative adjustment.



For example, in May 2015, we entered into an exclusive license agreement with Bayer to develop and commercialize IONIS-FXIRx for the prevention of thrombosis. As part of the agreement, Bayer paid us a $100 million upfront payment. At the onset of the agreement, we were responsible for completing a Phase 2 study of IONIS-FXIRx in people with end-stage renal disease on hemodialysis and for providing an initial supply of API. In February 2017, we amended our agreement with Bayer to advance IONIS-FXIRx and to initiate development of IONIS-FXI-LRx, which Bayer licensed. As part of the 2017 amendment, Bayer paid us $75 million. We are also eligible to receive milestone payments and tiered royalties on gross margins of IONIS-FXIRx and IONIS-FXI-LRx. Under the 2017 amendment, we concluded we had a new agreement with 3 performance obligations. These performance obligations were to deliver the license of IONIS-FXI-LRx, to provide R&D services and to deliver API. We allocated the $75 million transaction price to these performance obligations. Refer to Note 6, Collaborative Arrangements and Licensing Agreements, in our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 20192020 for further discussion of the Bayer collaboration.

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Multiple agreements


From time to time, we may enter into separate agreements at or near the same time with the same partner. We evaluate such agreements to determine whether we should account for them individually as distinct arrangements or whether the separate agreements should be combined and accounted for together. We evaluate the following to determine the accounting for the agreements:


Whether the agreements were negotiated together with a single objective;
Whether the amount of consideration in one contract depends on the price or performance of the other agreement; or
Whether the goods and/or services promised under the agreements are a single performance obligation.


Our evaluation involves significant judgment to determine whether a group of agreements might be so closely related that accounting guidance requires us to account for them as a combined arrangement.


For example, in the second quarter of 2018, we entered into 2 separate agreements with Biogen at the same time: a new strategic neurology collaboration agreement and a stock purchase agreement, or SPA. We evaluated the Biogen agreements to determine whether we should treat the agreements separately or combine them. We considered that the agreements were negotiated concurrently and in contemplation of one another. Based on these facts and circumstances, we concluded that we should evaluate the provisions of the agreements on a combined basis.


Contracts Receivable



Our contracts receivable balance represents the amounts we have billed our partners or customers and that are due to us unconditionally for goods we have delivered or services we have performed. When we bill our partners or customers with payment terms based on the passage of time, we consider the contractcontracts receivable to be unconditional. We typically receive payment within one quarter of billing our partner or customer.


As of March 31, 2021, approximately 46.8 percent of our contracts receivables were from 3 significant customers. As of December 31, 2020, approximately 99.5 percent of our contracts receivables were from 2 significant customers.


Unbilled SPINRAZA Royalties



Our unbilled SPINRAZA royalties represent our right to receive consideration from Biogen in advance of when we are eligible to bill Biogen for SPINRAZA royalties. We include these unbilled amounts in other current assets on our condensed consolidated balance sheet.


Deferred Revenue


We are often entitled to bill our customers and receive payment from our customers in advance of our obligation to provide services or transfer goods to our partners. In these instances, we include the amounts in deferred revenue on our condensed consolidated balance sheet. During the three months ended March 31, 20202021 and 2019,2020, we recognized $28.0$26.0 million and $40.3$28.0 million of revenue from amounts that were in our beginning deferred revenue balance for each respective period. For further discussion, refer to our revenue recognition policy above.

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Cost of Products SoldSales


Our cost of products soldsales includes manufacturing costs, transportation and freight costs and indirect overhead costs associated with the manufacturing and distribution of our products. We also may include certain period costs related to manufacturing services and inventory adjustments in cost of products sold. Prior to obtaining regulatory approval of TEGSEDI in July 2018 and WAYLIVRA in May 2019, we expensed as research and development expenses a significant portion of the costs we incurred to produce the initial commercial launch supply for each medicine. We previously expensed $0.6 million and $0.3 million of costs to produce our products related to the product sales revenue we recognized in the three months ended March 31, 2020 and 2019, respectively.


Noncontrolling Interest in Akcea Therapeutics, Inc.



Prior to Akcea’s IPO in July 2017, we owned 100 percent of Akcea. Since Akcea’s IPO, our ownership has ranged from 68 percent to 77 percent. At March 31, 2020, our ownership was approximately 76 percent. We reflect changes in our ownership percentage in our financial statements as an adjustment to noncontrolling interest in the period the change occurs. During 2019, we received the following additional shares of Akcea common stock:


2.8 million shares in the first quarter of 2019 as payment for the sublicense fee Akcea owed us for Novartis’s license of AKCEA-APO(a)-LRx, and
6.9 million shares in the fourth quarter of 2019 as payment for the sublicense fee Akcea owed us for Pfizer’s license of vupanorsen.



The shares third parties own represent an interest in Akcea’s equity that we do control. However, as we continue to maintain overall control of Akcea through our voting interest, we reflect the assets, liabilities and results of operations of Akcea in our condensed consolidated financial statements. We reflect the noncontrolling interest attributable to other owners of Akcea’s common stock in a separate line on the statement of operations and a separate line within stockholders’ equity in our condensed consolidated balance sheet. In addition, we record a noncontrolling interest adjustment to account for the stock options Akcea grants, which if exercised, will dilute our ownership in Akcea. This adjustment is a reclassification within stockholders’ equity from additional paid-in capital to noncontrolling interest in Akcea equal to the amount of stock-based compensation expense Akcea had recognized.sales.


Cash, Cash Equivalents and Investments



We consider all liquid investments with maturities of three months or less when we purchase them to be cash equivalents. Our short-term investments have initial maturities of greater than three months from date of purchase. We classify our short-term debt investments as “available-for-sale” and carry them at fair market value based upon prices on the last day of the fiscal period for identical or similar items. We record unrealized gains and losses on debt securities as a separate component of comprehensive income (loss) and include net realized gains and losses in gain (loss) on investments.investments in our condensed consolidated statement of operations. We use the specific identification method to determine the cost of securities sold.


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We also have equity investments of less than 20 percent ownership in publicly and privately held biotechnology companies that we received as part of a technology license or partner agreement. At March 31, 2020,2021, we held equity investments in 2 publicly held companies, ProQR Therapeutics N.V., or ProQR, and Antisense Therapeutics Limited, or ATL. We also held equity investments in 5 privately-held7 privately held companies, Aro Biotherapeutics, Atlantic Pharmaceuticals Limited, Dynacure SAS, Empirico, Inc., Flamingo Therapeutics BV, Seventh Sense Biosystems and Suzhou RiboSuzhou-Ribo Life Science Co, Ltd.



We are required to measure and record our equity investments at fair value and to recognize the changes in fair value in our condensed consolidated statement of operations. We account for our equity investments in privately held companies at their cost minus impairments, plus or minus changes resulting from observable price changes in orderly transactions for the identical or similar investment of the same issuer. For example, during the second and fourth quarters of 2020, we revalued our investments in 3 privately held companies, Dynacure, Suzhou-Ribo and Aro Biotherapeutics because the companies sold additional equity securities that were similar to the equity we own. These observable price changes resulted in us recognizing a $6.3 million gain on our investment in Dynacure, a $3.0 million gain on our investment in Suzhou-Ribo and a $5.5 million gain on our investment in Aro Biotherapeutics in our condensed consolidated statement of operations during 2020 because the sales were at higher prices compared to our recorded value.


Inventory Valuation



We reflect our inventory on our condensed consolidated balance sheet at the lower of cost or marketnet realizable value under the first-in, first-out method, or FIFO. We capitalize the costs of raw materials that we purchase for use in producing our medicines because until we use these raw materials, they have alternative future uses, which we refer to as clinical raw materials. We include in inventory raw material costs for medicines that we manufacture for our partners under contractual terms and that we use primarily in our clinical development activities and drug products. We can use each of our raw materials in multiple products and, as a result, each raw material has future economic value independent of the development status of any single medicine. For example, if one of our medicines failed, we could use the raw materials for that medicine to manufacture our other medicines. We expense these costs as R&D expenses when we begin to manufacture API for a particular medicine if the medicine has not been approved for marketing by a regulatory agency.

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We obtained the first regulatory approval for TEGSEDI in July 2018 and for WAYLIVRA in May 2019. At March 31, 2020,2021, our physical inventory for TEGSEDI and WAYLIVRA included API that we produced prior to when we obtained regulatory approval. As such, this API has no cost basis as we had previously expensed the costs as R&D expenses.



We review our inventory periodically and reduce the carrying value of items we consider to be slow moving or obsolete to their estimated net realizable value based on forecasted demand compared to quantities on hand. We consider several factors in estimating the net realizable value, including shelf life of our inventory, alternative uses for our medicines in development and historical write-offs. We did not record any materialrecorded an insignificant amount of inventory write-offs for the three months ended March 31, 2021 and 2020. Total


Our inventory was $22.9 million and $18.2 million as of March 31, 2020 and December 31, 2019, respectively, and consisted of the following (in thousands):


 March 31, 2020  December 31, 2019  March 31, 2021  December 31, 2020 
Raw materials:            
Raw materials- clinical $9,162  $9,363  $10,695  $9,206 
Raw materials- commercial  10,476   6,520   7,502   7,502 
Total raw materials  19,638   15,883   18,197   16,708 
Work in process  2,645   2,039   2,096   2,252 
Finished goods  602   258   1,906   3,005 
Total inventory $22,885  $18,180  $22,199  $21,965 


Leases



We determine if an arrangement contains a lease at inception. We currently only have operating leases. We recognize a right-of-use operating lease asset and associated short- and long-term operating lease liability on our condensed consolidated balance sheet for operating leases greater than one year. Our right-of-use assets represent our right to use an underlying asset for the lease term and our lease liabilities represent our obligation to make lease payments arising from the lease arrangement. We recognize our right-of-use operating lease assets and lease liabilities based on the present value of the future minimum lease payments we will pay over the lease term.We determineddetermine the lease term at the inception of theeach lease, and in certain cases our lease term could include renewal options if we concluded we were reasonably certain that we will exercise the renewal option. When we exercise a lease option that was not previously included in the initial lease term, we reassess our right-of-use asset and lease liabilities for the new lease term.


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As our current leases do not provide an interest rate implicit in the lease, we used our incremental borrowing rate, based on the information available on the date we adopted Topic 842 (January 2019) or, as of the lease inception date or at the lease option extension date in determining the present value of future payments. We recognize rent expense for our minimum lease payments on a straight-line basis over the expected term of our lease. We recognize period expenses, such as common area maintenance expenses, in the period we incur the expense.

Research, Development and Patent Expenses


Our research and development expenses include wages, benefits, facilities, supplies, external services, clinical trial and manufacturing costs and other expenses that are directly related to our research and development operations. We expense research and development costs as we incur them. When we make payments for research and development services prior to the services being rendered, we record those amounts as prepaid assets on our condensed consolidated balance sheet and we expense them as the services are provided.


We capitalize costs consisting principally of outside legal costs and filing fees related to obtaining patents. We amortize patent costs over the useful life of the patent, beginning with the date the U.S. Patent and Trademark Office, or foreign equivalent, issues the patent. We review our capitalized patent costs regularly to ensure that they include costs for patents and patent applications that have future value. When we identify patents and patent applications that we are not actively pursuing, we write off any associated costs.


Income Taxes



We account for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in our financial statements or tax returns. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. We record a valuation allowance when necessary to reduce our net deferred tax assets to the amount we expect to realize.


We evaluate our deferred tax assets regularly to determine whether adjustments to the valuation allowance are appropriate due to changes in facts or circumstances, such as changes in expected future pre-tax earnings, tax law, interactions with taxing authorities and developments in case law. In making this evaluation, we rely on our recent history of pre-tax earnings. Our material assumptions are our forecasts of future pre-tax earnings and the nature and timing of future deductions and income represented by the deferred tax assets and liabilities, all of which involve the exercise of significant judgment.


We assessed our valuation allowance requirements and recorded a valuation allowance against all of Ionis’ U.S. federal net deferred tax assets in the fourth quarter of 2020, due to uncertainties related to our ability to realize the tax benefits associated with these assets. We based our determination largely on Akcea rejoining the Ionis U.S. consolidated federal tax group in the fourth quarter of 2020. Due to Akcea’s historical and projected financial statement losses, and the negative impact we expect this to have on Ionis’ consolidated taxable income, there is uncertainty of generating sufficient consolidated pre-tax income in future periods to realize the Ionis deferred tax benefits. We also expect that Ionis’ pre-tax income in future periods may be realized.lower due to increased research and development expenses associated with our pipeline of wholly owned medicines. We continue to maintain a valuation allowance against all our consolidated U.S. federal and state net deferred tax assets.


Long-lived Assets



We evaluate long-lived assets, which include property, plant and equipment and patent costs, for impairment on at least a quarterly basis and whenever events or changes in circumstances indicate that we may not be able to recover the carrying amount of such assets.

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Use of Estimates



The preparation ofWe prepare our condensed consolidated financial statements in conformity with accounting principles generally accepted in the U.S. requires managementthat require us to make estimates and assumptions that affect the amounts reported in theour condensed consolidated financial statements and accompanying notes. Actual results could differ from thoseour estimates.

15

Basic and Diluted Net Income (Loss)Loss Per Share


Basic net income (loss)loss per share



We computeIn the first quarter of 2021, we computed basic net income (loss)loss per share by dividing the totalour net income (loss) attributable to our common stockholdersloss by our weighted-average number of common shares outstanding during the period.



The For the first quarter of 2021, we did not have to consider Akcea results separately in our calculation because we owned 100 percent of totalAkcea for the entire period. Our basic net income (loss) attributable to our common stockholdersloss per share for the three months ended March 31, 2021 was $0.64.


In the first quarter of 2020, and 2019 consideredprior to the Akcea Acquisition, we calculated our net income (loss)loss for Ionis on a stand-alone basis plus our share of Akcea’s net income (loss)loss for the period.period to determine our total net loss attributable to our common stockholders. To calculate the portion of Akcea’s net loss attributable to our ownership, we multiplied Akcea’s net income (loss)loss per share by the weighted average shares we owned in Akcea during the period. As a result of this calculation, our total net income (loss)loss available to Ionis common stockholders for the calculation of net income (loss)loss per share is different than our net income (loss)loss attributable to Ionis Pharmaceuticals, Inc. common stockholders in the condensed consolidated statements of operations.


Our basic net loss per share for the three months ended March 31, 2020, was calculated as follows (in thousands, except per share amounts):

Three months ended March 31, 2020 
Weighted
Average Shares
Owned in Akcea
  
Akcea’s
Net Loss
Per Share
  
Basic
Net Loss Per
Share Calculation
(as revised*)
 
Ionis’ portion of Akcea’s net loss  77,095  $(0.42) $(32,674)
Akcea’s net loss attributable to our ownership         $(32,674)
Ionis’ stand-alone net loss          (7,032)
Net loss available to Ionis common stockholders         $(39,706)
Weighted average shares outstanding          139,429 
Basic net loss per share         $(0.28)

Three months ended March 31, 2020 
Weighted
Average Shares
Owned in Akcea
  
Akcea’s
Net Loss
Per Share
  
Ionis’ Portion of
Akcea’s Net Loss
 
Common shares  77,095  $(0.42) $(32,674)
Akcea’s net loss attributable to our ownership         $(32,674)
Ionis’ stand-alone net loss          (15,630)
Net loss available to Ionis common stockholders         $(48,304)
Weighted average shares outstanding          139,429 
Basic net loss per share         $(0.35)


Our basic net income per share for the three months ended March 31, 2019, was calculated as follows (in thousands, except per share amounts):


Three months ended March 31, 2019 
Weighted
Average Shares
Owned in Akcea
  
Akcea’s
Net Income
Per Share
  
Ionis’ Portion of
Akcea’s Net Income
 
Common shares  68,582  $0.35  $23,846 
Akcea’s net income attributable to our ownership         $23,846 
Ionis’ stand-alone net income          63,697 
Net income available to Ionis common stockholders         $87,543 
Weighted average shares outstanding          138,582 
Basic net income per share         $0.63 
*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.


Diluted net income (loss)loss per share


For the three months ended March 31, 2021 and 2020, we incurred a net loss; therefore, we did not include dilutive common equivalent shares in the computation of diluted net loss per share because the effect would have been anti-dilutive. Common stock from the following would have had an anti-dilutive effect on net loss per share:


0.125 percent convertible senior notes;
Note hedges related to the 0.125 percent convertible senior notes;
1 percent convertible senior notes;
Dilutive stock options;
Unvested restricted stock units;units, or RSUs;
Unvested performance restricted stock units, or PRSUs; and
Employee Stock Purchase Plan, or ESPP.



For the three months endedAdditionally as of March 31, 2019,2021, we had net income availablewarrants related to Ionis common stockholders. As a result, we computedour 0.125 percent convertible senior notes outstanding. We will include the shares issuable under these warrants in our calculation of diluted net incomeearnings per share usingwhen the weighted-average numberaverage market price per share of our common shares and dilutive common equivalent shares outstanding duringstock for the period.reporting period exceeds the strike price of the warrants.

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Convertible Debt
We calculated our diluted net income per share for the three months ended March 31, 2019 as follows (in thousands except per share amounts):

Three months ended March 31, 2019 
Income
(Numerator)
  
Shares
(Denominator)
  
Per-Share
Amount
 
Net income available to Ionis common stockholders $87,543   138,582  $0.63 
Effect of dilutive securities:            
Shares issuable upon exercise of stock options     2,252     
Shares issuable upon restricted stock award issuance     665     
Shares issuable related to our Employee Stock Purchase Plan     38     
Income available to Ionis common stockholders $87,543   141,537  $0.62 


ForAdoption of ASU 2020-06


In August 2020, the three months ended March 31, 2019,FASB issued ASU 2020-06, which simplifies the calculation excluded our 1 percentaccounting for convertible senior notes, or 1% Notes, becausedebt instruments, amends the effectguidance on derivative scope exceptions for contracts in an entity’s own equity, and modifies the guidance on diluted earnings per share was anti-dilutive.


Convertible Debt



At issuance,calculations. We adopted ASU 2020-06 on January 1, 2021 under the full retrospective approach, which required us to revise our prior period financial statements. This guidance impacted our accounting for outstanding convertible debt. As of March 31, 2021, we accounted for ourhad 2 outstanding convertible debt instruments, includingnotes, our 0.125 percent senior convertible notes, or 0.125% Notes, which mature in December 2024, and our 1 percent senior convertible notes, or 1% Notes, that may be settledwhich mature in November 2021.


The updated guidance eliminates the cash upon conversion (including partial cash settlement) by separating theaccounting model we previously followed in Accounting Standard Codification, or ASC, 470-20, which required us to separate each of our convertible debt instruments at issuance into two units of accounting, a liability and equity components of the instruments in a manner that reflectscomponent, based on our nonconvertible debt borrowing rate onat issuance, and an equity component. Under ASU 2020-06, we now account for each of our convertible debt instruments as a single unit of accounting, a liability, because we concluded that the dateconversion features do not require bifurcation as a derivative under ASC 815-15 and our convertible debt instruments were not issued at a substantial premium. Since we adopted ASU 2020-06 using the notes were issued. In reviewing debt issuances,full retrospective approach, we were not ablerequired to identify any comparable companies that issued non-convertibleapply the guidance to all convertible debt instruments we had outstanding as of January 1, 2019. We recomputed the basis of each convertible debt instrument as if we accounted for each as a single unit of accounting at issuance. This update included recalculating the timeamortization of debt issuance costs using an updated effective interest rate. As a result of adopting ASU 2020-06, we recorded a cumulative adjustment to decrease our additional paid in capital and our accumulated deficit at January 1, 2019. We have updated these financial statements to reflect the cumulative adjustment for the periods presented. We have labeled our prior period financial statements “as revised” to indicate the change required under the new accounting guidance. Below is a summary of the change in our balance sheet at December 31, 2020 and statement of operations from our first quarter 2020 under the ASC 470-20 legacy guidance compared to the new ASU 2020-06 guidance we adopted:


The following table summarizes the adjustments we made to the condensed consolidated balance sheet we originally reported at December 31, 2020 to adopt ASU 2020-06 (in thousands):

 December 31, 2020 
  
As Previously
Reported
  
ASU 2020-06
Adjustment
  As Revised 
1 percent convertible senior notes $293,161  $15,648  $308,809 
0.125 percent convertible senior notes $455,719  $84,417  $540,136 
Additional paid-in-capital $2,113,646  $(218,127) $1,895,519 
Accumulated deficit $(1,249,368) $118,062  $(1,131,306)


Under ASU 2020-06, our revised ending balances for our 1% Notes and 0.125% Notes as of December 31, 2020 represent the principal balance of each convertible debt instrument less debt issuance of thecosts. Additionally, because we have deferred tax assets related to our convertible notes. Therefore,debt instruments, we estimated the fair value of the liability componentalso adjusted these amounts as part of our notes by using assumptions that market participants would use in pricingadoption of ASU 2020-06. However, because we have a full valuation allowance on our deferred tax assets, there was 0 impact to our condensed consolidated balance sheet related to our deferred tax assets.


The following table summarizes the adjustments we made to the condensed consolidated statement of operations we originally reported at March 31, 2020 to adopt ASU 2020-06 (in thousands):

 Three Months Ended March 31, 2020 
  
As Previously
Reported
  
ASU 2020-06
Adjustment
  As Revised 
Interest expense $(10,990) $8,783  $(2,207)
Loss before income tax benefit $(61,737) $8,783  $(52,954)
Income tax benefit $3,257  $(185) $3,072 
Net loss $(58,480) $8,598  $(49,882)
Net loss attributable to Ionis Pharmaceuticals, Inc. common stockholders $(48,226) $8,598  $(39,628)
Basic and diluted net loss per share $(0.35) $0.07  $(0.28)

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Under ASU 2020-06, our revised interest expense is lower as we are no longer recording non-cash interest expense related to a debt instrument, including marketdiscount. This decrease was partially offset by the increase in interest expense related to the amortization of debt issuance costs because we no longer allocate a portion of our debt issuance costs to stockholders’ equity at issuance. Instead, the entire debt issuance costs were recorded as a contra-liability on our condensed consolidated balance sheet at issuance and we are amortizing them over the contractual term using an updated effective interest rate. Our updated effective interest rates credit standing, yield curvesfor our 1% Notes and volatilities.0.125% Notes were 1.4 percent and 0.5 percent, respectively.


The following tables summarize the adjustments we made to our condensed consolidated statements of stockholders’ equity we originally reported at December 31, 2020 and 2019 to adopt ASU 2020-06 (in thousands):

 December 31, 2020 
  
As Previously
Reported
  
ASU 2020-06
Adjustment
  As Revised 
Additional paid-in-capital $2,113,646  $(218,127) $1,895,519 
Accumulated deficit $(1,249,368) $118,062  $(1,131,306)
Total stockholders' equity $843,347  $(100,065) $743,282 

 December 31, 2019 
  
As Previously
Reported
  
ASU 2020-06
Adjustment
  As Revised 
Additional paid-in-capital $2,203,778  $(218,128) $1,985,650 
Accumulated deficit $(707,534) $111,039  $(596,495)
Total stockholders' equity $1,684,547  $(107,089) $1,577,458 



We assigned a value toCall Spread


In conjunction with the debt componentissuance of our convertible notes equal0.125% Notes in December 2019, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants. We account for the note hedges and warrants as separate freestanding financial instruments and treat each instrument as a separate unit of accounting. We determined that the note hedges and warrants do not meet the definition of a liability using the guidance contained in ASC Topic 480, therefore we account for the note hedges and warrants using the Derivatives and Hedging – Contracts in Entity’s Own Equity accounting guidance contained in ASC Topic 815. We determined that the note hedges and warrants meet the definition of a derivative, are indexed to our stock and meet the estimated fair value of similar debt instruments withoutcriteria to be classified in shareholders’ equity. We recorded the conversion feature, which resulted in us recording our debt at a discount. We are amortizing our debt issuance costsaggregate amount paid for the note hedges and debt discount over the life ofaggregate amount received for the convertible noteswarrants as additional non-cash interest expense utilizingpaid-in capital in our condensed consolidated balance sheet. We reassess our ability to continue to classify the effective interest method.note hedges and warrants in shareholders’ equity at each reporting period.


Segment Information



We have 2In 2021, we began operating segments, ouras a single segment, Ionis Core segment and Akcea Therapeutics, our majority-owned affiliate. Akcea is a biopharmaceutical company focused on developing and commercializing medicines to treat patients with serious and rare diseases. We provide segment financial information and results for our Ionis Core segment and our Akcea Therapeutics segment based on the segregation of revenues and expenses thatoperations, because our chief decision maker reviews to assess operating performanceresults on an aggregate basis and to makemanages our operations as a single operating decisions. We allocate a portion of Ionis’ development, R&D supportsegment. Previously, we had operated as 2 operating segments, Ionis Core and general and administrative expenses to Akcea for work Ionis performs on behalfTherapeutics. In October 2020, we acquired the remaining common stock of Akcea that we did not own and we bill Akcea for these expenses.fully integrated Akcea’s operations into ours as of January 1, 2021.


Stock-based Compensation Expense



We measure stock-based compensation expense for equity-classified awards, principally related to stock options, restricted stock units, or RSUs, and stock purchase rights under our ESPP based on the estimated fair value of the award on the date of grant. We recognize the value of the portion of the award that we ultimately expect to vest as stock-based compensation expense over the requisite service period in our condensed consolidated statements of operations. We reduce stock-based compensation expense for estimated forfeitures at the time of grant and revise in subsequent periods if actual forfeitures differ from those estimates.


We use the Black-Scholes model to estimate the fair value of stock options granted and stock purchase rights under our ESPP. The


On the grant date, we use our stock price and assumptions regarding a number of variables to determine the estimated fair value of stock-based payment awards. These variables include, but are not limited to, our expected stock price volatility over the term of the awards, and actual and projected employee stock option exercise behaviors.


We recognize compensation expense for stock options granted, representsRSUs, PRSUs and stock purchase rights under the ESPP using the accelerated multiple-option approach. Under the accelerated multiple-option approach (also known as the graded-vesting method), we recognize compensation expense over the requisite service period for each separately vesting tranche of time thatthe award as though the award were in substance multiple awards, which results in the expense being front-loaded over the vesting period.

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In December 2020, we expect themamended and restated the Akcea 2015 equity plan, including renaming the plan as the Ionis Pharmaceuticals, Inc. 2020 Equity Incentive Plan, or 2020 Plan. As a result, all employees are now under an Ionis stock plan and subject to be outstanding. We estimate the expected termsame Black-Scholes assumptions. During the three months ended March 31, 2021 and 2020, we did 0t grant any stock options or RSUs to our Board of options granted based on historical exercise patterns.Directors. For the three months ended March 31, 20202021 and 2019,2020, we used the following weighted-average assumptions in our Black-Scholes calculations:


Ionis Employee Stock Options:

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Risk-free interest rate  1.6%  2.4%  0.5%  1.6%
Dividend yield  0.0%  0.0%  0.0%  0.0%
Volatility  58.9%  60.3%  55.1%  58.9%
Expected life 4.7 years  4.6 years  4.9 years  4.7 years 


Ionis ESPP:

 
Three Months Ended
March 31,
 
  2020  2019 
Risk-free interest rate  1.1%  2.5%
Dividend yield  0.0%  0.0%
Volatility  47.2%  45.5%
Expected life 6 months  6 months 

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Three Months Ended
March 31,
 
  2021  2020 
Risk-free interest rate  0.1%  1.1%
Dividend yield  0.0%  0.0%
Volatility  39.1%  47.2%
Expected life 6 months  6 months 


Ionis RSU’s:



The fair value of RSUs is based on the market price of our common stock on the date of grant. The RSUs we have granted to employees vest annually over a four-year period. The RSUs we granted to our board of directors prior to June 2020 vest annually over a four-year period. RSUs granted after June 2020 to our board of directors fully vest after one year. The weighted-average grant date fair value of RSUs granted to employees for the three months ended March 31, 20202021 was $62.30$62.02 per share.


In addition to our stock plans, Akcea has its own stock plan under which it grants stock options and RSUs and under which it derives its stock-based compensation expense. The following are the weighted-average Black-Scholes assumptions Akcea used under its plan for the three months endedMarch 31, 2020 and 2019:PRSU’s:



Akcea Employee Stock Options:

 
Three Months Ended
March 31,
 
  2020  2019 
Risk-free interest rate  1.5%  2.5%
Dividend yield  0.0%  0.0%
Volatility  73.6%  76.4%
Expected life 6.1 years  6.1 years 


Akcea BoardBeginning in 2020, we added performance-based restricted stock units, or PRSU, awards to the compensation for our Chief Executive Officer, Dr. Brett Monia. Under the terms of Directors Stock Options:

Three Months Ended
March 31,
2020
Risk-free interest rate1.5%
Dividend yield0.0%
Volatility73.3%
Expected life6.3 years


Akcea ESPP:

 
Three Months Ended
March 31,
 
  2020  2019 
Risk-free interest rate  1.0%  2.5%
Dividend yield  0.0%  0.0%
Volatility  71.9%  64.1%
Expected life 6 months  6 months 


Akcea RSU’s:the grants, one third of the PRSUs may vest at the end of 3 separate performance periods spread over the three years following the date of grant (i.e., the one-year period commencing on the date of grant and ending on the first anniversary of the date of grant; the two-year period commencing on the date of grant and ending on the second anniversary of the date of grant; and the three-year period commencing on the date of grant and ending on the third anniversary of the date of grant) based on our relative total shareholder return, or TSR, as compared to a peer group of companies, and as measured, in each case, at the end of the applicable performance period. Under the terms of the grants 0 number of PRSUs is guaranteed to vest and the actual number of PRSUs that will vest at the end of each performance period may be anywhere from 0percentto 150 percent of the target number depending on our relative TSR.



TheWe determined the fair value of RSUsDr. Monia’s PRSUs using a Monte Carlo model because the performance target is based on our relative TSR, which represents a market condition. We are recognizing the market pricegrant date fair value of Akcea’s common stock onthese awards as stock-based compensation expense using the date of grant. Akcea has granted RSUs with variousaccelerated multiple-option approach over the vesting terms between six months and four years.period. The weighted-average grant date fair value of RSUsPRSUs granted to employeesDr. Monia for the three months ended March 31, 20202021 was $15.84$77.17 per share.

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The following table summarizes stock-based compensation expense for the three months ended March 31, 20202021 and 20192020 (in thousands). Our non-cash stock-based compensation expense includes $7.3 million and $18.6 million of stock-based compensation expense for Akcea employees for the three months ended March 31, 2020 and 2019, respectively.



 
Three Months Ended
March 31,
 
  2020  2019 
Cost of products sold $237  $118 
Research, development and patent  25,556   24,435 
Selling, general and administrative  14,997   20,952 
Total $40,790  $45,505 
 
Three Months Ended
March 31,
 
  2021  2020 
Cost of sales $182  $237 
Research, development and patent expense  25,899   25,556 
Selling, general and administrative expense  11,780   14,997 
Total $37,861  $40,790 


As of March 31, 2020,2021, total unrecognized estimated non-cash stock-based compensation expense related to non-vested stock options, RSUs and RSUsPRSUs was $146.3$101.8 million, $109.6 million and $114.3$3.8 million, respectively. Our actual expenses may differ from these estimates because we will adjust our unrecognized non-cash stock-based compensation expense for future forfeitures. We expect to recognize the cost of non-cash stock-based compensation expense related to our non-vested stock options, RSUs and RSUsPRSUs over a weighted average amortization period of 1.4 years, 1.8 years and 1.91.7 years, respectively.

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Share Repurchase Program



In September 2019, our board of directors approved an initial share repurchase program of up to $125 million of our common stock. In 2019, we repurchased 535,000 shares for $34.4 million. In the first quarter of 2020, we repurchased an additional 1.5 million shares for $90.6 million.


Impact of Recently Issued Accounting Standards



In June 2016,As disclosed in the FASB issued“Convertible Debt” policy above within this footnote, we adopted the simplified accounting for convertible debt instrument guidance that changes(ASU 2020-06) on January 1, 2021. Refer to the measurementsection above for the impact of credit losses for most financial assets and certain other instruments. If we have credit losses, this updated guidance requires us to record allowances for these instruments under a new expected credit loss model. This model requires us to estimate the expected credit loss of an instrument over its lifetime, which represents the portion of the amortized cost basis weadoption. We do not expect to collect. The new guidance requires us to remeasure our allowance in each reporting period we have credit losses. We adopted this new guidance on January 1, 2020. This guidance did not have an impact on our condensed consolidated financial statements.


In August 2018, the FASBany other recently issued clarifying guidance on howaccounting standards to account for implementation costs related to cloud-servicing arrangements. The guidance states that if these fees qualify to be capitalized and amortized over the service period, they need to be expensed in the same line item as the service expense and recognized in the same balance sheet category. The update can be applied either retrospectively or prospectively to all implementation costs incurred after the date of adoption. We adopted this guidance on January 1, 2020 on a prospective basis. This guidance did not have an impact on our condensed consolidated financial statements.


In November 2018, the FASB issued clarifying guidance of the interaction between the collaboration accounting guidance and the new revenue recognition guidance we adopted on January 1, 2018 (Topic 606). Below is the clarifying guidance and how we implemented it (in italics):


1)When a participant is considered a customer in a collaborative arrangement, all of the associated accounting under Topic 606 should be applied
We are applying all of the associated accounting under Topic 606 when we determine a participant in a collaborative arrangement is a customer
2)Adds “unit of account” concept to collaboration accounting guidance to align with Topic 606. The “unit of account” concept is used to determine if revenue is recognized or if a contra expense is recognized from consideration received under a collaboration
We use the “unit of account” concept when we receive consideration under a collaborative arrangement to determine when we recognize revenue or a contra expense
3)The clarifying guidance precludes us from recognizing revenue under Topic 606 when we determine a transaction with a collaborative partner is not a customer and is not directly related to the sales to third parties
When we conclude a collaboration partner is not a customer and is not directly related to the sales to third parties, we do not recognize revenue for the transaction



We adopted this new guidance on January 1, 2020. This guidance did not have a significantmaterial impact onto our condensed consolidated financial statements.results.

3.  Investments


The following table summarizes the contract maturity of the available-for-sale securities we held as of March 31, 2020:2021:

One year or less  7067%
After one year but within two years  2220%
After two years but within three and a half years
  813%
Total  100%


As illustrated above, at March 31, 2020, 922021, 87 percent of our available-for-sale securities had a maturity of less than two years.


All of our available-for-sale securities are available to us for use in our current operations. As a result, we categorize all of these securities as current assets even though the stated maturity of some individual securities may be one year or more beyond the balance sheet date.



We invest in available-for-sale securities with strong credit ratings and an investment grade rating at or above A-1, P-1 or F-1 by Moody’s, Standard & Poor’s, or S&P, Moody’s or Fitch, respectively.


At March 31, 2020,2021, we had an ownership interest of less than 20 percent in 57 private companies and 2 public companies with which we conduct business. The privately-heldprivately held companies are Aro Biotherapeutics, Atlantic Pharmaceuticals Limited, Dynacure SAS, Empirico, Inc., Flamingo Therapeutics BV, Seventh Sense Biosystems and Suzhou Ribo Life Science Co, Ltd. The publicly-tradedpublicly traded companies are ATLAntisense Therapeutics Ltd. and ProQR.

ProQR Therapeutics N.V.

1920



The following is a summary of our investments (in thousands):


    Gross Unrealized  Estimated     Gross Unrealized  Estimated 
March 31, 2020 
Cost (1)
  Gains  Losses  Fair Value 
March 31, 2021 
Cost (1)
  Gains  Losses  Fair Value 
Available-for-sale securities:                        
Corporate debt securities (2) $717,739  $545  $(1,890) $716,394  $446,816  $1,838  $(76) $448,578 
Debt securities issued by U.S. government agencies  167,333   572   (28)  167,877   80,703   292   (2)  80,993 
Debt securities issued by the U.S. Treasury (2)  355,634   1,621   (2)  357,253   234,164   126   0   234,290 
Debt securities issued by states of the U.S. and political subdivisions of the states  15,746   43   (2)  15,787   121,776   220   (22)  121,974 
Other municipal debt securities  5,137   0   (7)  5,130 
Total securities with a maturity of one year or less  1,256,452   2,781   (1,922)  1,257,311   888,596   2,476   (107)  890,965 
Corporate debt securities  500,378   2,318   (2,903)  499,793   325,335   3,108   (245)  328,198 
Debt securities issued by U.S. government agencies  165,369   994   (15)  166,348   96,698   36   (164)  96,570 
Debt securities issued by the U.S. Treasury  62,382   810      63,192   59,030   326   (35)  59,321 
Debt securities issued by states of the U.S. and political subdivisions of the states  18,687   100      18,787   34,515   81   (25)  34,571 
Other municipal debt securities  903   4      907 
Other municipal debt  6,233   0   (20)  6,213 
Total securities with a maturity of more than one year  747,719   4,226   (2,918)  749,027   521,811   3,551   (489)  524,873 
Total available-for-sale securities $2,004,171  $7,007  $(4,840) $2,006,338  $1,410,407  $6,027  $(596) $1,415,838 
Equity securities:                                
Total equity securities included in other current assets (3) $4,712  $  $(2,623) $2,089  $4,712  $0  $(1,514) $3,198 
Total equity securities included in deposits and other assets (4)  15,019         15,019   15,062   15,938   0   31,000 
Total equity securities  19,731      (2,623)  17,108   19,774   15,938   (1,514)  34,198 
Total available-for-sale and equity securities $2,023,902  $7,007  $(7,463) $2,023,446  $1,430,181  $21,965  $(2,110) $1,450,036 


    Gross Unrealized  Estimated     Gross Unrealized  Estimated 
December 31, 2019 
Cost (1)
  Gains  Losses  Fair Value 
December 31, 2020 
Cost (1)
  Gains  Losses  Fair Value 
Available-for-sale securities:                        
Corporate debt securities (2) $669,665  $1,451  $(43) $671,073  $514,182  $2,194  $(41) $516,335 
Debt securities issued by U.S. government agencies  188,216   303   (43)  188,476   94,234   354   (2)  94,586 
Debt securities issued by the U.S. Treasury (2)  327,670   232   (27)  327,875   307,576   233   (9)  307,800 
Debt securities issued by states of the U.S. and political subdivisions of the states (2)  21,065   26   (5)  21,086 
Debt securities issued by states of the U.S. and political subdivisions of the states  104,271   196   (12)  104,455 
Other municipal debt securities  5,191   0   (7)  5,184 
Total securities with a maturity of one year or less  1,206,616   2,012   (118)  1,208,510   1,025,454   2,977   (71)  1,028,360 
Corporate debt securities  428,627   2,911   (43)  431,495   325,079   4,941   (40)  329,980 
Debt securities issued by U.S. government agencies  140,988   57   (117)  140,928   80,099   185   (9)  80,275 
Debt securities issued by the U.S. Treasury  35,822   9   (12)  35,819   50,318   383   (4)  50,697 
Debt securities issued by states of the U.S. and political subdivisions of the states  19,309   18   (6)  19,321   31,779   91   (16)  31,854 
Other municipal debt securities  1,041   0   0   1,041 
Total securities with a maturity of more than one year  624,746   2,995   (178)  627,563   488,316   5,600   (69)  493,847 
Total available-for-sale securities $1,831,362  $5,007  $(296) $1,836,073  $1,513,770  $8,577  $(140) $1,522,207 
Equity securities:                                
Total equity securities included in other current assets (3)  4,712      (870)  3,842  $4,712  $0  $(2,681) $2,031 
Total equity securities included in deposits and other assets (4)  10,000         10,000   15,062   15,938   0   31,000 
Total equity securities  14,712      (870)  13,842   19,774   15,938   (2,681)  33,031 
Total available-for-sale and equity securities $1,846,074  $5,007  $(1,166) $1,849,915  $1,533,544  $24,515  $(2,821) $1,555,238 

(1)We hold our available-for-sale securities at amortized cost.


(2)Includes investments classified as cash equivalents on our condensed consolidated balance sheet.


(3)Our equity securities included in other current assets consisted of our investmentinvestments in ProQR, which is a public company.publicly traded companies. We recognize our public companypublicly traded equity securities at fair value.


(4)
Our equity securities included in deposits and other assets consisted of our investments in Empirico and Dynacure SAS, which are privateprivately held companies. We recognize our private company equity securities at cost minus impairments, plus or minus changes resulting from observable price changes in orderly transactions for the identical or similar investment of the same issuer on our condensed consolidated balance sheet..

2021



The following is a summary of our investments we consider to be temporarily impaired at March 31, 20202021 (in thousands). All of these investments have less than 12 months of temporary impairment. We believe that the decline in value of these securities is temporary and is primarily related to the change in market interest rates since purchase. We believe it is more likely than not that we will be able to hold our debt securities to maturity. Therefore, we anticipate full recovery of our debt securities’ amortized cost basis at maturity.


    
Less than 12 Months of
Temporary Impairment
  
More than 12 Months of
Temporary Impairment
  
Total Temporary
Impairment
 
 
Number of
Investments
  
Estimated
Fair Value
  
Unrealized
Losses
  
Estimated
Fair Value
  
Unrealized
Losses
  
Estimated
Fair Value
  
Unrealized
Losses
  
Number of
Investments
  
Estimated
Fair Value
  
Unrealized
Losses
 
Corporate debt securities  305  $750,404  $(4,793) $  $  $750,404  $(4,793)  101  $233,665  $(321)
Debt securities issued by U.S. government agencies  11   47,473   (32)  34,053   (11)  81,526   (43)  7   60,681   (166)
Debt securities issued by the U.S. Treasury  1   15,598   (2)        15,598   (2)  6   52,838   (35)
Debt securities issued by states of the U.S. and political subdivisions of the states  3   3,634   (2)        3,634   (2)  297   76,712   (47)
Other municipal debt securities  3   11,343   (27)
Total temporarily impaired securities  320  $817,109  $(4,829) $34,053  $(11) $851,162  $(4,840)  414  $435,239  $(596)

4.  Fair Value Measurements


We use a three-tier fair value hierarchy to prioritize the inputs used in our fair value measurements. These tiers include: Level 1, defined as observable inputs such as quoted prices in active markets for identical assets, which includes our money market funds and treasury securities classified as available-for-sale securities and our investment in equity securities in publicly-heldpublicly held biotechnology companies; Level 2, defined as inputs other than quoted prices in active markets that are either directly or indirectly observable, which includes our fixed income securities and commercial paper classified as available-for-sale securities; and Level 3, defined as unobservable inputs in which little or no market data exists, therefore requiring us to develop our own assumptions. We classify most of our securities as Level 2. We obtain the fair value of our Level 2 investments from our custodian bank or from a professional pricing service. We validate the fair value of our Level 2 investments by understanding the pricing model used by the custodian banks or professional pricing service provider and comparing that fair value to the fair value based on observable market prices.


The following tables present the major security types we held at March 31, 20202021 and December 31, 20192020 that we regularly measure and carry at fair value. AtAs of March 31, 20202021 and December 31, 20192020, a portion of our ProQR investment was subject to trading restrictionswe did 0t have any investments that extend to the fourth quarter of 2020; as a result, we included a lack of marketability discount in valuing this investment, which is a valued using Level 3 input. The amount we owned in ProQR did not change from December 31, 2019 to March 31, 2020inputs. The following tables below segregate each security type by the level within the fair value hierarchy of the valuation techniques we utilized to determine the respective securities’ fair value (in thousands):



 
At
March 31, 2020
  
Quoted Prices in
Active Markets
(Level 1)
  
Significant Other
Observable Inputs
(Level 2)
  
Significant
Unobservable Inputs
(Level 3)
 
Cash equivalents (1) $336,371  $336,371  $  $ 
Corporate debt securities (2)  1,216,187      1,216,187    
Debt securities issued by U.S. government agencies (3)  334,225      334,225    
Debt securities issued by the U.S. Treasury (4)  420,445   420,445       
Debt securities issued by states of the U.S. and political subdivisions of the states (5)  34,574      34,574   
 
Other municipal debt securities (5)
  907      907    
Investment in ProQR Therapeutics N.V. (6)
  2,089   617      1,472 
Total $2,344,798  $757,433  $1,585,893  $1,472 


 
At
March 31, 2021
  
Quoted Prices in
Active Markets
(Level 1)
  
Significant Other
Observable Inputs
(Level 2)
 
Cash equivalents (1) $372,050  $372,050  $0 
Corporate debt securities (2)  776,776   0   776,776 
Debt securities issued by U.S. government agencies (3)  177,563   0   177,563 
Debt securities issued by the U.S. Treasury (3)  293,611   293,611   0 
Debt securities issued by states of the U.S. and political subdivisions of the states (3)  156,545   0   156,545 
Other municipal debt securities (3)
  11,343   0   11,343 
Investment in ProQR Therapeutics N.V. (4)
  3,198   3,198   0 
Total $1,791,086  $668,859  $1,122,227 
2122



 
At
December 31, 2019
  
Quoted Prices in
Active Markets
(Level 1)
  
Significant Other
Observable Inputs
(Level 2)
  
Significant
Unobservable Inputs
(Level 3)
  
At
December 31, 2020
  
Quoted Prices in
Active Markets
(Level 1)
  
Significant Other
Observable Inputs
(Level 2)
 
Cash equivalents (1) $418,406  $418,406  $  $  $221,125  $221,125  $0 
Corporate debt securities (7)(2)  1,102,568      1,102,568      846,315   0   846,315 
Debt securities issued by U.S. government agencies (8)(3)  329,404      329,404      174,861   0   174,861 
Debt securities issued by the U.S. Treasury (5)  363,694   363,694         358,497   358,497   0 
Debt securities issued by states of the U.S. and political subdivisions of the states (5)(3)  40,407      40,407      136,309   0   136,309 
Investment in ProQR Therapeutics N.V. (6)
  4,506         4,506 
Other municipal debt securities (3)
  6,225   0   6,225 
Investment in ProQR Therapeutics N.V. (4)
  2,031   2,031   0 
Total $2,258,985  $782,100  $1,472,379  $4,506  $1,745,363  $581,653  $1,163,710 

The following footnotes reference lines on our condensed consolidated balance sheet:


(1)Included in cash and cash equivalents.equivalents on our condensed consolidated balance sheet.


(2)$21.010.0 million was included in cash and cash equivalents, with the difference included in short-term investments.


(3)Included in short-term investments.

(4)Included in other current assets on our condensed consolidated balance sheet.

(5)$6.517.5 million was included in cash and cash equivalents on our condensed consolidated balance sheet, with the difference included in short-term investments.investments on our condensed consolidated balance sheet.


(4)$81 million was included in cash and cash equivalents, with the difference included in short-term investments.


(5)Included in short-term investments.


(6)Included in other current assets.


(7)$19.0 million was included in cash and cash equivalents, with the difference included in short-term investments.


(8)$0.8 million was included in cash and cash equivalents, with the difference included in short-term investments.

Convertible Notes


Our 1% Notes and 0.125% Notes had a fair value of $315.3$314.6 million and $495.3$527.3 million at March 31, 2020,2021, respectively. We determine the fair value of our notes based on quoted market prices for these notes, which are Level 2 measurements because the notes do not trade regularly.


5.  Income Taxes


The Coronavirus Aid, Relief, and Economic Security, or CARES, Act was enacted in March 2020. We considered our ability to estimate annual effective tax rates based on our pre-tax income projections, the income tax effects of the CARES Act, the realizability of our net deferred tax assets and the appropriateness of our valuation allowances.



Under the Tax Cut and Jobs Act of 2017, the utilization of federal net operating losses was limited to 80 percent of taxable income. The CARES Act temporarily removed this limitation and provides for the utilization of net operating loss carryforwards to offset 100 percent of taxable income. The 80 percent limitation enacted by the Tax Act is reinstated for tax years beginning in 2021.

In 2019, we recorded income tax expense related to Akcea due to the 80 percent limitation on the utilization of net operating losses in effect at the time. As a result of the temporary change in tax law provided by the CARES Act, we recorded a $1.7 million tax benefit in the first quarter of 2020 as we will now utilize federal net operating loss carryforwards to offset 100 percent of Akcea’s taxable income for 2019. We recorded the tax benefit as a discrete item in the first quarter of 2020 because that was when the CARES Act was enacted.



We recorded an income tax benefit of $3.3 million for the three months ended March 31, 2020, compared to income tax expense of $31.0 million for the same period in 2019. We recorded an income tax benefit for the three months ended March 31, 2020 primarily due to Ionis’ pre-tax loss for the period and the $1.7 million tax benefit related to Akcea. We did not record a tax benefit as a result of Akcea’s pre-tax loss in the first quarter of 2020 because Akcea maintains a full valuation allowance against its deferred tax assets.



Our effective tax rate may vary from the U.S. federal statutory rate due to the change in the mix of earnings in tax jurisdictions with different statutory rates, benefits related to tax credits, the tax impact of non-deductible expenses and other permanent differences between income before taxes and taxable income, and changes to tax laws or rates. Our effective income tax rate of 5.28 percent for the three months ended March 31, 2020 differed from the U.S. federal statutory rate of 21 percent primarily due to Ionis’ pre-tax loss for the period and the $1.7 million tax benefit related to Akcea.

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6.  Collaborative Arrangements and Licensing Agreements


Below, we have included our collaborationsBiogen collaboration, which is our only collaboration with substantive changes during the first three months of 20202021 from those included in Note 6 of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2019.

2020.

Strategic Partnership


Biogen



We have several strategic collaborations with Biogen focused on using antisense technology to advance the treatment of neurological disorders. These collaborations combine our expertise in creating antisense medicines with Biogen’s expertise in developing therapies for neurological disorders. We developed and licensed to Biogen SPINRAZA, our approved medicine to treat people with spinal muscular atrophy, or SMA. In December 2017, we entered into a collaboration with Biogen to identify new antisense medicines for the treatment of SMA. We and Biogen are currently developing 8 investigational medicines to treat neurodegenerative diseases under these collaborations, including medicines in development to treat people with ALS, Alzheimer’s disease and Parkinson’s disease. In addition to these medicines, our collaborations with Biogen include a substantial research pipeline that addresses a broad range of neurological diseases. From inception through March 2020,31, 2021, we have received more than $2.5$2.9 billion from our Biogen collaborations.

23


During the three months ended March 31, 20202021 and 2019,2020, we earned the following revenue from our relationship with Biogen (in millions, except percentage amounts):


 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
SPINRAZA royalties (commercial revenue) $66.0  $59.7  $60.0  $66.0 
R&D revenue  21.4   24.5   18.1   21.4 
Total revenue from our relationship with Biogen $87.4  $84.2  $78.1  $87.4 
Percentage of total revenue  66%  28%  70%  66%


2012 Neurology Collaboration



In the first quarterOur condensed consolidated balance sheet at March 31, 2021 and December 31, 2020included deferred revenue of 2020, we achieved a $7.5$447.7 million milestone payment from Biogen when we advanced IONIS-MAPTRx in development. This milestone payment did not create a new performance obligation because it is part ofand $465.8 million, respectively, related to our performance obligation to conduct development of IONIS-MAPTRx. Therefore, we included the $7.5 million milestone payment in our transaction price for our IONIS-MAPTRx development performance obligation. We are recognizing revenue for our IONIS-MAPTRx development performance obligation based on the percentage of completion. From inception through March 2020, we have included $45.0 million in the transaction price for our IONIS-MAPTRx development performance obligation. We currently estimate we will satisfy our performance obligation in 2022.

relationship with Biogen.


During the first three months of 2020,2021, we did not have any changes to our performance obligations, transaction price or the timing in which we expect to recognize revenue under our Biogen collaborations, except as noted above.


Our condensed consolidated balance sheet at March 31, 2020 and December 31, 2019included deferred revenue of $512.3 million and $525.8 million, respectively, related to our relationship with Biogen.

Research, Development and Commercialization Partners


AstraZeneca


We have 2 collaborations with AstraZeneca, 1 focused on the treatment of cardiovascular, renal and metabolic diseases and a second focused on the treatment of oncology diseases. We and AstraZeneca are currently developing several medicines under these collaborations, including medicines to treat people with cardiovascular disease, a genetically associated form of kidney disease, nonalcoholic steatohepatitis, or NASH and cancer. From inception through March 2020, we have received more than $300 million from our AstraZeneca collaborations.


During the three months ended March 31, 2020 and 2019, we earned the following revenue from our relationship with AstraZeneca (in millions, except percentage amounts):


 
Three Months Ended
March 31,
 
  2020  2019 
R&D revenue $13.8  $4.0 
Percentage of total revenue  10%  1%


Our condensed consolidated balance sheet at March 31, 2020 and December 31, 2019 included deferred revenue of $21.3 million and $25.0 million, respectively, related to our relationship with AstraZeneca.


23



During the first three months of 2020, we did not have any changes to our performance obligations or the timing in which we expect to recognize revenue under our AstraZeneca collaborations, except as noted below.



Cardiovascular, Renal and Metabolic Diseases Collaboration



In the first quarter of 2020,April 2021, we achieved a $10 million milestone payment from AstraZenecaBiogen when AstraZenecaBiogen advanced ION532, aION541, an investigational medicine targeting APOL1 for the treatment of kidney disease, in development. ataxin 2 to treat patients with ALS. We concluded that this milestone payment was not related to our R&D services performance obligation. Therefore, we recognized the $10 million milestone payment in full in the first quarter of 2020 because we did not have any performance obligations related to this payment. We will achieve the next payment of up to $30 millionif AstraZeneca licenses a medicine$8 million if Biogen advances one of the medicines under thisour 2013 strategic neurology collaboration.

7.  Segment Information6. Convertible Debt


0 Percent Convertible Senior Notes and Call Spread


In April 2021, we completed a $632.5 million offering of convertible senior notes. We have used a portion of the net proceeds from the issuance of the 0 percent convertible senior notes, or 0% Notes, to repurchase $247.9 million in principal of our 1% Notes for $257.0 million.


Following the closing of the debt transaction in April 2021, we had the following 0%2 reportable segments, Ionis Core Notes outstanding (amounts in millions except interest rate and Akcea Therapeutics. At March 31, 2020we owned approximately 76 percent of Akcea. Segment income (loss) from operations includes revenue less operating expenses attributable to each segment.price per share data):

 
0% Notes
 
Outstanding principal balance $632.5 
Maturity date April 2026 
Interest rate 0 percent 
Conversion price per share $57.84 
Effective conversion price per share with call spread $76.39 
Total shares of common stock subject to conversion  10.9 



In conjunction with the April 2021 offering, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants, to minimize the impact of potential economic dilution upon conversion of our Ionis Core segment0% Notes by increasing the effective conversion price on our 0% Notes. We increased our effective conversion price to $76.39 with the same number of underlying shares as our 0% Notes. The call spread cost us $46.9 million, of which $136.7 million was for the note hedge purchase, offset by $89.8 million we received for selling the warrants. Similar to our 0% Notes, our note hedges are exploitingsubject to adjustment. Additionally, our antisense technologynote hedges are exercisable upon conversion of the 0% Notes. The note hedges will expire upon maturity of the 0% Notes, or April 2026. The note hedges and warrants are separate transactions and are not part of the terms of our 0% Notes. The holders of the 0% Notes do not have any rights with respect to generate a broad pipeline of first-in-class and/or best-in-class medicines for usthe note hedges and our partners. Our Ionis Core segment generates revenue from a multifaceted partnering strategy.warrants.


Akcea is a biopharmaceutical company focused on developing and commercializing medicines to treat patients with serious and rare diseases. Akcea generates revenue from TEGSEDI and WAYLIVRA product sales and from its collaborations.


The following tables show our segment revenue and income (loss) from operations for the three months ended March 31, 2020 and 2019 (in thousands), respectively.


Three Months Ended March 31, 2020 Ionis Core  Akcea Therapeutics  
Elimination of
Intercompany Activity
  Total 
Revenue:            
Commercial revenue:            
SPINRAZA royalties $66,008  $  $  $66,008 
Product sales, net     15,159      15,159 
Licensing and other royalty revenue  3,598      (804)  2,794 
Total commercial revenue $69,606  $15,159  $(804) $83,961 
R&D revenue under collaborative agreements $48,491  $915  $  $49,406 
Total segment revenue $118,097  $16,074  $(804) $133,367 
Total operating expenses $135,426  $61,334  $(2,266) $194,494 
Loss from operations $(17,329) $(45,260) $1,462  $(61,127)

Three Months Ended March 31, 2019 Ionis Core  Akcea Therapeutics  
Elimination of
Intercompany Activity
  Total 
Revenue:            
Commercial revenue:            
SPINRAZA royalties $59,711  $  $  $59,711 
Product sales, net     6,754      6,754 
Licensing and other royalty revenue  1,623         1,623 
Total commercial revenue $61,334  $6,754  $  $68,088 
R&D revenue under collaborative agreements $160,556  $157,062  $(88,492) $229,126 
Total segment revenue $221,890  $163,816  $(88,492) $297,214 
Total operating expense $114,515  $137,610  $(76,446) $175,679 
Income from operations $107,375  $26,206  $(12,046) $121,535 


The following table shows our total assets by segment at March 31, 2020 and December 31, 2019 (in thousands), respectively.


Total Assets Ionis Core  Akcea Therapeutics  
Elimination of
Intercompany Activity
  Total 
March 31, 2020 $3,376,169  $559,921  $(845,177) $3,090,913 
December 31, 2019 $3,478,081  $599,250  $(844,219) $3,233,112 

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0.125 Percent Convertible Senior Notes and Call Spread


At March 31, 2021, we had the following 0.125% Notes outstanding with interest payable semi-annually (amounts in millions except interest rate and price per share data):

 0.125% Notes 
Outstanding principal balance $548.8 
Maturity date December 2024 
Interest rate 0.125 percent 
Conversion price per share $83.28 
Effective conversion price per share with call spread $123.38 
Total shares of common stock subject to conversion  6.6 
Unamortized debt issuance costs $8.1 



In conjunction with the issuance of our 0.125% Notes in December 2019, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants, to minimize the impact of potential economic dilution upon conversion of our 0.125% Notes by increasing the effective conversion price on our 0.125% Notes. We increased our effective conversion price to $123.38 with the same number of underlying shares as our 0.125% Notes. The call spread cost us $52.6 million, of which $108.7 million was for the note hedge purchase, offset by $56.1 million we received for selling the warrants. Similar to our 0.125% Notes, our note hedges are subject to adjustment. Additionally, our note hedges are exercisable upon conversion of the 0.125% Notes. The note hedges will expire upon maturity of the 0.125% Notes, or December 2024. The note hedges and warrants are separate transactions and are not part of the terms of our 0.125% Notes. The holders of the 0.125% Notes do not have any rights with respect to the note hedges and warrants.


We recorded the amount paid for the note hedges and the amount received for the warrants in additional paid-in capital in our condensed consolidated balance sheet. See our Call Spread accounting policy in Note 2, Significant Accounting Policies, in the Notes to the Condensed Consolidated Financial Statements. We reassess our ability to continue to classify the note hedges and warrants in shareholders’ equity at each reporting period.


1 Percent Convertible Senior Notes


At March 31, 2021, we had the following 1% Notes outstanding with interest payable semi-annually (amounts in millions except interest rate and price per share data):

  1% Notes 
Outstanding principal balance $309.9 
Maturity date November 2021 
Interest rate 1 percent 
Conversion price per share $66.81 
Total shares of common stock subject to conversion  4.6 
Unamortized debt issuance costs $0.8 


In April 2021, we repurchased $247.9 million in aggregate principal amount of our 1% Notes in privately negotiated transactions. As a result, in April 2021, the remaining principal outstanding for our 1% Notes was $62.0 million, resulting in 0.9 million shares of common stock subject to conversion. As a result of the repurchase, we reclassified the repurchased portion of our 1% Notes from current to non-current liabilities on our condensed consolidated balance sheet as of March 31, 2021 because we replaced this portion of our outstanding debt with long-term debt.


Other Terms of Convertible Senior Notes


The 0%, 0.125% and 1% Notes are convertible under certain conditions, at the option of the note holders. We can settle conversions of the notes, at our election, in cash, shares of our common stock or a combination of both. We may not redeem the notes prior to maturity, and we do not have to provide a sinking fund for them. Holders of the notes may require us to purchase some or all of their notes upon the occurrence of certain fundamental changes, as set forth in the indentures governing the notes, at a purchase price equal to 100 percent of the principal amount of the notes to be purchased, plus any accrued and unpaid interest.

25

7. Severance and Retention Costs


Akcea Acquisition


As a result of the Akcea Acquisition in October 2020, we began recognizing severance and retention expenses in the fourth quarter of 2020. The following table summarizes our total estimated severance and retention expenses related to the Akcea Acquisition (in millions):

  Severance and Retention Expenses 
Total estimated expenses $28.5 
Expenses incurred in the three months ended December 31, 2020  15.3 
Expenses incurred in the three months ended March 31, 2021  5.4 
Remaining estimated expenses to be recognized through October 2021 $7.8 


The following table summarizes our severance and retention expenses related to the Akcea Acquisition that we recognized during the three months ended March 31, 2021 (in millions):

  
Three Months Ended
March 31, 2021
 
Research, development and patent expenses $2.5 
Selling, general and administrative expenses  2.9 
Total $5.4 


The following table summarizes the severance and retention reserve amounts related to the Akcea Acquisition that we included in accrued compensation for the period indicated (in millions):

  
Three Months Ended
March 31, 2021
 
Beginning balance $14.7 
Amounts expensed during the period  6.1 
Reserve adjustments during the period  (0.7)
Net amount expensed during the period  5.4 
Amounts paid during the period  (9.0)
Ending balance $11.1 


The reserve adjustments during the period primarily related to forfeitures of severance and retention payments as a result of employee terminations before they earned the amounts.


Restructured European Operations


As a result of restructuring our European operations, or Restructured European Operations, in December 2020, we began recognizing severance and retention expenses in the fourth quarter of 2020. The following table summarizes our total severance and retention expenses related to our Restructured European Operations (in millions):

  Severance and Retention Expenses 
Total estimated expenses $13.6 
Expenses incurred in the three months ended December 31, 2020  12.5 
Expenses incurred in the three months ended March 31, 2021  0.7 
Remaining estimated expenses through October 2021 $0.4 

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The following table summarizes the severance and retention expenses related to our Restructured European Operations that we recognized during the three months ended March 31, 2021 (in millions):

  
Three Months Ended
March 31, 2021
 
Research, development and patent expenses $0.1 
Selling, general and administrative expenses  0.6 
Total $0.7 


The following table summarizes the severance and retention reserve amounts related to our Restructured European operations that we included in accrued compensation for the periods indicated (in millions):

  
Three Months Ended
March 31, 2021
 
Beginning balance $12.4 
Amounts expensed during the period  2.2 
Reserve adjustments during the period  (1.5)
Net amount expensed during the period  0.7 
Amounts paid during the period  (11.9)
Ending balance $1.2 



The reserve adjustments during the period primarily related to tax expense adjustments.


Restructured North American TEGSEDI Operations


In April 2021, we entered into a distribution agreement with Sobi for TEGSEDI in North America. Under the terms of the distribution agreement, we will retain the marketing authorizations for TEGSEDI in the U.S. and Canada. We will continue to supply commercial product to Sobi and manage regulatory and manufacturing processes, as well as relationships with key opinion leaders. We will also continue to lead the TEGSEDI global commercial strategy. Sobi will otherwise have responsibility for commercializing TEGSEDI in the U.S. and Canada and will assume these activities by August 2021.


In connection with restructuring our North American TEGSEDI operations, or Restructured North American TEGSEDI Operations, we enacted a plan to reorganize our Akcea workforce in North America to better align with the needs of our business, or the Reorganization Plan, and to focus on our wholly owned pipeline. Under the Reorganization Plan, we expect to incur restructuring charges in the range of $11 million to $14 million principally in the second quarter of 2021.

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ITEM 2MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

In this Report on Form 10-Q, unless the context requires otherwise, “Ionis,” “Company,” “we,” “our,” and “us,” means Ionis Pharmaceuticals, Inc. and its majoritywholly owned affiliate, Akcea Therapeutics, Inc.

Forward-Looking Statements

In addition to historical information contained in this Report on Form 10-Q, the Report includes forward-looking statements regarding our business and the therapeutic and commercial potential of SPINRAZA (nusinersen), TEGSEDI (inotersen), WAYLIVRA (volanesorsen) and our technologies and products in development, including the business of Akcea Therapeutics, Inc., our majority-owned affiliate.development. Any statement describing our goals, expectations, financial or other projections, intentions or beliefs, is a forward-looking statement and should be considered an at-risk statement. Such statements are subject to certain risks and uncertainties, including those related to the impact COVID-19 could have on our business, and including but not limited to those related to our commercial products and the medicines in our pipeline, and particularly those inherent in the process of discovering, developing and commercializing medicines that are safe and effective for use as human therapeutics, and in the endeavor of building a business around such medicines. Our forward-looking statements also involve assumptions that, if they never materialize or prove correct, could cause our results to differ materially from those expressed or implied by such forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in this report and described in additional detail in our annual report on Form 10-K for the year ended December 31, 2019,2020, which is on file with the U.S. Securities and Exchange Commission and is available from us, and those identified within Part II Item 1A. Risk Factors of this Report. Although our forward-looking statements reflect the good faith judgment of our management, these statements are based only on facts and factors currently known by us. As a result, you are cautioned not to rely on these forward-looking statements.

Overview

We are a leader in discoveringRNA-targeted therapy and developing RNA-targeted therapeutics. We have created an efficientbelieve our medicines are pioneering new markets, changing standards of care and broadly applicable drug discovery platform leveraging our expertise in antisense oligonucleotide therapeutics that we believe has fundamentally changed medicine and transformedtransforming the lives of people with devastating diseases. Our large, diverse and advancingclinical pipeline has over 40of potential first-in-class and/or best-in-class medicines designed to address a broad range of diseases, including neurological, cardiovascular, infectiousdiseases. We are primarily focused on two core franchises: neurology and pulmonary diseases. The medicines in our pipeline address patients with diseases ranging from rare to common. We have threecardiometabolic. Our commercial medicinesproducts SPINRAZA, TEGSEDI and WAYLIVRA, are approved in major markets around the world, SPINRAZA, TEGSEDI and WAYLIVRA. Weworld. Within our late-stage pipeline, we have four medicines in pivotalsix Phase 3 studies tominersen for Huntington’s disease,ongoing with five medicines: tofersen for SOD1-ALS, AKCEA-APO(a)-LIONIS-TTR-LRx for cardiovascular disease,transthyretin, or CVD, and AKCEA-TTR-LTTR, amyloidosis, IONIS-APOCIII-LRx for TTR amyloidosis.familial chylomicronemia syndrome, or FCS, pelacarsen for lipoprotein(a), or Lp(a), driven cardiovascular disease and ION363 for amyotrophic lateral sclerosis, or ALS, with mutations in the fused in sarcoma gene, or FUS.

With our strongOur multiple sources of revenue provide us with substantial financial position, we have the resources to continuestrength. Our financial strength enables us to execute on our plan to investcapital allocation strategy, which is focused on internal investment in areasthree key areas: our wholly owned pipeline, building our commercial capabilities and broadening the reach of our business that wetechnology. We believe haveinvesting in these areas moves us closer to our goal of 12 or more marketed products in 2026 and will drive the potential to creategreatest value for patients and shareholders.

In April 2021, we entered into a distribution agreement with Sobi for TEGSEDI in North America. Under the terms of the distribution agreement, we retained the marketing authorizations for TEGSEDI in the U.S. and Canada. We currently have four medicineswill continue to supply commercial product to Sobi and manage regulatory and manufacturing processes, as well as relationships with key opinion leaders. We will also continue to lead the TEGSEDI global commercial strategy. In connection with the agreement, we enacted the Reorganization Plan to reorganize our Akcea workforce in pivotal studies. ByNorth America to better align with the end of this year, we plan to have six pivotal studies underway and report clinical proof-of-concept data for six medicines. We also plan to expand the reachneeds of our antisense technology by optimizing additional routes of administration, such as oralbusiness and pulmonary for which we expect clinical data this year. Additionally, this year, we are continuing to prioritize the growth and advancement of our Ionis-owned pipeline. Building on our achievements to date, we believe that continued advances in our pipeline and technology will enable us to achieve our goal of 10 or more new drug applications through the end of 2025.

Our goal is to determine the optimal development and commercialization strategy for each medicine in our pipeline, while ensuring we remain focused on innovation and delivering substantial value for patients in need and shareholders. With this goal firmly in mind, this year we plan to further develop our commercial strategy and capabilities to ensure we maximize the value of each of our medicines.

By building on our strong foundation and continuing to focus on our strategic priorities,wholly owned pipeline. Under the Reorganization Plan, we believe we are achieving our vision of becoming one of the most successful and innovative companiesexpect to incur restructuring charges in the healthcare industry. We intendrange of $11 million to continue to pursue our vision by executing on our strategic priorities: advancing our Ionis-owned pipeline, further developing our commercial strategies and capabilities, and expanding$14 million principally in the reachsecond quarter of our antisense technology.2021.

Commercial Medicines

SPINRAZA is a global foundation-of-care for the treatment of patients of all ages with spinal muscular atrophy, or SMA, a progressive, debilitating and often fatal genetic disease. Biogen, our partner responsible for commercializing SPINRAZA worldwide, reported that as of March 31, 2020, approximately 10,8002021, more than 11,000 patients were on SPINRAZA therapy in markets around the world. Additionally, as of March 31, 2020, SPINRAZA was approved in over 50 countries with formal reimbursement in 40 countries. Through March 31, 2020,2021, we have earned more than $1.1$1.4 billion in revenues from our SPINRAZA collaboration, including more than $710 millionapproximately $1 billion in royalties on sales of SPINRAZA.

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TEGSEDI is a once weekly, self-administered subcutaneous medicine was approved in 2018 in the U.S., EUEurope, Canada and CanadaBrazil for the treatment of patients with polyneuropathy caused by hereditary TTR amyloidosis, or hATTR, a debilitating, progressive, and fatal disease. Akcea, our majority-owned affiliate focused on developing and commercializing medicines to treat patients with serious and rare diseases, We launched TEGSEDI in the U.S. and the European Union, or EU, in late 2018. In 2021, we began selling TEGSEDI is commercially available in 12 countries. Akcea plans to expandEurope through our distribution agreement with Sobi. Additionally, in the global launchsecond quarter of 2021, Sobi also began distributing TEGSEDI by launching in additional countries.the U.S. and Canada. In Latin America, PTC Therapeutics International Limited, or PTC, through its exclusive license from Akcea,agreement with us, is launchingcommercializing TEGSEDI in Brazil and is working towards access in additional Latin American countries.

WAYLIVRA is a once weekly, self-administered, subcutaneous medicine that received conditional marketing authorization in May 2019 from the European Commission, or EC, as an adjunct to diet in adult patients with genetically confirmed familial chylomicronemia syndrome, or FCS and at high risk for pancreatitis. AkceaWe launched WAYLIVRA in the EU in the third quarter of 2019 and is leveraging its existing commercial infrastructure2019. In 2021, we began selling WAYLIVRA in Europe to market WAYLIVRA. PTC through itsour distribution agreement with Sobi. Through our exclusive license agreement with Akcea isPTC, we are working to expand access to WAYLIVRA across Latin America, beginning in Brazil. In the second quarter of 2020, PTC plans to filesubmitted the WAYLIVRA marketing application for marketing approval of WAYLIVRA in Brazil this year.to the National Health Surveillance Agency (Agência Nacional de Vigilância Sanitária), or ANVISA.

Medicines in Pivotal Phase 3 Studies

OurWe advanced our pipeline of medicines in pivotal studies include tominersen for Huntington’s disease, tofersen for SOD1-ALS, AKCEA-APO(a)-LRx for cardiovascular disease, or CVD,that we believe will pioneer new markets and AKCEA-TTR-LRx for TTR amyloidosis. In April 2020, Roche completed enrollmentchange standards of thecare.
Our Phase 3 study for tominersen our medicine to treat people with Huntington’s disease. The Phase 3 study for tofersen continues to progress in patients with SOD1-ALS. In January 2020, Novartis began enrollment in the HORIZON Phase 3 cardiovascular outcome study of AKCEA-APO(a)-LRx in patients with established cardiovascular disease and elevated Lp(a). Our broad Phase 3 program for AKCEA-TTR-LRx is also progressing.medicines include:

Tofersen: Biogen completed enrollment in the VALOR Phase 3 study in patients with SOD1-ALS in December 2020
IONIS-TTR-LRx: Enrollment is ongoing in both the NEURO-TTRansform and the CARDIO-TTRansform Phase 3 studies
IONIS-APOCIII-LRx: Enrollment is ongoing in the BALANCE Phase 3 study in patients with FCS
Pelacarsen: Enrollment is ongoing in Novartis Pharma AG’s Lp(a)HORIZON Phase 3 cardiovascular outcome study
ION363: We recently initiated a Phase 3 study in patients with FUS-ALS, the most common cause of juvenile-onset ALS

COVID-19

As a company focused on improving the health of people around the world, our priority during the COVID-19 pandemic is the safety of our employees, their families, and the patients and healthcare workers who work with us and the patients who rely on our medicines. We are also focused on maintaining the quality of our studies and meetingminimizing the impact to timelines. WeWhile the COVID-19 pandemic has impacted some areas of our business, we believe our mitigation efforts and financial strength provideswill enable us with the abilityto continue to manage through this crisisthe pandemic and continue to execute on our strategic initiatives. To date, we have not experienced a significant impact to our overall business as a result of the COVID-19 pandemic. Because the situation is extremely fluid, we are continuing to evaluate the impact COVID-19 could have on our business, including but not limited to the impact on our commercial products and the medicines in our pipeline.

Financial Highlights

The following is a summary of our financial results (in thousands)millions):

  Three Months Ended March 31, 
  2020  2019 
Total revenue $133,367  $297,214 
Total operating expenses $194,494  $175,679 
Income (loss) from operations $(61,127) $121,535 
Net income (loss) $(58,480) $90,884 
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders $(48,226) $84,443 
  Three Months Ended March 31, 
  2021  2020 
     (as revised*) 
Total revenue $111.6  $133.4 
Total operating expenses $203.6  $194.5 
Loss from operations $(92.0) $(61.1)
Net loss $(89.9) $(49.9)

*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

Our revenue for the three months ended March 31, 2020first quarter of 2021 was $133.4$111.6 million. Our commercial revenue forin the three months ended March 31, 2020 increased more than 20 percent overfirst quarter of 2021 was consistent with the same period last year. As we complete the transition of TEGSEDI operations in 2019.North America to Sobi, our commercial revenue from product sales will shift to distribution fee revenue.

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We earn our R&D revenue from multiple sources that can fluctuate depending on the timing of events. Our R&D revenue decreased in the first quarter of 2021 compared to the same period in 2020 primarily because we earned more milestone payments in the first quarter of 2020 included over $25 million from our neurology disease franchise and $15 million from our cardiometabolic franchise. Our R&D revenuethan in the first quarter of 2019 included $185 million from two large items, including a $150 million license fee we earned from Novartis when it licensed AKCEA-APO(a)-LRx.2021. We anticipateexpect our R&D revenue will be higherto increase in the second half of 2020,2021 compared to the first half of 2020.half.

Our operating expenses for the first quarter of 20202021 were $194.5$203.6 million and increased over the same period in 2019,2020, principally due to our investments in advancing our late-stage wholly owned pipeline. In addition, we incurred approximately $7 million in costs related to the global launchesAkcea Acquisition and Restructured European Operations, primarily comprised of TEGSEDIseverance and WAYLIVRA, the Phase 3 program for AKCEA-TTR-LRx and our Ionis-owned pipeline.retention costs.

We expect our operating expenses to continue to increase during the rest of 20202021 as we continue to advance our strategic priorities. Additionally, we expect to incur an additional $11 million to $14 million of restructuring costs, principally in the second quarter of 2021, related to the Restructured North American TEGSEDI Operations to better align with the immediate needs of our business and to focus on our wholly owned pipeline. We also expect to recognize the majority of the remaining severance and retention costs related to the Akcea Acquisition and Restructured European Operations transactions in the second quarter of 2021. See Note 7, Severance and Retention Costs, for additional details.

We ended the first quarter of 2020,2021 with $2.4$1.8 billion in cash and short-term investments. In April 2021, we issued $632.5 million of 0% senior convertible notes due in April 2026 and repurchased $247.9 million of our 1% senior convertible notes. In conjunction with these transactions, we also executed a call spread to increase the effective conversion price of the 0% senior convertible notes to $76.39. After giving effect to these transactions, our pro forma cash, cash equivalents and short-term investments was $2.1 billion. We believe our strong financial position should enable us to continue to execute on our corporate goals throughout 2020this year and beyond.beyond, including developing and commercializing medicines within our wholly owned pipeline.

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Recent Business Updates

Recent Business Highlights (Q1 2020 and subsequent activities)

Commercial MedicineFirst Quarter 2021 Marketed Products Highlights

SPINRAZA: a global foundation-of-care for the treatment of SMA patients of all ages
oWorldwide$521 million in worldwide sales increased to $565 million in the first quarter a 9 percent increase compared to the first quarter of 2019
oWorldwideMore than 11,000 patients worldwide were on treatment increased to approximately 10,800therapy at the end of the first quarter including patients across commercial,post-marketing, expanded access and clinical trial settings
oPatient treatment is underway
Higher-dose SPINRAZA demonstrated safety and tolerability consistent with the currently approved dose in the Phase 2/3open-label safety cohort of the DEVOTE study, evaluatingenabling enrollment in the safety, tolerability and potentialblinded, pivotal cohort to achieve even greater efficacy with a higher dose of SPINRAZAget underway
oData from an independent study published in Lancet Neurology demonstrated statistically significant improvement in motor function with SPINRAZA treatment in teens and adults

TEGSEDI: launched in multiple marketsTEGSEDI and WAYLIVRA: important medicines approved for the treatment of hATTRpatients with polyneuropathy in adult patientssevere rare diseases
oCommercially available in 12 countriesCompleted the transition of European operations to Sobi and expanded the distribution agreement to include North American TEGSEDI operations

oLaunching in additional EU countries this year and expanding in Latin America through PTC Therapeutics
oResults from the NEURO-TTR Phase 3 open-label extension study were published in the European Journal of Neurology.
First Quarter 2021 and Recent Pipeline Events

WAYLIVRA: launchedPhase 3 Pipeline: growing and positioned for 12 or more products on the market in the EU as the only approved treatment for adults with genetically confirmed FCS at high risk for pancreatitis2026
oLaunch progressing in Germany, Austria and through the ATU in France
oLaunching in additional EU countries this year

Pipeline Highlights

Roche completed enrollment in the global, GENERATION HD1Advanced ION363 into a Phase 3 study in patients with Huntington’s diseaseFUS-ALS
oAdvanced tofersen into the Phase 3 ATLAS study in presymptomatic SOD1-ALS patients
oRoche reported tominersen data related to the dosing halt in the Phase 3 program
InitiatedMid-stage Pipeline: advancing multiple medicines with potential to change the CARDIO-TTRansform Phase 3 clinical trialstandard of care for AKCEA-TTR-Lpatients with severe diseases
o
Reported positive topline IONIS-PKK-LRx results in patients with TTR-mediated amyloid cardiomyopathyhereditary angioedema
oTwo medicines granted Fast Track Designation byAdvanced ION373 into the U.S. FDAPhase 2 portion of a pivotal study in patients with Alexander disease
o
AKCEA-APO(a)-LAdvanced the IONIS-AGT-LRx for the treatment of cardiovascular disease due to elevated Lp(a) levelsdevelopment program:
o
IONIS-C9Rx for the treatment of C9orf72-ALSReported positive Phase 2 data in JACC: Basic to Translational Science
We generated
Advanced into a Phase 2b study in patients with hypertension uncontrolled with three or more than $20 million as numerous partnered medicines advancedantihypertensive medications
o$10 million from AstraZeneca for ION532 targeting APOL1 for the treatment of kidney disease
Advanced into a Phase 2 study in patients with chronic heart failure with reduced injection fraction
o
$7.5 million from Biogen for IONIS-MAPTRx forAdvanced the treatment of Alzheimer’s disease
o
$5 million from Dynacure for IONIS-DNM2-2.5Rx for the treatment of centronuclear myopathies
We and Akcea reported positive topline results for AKCEA-APOCIII-LRx and vupanorsen
Results from theongoing Phase 2 study of AKCEA-APO(a)-LRxION541 in patients with Lp(a)-driven cardiovascular disease, highlighting the favorable safety and tolerability profile and the potential to addressALS regardless of family history, resulting in a major area of unmet need, were published in the New England Journal of Medicine$10 million payment from Biogen


Business Segment

In 2021, we began operating as a single segment, Ionis operations, because our chief decision maker reviews operating results on an aggregate basis and manages our operations as a single operating segment. Previously, we had operated as two operating segments, Ionis Core and Akcea Therapeutics. In October 2020, we acquired the remaining common stock of Akcea that we did not own and fully integrated Akcea’s operations into ours as of January 1, 2021.

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Initiated a Phase 1 study of ION224, an Ionis-owned medicine in development for the treatment of NASH


Critical Accounting Estimates

We prepare our condensed consolidated financial statements in conformity with accounting principles generally accepted in the United States.U.S. As such, we make certain estimates, judgments and assumptions that we believe are reasonable, based upon the information available to us. These judgments involve making estimates about the effect of matters that are inherently uncertain and may significantly impact our quarterly or annual results of operations and financial condition. Each quarter, our senior management reviews the development, selection and disclosure of such estimates with the audit committee of our board of directors. In the following paragraphs, we describe the specific risks associated with these critical accounting estimates and we caution that future events rarely develop exactly as one may expect, and that best estimates may require adjustment.

The following are our significant accounting estimates, which we believe are the most critical to aid in fully understanding and evaluating our reported financial results:

Assessing the propriety of revenue recognition and associated deferred revenue;
Determining the appropriate cost estimates for unbilled preclinical studies and clinical development activities; and

Estimating our income taxes
In the first quarter of 2021, we determined the estimation of our income taxes was no longer a critical accounting estimate because we recorded a valuation allowance against the entirety of our net deferred tax assets in the fourth quarter of 2020. We recorded the expected impact from the valuation allowance on our tax provision for 2021.

There have been no other material changes to our critical accounting policies and estimates from the information provided in Item 7, “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2019.2020.

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Results of Operations

Revenue

Total revenue for the three months ended March 31, 20202021 was $133.4$111.6 million compared to $297.2$133.4 million for the same period in 20192020 and was comprised of the following (amounts in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Revenue:            
Commercial revenue:            
SPINRAZA royalties $66,008  $59,711  $60.0  $66.0 
Product sales, net  15,159   6,754 
TEGSEDI and WAYLIVRA revenue, net  19.8   15.2 
Licensing and other royalty revenue  2,794   1,623   4.6   2.8 
Total commercial revenue  83,961   68,088   84.4   84.0 
R&D revenue:                
Amortization from upfront payments  21,146   35,851   20.1   21.1 
Milestone payments  23,119   40,017   5.2   23.1 
License fees     150,000 
Other services  5,141   3,258   1.9   5.2 
Total R&D revenue  49,406   229,126   27.2   49.4 
Total revenue $133,367  $297,214  $111.6  $133.4 

InOur commercial revenue in the first quarter of 2020,2021 was consistent with the same period last year. As we complete the transition of TEGSEDI operations in North America to Sobi, our commercial revenue increased over 20 percent, compared to the same quarter of 2019. Commercial revenue from SPINRAZA royalties increased over 10 percent and product sales from TEGSEDI and WAYLIVRA more than doubled.will shift to distribution fee revenue.

We earn our R&D revenue from multiple sources whichthat can fluctuate depending on the timing of events. Our R&D revenue decreased in the first quarter of 2021 compared to the same period in 2020 primarily because we earned more milestone payments in the first quarter of 2020 included over $25 million from our neurology disease franchise and $15 million from our cardiometabolic franchise. Our R&D revenuethan in the first quarter of 2019 included $185 million from two large items, including a $150 million license fee we earned from Novartis when it licensed AKCEA-APO(a)-LRx.2021. We anticipate our R&D revenue to be higherincrease in the second half of 2020,2021 compared to the first half of 2020.2021 as many of our partnered programs advance.

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Operating Expenses

Our operating expenses were as follows (in millions):

  
Three Months Ended
March 31,
 
  2021  2020 
Operating expenses, excluding non-cash compensation expense related to equity awards $159.0  $153.7 
Restructuring expenses  6.7    
Non-cash compensation expense related to equity awards  37.9   40.8 
Total operating expenses $203.6  $194.5 

Operating expenses, excluding non-cash compensation expense related to equity awards, for the three months ended March 31, 2020 were $194.5 million and2021 increased compared to $175.7 million for the same period in 2019.2020. The increase was principally due to our investments in the global launches of TEGSEDI and WAYLIVRA, the Phase 3 program for AKCEA-TTR-LIONIS-TTR-LRx and other medicines in our Ionis-ownedwholly owned pipeline. Compensation expenseAdditionally, we incurred approximately $7 million in costs related to equity awards declined for the three months ended March 31, 2020 compared to the same period in 2019Akcea Acquisition and Restructured European Operations, primarily due to the departurescomprised of certain members of Akcea’s senior managementseverance and board of directors.retention costs. We expect our operating expenses, excluding non-cash compensation expense related to equity awards, to continue to increase during the rest of 20202021 as we continue to advance our strategic priorities. Additionally, we expect to incur an additional $11 million to $14 million of restructuring costs, principally in the second quarter of 2021, related to our the Restructured North American TEGSEDI Operations to better align with the immediate needs of our business and to focus on our wholly owned pipeline. We also expect to recognize the majority of the remaining severance and retention costs related to the Akcea Acquisition and Restructured European Operations transactions in the second quarter of 2021. See Note 7, Severance and Retention Costs, for additional details.

Our operating expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $95,020  $78,514 
Akcea Therapeutics  60,950   128,106 
Elimination of intercompany activity  (2,266)  (76,446)
Subtotal  153,704   130,174 
Non-cash compensation expense related to equity awards  40,790   45,505 
Total operating expenses $194,494  $175,679 

To analyze and compare our results of operations to other similar companies, we believe it is important to exclude non-cash compensation expense related to equity awards from our operating expenses. We believe non-cash compensation expense related to equity awards is not indicative of our operating results or cash flows from our operations. Further, we internally evaluate the performance of our operations excluding it.

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Cost of Products SoldSales

Our cost of products soldsales consisted of manufacturing costs, including certain fixed costs, transportation and freight, indirect overhead costs associated with the manufacturing and distribution of TEGSEDI and WAYLIVRA and certain associated period costs. Prior to the regulatory approval of TEGSEDI and WAYLIVRA, we expensed as R&D expense a significant portion of the cost of producing TEGSEDI and WAYLIVRA that Akcea iswe are using in the commercial launches. We expect cost of products soldsales to increase as we deplete these inventories.

Our cost of products sold by segmentsales were as follows (in thousands)millions):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $  $ 
Akcea Therapeutics  4,534   2,326 
Elimination of intercompany activity  (2,223)  (1,403)
Subtotal  2,311   923 
Non-cash compensation expense related to equity awards  237   118 
Total cost of products sold $2,548  $1,041 
  
Three Months Ended
March 31,
 
  2021  2020 
Cost of sales, excluding non-cash compensation expense related to equity awards $2.4  $2.3 
Non-cash compensation expense related to equity awards  0.2   0.2 
Total cost of sales $2.6  $2.5 

We began recognizing cost of products sold for TEGSEDI in the third quarter of 2018 when TEGSEDI was approved and for WAYLIVRA in the second quarter of 2019 when WAYLIVRA was approved. Our cost of products sold increased insales, excluding non-cash compensation expense related to equity awards, for the three months ended March 31, 20202021, compared to were consistent with the same period in 2019, primarily due to the increase in commercial product sales. We previously expensed $0.6 million and $0.3 million of costs to produce our products related to the product sales revenue we recognized in the three months ended March 31, 2020 and 2019, respectively. We recognized these costs in prior periods because we incurred these costs before we obtained regulatory approval. In its cost of products sold Akcea includes the amortization for milestone payments it made to us related to the U.S. and European approvals of TEGSEDI. Akcea is recognizing this amortization over TEGSEDI’s remaining estimated patent life. We eliminate this amortization in our consolidated results. All amounts exclude non-cash compensation expense related to equity awards.2020.

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Research, Development and Patent Expenses

Our research, development and patent expenses consist of expenses for antisense drug discovery, antisense drug development, manufacturing and operationsdevelopment chemistry and R&D support expenses.

The following table sets forth information on research, development and patent expenses (in thousands)millions):

  
Three Months Ended
March 31,
 
  2020  2019 
Research, development and patent expenses, excluding non-cash compensation expense related to equity awards $91,396  $81,982 
Non-cash compensation expense related to equity awards  25,556   24,435 
Total research, development and patent expenses $116,952  $106,417 

Our research, development and patent expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $75,433  $61,327 
Akcea Therapeutics  16,006   95,698 
Elimination of intercompany activity  (43)  (75,043)
Subtotal  91,396   81,982 
Non-cash compensation expense related to equity awards  25,556   24,435 
Total research, development and patent expenses $116,952  $106,417 
  
Three Months Ended
March 31,
 
  2021  2020 
Research, development and patent expenses, excluding non-cash compensation expense related to equity awards $111.3  $91.4 
Restructuring expenses  2.6    
Non-cash compensation expense related to equity awards  25.9   25.6 
Total research, development and patent expenses $139.8  $117.0 

Antisense Drug Discovery

We use our proprietary antisense technology to generate information about the function of genes and to determine the value of genes as drug discovery targets. We use this information to direct our own antisense drug discovery research, and that of our partners. Antisense drug discovery is also the function that is responsible for advancing our antisense core technology. This function is also responsible for making investments in complementary technologies to expand the reach of antisense technology.

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As we continue to advance our antisense technology, we are investing in our drug discovery programs to expand our and our partners’ drug pipelines.pipeline.

Our antisense drug discovery expenses are part of our Ionis Core business segment and were as follows (in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Antisense drug discovery expenses, excluding non-cash compensation expense related to equity awards $18,366  $14,632  $26.6  $18.4 
Non-cash compensation expense related to equity awards  6,306   5,493   6.3   6.3 
Total antisense drug discovery expenses $24,672  $20,125  $32.9  $24.7 

Antisense drug discovery expenses were higher, excluding non-cash compensation expense related to equity awards, increased in the three months endedMarch 31, 2020,2021 compared to the same period in 2019,2020 due to expenses we incurred primarily related to advancing our Ionis-owned research programs. All amounts exclude non-cash compensation expense relatedprograms and investments we made to equity awards.expand the reach of our antisense technology.

Antisense Drug Development

The following table sets forth drug development expenses, including expenses for our marketed medicines and those in Phase 3 development and/or commercialization for which we have incurred significant costs (in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
      
AKCEA-TTR-LRx
 $5,851  $940 
TEGSEDI $1.8  $4.3 
WAYLIVRA  978   1,971   0.6   1.0 
TEGSEDI  4,346   4,691 
IONIS-TTR-LRx
  13.3   5.9 
IONIS-APOCIII-LRx
  1.4   0.8 
ION363  2.1    
Other antisense development projects  21,840   21,370   20.3   21.0 
Development overhead expenses  17,932   18,944   22.5   17.9 
Restructuring expenses  2.3    
Total antisense drug development, excluding non-cash compensation expense related to equity awards  50,947   47,916   64.3   50.9 
Non-cash compensation expense related to equity awards  11,787   12,234   12.4   11.8 
Total antisense drug development expenses $62,734  $60,150  $76.7  $62.7 

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Our development expenses, excluding non-cash compensation expense related to equity awards, increased slightly for the three months endedMarch 31, 20202021 compared to the same period in 2019. The increase in development expenses2020 primarily relateddue to our broad Phase 3 program for AKCEA-TTR-LIONIS-TTR-LRx, which we initiated in late 2019. This increase was slightly offset by decreases in expenses from WAYLIVRA. All amounts exclude non-cash compensation expense related to equity awards.

Our antisense drug development expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $39,102  $29,070 
Akcea Therapeutics  11,845   93,846 
Elimination of intercompany activity     (75,000)
Subtotal  50,947   47,916 
Non-cash compensation expense related to equity awards  11,787   12,234 
Total antisense drug development expenses $62,734  $60,150 

Akcea’s development expenses in the first quarter of 2019 included a $75 million sublicense fee it paid us related to Novartis’ license of AKCEA-APO(a)-LRx. We eliminated this expenseAdditionally, we advanced other medicines in our consolidated results. Excluding this fee, Akcea's development expenses decreased primarily because Akcea completed thewholly owned pipeline, including ION363, which we recently initiated a Phase 23 study of vupanorsenfor in early 2020.patients with FUS-ALS.

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We may conduct multiple clinical trials on a drug candidate, including multiple clinical trials for the various indications we may be studying. Furthermore, as we obtain results from trials, we may elect to discontinue clinical trials for certain drug candidates in certain indications in order to focus our resources on more promising drug candidates or indications. Our Phase 1 and Phase 2 programs are clinical research programs that fuel our Phase 3 pipeline. When our medicines are in Phase 1 or Phase 2 clinical trials, they are in a dynamic state in which we may adjust the development strategy for each medicine. Although we may characterize a medicine as “in Phase 1” or “in Phase 2,” it does not mean that we are conducting a single, well-defined study with dedicated resources. Instead, we allocate our internal resources on a shared basis across numerous medicines based on each medicine’s particular needs at that time. This means we are constantly shifting resources among medicines. Therefore, what we spend on each medicine during a particular period is usually a function of what is required to keep the medicines progressing in clinical development, not what medicines we think are most important. For example, the number of people required to start a new study is large, the number of people required to keep a study going is modest and the number of people required to finish a study is large. However, such fluctuations are not indicative of a shift in our emphasis from one medicine to another and cannot be used to accurately predict future costs for each medicine. And, because we always have numerous medicines in preclinical and early stage clinical research, the fluctuations in expenses from medicine to medicine, in large part, offset one another. If we partner a medicine, it may affect the size of a trial, its timing, its total cost and the timing of the related costs.

Manufacturing and Development Chemistry

Expenditures in our manufacturing and development chemistry function consist primarily of personnel costs, specialized chemicals for oligonucleotide manufacturing, laboratory supplies and outside services. Our manufacturing and development chemistry function is responsible for providing drug supplies to antisense drug development Akcea and our collaboration partners. Our manufacturing procedures include testing to satisfy good laboratory and good manufacturing practice requirements.

Our manufacturing and development chemistry expenses were as follows (in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Manufacturing and development chemistry expenses, excluding non-cash compensation expense related to equity awards $11,983  $10,154  $11.8  $12.0 
Restructuring expenses  0.3    
Non-cash compensation expense related to equity awards  2,832   2,057   3.1   2.8 
Total manufacturing and development chemistry expenses $14,815  $12,211  $15.2  $14.8 

Manufacturing and development chemistry expenses increased slightly, excluding non-cash compensation expense related to equity awards, were essentially flat for the three months endedMarch 31, 2020,2021 compared to the same period in 2019. All amounts exclude non-cash compensation expense related to equity awards.2020.

Our manufacturing and development chemistry expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $10,311  $8,799 
Akcea Therapeutics  1,672   1,355 
Subtotal  11,983   10,154 
Non-cash compensation expense related to equity awards  2,832   2,057 
Total manufacturing and development chemistry expenses $14,815  $12,211 

R&D Support

In our research, development and patent expenses, we include support costs such as rent, repair and maintenance for buildings and equipment, utilities, depreciation of laboratory equipment and facilities, amortization of our intellectual property, informatics costs, procurement costs and waste disposal costs. We call these costs R&D support expenses.

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The following table sets forth information on R&D support expenses (in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Personnel costs $3,838  $3,910  $4.3  $3.8 
Occupancy  2,442   2,177   3.2   2.4 
Patent expenses  672   523   0.8   0.7 
Depreciation and amortization  162   121 
Insurance  610   411   0.8   0.6 
Computer software and licenses  0.5   0.6 
Other  2,376   2,138   1.3   2.0 
Total R&D support expenses, excluding non-cash compensation expense related to equity awards  10,100   9,280   10.9   10.1 
Non-cash compensation expense related to equity awards  4,632   4,651   4.1   4.6 
Total R&D support expenses $14,732  $13,931  $15.0  $14.7 

R&D support expenses, excluding non-cash compensation expense related to equity awards, for the three months endedMarch 31, 20202021 increased slightly compared to the same period in 2019. All amounts exclude non-cash compensation expense related to equity awards.2020.

Our R&D support expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $7,654  $8,826 
Akcea Therapeutics  2,489   497 
Elimination of intercompany activity  (43)  (43)
Subtotal  10,100   9,280 
Non-cash compensation expense related to equity awards  4,632   4,651 
Total R&D support expenses $14,732  $13,931 

Selling, General and Administrative Expenses

Selling, general and administrative, or SG&A, expenses include personnel and outside costs associated with the pre-commercialization and commercialization activities for our medicines and costs to support our company, our employees and our stockholders including, legal, human resources, investor relations, and finance. Additionally, we include in selling, general and administrative expenses such costs as rent, repair and maintenance of buildings and equipment, depreciation and utilities costs that we need to support the corporate functions listed above. We also include fees we owe under our in-licensing agreements related to SPINRAZA.

The following table sets forth information on SG&A expenses (in thousands)millions):

 
Three Months Ended
March 31,
  
Three Months Ended
March 31,
 
 2020  2019  2021  2020 
Selling, general and administrative expenses, excluding non-cash compensation expense related to equity awards $59,997  $47,270  $45.3  $60.0 
Restructuring expenses  4.1    
Total selling, general and administrative expenses, excluding non-cash compensation related to equity awards  49.4   60.0 
Non-cash compensation expense related to equity awards  14,997   20,951   11.8   15.0 
Total selling, general and administrative expenses $74,994  $68,221  $61.2  $75.0 

SG&A expenses, excluding non-cash compensation expense related to equity awards, were higherlower for the three months ended March 31, 20202021, compared to the same period in 20192020 principally due to operating efficiencies attained from our investments in the global launchesintegration ofTEGSEDI Akcea and WAYLIVRA. All amounts exclude non-cash compensation expense related to equity awards.

Our SG&A expenses by segment were as follows (in thousands):

  
Three Months Ended
March 31,
 
  2020  2019 
Ionis Core $19,587  $17,187 
Akcea Therapeutics  40,410   30,082 
Subtotal  59,997   47,269 
Non-cash compensation expense related to equity awards  14,997   20,952 
Total selling, general and administrative expenses $74,994  $68,221 

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Akcea Therapeutics, Inc.

The following table sets forth information on operating expenses (in thousands) for our Akcea Therapeutics business segment:

  
Three Months Ended
March 31,
 
  2020  2019 
Cost of products sold $4,534  $2,326 
Development and patent expenses  16,006   20,698 
Sublicense fees to Ionis     75,000 
Selling, general and administrative expenses  40,410   30,082 
Profit (loss) share for TEGSEDI commercialization activities  (6,898)  (9,056)
Total operating expenses, excluding non-cash compensation expense related to equity awards  54,052   119,050 
Non-cash compensation expense related to equity awards  7,282   18,560 
Total Akcea Therapeutics operating expenses $61,334  $137,610 

Akcea's development expenses decreased for the three months ended March 31, 2020, compared to the same period in 2019 primarily because Akcea completed the Phase 2 studies of vupanorsen and AKCEA-APOCIII-LRx in early 2020.updated European distribution model. These decreases were slightly offset by an increase in development expensesrestructuring costs related to the broad Phase 3 program for AKCEA-TTR-LRx.

In the first quarter of 2019 Akcea incurred a $75 million sublicense fee it paid to us related to Novartis’ license of AKCEA-APO(a)-LRx. We eliminated the sublicense fee in our consolidated results.

Akcea’s SG&A expenses increased in the three months ended March 31, 2020 compared to the same period in 2019, primarily due to Akcea’s commercialization of TEGSEDIAcquisition and WAYLIVRA. For each period presented, we allocated a portion of Ionis’ SG&A expenses to Akcea for work we performed on Akcea’s behalf and we bill Akcea for these expenses. We included these allocated expenses in Akcea’s SG&A expenses in the table above. All amounts exclude non-cash compensation expense related to equity awards.

In the first quarter of 2019, we began sharing profits and losses for TEGSEDI with Akcea under our TTR licensing agreement. As Akcea is the principal for all commercial activities related to the TTR License Agreement, Akcea records all activities related to TEGSEDI on a gross basis in its statement of operations based on the nature of the activity, including revenues, cost of products sold and sales and marketing expenses. Ionis’ share of the net profit/loss from commercializing TEGSEDI is separately presented on Akcea’s statement of operations on the line titled “Profit (loss) share for TEGSEDI commercialization activities”Restructured European Operations. Since TEGSEDI is currently generating a loss, this represents the amount Ionis owes Akcea under the licensing agreement for Ionis’ share of the net loss of TEGSEDI commercialization activities during the period. With the launch of WAYLIVRA in the third quarter of 2019, Akcea began paying Ionis royalties on WAYLIVRA product sales. We eliminate these amounts in our consolidated results.

All amounts exclude non-cash compensation expense related to equity awards.

Investment Income

Investment income for the three months ended March 31, 20202021 was $10.5$4.6 million compared to $12.1$10.5 million for 2019.2020. The decrease in investment income was primarily due to a decline in interest rates and a lower cash balance during the three months ended March 31, 20202021 compared to the same period in 2019.2020.

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Interest Expense

The following table sets forth information on interest expense (in thousands)millions):

 
Three Months Ended
March 31,
 
 
Three Months Ended
March 31,
  2021  2020 
 2020  2019     (as revised*) 
Convertible notes:            
Non-cash amortization of the debt discount and debt issuance costs $9,412  $9,200 
Non-cash amortization of debt issuance costs $0.9  $0.7 
Interest expense payable in cash  946   1,714   0.9   0.9 
Interest on mortgage for primary R&D and manufacturing facilities  601   582   0.6   0.6 
Other  31   103 
Total interest expense $10,990  $11,599  $2.4  $2.2 

Our interest expense payable in cash decreased in the three months ended March 31, 2020, compared to the same period in 2019 because we exchanged a significant portion of our 1% Notes for 0.125% Notes in December 2019.
*
We revised our 2020 amounts to reflect the simplified convertible instruments accounting guidance, which we adopted retrospectively. Refer to Note 2, Significant Accounting Policies, for further information.

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Income Tax Expense (Benefit)

We recorded annegligible income tax benefit of $3.3 millionexpense for the three months ended March 31, 2020, compared2021 primarily due to our valuation allowance and our expected taxable losses for the year. We recorded an income tax expensebenefit of $31.0$3.1 million for the same period in 2019. We recorded an income tax benefit for the three months ended March 31, 2020 primarily due to Ionis’our pre-tax loss for the period and a $1.7 million tax benefit related to Akcea. We did not record a tax benefit as a resultutilization of Akcea’s pre-taxadditional net operating loss carryforwards provided by the Coronavirus Aid, Relief, and Economic Security Act, or the CARES Act, enacted by the U.S. Congress in the first quarter of 2020 because Akcea maintains a full valuation allowance against its deferred tax assets.March 2020.

Net Income (Loss)Loss

We had a net loss of $58.5$89.9 million for the three months ended March 31, 2020,2021 compared to net incomeloss of $90.9$49.9 million for the same period in 2019. Our net loss was primarily due to decreased revenue year-over-year, as2020, which reflects the fluctuations discussed above in the revenue section.above.

Net (Income) Loss Attributable to Noncontrolling Interest in Akcea Therapeutics, Inc.

At March 31,During the first quarter of 2020, we owned approximately 76 percent of Akcea. The shares of Akcea third parties own representowned represented an interest in Akcea'sAkcea’s equity that we dodid not control. However, because we continue to maintainmaintained overall control of Akcea through our voting interest, we reflect the assets, liabilities andreflected Akcea’s results of operations of Akcea in our condensed consolidated financial statements. We reflectreflected the noncontrolling interest attributable to other owners of Akcea'sAkcea’s common stock in a separate line called “Net loss attributable to noncontrolling interest in Akcea” on our statement of operations. Our noncontrolling interest in Akcea on our statement of operations for the three months ended March 31, 2020, was a loss of $10.3 million, comparedmillion. After our acquisition of Akcea in October 2020, we no longer recorded any adjustment related to noncontrolling interest for Akcea’s net income of $6.4 million for same period in 2019.loss.

Net Income (Loss)Loss Attributable to Ionis Pharmaceuticals, Inc.Our Common Stockholders and Net Income (Loss)Loss per Share

We had a net loss attributable to our common stockholders’stockholders of $48.2$89.9 million for the three months ended March 31, 2020,2021 compared to net incomeloss of $84.4$39.6 million for the same period in 2019.2020. Basic and diluted net loss per share for the three months ended March 31, 20202021 were $0.350.64. Our basic and diluted net incomeloss per share for the three months ended March 31, 2019 was $0.63 and2020 were $0.620.28, respectively..

Liquidity and Capital Resources

We have financed our operations primarily from research and development collaborative agreements. We also finance our operations from commercial revenue from SPINRAZA royalties and product sales.TEGSEDI and WAYLIVRA commercial revenue. From our inception through March 31, 2020,2021, we have earned approximately $4.4$5.1 billion in revenue. We have also financed our operations through the sale of our equity securities and the issuance of long-term debt. From the time we were founded through March 31, 2020,2021, we have raised net proceeds of approximately $1.8$2.0 billion from the sale of our equity securities, not including the $182.4 million Akcea received in net proceedssecurities. Additionally, from its IPO in July 2017. Additionally,our inception through March 31, 2021, we have borrowed approximately $1.5 billion under long-term debt arrangements to finance a portion of our operations over the same time period.operations.

Our key liquidity metrics and capital resources, including our cash, cash equivalents and short-term investments working capital and debt obligations were essentially unchanged did not change significantly at March 31, 2020,2021 compared to December 31, 2019.2020, except working capital. Our working capital increased because we reclassified a portion of our 1% Notes as a non-current liability on our condensed consolidated balance sheet in the first quarter of 2021.

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In April 2021, we issued $632.5 million of 0% Notes due in April 2026 and repurchased $247.9 million of our 1% Notes. Therefore, as of March 31, 2021, we classified the repurchased portion of our 1% Notes as a non-current liability on our condensed consolidated balance sheet.

The following table summarizes our contractual obligations as of March 31, 2020.2021. The table provides a breakdown of when obligations become due. We provide a more detailed description of the major components of our debt in the paragraphs following the table:

 Payments Due by Period (in millions) 
Contractual Obligations
(selected balances described below)
 Total  Less than 1 year  1-3 years  3-5 years  After 5 years 
Contractual Obligations Payments Due by Period (in millions) 
(selected balances described below) Total  Less than 1 year  More than 1 year 
0.125% Notes (principal and interest payable) $552.3  $0.7  $1.4  $550.2  $  $551.6  $0.7  $550.9 
1% Notes (principal and interest payable)  316.1   3.1   313.0       
1% Notes (principal and interest payable)*  313.0   313.0    
Building mortgage payments  77.6   2.4   5.5   6.9   62.8   75.5   2.4   73.1 
Operating leases  22.6   3.3   5.7   4.8   8.8   22.4   3.3   19.1 
Other obligations (principal and interest payable)  1.0   0.1   0.1   0.1   0.7   0.9   0.1   0.8 
Total $969.6  $9.6  $325.7  $562.0  $72.3  $963.4  $319.5  $643.9 

*In April 2021, we repurchased $247.9 million in aggregate principal amount of our 1% Notes in privately negotiated transactions. As a result, in April 2021, the remaining principal outstanding for our 1% Notes was $62.0 million. As a result of the repurchase, we reclassified the repurchased portion of our 1% Notes from current to non-current liabilities on our condensed consolidated balance sheet as of March 31, 2021 because we replaced this portion of our outstanding debt with long-term debt.

Our contractual obligations consist primarily of our convertible debt. In addition, we also have facility mortgages, facility leases, equipment financing arrangements and other obligations. Due to the uncertainty with respect to the timing of future cash flows associated with our unrecognized tax benefits, we are unable to make reasonably reliable estimates of the period of cash settlement with the respective taxing authorities. Therefore, we have excluded our gross unrecognized tax benefits from our contractual obligations table above. We have not entered into, nor do we currently have, any off-balance sheet arrangements (as defined under SEC rules).

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0.125 Percent Convertible Senior NotesDebt and Call Spread

In December 2019, we entered into privately negotiated exchange and/or subscription agreements with certain new investors and certain holders of our existing 1% Notes to exchange $375.6 million of our 1% Notes for $439.3 million of our 0.125% Notes, and to issue $109.5 million of our 0.125% Notes. We completed this exchange to reduce our cash interest payments, increase our conversion price and extend our maturity for a large portion of our debt. Additionally, in conjunction with the December 2019 exchange, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants, to minimize the impact of potential economic dilution upon conversion of our 0.125% Notes by increasing the conversion price on our 0.125% even further.

The call spread cost us $52.6 million, of which $108.7 million was for the note hedge purchase, offset by $56.1 million we received for selling the warrants. We increased our effective conversion price to $123.38 with the same number of underlying shares as our 0.125% Notes.

SimilarRefer to our Convertible Debt and Call Spread accounting policies in Note 2, Significant Accounting Policies0.125% Notes, our note hedges are subjectand Note 6, Convertible Debt, in the Notes to adjustment. Additionally, our note hedges are exercisable upon conversion of the 0.125% Notes. The note hedges will expire upon maturity of 0.125% Notes, or December 2024. The note hedges and warrants are separate transactions and are not part of the terms of our 0.125% Notes. The holders of the 0.125% Notes do not have any rights with respect to the note hedges and warrants.

We recorded the aggregate amount paid for the note hedges and the aggregate amount received for the warrants in additional paid-in capital in our condensed consolidated balance sheet. We exclude any shares of our common stock receivable by us under the note hedges from our calculation of diluted earnings per share as they are antidilutive. We will include the shares issuable under the warrants in our calculation of diluted earnings per share when the average market price per share of our common stockfinancial statements for the reporting period exceeds the strike pricesignificant terms of the warrants.each convertible debt instrument.

At March 31, 2020, we had the following 0.125% Notes outstanding (amounts in millions except price per share data):

 0.125% Notes 
Outstanding principal balance $548.8 
Maturity date December 2024 
Interest rate 0.125 percent 
Conversion price per share $83.28 
Total shares of common stock subject to conversion  6.6 

Interest is payable semi-annually for the 0.125% Notes. The 0.125% Notes are convertible under certain conditions, at the option of the note holders. We can settle conversions of the 0.125% Notes, at our election, in cash, shares of our common stock or a combination of both. We may not redeem the 0.125% Notes prior to maturity, and no sinking fund is provided for them. Holders of the 0.125% Notes may require us to purchase some or all of their notes upon the occurrence of certain fundamental changes, as set forth in the indenture governing the 0.125% Notes, at a purchase price equal to 100 percent of the principal amount of the notes to be purchased, plus accrued and unpaid interest.

1 Percent Convertible Senior Notes

In November 2014, we completed a $500 million offering of convertible senior notes, which mature in 2021 and bear interest at 1 percent. We used a substantial portion of the net proceeds from the issuance of the 1% Notes to repurchase $140 million in principal of our 2¾ percent convertible senior notes, or 2¾% Notes. In December 2016, we issued an additional $185.5 million of 1% Notes in exchange for the redemption of $61.1 million of our 2¾% Notes. In December 2019, we exchanged a portion of our 1% Notes for new 0.125% Notes. As a result, the principal balance of the 1% Notes following the exchange was $309.9 million.

At March 31, 2020, we had the following 1% Notes outstanding (amounts in millions except price per share data):

  1% Notes 
Outstanding principal balance $309.9 
Maturity date November 2021 
Interest rate 1 percent 
Conversion price per share $66.81 
Total shares of common stock subject to conversion  4.6 

Interest is payable semi-annually for the 1% Notes. The 1% Notes are convertible under certain conditions, at the option of the note holders. We settle conversions of the 1% Notes, at our election, in cash, shares of our common stock or a combination of both. We may not redeem the 1% Notes prior to maturity, and no sinking fund is provided for them. Holders of the 1% Notes may require us to purchase some or all of their notes upon the occurrence of certain fundamental changes, as set forth in the indenture governing the 1% Notes, at a purchase price equal to 100 percent of the principal amount of the notes to be purchased, plus accrued and unpaid interest.

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Research and Development and Manufacturing Facilities

In July 2017, we purchased the building that houses our primary R&D facility for $79.4 million and our manufacturing facility for $14.0 million. We financed the purchase of these two facilities with mortgage debt of $60.4 million in total. Our primary R&D facility mortgage has an interest rate of 3.88 percent. Our manufacturing facility mortgage has an interest rate of 4.20 percent. During the first five years of both mortgages, we are only required to make interest payments. Both mortgages mature in August 2027.

Other Obligations

In addition to contractual obligations, we had outstanding purchase orders as of March 31, 20202021 for the purchase of services, capital equipment and materials as part of our normal course of business.

We may enter into additional collaborations with partners which could provide for additional revenue to us and we may incur additional cash expenditures related to our obligations under any of the new agreements we may enter into. We currently intend to use our cash, cash equivalents and short-term investments to finance our activities. However, we may also pursue other financing alternatives, like issuing additional shares of our common stock, issuing debt instruments, refinancing our existing debt, or securing lines of credit. Whether we use our existing capital resources or choose to obtain financing will depend on various factors, including the future success of our business, the prevailing interest rate environment and the condition of financial markets generally.

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ITEM 3.QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

We are exposed to changes in interest rates primarily from our investments in certain short-term investments. We primarily invest our excess cash in highly liquid short-term investments of the U.S. Treasury and reputable financial institutions, corporations, and U.S. government agencies with strong credit ratings. We typically hold our investments for the duration of the term of the respective instrument. We do not utilize derivative financial instruments, derivative commodity instruments or other market risk sensitive instruments, positions or transactions to manage exposure to interest rate changes. Accordingly, we believe that, while the securities we hold are subject to changes in the financial standing of the issuer of such securities, we are not subject to any material risks arising from changes in interest rates, foreign currency exchange rates, commodity prices, equity prices or other market changes that affect market risk sensitive instruments.

We are also exposed to changes in foreign currency exchange rates as we have foreign subsidiaries with functional currencies other than the U.S. dollar. We translate our subsidiaries’ functional currencies into our reporting currency, the U.S. dollar. As a result, our financial position, results of operations and cash flows can be affected by market fluctuations in the foreign currencies to U.S. dollar exchange rate, which are difficult to predict. A hypothetical 10 percent change in foreign exchange rates during any of the periods presented would not have had a material impact on our condensed consolidated financial statements. Our business strategy incorporates potentially significant international expansion, particularly related to TEGSEDI and WAYLIVRA, therefore we expect that the impact of foreign currency exchange rate fluctuations may become more substantial in the future.

ITEM 4.CONTROLS AND PROCEDURES

We maintain disclosure controls and procedures that are designed to ensure that information we are required to disclose in our Exchange Act reports is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. We design and evaluate our disclosure controls and procedures recognizing that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance and not absolute assurance of achieving the desired control objectives.

As of our most recently completed fiscal year and as of the end of the period covered by this Quarterly Report on Form 10-Q, we carried out an evaluation of the effectiveness of the design and operation of our disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, under the supervision and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer. Based on our evaluation, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective as of March 31, 2020.2021. There have been no significant changes in our internal controls or in other factors that could significantly affect internal controls subsequent to March 31, 2020.2021.

We also performed an evaluation of any changes in our internal controls over financial reporting that occurred during our last fiscal quarter and that have materially affected, or are reasonably likely to materially affect, our internal controls over financial reporting. We conducted this evaluation under the supervision of and with the participation of our management, including our Chief Executive Officer and Chief Financial Officer. That evaluation did not identify any changes in our internal controls over financial reporting that occurred during our latest fiscal quarter and that have materially affected, or are reasonably likely to materially affect, our internal controls over financial reporting.

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PART II — OTHER INFORMATION

ITEM 1.LEGAL PROCEEDINGS

From time to time, we are involved in legal proceedings arising in the ordinary course of our business. Periodically, we evaluate the status of each legal matter and assess our potential financial exposure. If the potential loss from any legal proceeding is considered probable and the amount can be reasonably estimated, we accrue a liability for the estimated loss. Significant judgment is required to determine the probability of a loss and whether the amount of the loss is reasonably estimable. The outcome of any proceeding is not determinable in advance. As a result, the assessment of a potential liability and the amount of accruals recorded are based only on the information available to us at the time. As additional information becomes available, we reassess the potential liability related to the legal proceeding, and may revise our estimates.

In November 2019,
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On July 16, 2020, a purported stockholder of Akcea filed an action in the Delaware Court of Chancery captioned City of Cambridge Retirement SystemJohn Makris, et al. v. Stanley T. Crooke, et al., C.A. No. 2019-0905,2020-0587, or the Delaware“Delaware Action. The plaintiff in the Delaware Action assertedasserts claims against (i) current and former members of Akcea’s Boardboard of Directors,directors; and (ii) Ionis, or collectively, the Defendants.“Defendants”. The plaintiff purported to assert theseasserts derivative claims derivatively on behalf of Akcea, which was theis a nominal defendant in the Delaware Action, as well as directly against the Defendantsputatively direct claims on behalf of a purported class of AkceaAkcea’s stockholders. The plaintiff in the Delaware Action assertedaction asserts that the Defendants breached their fiduciary duties in connection with the licensing transaction that Akceawe and IonisAkcea entered into regarding TEGSEDI and AKCEA-TTR-LIONIS-TTR-LRx. The plaintiff also assertedasserts an unjust enrichment claim against IonisIonis. The plaintiff’s claims are similar to those asserted in connectiona prior action in the Delaware Court of Chancery captioned City of Cambridge Retirement System v. Crooke, et al., C.A. No. 2019-0905, which was dismissed with prejudice to the named plaintiff only on April 8, 2020. We believe that transaction. Wethe claims asserted in the Delaware Action are without merit and Akcea movedanticipate filing a motion to dismiss the plaintiff’s complaint and, on Januaryclaims.

In light of the August 31, 2020 public announcement of the Akcea Acquisition, the parties to the Delaware Action entered into a stipulation whereby the Defendants need not respond to the complaint filed briefs in support of our respective motions to dismiss. On April 7,on July 16, 2020, and the plaintiff in the Delaware action voluntarily dismissed its claims. That dismissal was with prejudice only as to the individual stockholder that filed the Delaware Action. It is therefore possible that a similar action could be filed at a later date prior to the expiration of the applicable statute of limitations.will file an amended complaint. The amended complaint has not yet been filed.

ITEM 1A.RISK FACTORS

Investing in our securities involves a high degree of risk. You should carefully consider carefully the following information about the risks described below, together with the other information contained in this report and in our other public filings in evaluating our business. If any of the following risks actually occur, our business could be materially harmed, and our financial condition and results of operations could be materially and adversely affected. As a result, the trading price of our securities could decline, and you might lose all or part of your investment. We have marked with an asterisk those risk factors that reflect substantive changes from the risk factors included in our Annual Report on Form 10-K for the year ended December 31, 2019.2020.

Summary of Risk Factors

There are a number of risks related to our business and our securities. Some of the principal risks related to our business include the following:

the impact on our operations and financial condition from the effects of the current COVID-19 pandemic;
our ability to generate substantial revenue from the sale of our medicines;
our and our partners’ ability to compete effectively;
the availability of adequate coverage and payment rates for our medicines;
our ability to successfully manufacture our medicines;
our ability to successfully develop and obtain marketing approvals for our medicines;
our ability to secure and maintain effective corporate partnerships;
our ability to sustain cash flows and achieve consistent profitability;
our ability to protect our intellectual property;
our ability to maintain the effectiveness of our personnel; and
the other factors set forth below.

Risks Related to the COVID-19 Pandemic

Our business could be materially adversely affected by the effects of health epidemics, includingepidemics. To date, we believe the impacts of the recent COVID-19 pandemic.*pandemic on our business are limited and manageable.

Our business could be materially adversely affected by health epidemics in regions where we or our partners are commercializing our medicines, have concentrations of clinical trial sites or other business operations, and could cause significant disruption in the operations of third-party manufacturers and contract research organizations upon whom we rely. For example, since December 2019, a novel strain of coronavirus, SARS-CoV-2, causing a disease referred to as COVID-19, has spread to multiple countries, including the U.S. and several European countries.worldwide. In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic, or the COVID-19 Pandemic, and the U.S. government-imposed travel restrictions on travel between the U.S., Europe and certain other countries. In addition, the Governor of the State of California and the Governor of the Commonwealth of Massachusetts, the states in which our and Akcea’s headquartersoffices are located, respectively, each declared a state of emergency related to the spread of COVID-19 and issued executive orders that directed residents to stay at home.

In response to these public health directives and orders, we implemented work-from-home policies for most of our employees globally and generally suspended business-related travel. Akcea has also implementedOut of an abundance of caution and to protect the health and welfare of our employees, we continue to maintain work-from-home policies for its employees globally and suspended business-related travel. Themost of our employees. We believe the effects of these orders and our work-from-home and travel policies may negativelyhave thus far had a limited impact productivity, disrupton our business, delay or disrupt Akcea’sbusiness.

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These public health directives and orders have also impacted our and our partners’ sales efforts. For example, some physician and hospital policies that have been put in place as a result of the COVID-19 Pandemic restrict in-person access by third parties, which has in some cases impacted our commercialization efforts for TEGSEDI and WAYLIVRA, and our clinical programs and timelines,WAYLIVRA. Additionally, Biogen has reported that as a result of the magnitude of which will depend,COVID-19 Pandemic, SPINRAZA sales revenues have decreased in part onbecause SPINRAZA doses have been delayed due, directly or indirectly, to the lengthCOVID-19 Pandemic, and severity of the restrictions and other limitations on our ability to conduct our business in the ordinary course.that future SPINRAZA sales revenues may be adversely affected by continued dosing delays. These and similar, and perhaps more severe, disruptions in our or our partner’s commercial operations could negativelymaterially impact our business, operating results and financial condition.condition in the future.

Quarantines, shelter-in-place, executive and similar government orders, or the perception that such orders, shutdowns or other restrictions on the conduct of business operations could occur, related to COVID-19 or other infectious diseases could impact personnel at third-party manufacturing facilities in the U.S. and other countries, or the availability or cost of materials, which would disrupt our supply chain.In addition, the commercialization efforts for TEGSEDI and WAYLIVRA by Akcea’s field force may be affected by the COVID-19 Pandemic as a result of physician and hospital policies that restrict in-person access to third parties.

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Our clinical trials may also be affected by the COVID-19 Pandemic. Although we are movingWe have experienced impacts to remote clinical site initiation and training via teleconferencing, videoconferencing and webcasts, clinical site initiation and patient enrollment may be delayed due to prioritization of hospital resources toward the COVID-19 Pandemic. Additionally, while we are utilizing home health care where possible, some patients may not be able to comply with clinical trial protocols if quarantines impede patient movement or interrupt healthcare services. Similarly, our inability to recruit and retain patients and principal investigators and site staff who, as healthcare providers, may have heightened exposure to COVID-19, may adversely impact our clinical trial operations. For example, in March 2020, Akcea instituted a temporary suspensionoperations due to the COVID-19 Pandemic; however, we believe such impacts are limited and manageable. Some examples of enrollment for new subjects in its Phase 3 studies of AKCEA-TTR-LRx based on advice from Akcea’s trial advisory committee; however, enrollment has resumed as sites have come back online as local these impacts include:

we have experienced some impact on clinical site initiation and patient enrollment due to restrictions imposed as a result of the COVID-19 Pandemic;
o
For example, in March 2020, we instituted a temporary suspension of enrollment for new subjects in our Phase 3 studies of IONIS-TTR-LRx based on advice from our trial advisory committee; however, enrollment has resumed.
some patients have not been able to meet protocol requirements, as quarantines have impeded patient movement and interrupted healthcare services;
we have experienced some delays in site initiations due to principle investigators and site staff focusing on
and regional restrictions have eased. Additionally, there may delays in necessary interactions with regulators, ethics committeesprioritizing COVID-19 patient care; and other
we have experienced some delays in necessary interactions with regulators, ethics committees and other
important agencies and contractors due to limitations in employee resources or forced furlough of
government or contractor personnel.

The spread of COVID-19 has caused a broad impact globally. While the potential economic impact brought by, and the duration of, the COVID-19 Pandemic may be difficult to assess or predict, it could result in significant disruption of global financial markets, reducing our ability to access capital, which could in the future negatively affect our liquidity. In addition, a recession or market correction resulting from the spread of COVID-19 could materially affect our business and has and could continue to affect the value of our securities.

The global COVID-19 Pandemic continues to rapidly evolve. TheWhile we have not yet experienced material adverse effects to our business as a result of the COVID-19 Pandemic, the ultimate impact of the COVID-19 Pandemic or a similar health epidemic is highly uncertain and subject to change. WeAs such, we do not yet know the full extent of potential delays or impacts on our business, our clinical trials, healthcare systems or the global economy as a whole. However, these effects could have a material impact on our operations, and we will continue to monitor the COVID-19 Pandemic closely.

Risks AssociatedRelated to the Commercialization of our Medicines

We have limited experience as a company in commercializing medicines, and we may have to invest significant resources to develop these capabilities. If we are unable to establish effective marketing, sales and distribution capabilities or enter into agreements with third parties to market, sell and distribute our Ionis Core and Akcea Therapeutics Businessesmedicines, we may not be able to generate revenue from our medicines.

We have limited experience as a company in the marketing, sale and distribution of pharmaceutical products and there are significant risks involved in building and managing a sales organization, including our ability to hire, retain and incentivize qualified individuals, generate sufficient sales leads, provide adequate training to sales and marketing personnel and effectively manage a geographically dispersed sales and marketing team. Any failure to effectively manage our internal sales, marketing and distribution capabilities would adversely impact the commercialization of our medicines. In addition, we may not be able to enter into collaborations or hire consultants or external service providers to assist us in sales, marketing and distribution functions on acceptable financial terms, or at all. Even if we are able to engage third parties to market, sell and distribute our medicines, our product revenues and profitability may be lower if we rely on such third parties for these functions than if we were to perform them on our own. We also will likely have little control over such third parties, and any of them may fail to devote the necessary resources and attention to market, sell and distribute our medicines effectively. If we are not successful in commercializing our medicines, either on our own or through arrangements with one or more third parties, we may not be able to generate revenue from our medicines.

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If the market does not accept our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, we are not likely to generate substantial revenues or become consistently profitable.*

Even if our medicines are authorized for marketing, including SPINRAZA, TEGSEDI and WAYLIVRA, our success will depend upon the medical community, patients and third-party payers accepting our medicines as medically useful, cost-effective, safe and convenient. Even when the FDA or foreign regulatory authorities authorize our or our partners’ medicines for commercialization, doctors may not prescribe our medicines to treat patients. WeFurthermore, we and our partners may not successfully commercialize additional medicines.

Additionally, in many of the markets where we or our partners may sell our medicines in the future, if we or our partners cannot agree with the government or other third-party payers regarding the price we can charge for our medicines, then we may not be able to sell our medicines in that market. Similarly, cost control initiatives by governments or third-party payers could decrease the price received for our medicines or increase patient coinsurance to a level that makes our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, economically unviable.

The degree of market acceptance for our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, depends upon a number of factors, including the:

receipt and scope of marketing authorizations;
establishment and demonstration in the medical and patient community of the efficacy and safety of our medicines and their potential advantages over competing products;
cost and effectiveness of our medicines compared to other available therapies;
patient convenience of the dosing regimen for our medicines; and
reimbursement policies of government and third-party payers.

Based on the profile of our medicines, physicians, patients, patient advocates, payers or the medical community in general may not accept or use any medicines that we may develop.

For example, the product label for TEGSEDI in the U.S. has a boxed warning for thrombocytopenia and glomerulonephritis, requires periodic blood and urine monitoring, and TEGSEDI is only available through a Risk Evaluation and Mitigation Strategy, or REMS, program. Our main competition in the U.S. market for TEGSEDI is ONPATTRO (patisiran),patisiran, marketed by Alnylam Pharmaceuticals, Inc. Although ONPATTROpatisiran requires intravenous administration and pre-treatment with steroids, it does not have a boxed warning or REMS. Additionally, the product label for WAYLIVRA in the E.U.EU requires regular blood monitoring. In each case, these label requirements could negatively affect our ability to attract and retain patients for these medicines. We believe that the enhanced monitoring we have implemented to support early detection and management of these issues can help manage thesemitigate safety issues so that patients can continue treatment. Since implementation of the enhanced monitoring, serious platelet events have been infrequent. While we believe we and Akcea can better maintain patients on TEGSEDI and WAYLIVRA through our patient-centric commercial approach where we or our partner plan to have greater involvement with physicians and patients, if we or our partner cannot effectively maintain patients on TEGSEDI or WAYLIVRA, including due to limitations or restrictions on ourthe ability to conduct periodic blood and urine monitoring of our patients as a result of the current COVID-19 Pandemic, we may not be able to generate substantial revenue from TEGSEDI or WAYLIVRA sales.

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If we or our partners fail to compete effectively, our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, will not contribute significant revenues.*

Our competitors engage in drug discovery throughout the world, are numerous, and include, among others, major pharmaceutical companies and specialized biopharmaceutical firms. Other companies engageare engaged in developing antisense technology. Our competitors may succeed in developing medicines that are:

priced lower than our medicines;
reimbursed more favorably by government and other third-party payers than our medicines;
safer than our medicines;
more effective than our medicines; or
more convenient to use than our medicines.

These competitive developments could make our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, obsolete or non-competitive.

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Certain of our partners are pursuing other technologies or developing other medicines either on their own or in collaboration with others, including our competitors, to treat the same diseases our own collaborative programs target. Competition may negatively impact a partner’s focus on and commitment to our medicines and, as a result, could delay or otherwise negatively affect the commercialization of our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA.

Many of our competitors have substantially greater financial, technical and human resources than we do. In addition, many of these competitors have significantly greater experience than we do in conducting preclinical testing and human clinical studies of new pharmaceutical products, in obtaining FDA and other regulatory authorizations of such products and in commercializing such products. Accordingly, our competitors may succeed in obtaining regulatory authorization for products earlier than we do. Marketing and sales capability is another factor relevant to the competitive position of our medicines, and we will primarily rely on our partners and Akcea to provide this capability.

There are several pharmaceutical and biotechnology companies engaged in the development or commercialization in certain geographic markets of products against targets that are also targets of products in our development pipeline. For example:

ZOLGENSMA couldOnasemnogene abeparvovec and risdiplam compete with SPINRAZA;
ONPATTRO, VYNDAQELPatisiran, tafamidis and VYNDAMAX, AG10 and vutrisiran couldtafamidis meglumine compete with TEGSEDI;
Vutrisiran and acoramidis could compete with TEGSEDI and IONIS-TTR-LRx;
ARO-APOC3, Myaleptlomitapide and gemcabene could compete with WAYLIVRA;WAYLIVRA and IONIS-APOCIII-LRx; and
WVE-120101/WVE-120102, Selistat and VX15 could compete with tominersen;
Arimoclomol, ultomiris, mastinib and trehalose could compete with tofersen;tofersen and ION363.

Specifically, SPINRAZA faces competition from onasemnogene abeparvovec, a new gene therapy product that was approved in the U.S. in May 2019 and in the EU in May 2020 for the treatment of SMA, as well as risdiplam, a new oral product for the treatment of SMA that was approved in the U.S. in August 2020. Biogen has disclosed that SPINRAZA revenue has decreased due in part to lower sales volumes as a result of increased competition and that future sales of SPINRAZA may be adversely affected by the commercialization of competing products. SPINRAZA injection for intrathecal use is an antisense medicine indicated for the treatment of SMA patients of all ages approved in over 50 countries.
ONPATTRO, VYNDAQEL and VYNDAMAX, vutrisiran and AG10 could complete with AKCEA-TTR-LRx;.

Additionally, companies that are developing medicines that target the same patient populations as our medicines in development may compete with us to enroll participants in the clinical trials for such medicines, which could make it more difficult for us to complete enrollment for these clinical trials.

Certain of our medicines may compete with our other medicines, which could reduce our expected revenues.

Certain of our medicines inhibit the production of the same protein. For example, WAYLIVRA inhibits the production of the same protein as AKCEA-APOCIII-LIONIS-APOCIII-LRx and TEGSEDI inhibits the production of the same protein as AKCEA-TTR-LIONIS-TTR-LRx. We believe the enhancements we incorporated into AKCEA-APOCIII-LIONIS-APOCIII-LRx and AKCEA-TTR-LIONIS-TTR-LRx can provide greater patient convenience by allowing for significantly lower doses and less frequent administration compared to WAYLIVRA and TEGSEDI, respectively. As such, to the extent physicians and patients elect to use AKCEA-APOCIII-LIONIS-APOCIII-LRx or AKCEA-TTR-LIONIS-TTR-LRx instead of WAYLIVRA or TEGSEDI, respectively, it will reduce the revenue we derive from those medicines. In addition, while vupanorsen, AKCEA-APOCIII-LIONIS-APOCIII-LRx and WAYLIVRA use different mechanisms of action, if vupanorsen and IONIS-APOCIII- LRxcan effectively lower triglyceride levels in patients, including patients with FCS, patients, it may likewise reduce the revenue we derive from WAYLIVRA, vupanorsen and AKCEA-APOCIII-LIONIS-APOCIII-LRx. may compete with each other.

Our medicines could be subject to regulatory limitations following approval.*

Following approval of a medicine, we and our partners must comply with comprehensive government regulations regarding the manufacture, marketing and distribution of medicines. Promotional communications regarding prescription medicines must be consistent with the information in the product’s approved labeling. We or our partners may not obtain the labeling claims necessary or desirable to successfully commercialize our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development.

The FDA and foreign regulatory bodies have the authority to impose significant restrictions on an approved medicine through the product label and on advertising, promotional and distribution activities. For example:

in the U.S., TEGSEDI’s label contains a boxed warning for thrombocytopenia and glomerulonephritis;
TEGSEDI requires periodic blood and urine monitoring; and
in the U.S., TEGSEDI is available only through a Risk Evaluation and Mitigation Strategy, or REMS program; andprogram.
we expect WAYLIVRA will require periodic blood monitoring if approved in the U.S.

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Prescription medicines may be promoted only for the approved indications in accordance with the approved label. The FDA and other agencies actively enforce the laws and regulations prohibiting the promotion of off-label uses, and a company that is found to have improperly promoted off-label may be subject to significant liability.

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In addition, when approved, the FDA or a foreign regulatory authority may condition approval on the performance of post-approval clinical studies or patient monitoring, which could be time consuming and expensive. For example, in connection with the conditional marketing approval for WAYLIVRA in the E.U.,EU, we are required to conduct a post-authorization safety study to evaluate the safety of WAYLIVRA on thrombocytopenia and bleeding in FCS patients taking WAYLIVRA. If the results of such post-marketing studies are not satisfactory, the FDA, EC or other foreign regulatory authority may withdraw marketing authorization or may condition continued marketing on commitments from us or our partners that may be expensive and time consuming to fulfill.

If we or others identify side effects after any of our medicines are on the market, or if manufacturing problems occur subsequent to regulatory approval, or if we, our manufacturers or our partners fail to comply with regulatory requirements, we or our partners may, among other things, lose regulatory approval and be forced to withdraw products from the market, need to conduct additional clinical studies, incur restrictions on the marketing, distribution or manufacturing of the product, and/or change the labeling of our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA.

We depend on our collaboration with Biogen for the development and commercialization of SPINRAZA.

We have entered into a collaborative arrangement with Biogen to develop and commercialize SPINRAZA. We entered into this collaboration primarily to:

fund our development activities for SPINRAZA;
seek and obtain regulatory approvals for SPINRAZA; and
successfully commercialize SPINRAZA.

We are relying on Biogen to obtain additional regulatory approvals for SPINRAZA, manufacture and successfully commercialize SPINRAZA. In general, we cannot control the amount and timing of resources that Biogen devotes to our collaboration. If Biogen fails to further develop SPINRAZA, obtain additional regulatory approvals for SPINRAZA, manufacture or commercialize SPINRAZA, or if Biogen’s efforts are not effective, our business may be negatively affected.

Our collaboration with Biogen may not continue for various reasons. Biogen can terminate our collaboration at any time. If Biogen stops developing or commercializing SPINRAZA, we would have to seek or spend additional funding, and SPINRAZA’s commercialization may be harmed or delayed.

Our collaboration with Biogen may not result in the continued successful commercialization of SPINRAZA. If Biogen does not continue to successfully commercialize SPINRAZA, we will receive limited revenues for SPINRAZA.

If Akcea cannot optimizeWe are relying on third parties to market, sell and maintain effective marketingdistribute TEGSEDI and sales capabilities or enterWAYLIVRA.*

We have entered into agreements with third parties to market and sell TEGSEDI and WAYLIVRA, we may not generate significant product revenue from TEGSEDI or WAYLIVRA.*

To successfully commercialize TEGSEDI and WAYLIVRA Akcea must effectively manage its marketing, sales and distribution capabilities or make arrangements with third parties to perform these services. Akcea may not be successful in doing so. To commercialize WAYLIVRA in the initial indications Akcea is pursuing and to continue the commercialization of TEGSEDI, Akcea will need to optimize and maintain specialty sales forces in the global regions where it currently markets or expects to market TEGSEDI and WAYLIVRA, supported by case managers, reimbursement specialists, partnerships with specialty pharmacies, injection training, routine blood and urine monitoring and a medical affairs team.as follows:

Even though certain members of Akcea’s management team and other employees have experience commercializing medicines, as a company Akcea has limited experience marketing, selling and distributing medicines, and there are significant risks involved in building, tailoring, optimizing and managing a commercial infrastructure. Since September 2019, Akcea has announced several changes to its senior leadership team, including the departure of its Chief Executive Officer, its President, and its Chief Operating Officer and the recent resignation of its Chief Financial Officer, whose resignation became effective on April 1, 2020, and the appointment of a new Chief Executive Officer, a new Chief Commercial Officer, a new Chief Operating Officer and a new General Counsel. The effectiveness of the senior leadership team following these transitions, new leaders as they fill in these roles, and any further transition as a result of these changes could impair Akcea’s ability to manage its business.
In April 2021, we entered into a distribution agreement with Sobi to commercialize TEGSEDI in the U.S. and Canada;
In December 2020, we entered into a distribution agreement with Sobi to commercialize TEGSEDI and WAYLIVRA in Europe; and
In August 2018, we granted PTC the exclusive right to commercialize TEGSEDI and WAYLIVRA in Latin America and certain Caribbean countries.

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It is expensiveWe are relying on Sobi and time consuming for AkceaPTC to maintain its own sales forceseffectively market, sell and related compliance protocols to marketdistribute TEGSEDI and WAYLIVRA and it will be increasingly expensivehave less control over sales efforts and time consuming when Akcea commercially launches additional medicines, if approved. Akcea may never successfully optimize or manage this capability and any failure could harm the commercial launch of WAYLIVRA or adversely affect TEGSEDI sales. Additionally, Akcea and its partners, if any, will have to compete with other companies to recruit, hire, train, manage and retain marketing and sales personnel. As a result of Akcea’s receipt of a CRL from the FDA regarding the new drug application for WAYLIVRA, on September 6, 2018, Akcea enacted a plan to reorganize its workforce to better align with the immediate needs of the business. In connection with this reorganization plan, Akcea reduced its workforce by approximately 12% and will need to increase its operations and expand its use of third -party contractors if WAYLIVRA is approved in the U.S.

Akcea has incurred expenses launching, optimizing and managing the marketing and sales infrastructure for TEGSEDI in the E.U., Canada and the U.S., and WAYLIVRA in the E.U. If regulatory requirements or other factors cause the commercialization of TEGSEDI or WAYLIVRA to be less successful than expected in important markets, Akcea would incur additional expenses for having invested in these capabilities prior to realizing any significant revenue from sales of TEGSEDI or WAYLIVRA. Akcea’s sales force and marketing teams may not successfully commercialize TEGSEDI or WAYLIVRA.

To the extent we and Akcea decide to rely on third parties to commercialize TEGSEDI or WAYLIVRA in a particular geographic market, we may receive less revenue than if Akceawe commercialized TEGSEDI or WAYLIVRA by itself. For example, in August 2018, Akcea granted PTC Therapeutics International Limited,ourselves. If Sobi or PTC Therapeutics, the exclusive right to commercialize TEGSEDI and WAYLIVRA in Latin America and certain Caribbean countries, and Akcea will continue to rely on PTC Therapeutics to commercialize TEGSEDI and WAYLIVRA in those geographic markets. If PTC Therapeutics does not successfully commercialize TEGSEDI or WAYLIVRA, including as a result of delays or disruption caused by the current COVID-19 Pandemic, that may affect PTC Therapeutics’ ability to commercialize TEGSEDI or WAYLIVRA, and Akceawe may receive limited revenue for TEGSEDI or no revenue for WAYLIVRA in the U.S., Canada, Europe, Latin America or certain Caribbean countries. In addition, in August 2018 Akcea entered into an agreement with Accredo Health Group, Inc., or Accredo, a subsidiary of Express Scripts, to be Akcea’s specialty pharmacy partner for distribution of TEGSEDI in the U.S. Further, Akcea has less control over the sales efforts of other third parties, including PTC Therapeutics and Accredo, involved in commercializing TEGSEDI or WAYLIVRA.

If Akcea cannot effectively build and manage its distribution, medical affairs, market access, marketing and sales infrastructure, or find a suitable third party to perform such functions, the sales of TEGSEDI and WAYLIVRA may be adversely affected. Any such events may result in decreased sales and lower revenue,countries, which could have a material adverse effect on our business, prospects, financial condition and results of operations.

Our operations are subject to additional healthcare laws.

Our operations are subject to additional healthcare laws, including federal and state anti-kickback laws, false claims laws, transparency laws, such as the federal Sunshine Act, and health information privacy and security laws. Efforts to ensure that our operations comply with applicable healthcare laws and regulations involve substantial costs. It is possible that governmental authorities will conclude that our business practices may not comply with current or future statutes, regulations or case law involving applicable fraud and abuse or other healthcare laws and regulations. Penalties for violations of applicable healthcare laws and regulations may include significant civil, criminal and administrative penalties, damages, disgorgement, fines, imprisonment, exclusion of products from government funded healthcare programs, such as Medicare and Medicaid, and additional reporting requirements and oversight if we enter into a corporate integrity agreement or similar agreement to resolve allegations of non-compliance with these laws. In addition, violations may also result in response to the public health directivesreputational harm, diminished profits and orders related to the COVID-19 Pandemic, Akcea implemented work-from-home policies for its employees globally and suspended business-related travel. The effects of the government orders and Akcea’s work-from-home and travel policies in response to the COVID-19 Pandemic have thus far had a limited impact on Akcea’s productivity, business and commercialization efforts for TEGSEDI and WAYLIVRA, but the effects of these orders and policies may become more significant in the future.future earnings.

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If government or other third-party payers fail to provide adequate coverage and payment rates for our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, our revenue will be limited.*

In both domestic and foreign markets, sales of our current and future products will depend in part upon the availability of coverage and reimbursement from third-party payers. The majority of patients in the U.S. who would fit within our target patient populations for our medicines have their healthcare supported by a combination of Medicare coverage, other government health programs such as Medicaid, managed care providers, private health insurers and other organizations. Coverage decisions may depend upon clinical and economic standards that disfavor new medicines when more established or lower cost therapeutic alternatives are already available or subsequently become available. Assuming coverage is approved, the resulting reimbursement payment rates might not be enough to make our medicines affordable. Accordingly, SPINRAZA, TEGSEDI and WAYLIVRA for FCS in the E.U. and, if approved, WAYLIVRA in the U.S. or Canada and for additional indications,EU, and our medicines in development, will face competition from other therapies and medicines for limited financial resources. We or our partners may need to conduct post-marketing studies to demonstrate the cost-effectiveness of any future products to satisfy third-party payers. These studies might require us to commit a significant amount of management time and financial and other resources. Third-party payers may never consider our future products as cost-effective. Adequate third-party coverage and reimbursement might not be available to enable us to maintain price levels sufficient to realize an appropriate return on investment in product development.

Third-party payers, whether foreign or domestic, or governmental or commercial, are developing increasingly sophisticated methods of controlling healthcare costs. In addition, in the U.S., no uniform policy of coverage and reimbursement for medicines exists among third-party payers. Therefore, coverage and reimbursement for medicines can differ significantly from payer to payer. For example, the Patient Protection and Affordable Care Act, as amended by the Health Care and Education Reconciliation Act of 2010, or collectively, the PPACA,Affordable Care Act, was passed in March 2010, and substantially changed the way healthcare is financed by both governmental and private insurers, and continues to significantly impact the U.S. pharmaceutical industry. There remain judicial and Congressional challenges to certain aspects of the Affordable Care Act, as well as efforts by the Trump administration to repeal or replace certain aspects of the Affordable Care Act. On December 18, 2019, the U.S. Court of Appeals for the 5th Circuit upheld the District Court ruling that the individual mandate was unconstitutional and remanded the case back to the District Court to determine whether the remaining provisions of the Affordable Care Act are invalid as well. However, in March 2020, before the District Court could rule on the remaining provisions of the Affordable Care Act, the U.S. Supreme Court agreed to review the case. In November 2020, the U.S. Supreme Court heard oral arguments and is expected to rule on the case in its current session, which began in October 2020. Although the U.S. Supreme Court has not yet ruled on the constitutionality of the Affordable Care Act, on January 28, 2021, President Biden issued an executive order to initiate a special enrollment period from February 15, 2021 through May 15, 2021 for purposes of obtaining health insurance coverage through the Affordable Care Act marketplace. It is unclear how this decision, future decisions, subsequent appeals,the Supreme Court ruling, or other such litigation and other efforts to repeal and replace the Affordable Care Acthealthcare reform measures, will impact the Affordable Care Act and our business.

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Further, we believe that future coverage and reimbursement will likely be subject to increased restrictions both in the U.S. and in international markets. For example, in the U.S., recent health reform measures have resulted in reductions in Medicare and other healthcare funding, and there have been several recent U.S. Congressional inquiries and legislation designed to, among other things, reform government program reimbursement methodologies for medicines and bring more transparency to drug pricing. At the federal level, the Trump administration’s budgetSuch restrictions may include legislative proposals seeking to reduce drug prices (e.g., by placing limits on pharmaceutical price increases and tying Medicare Part B drug prices to international drug prices), increase competition (e.g., by allowing for fiscal year 2020 contains furtherpersonal importation of drugs from Canada), lower out-of-pocket drug price control measures that could be enacted during the budget process or in other future legislation, including,costs for example, measures to permitpatients (e.g., by capping Medicare Part D plansbeneficiary out-of-pocket pharmacy expenses) and increase patient access to negotiatelower-cost generic and biosimilar drugs. In November 2020, the price of certain medicines under Medicare Part B, to allow some states to negotiate prices under Medicaid, and to eliminate cost sharing for generic medicines for low-income patients. Further, the Trump administration released a “Blueprint” to lower medicine prices and reduce out of pocket costs of medicines that contains additional proposals to increase drug manufacturer competition, increase the negotiating power of certain federal healthcare programs, incentivize manufacturers to lower the list price of their products, and reduce the out of pocket costs of medicines paid by consumers. TheU.S. Department of Health and Human Services has solicited feedback on some of these measuresissued a final rule modifying the anti-kickback law safe harbors for plans, pharmacies, and at the same time, has implemented others under its existing authority. While some of these and other measures may require additional authorization to become effective, Congress and the Trump administration have each indicated that it will continue to seek new legislative and administrative measures to control drug costs.pharmaceutical benefit managers. At the state level, legislatures have increasingly passed legislation and implemented regulations designed to control pharmaceutical and biological product pricing, including price or patient reimbursement constraints, discounts, restrictions on certain product access and marketing cost disclosure and transparency measures, and, in some cases, designed to encourage importation from other countries and bulk purchasing. Third-party coverage and reimbursement for medicines may not be available or adequate in either the U.S. or international markets, and third-party payers, whether foreign or domestic, or governmental or commercial, may allocate their resources to address the current COVID-19 Pandemic or experience delays or disruptions in their ability to devote resources to coverage and reimbursement matters related to our products or medicines as a result of the COVID-19 Pandemic, which would negatively affect the potential commercial success of our products, our revenue and our profits.

If Biogenwe cannot manufacture finishedour medicines or contract with a third party to manufacture our medicines at costs that allow us to charge competitive prices to buyers, we cannot market our products profitably.

To successfully commercialize any of our medicines, we would need to optimize and manage large-scale commercial manufacturing capabilities either on a standalone basis or through a third-party manufacturer. We rely on third-party manufacturers to supply the drug substance and drug product for SPINRAZATEGSEDI and drug product for WAYLIVRA. Any delays or the post-launchdisruption to our own or third-party commercial manufacturing capabilities, including any interruption to our supply chain as a result of the active drug substance for SPINRAZA, SPINRAZA may not maintaincurrent COVID-19 Pandemic, could limit the commercial success.success of our medicines.

Biogen is responsible
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In addition, as our drug development pipeline increases and matures, we will have a greater need for clinical trial and commercial manufacturing capacity. We have limited experience manufacturing pharmaceutical products of the chemical class represented by our medicines, called oligonucleotides, on a commercial scale for the long-term supplysystemic administration of both SPINRAZAa medicine. There are a small number of suppliers for certain capital equipment and raw materials that we use to manufacture our medicines, and some of these suppliers will need to increase their scale of production to meet our projected needs for commercial manufacturing. Further, we must continue to improve our manufacturing processes to allow us to reduce our drug substance and finished drug product. Biogencosts. We or our partners may not be able to reliably manufacture SPINRAZA drug substanceour medicines at a cost or in quantities necessary to make commercially successful products.

Also, manufacturers, including us, must adhere to the FDA’s cGMP regulations and drug product to supportsimilar regulations in foreign countries, which the long-term commercialization of SPINRAZA. If Biogen cannot reliably manufacture SPINRAZA drug substanceapplicable regulatory authorities enforce through facilities inspection programs. We, our partners and drug product, SPINRAZAour contract manufacturers may not comply or maintain compliance with cGMP, or similar foreign regulations. Non-compliance could significantly delay or prevent receipt of marketing authorizations for our medicines, including authorizations for SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, or result in enforcement action after authorization that could limit the commercial success which will harmof our abilitymedicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development.

Risks Related to generate revenue.the Development and Regulatory Approval of our Medicines

If we or our partners fail to obtain regulatory approval for our medicines and additional approvals for SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, we or our partners cannot sell them in the applicable markets.

We cannot guarantee that any of our medicines will be considered safe and effective or will be approved for commercialization. In addition, it is possible that SPINRAZA, TEGSEDI and WAYLIVRA may not be approved in additional markets or for additional indications. We and our partners must conduct time-consuming, extensive and costly clinical studies to demonstrate the safety and efficacy of each of our medicines before they can be approved or receive additional approvals for sale. We and our partners must conduct these studies in compliance with FDA regulations and with comparable regulations in other countries.

We and our partners may not obtain necessary regulatory approvals on a timely basis, if at all, for our medicines. It is possible that regulatory agencies will not approve our medicines for marketing or SPINRAZA, TEGSEDI or WAYLIVRA in additional markets or for additional indications. If the FDA or another regulatory agency believes that we or our partners have not sufficiently demonstrated the safety or efficacy of any of our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, or our medicines in development, the agency will not approve the specific medicine or will require additional studies, which can be time consuming and expensive and which will delay or harm commercialization of the medicine. For example, in August 2018 Akceawe received a CRLcomplete response letter from the FDA regarding the new drug application for WAYLIVRA in which the FDA determined that the safety concerns identified with WAYLIVRA in Akcea’sour clinical development program outweighed the expected benefits of triglyceride lowering in patients with FCS. AkceaWe also received a Non-W from Health Canada for WAYLIVRA in November 2018. We and Akcea are engaged with the FDA and plan to work with Health Canada to confirm a path forward for WAYLIVRA.

The FDA or other comparable foreign regulatory authorities can delay, limit or deny approval of a medicine for many reasons, including:

such authorities may disagree with the design or implementation of our clinical studies;
we or our partners may be unable to demonstrate to the satisfaction of the FDA or other regulatory authorities that a medicine is safe and effective for any indication;
such authorities may not accept clinical data from studies conducted at clinical facilities that have deficient clinical practices or that are in countries where the standard of care is potentially different from the U.S.;
we or our partners may be unable to demonstrate that our medicine'smedicine’s clinical and other benefits outweigh its safety risks to support approval;
such authorities may disagree with the interpretation of data from preclinical or clinical studies;
such authorities may find deficiencies in the manufacturing processes or facilities of third-party manufacturers who manufacture clinical and commercial supplies for our medicines;medicines, or may delay the inspection of such facilities due to restrictions related to the COVID-19 Pandemic; and
the approval policies or regulations of such authorities or their prior guidance to us or our partners during clinical development may significantly change in a manner rendering our clinical data insufficient for approval.

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Failure to receive marketing authorization for our medicines, or failure to receive additional marketing authorizations for SPINRAZA, TEGSEDI or WAYLIVRA, and our medicines in development, or delays in these authorizations could prevent or delay commercial introduction of the medicine, and, as a result, could negatively impact our ability to generate revenue from product sales.

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If the results of clinical testing indicate that any of our medicines are not suitable for commercial use, we may need to abandon one or more of our drug development programs.*

Drug discovery and development has inherent risks and the historical failure rate for drugs is high. Antisense medicines are a relatively new approach to therapeutics. If we cannot demonstrate that our medicines are safe and effective for human use in the intended indication, we may need to abandon one or more of our drug development programs.

In the past, we have invested in clinical studies of medicines that have not met the primary clinical end points in their Phase 3 studies.studies or have been discontinued for other reasons. For example, in March 2021, Roche decided to discontinue dosing in the Phase 3 GENERATION HD1 study of tominersen in patients with manifest Huntington’s disease based on the results of a pre-planned review of data from the Phase 3 study conducted by an unblinded Independent Data Monitoring Committee. Similar results could occur in clinical studies for our other medicines, including the studies of tominersen, tofersen, AKCEA-APO(a)-Lpelacarsen, IONIS-TTR-LRx, IONIS-APOCIII-LRx and AKCEA-TTR-LRx.ION363. If any of our medicines in clinical studies, including tominersen, tofersen, AKCEA-APO(a)-Lpelacarsen, IONIS-TTR-LRx, IONIS-APOCIII-LRx and AKCEA-TTR-LRx,ION363, do not show sufficient efficacy in patients with the targeted indication, or if such studies are discontinued for any other reason, it could negatively impact our development and commercialization goals for these medicines and our stock price could decline.

Even if our medicines are successful in preclinical and human clinical studies, the medicines may not be successful in late-stage clinical studies.*

Successful results in preclinical or initial human clinical studies, including the Phase 2 results for some of our medicines in development, may not predict the results of subsequent clinical studies, including the studies of tominersentofersen, pelacarsen, IONIS-TTR-L,Rx, tofersen, AKCEA-APO(a)-LIONIS-APOCIII-LRx and AKCEA-TTR-LRx.ION363. For example, in March 2021, Roche decided to discontinue dosing in the Phase 3 GENERATION HD1 study of tominersen in patients with manifest Huntington’s disease based on the results of a pre-planned review of data from the Phase 3 study conducted by an unblinded Independent Data Monitoring Committee. There are a number of factors that could cause a clinical study to fail or be delayed, including:

the clinical study may produce negative or inconclusive results;
regulators may require that we hold, suspend or terminate clinical research for noncompliance with regulatory requirements;
we, our partners, the FDA or foreign regulatory authorities could suspend or terminate a clinical study due to adverse side effects of a medicine on subjects or lack of efficacy in the trial;
we, or our partners, may decide, or regulators may require us, to conduct additional preclinical testing or clinical studies;
enrollment in our clinical studies may be slower than we anticipate;
we or our partners, including our independent clinical investigators, contract research organizations and other third-party service providers on which we rely, may not identify, recruit and train suitable clinical investigators at a sufficient number of study sites or timely enroll a sufficient number of study subjects in the clinical study;
the institutional review board for a prospective site might withhold or delay its approval for the study;
enrollment in our clinical studies may be slower than we anticipate;
people who enroll in the clinical study may later drop out due to adverse events, a perception they are not benefiting from participating in the study, fatigue with the clinical study process or personal issues;
a clinical study site may deviate from the protocol for the study;
the cost of our clinical studies may be greater than we anticipate;
our partners may decide not to exercise any existing options to license and conduct additional clinical studies for our medicines; and
the supply or quality of our medicines or other materials necessary to conduct our clinical studies may be insufficient, inadequate or delayed.

The current COVID-19 Pandemic could make some of these factors more likely to occur.

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In addition, our current medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, are chemically similar to each other. As a result, a safety observation we encounter with one of our medicines could have, or be perceived by a regulatory authority to have, an impact on a different medicine we are developing. This could cause the FDA and other regulators to ask questions or take actions that could harm or delay our ability to develop and commercialize our medicines or increase our costs. For example, the FDA or other regulatory agencies could request, among other things, any of the following regarding one of our medicines: additional information or commitments before we can start or continue a clinical study, protocol amendments, increased safety monitoring, additional product labeling information, and post-approval commitments. This happened in connection with the conditional marketing approval for WAYLIVRA in the E.U.,EU, as the EC is requiring Akceaus to conduct a post-authorization safety study to evaluate the safety of WAYLIVRA on thrombocytopenia and bleeding in FCS patients taking WAYLIVRA. Akcea hasWe have an ongoing OLE extension study of WAYLIVRA in patients with FCS and an OLE study of TEGSEDI in patients with hATTR, and an early access program, or EAP, for both WAYLIVRA and TEGSEDI.WAYLIVRA. Adverse events or results from these studies or the EAPs could negatively impact Akcea’sour pending or future marketing approval applications for WAYLIVRA and TEGSEDI in patients with FCS or hATTR amyloidosis or the commercial opportunity for WAYLIVRA or TEGSEDI.

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Any failure or delay in the clinical studies, including the studies of tominersen, tofersen, AKCEA-APO(a)-Lpelacarsen, IONIS-TTR-LRx, IONIS-APOCIII-LRx and AKCEA-TTR-LRx,ION363, could reduce the commercial potential or viability of our medicines.

If we cannot manufacture our medicines or contract with a third party to manufacture our medicines at costs that allow us to charge competitive prices to buyers, we cannot market our products profitably.*

To successfully commercialize any of our medicines, we or our partner would need to optimize and manage large-scale commercial manufacturing capabilities either on our own or through a third-party manufacturer. We and Akcea rely on third-party manufacturers to supply the drug substance and drug product for TEGSEDI and WAYLIVRA. Any delays or disruption to our own or third-party commercial manufacturing capabilities, including any interruption to our supply chain as a result of the current COVID-19 Pandemic, could limit the commercial success of our medicines.

In addition, as our drug development pipeline increases and matures, we will have a greater need for clinical trial and commercial manufacturing capacity. We have limited experience manufacturing pharmaceutical products of the chemical class represented by our medicines, called oligonucleotides, on a commercial scale for the systemic administration of a medicine. There are a small number of suppliers for certain capital equipment and raw materials that we use to manufacture our medicines, and some of these suppliers will need to increase their scale of production to meet our projected needs for commercial manufacturing. Further, we must continue to improve our manufacturing processes to allow us to reduce our drug costs. We may not be able to manufacture our medicines at a cost or in quantities necessary to make commercially successful products.

Also, manufacturers, including us, must adhere to the FDA’s current Good Manufacturing Practices regulations and similar regulations in foreign countries, which the applicable regulatory authorities enforce through facilities inspection programs. We, our partners and our contract manufacturers may not comply or maintain compliance with Good Manufacturing Practices, or similar foreign regulations. Non-compliance could significantly delay or prevent receipt of marketing authorizations for our medicines, including authorizations for SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development, or result in enforcement action after authorization that could limit the commercial success of our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development.

We depend on third parties to conduct our clinical studies for our medicines and any failure of those parties to fulfill their obligations could adversely affect our development and commercialization plans.*

We depend on independent clinical investigators, contract research organizations and other third-party service providers to conduct our clinical studies for our medicines and expect to continue to do so in the future. For example, we use clinical research organizations, such as Pharmaceutical Research Associates, Inc., Icon Clinical Research Limited, Syneos Health, Inc., PPD and Medpace for the clinical studies for our medicines, including tominersen, tofersen, AKCEA-APO(a)-Lpelacarsen, IONIS-TTR-LRx, IONIS-APOCIII-LRx and AKCEA-TTR-LRx.ION363. We rely heavily on these parties for successful execution of our clinical studies, but do not control many aspects of their activities. For example, the investigators are not our employees. However, we are responsible for ensuring that these third parties conduct each of our clinical studies in accordance with the general investigational plan and approved protocols for the study. Third parties may not complete activities on schedule or may not conduct our clinical studies in accordance with regulatory requirements or our stated protocols. The failure of these third parties to carry out their obligations,, including as a result of delays or disruption caused by the current COVID-19 Pandemic that may affect the third party’s ability to conduct the clinical studies for our medicines, or a termination of our relationship with these third parties could delay or prevent the development, marketing authorization and commercialization of our medicines or additional marketing authorizations for SPINRAZA, TEGSEDI and WAYLIVRA.

Since corporate partnering is a significant part of our strategy to fund the advancement and commercialization of our development programs, if any of our collaborative partners fail to fund our collaborative programs, or if we cannot obtain additional partners, we may have to delay or stop progress on our drug development programs.*

To date, corporate partnering has played a significant role in our strategy to fund our development programs and to add key development resources. We plan to continue to rely on additional collaborative arrangements to develop and commercialize many of our unpartnered medicines. However, we may not be able to negotiate favorable collaborative arrangements for these drug programs. If we cannot continue to secure additional collaborative partners, our revenues could decrease and the development of our medicines could suffer.

Our corporate partners are developing and/or funding many of the medicines in our development pipeline. For example, we are relying on:

Roche for development and funding of tominersen;
Novartis for development and funding of pelacarsen; and
Biogen for development and funding of tofersen.

If any of these pharmaceutical companies stops developing and/or funding these medicines, our business could suffer and we may not have, or be willing to dedicate, the resources available to develop these medicines on our own. Our collaborators can terminate their relationships with us under certain circumstances, many of which are outside of our control. For example, as part of a reprioritization of its pipeline and strategic review of its rare disease business, GSK declined its option to license TEGSEDI and IONIS-FB-LRx.

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Even with funding from corporate partners, if our partners do not effectively perform their obligations under our agreements with them, it would delay or stop the progress of our drug development and commercial programs.

In addition to receiving funding, we enter into collaborative arrangements with third parties to:

conduct clinical studies;
seek and obtain marketing authorizations; and
manufacture, market and sell our medicines.

Once we have secured a collaborative arrangement to further develop and commercialize one of our drug development programs, such as our collaborations with AstraZeneca, Bayer, Biogen, GSK, Janssen, Novartis, Pfizer and Roche, these collaborations may not continue or result in commercialized medicines, or may not progress as quickly as we first anticipated.

For example, a collaborator such as AstraZeneca, Bayer, Biogen, GSK, Janssen, Novartis, Pfizer or Roche, could determine that it is in its financial interest to:

pursue alternative technologies or develop alternative products that may be competitive with the medicine that is part of the collaboration with us;
pursue higher-priority programs or change the focus of its own development programs; or
choose to devote fewer resources to our medicines than it does for its own medicines.

If any of these occur, it could affect our partner’s commitment to the collaboration with us and could delay or otherwise negatively affect the commercialization of our medicines, including SPINRAZA, tominersen, pelacarsen and tofersen.

If we do not progress in our programs as anticipated, the price of our securities could decrease.*

For planning purposes, we estimate and may disclose the timing of a variety of clinical, regulatory and other milestones, such as when we anticipate a certain medicine will enter clinical trials, when we anticipate completing a clinical study, or when we anticipate filing an application for, or obtaining, marketing authorization, or when we or our partners plan to commercially launch a medicine. We base our estimates on present facts and a variety of assumptions, many of which are outside of our control, including the current COVID-19 Pandemic. If we do not achieve milestones in accordance with our or our investors’ or securities analysts’ expectations, including milestones related to SPINRAZA, TEGSEDI, WAYLIVRA, tominersen, tofersen, pelacarsen, IONIS-TTR-LRx, IONIS-APOCIII-LRx and ION363, the price of our securities could decrease.

Risks Associated with our Businesses as a Whole

Risks related to our financial condition and business strategy

We have incurred losses, and our business will suffer if we fail to consistently achieve profitability in the future.

Because drug discovery and development requires substantial lead-time and money prior to commercialization, our expenses have generally exceeded our revenue since we were founded in January 1989. As of March 31, 2020,2021, we had an accumulated deficit of approximately $0.8$1.2 billion and stockholders’ equity of approximately $1.4$0.7 billion. Most of our historical losses resulted from costs incurred in connection with our research and development programs and from selling, general and administrative costs associated with our operations. Most of our income has come from collaborative arrangements, including commercial revenue from royalties and R&D revenue, with additional income from research grants and the sale or licensing of our patents, as well as interest income. If we do not continue to earn substantial revenue, we may incur additional operating losses in the future. We may not successfully develop any additional productsmedicines or achieve or sustain future profitability.

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Our abilityIf we fail to useobtain timely funding, we may need to curtail or abandon some of our net operating loss carryovers and certain other tax attributes may be limited.*programs.

UnderMany of our medicines are undergoing clinical studies or are in the Internal Revenue Codeearly stages of 1986, as amended,research and development. Most of our drug programs will require significant additional research, development, manufacturing, preclinical and clinical testing, marketing authorizations, preclinical activities and commitment of significant additional resources prior to their successful commercialization. These activities will require significant cash. As of March 31, 2021, we had cash, cash equivalents and short-term investments equal to $1.8 billion. If we or our partners do not meet our goals to successfully commercialize our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, or to license certain medicines and proprietary technologies, we will need additional funding in the Code, a corporation is generally allowed a deduction for net operating losses, or NOLs, carried over from a prior taxable year. Under that provision, we can carryforward our NOLs to offset ourfuture. Our future taxable income, if any, until such NOLs are used or expire. The same is true of other unused tax attributes,capital requirements will depend on many factors, such as tax credits.the following:

successful commercialization of SPINRAZA, TEGSEDI and WAYLIVRA;
additional marketing approvals for WAYLIVRA and TEGSEDI;
the profile and launch timing of our medicines, including TEGSEDI and WAYLIVRA;
changes in existing collaborative relationships and our ability to establish and maintain additional collaborative arrangements;
continued scientific progress in our research, drug discovery and development programs;
the size of our programs and progress with preclinical and clinical studies;
the time and costs involved in obtaining marketing authorizations; and
competing technological and market developments, including the introduction by others of new therapies that address our markets.
Under
If we need additional funds, we may need to raise them through public or private financing. Additional financing may not be available at all or on acceptable terms. If we raise additional funds by issuing equity securities, the Tax Cutshares of existing stockholders will be diluted and Jobs Act of 2017, or the Tax Act,price, as modified bywell as the Coronavirus Aid, Relief, and Economic Security Act, or the CARES Act, U.S. federal net operating losses incurred in 2018 and in future years may be carried forward indefinitely, but the deductibility of such U.S. federal net operating losses is limited to 80 percent of taxable income beginning in 2021. It is uncertain if and to what extent various states will conform to the federal Tax Act or the CARES Act. The CARES Act also reinstated the net operating loss carryback provisions whereby net operating losses incurred in calendar tax years 2018, 2019 and 2020 may be carried back to offset taxable income of the five tax years preceding the year of the loss.
In addition, under Sections 382 and 383 of the Code, and corresponding provisions of state law, if a corporation undergoes an “ownership change,” which is generally defined as a greater than 50 percent change, by value, in its equity ownership over a three-year period, the corporation’s ability to use its pre-change net operating loss carryforwards and other pre-change tax attributes to offset its post-change income or taxes may be limited. We may experience ownership changes in the future as a result of subsequent shifts in our stock ownership, some of which may be outsideprice of our control.other securities, may decline. If an ownership change occurs and our ability to use our net operating loss carryforwardsadequate funds are not available or other tax attributes is materially limited, it would harm our future operating results by effectively increasing our future tax obligations. In addition, at the state level, there may be periods during which the use of net operating losses is suspended or otherwise limited, which could accelerate or permanently increase state taxes owed. A change in tax laws, treaties or regulations, or their interpretation, of any other country in which we operate could also affect us.

Since corporate partnering is a significant part of our strategy to fund the development and commercialization of our development programs, if any of our collaborative partners fail to fund our collaborative programs, or if we cannot obtain additional partners,not available on acceptable terms, we may have to delaycut back on one or stop progress onmore of our research, drug discovery or development programs. Alternatively, we may obtain funds through arrangements with collaborative partners or others, which could require us to give up rights to certain of our technologies or medicines.

To date, corporate partnering has played a significant role in our strategy to fund our development programs and to add key development resources. We plan to continue to rely on additional collaborative arrangements to develop and commercialize our unpartnered medicines. However, we may not be able to negotiate favorable collaborative arrangements for these drug programs. If we cannot continue to secure additional collaborative partners, our revenues could decrease and the development of our medicines could suffer.

Our corporate partners are developing and/or funding many of the medicines in our development pipeline. For example, we are relying on:

Roche for development and funding of tominersen;
Novartis for development and funding of AKCEA-APO(a)-LRx; and
Biogen for development and funding of tofersen.

If any of these pharmaceutical companies stops developing and/or funding these medicines, our business could suffer and we may not have, or be willing to dedicate, the resources available to develop these medicines on our own. Our collaborators can terminate their relationships with us under certain circumstances, many of which are outside of our control. For example, as part of a reprioritization of its pipeline and strategic review of its rare disease business, GSK declined its option to license TEGSEDI and IONIS-FB-LRx.

Even with funding from corporate partners, if our partners do not effectively perform their obligations under our agreements with them, it would delay or stop the progress of our drug development and commercial programs.

In addition to receiving funding, we enter into collaborative arrangements with third parties to:

conduct clinical studies;
seek and obtain marketing authorization; and
manufacture, market and sell our medicines.

Once we have secured a collaborative arrangement to further develop and commercialize one of our drug development programs, such as our collaborations with AstraZeneca, Bayer, Biogen, GSK, Janssen, Novartis, Pfizer and Roche, these collaborations may not continue or result in commercialized medicines, or may not progress as quickly as we first anticipated.

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For example, a collaborator such as AstraZeneca, Bayer, Biogen, GSK, Janssen, Novartis, Pfizer or Roche, could determine that it is in its financial interest to:

pursue alternative technologies or develop alternative products that may be competitive with the medicine that is part of the collaboration with us;
pursue higher-priority programs or change the focus of its own development programs; or
choose to devote fewer resources to our medicines than it does for its own medicines.

If any of these occur, it could affect our partner’s commitment to the collaboration with us and could delay or otherwise negatively affect the commercialization of our medicines, including SPINRAZA, tominersen, AKCEA-APO(a)-LRx and tofersen.

If we do not progress in our programs as anticipated, the price of our securities could decrease.*

For planning purposes, we estimate and may disclose the timing of a variety of clinical, regulatory and other milestones, such as when we anticipate a certain medicine will enter clinical trials, when we anticipate completing a clinical study, or when we anticipate filing an application for, or obtaining, marketing authorization, or when our partners plan to commercially launch a medicine. We base our estimates on present facts and a variety of assumptions, many of which are outside of our control, including the current COVID-19 Pandemic. If we do not achieve milestones in accordance with our or our investors’ or securities analysts’ expectations, including milestonesRisks related to SPINRAZA, TEGSEDI, WAYLIVRA, tominersen, tofersen, AKCEA-APO(a)-LRx and AKCEA-TTR-LRx, the price of our securities could decrease.intellectual property

If we cannot protect our patent rights or our other proprietary rights, others may compete more effectively against us.

Our success depends to a significant degree upon whether we can continue to develop, secure and maintain intellectual property rights to proprietary products and services. However, we may not receive issued patents on any of our pending patent applications in the U.S. or in other countries and we may not be able to obtain, maintain or enforce our patents and other intellectual property rights which could impact our ability to compete effectively. In addition, the scope of any of our issued patents may not be sufficiently broad to provide us with a competitive advantage. Furthermore, other parties may successfully challenge, invalidate or circumvent our issued patents or patents licensed to us so that our patent rights do not create an effective competitive barrier or revenue source.

We cannot be certain that the U.S. Patent and Trademark Office, or U.S. PTO, and courts in the U.S. or the patent offices and courts in foreign countries will consider the claims in our patents and applications covering SPINRAZA, TEGSEDI, WAYLIVRA, or any of our medicines in development as patentable. Method-of-use patents protect the use of a product for the specified method. This type of patent does not prevent a competitor from making and marketing a product that is identical to our product for an indication that is outside the scope of the patented method. Moreover, even if competitors do not actively promote their product for our targeted indications, physicians may prescribe these products off-label. Although off-label prescriptions may infringe or contribute to the infringement of method-of-use patents, the practice is common and such infringement is difficult to prevent, including through legal action.

If we or any licensor partner loses or cannot obtain patent protection for SPINRAZA, TEGSEDI, WAYLIVRA, or any of our other medicines in development, it could have a material adverse impact on our business.

Intellectual property litigation could be expensive and prevent us from pursuing our programs.

From time to time we have to defend our intellectual property rights. If we are involved in an intellectual property dispute, we may need to litigate to defend our rights or assert them against others. Disputes can involve arbitration, litigation or proceedings declared by the U.S. PTO or the International Trade Commission or foreign patent authorities. Even if resolved in our favor, litigation or other legal proceedings relating to intellectual property claims may cause us to incur significant expenses and could distract our technical and management personnel from their normal responsibilities. In addition, there could be public announcements of the results of hearings, motions or other interim proceedings or developments and if securities analysts or investors perceive these results to be negative, it could have a substantial adverse effect on the price of our common stock.

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If a third partythird-party claims that our medicines or technology infringe its patents or other intellectual property rights, we may have to discontinue an important product or product line, alter our products and processes, pay license fees or cease certain activities. We may not be able to obtain a license to needed intellectual property on favorable terms, if at all. There are many patents issued or applied for in the biotechnology industry, and we may not be aware of patents or patent applications held by others that relate to our business. This is especially true since patent applications in the U.S. are filed confidentially for the first 18 months. Moreover, the validity and breadth of biotechnology patents involve complex legal and factual questions for which important legal issues remain.

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Risks related to our business strategy and personnel


If we fail to obtain timely funding, wesuccessfully integrate Akcea’s business and operations, it may need to curtail or abandon some ofadversely affect our programs.future results.

ManyWe believe our Akcea Acquisition will result in certain benefits, including a single vision and set of strategic priorities, led by one team, accelerating our next phase of growth and positioning us to more effectively deliver our medicines are undergoing clinical studies or areto patients. Under this transaction, Ionis will now retain more value from Akcea’s pipeline and commercial medicines, further strengthening our financial position and supporting continued investments in our future. The success of the early stages of research and development. Most of our drug programs will require significant additional research, development, manufacturing, preclinical and clinical testing, marketing authorization, preclinical activities and commitment of significant additional resources prior to their successful commercialization. These activities will require significant cash. As of March 31, 2020, we had cash, cash equivalents and short-term investments equal to $2.4 billion. If we or our partners do not meet our goals to successfully commercialize our medicines, including SPINRAZA, TEGSEDI and WAYLIVRA, or to license certain medicines and proprietary technologies, we will need additional funding in the future. Our future capital requirementstransaction will depend on many factors, such asour ability to realize these anticipated benefits. We may fail to realize the anticipated benefits of the Akcea Acquisition for a variety of reasons, including the following:

successful commercialization of SPINRAZA, TEGSEDIfailure to successfully manage relationships with partners, customers, distributors and WAYLIVRA;suppliers;
additional marketing approvals for WAYLIVRAdisruptions to Akcea’s commercial operations;
potential incompatibility of technologies and TEGSEDI;systems;
failure to leverage the capabilities of the combined company quickly and effectively;
potential difficulties integrating and harmonizing business systems and processes;
tax benefits of the combined structure may not be available or in the expected amounts; and
the profile and launch timingloss of our medicines, including TEGSEDI and WAYLIVRA;key employees.
changes in existing collaborative relationships and our ability to establish and maintain additional collaborative arrangements;
continued scientific progress in our research, drug discovery and development programs;
the size of our programs and progress with preclinical and clinical studies;
the time and costs involved in obtaining marketing authorizations; and
competing technological and market developments, including the introduction by others of new therapies that address our markets.

If we need additional funds, we may need to raise them through public or private financing. Additional financing may not be available at all or on acceptable terms. If we raise additional funds by issuing equity securities, the shares of existing stockholders will be diluted and the price, as well as the price of our other securities, may decline. If adequate funds are not available or not available on acceptable terms, we may have to cut back on one or more of our research, drug discovery or development programs. Alternatively, we may obtain funds through arrangements with collaborative partners or others, which could require us to give up rights to certain of our technologies or medicines.

If our management transition is not successful our business could suffer.

In January 2020, Dr. Crooke, our founder and Chief Executive Officer, transitioned from Chief Executive Officer to Executive Chairman of our Board of Directors. As Executive Chairman,Following the 2021 Annual Meeting of Stockholders, Dr. Crooke will continue to be responsible forstep down from the activities of the boardBoard and will remain active inserve as a Strategic Advisor to the company,Company, providing strategic advice and continuing to participate in the Company’s scientific activities. Starting in January 2020, Dr. Monia, who had been our Chief Operating Officer for the last year and has been a member of our team since our founding over 30 years ago, serves as our Chief Executive Officer. If this transition is not successful, our business could suffer.

The loss of key personnel, or the inability to attract and retain highly skilled personnel, could make it more difficult to run our business and reduce our likelihood of success.

We are dependent on the principal members of our management and scientific staff. We do not have employment agreements with any of our executive officers that would prevent them from leaving us. The loss of our management and key scientific employees might slow the achievement of important research and development goals. It is also critical to our success that we recruit and retain qualified scientific personnel to perform research and development work. We may not be able to attract and retain skilled and experienced scientific personnel on acceptable terms because of intense competition for experienced scientists among many pharmaceutical and health care companies, universities and non-profit research institutions. In addition, failure to succeed in clinical studies may make it more challenging to recruit and retain qualified scientific personnel. Similarly, Akcea iswe are dependent on the principal members of itsour staff responsible for marketing, sales and distribution activities. If Akcea iswe are not able to recruit and retain qualified marketing and sales personnel, the sales of TEGSEDI and WAYLIVRA may be adversely affected.

Risks related to taxes

Our ability to use our net operating loss carryovers and certain other tax attributes may be limited.*

Under the Internal Revenue Code of 1986, as amended, or the Code, a corporation is generally allowed a deduction for net operating losses, or NOLs, carried over from a prior taxable year. Under that provision, we can carryforward our NOLs to offset our future taxable income, if any, until such NOLs are used or expire. The same is true of other unused tax attributes, such as tax credits.

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Under the Tax Cut and Jobs Act of 2017, or the Tax Act, as modified by the Coronavirus Aid, Relief, and Economic Security Act, or the CARES Act, U.S. federal net operating losses incurred in 2018 and in future years may be carried forward indefinitely, but the deductibility of such U.S. federal net operating losses is limited to 80 percent of taxable income beginning in 2021. It is uncertain if and to what extent various states will conform to the federal Tax Act or the CARES Act. The CARES Act also reinstated the net operating loss carryback provisions whereby net operating losses incurred in calendar tax years 2018, 2019 and 2020 may be carried back to offset taxable income of the five tax years preceding the year of the loss.

In June 2020, California enacted Assembly Bill 85 (AB 85), which suspends NOLs and limits credit utilization to $5 million per year for the 2020, 2021 and 2022 tax years. AB 85 did not have a material impact on our 2020 tax provision, and we do not expect that it will materially impact our 2021 tax provision, but it is possible that it may in future years.

In addition, under Sections 382 and 383 of the Code, and corresponding provisions of state law, if a corporation undergoes an “ownership change,” which is generally defined as a greater than 50 percent change, by value, in its equity ownership over a three-year period, the corporation’s ability to use its pre-change net operating loss carryforwards and other pre-change tax attributes to offset its post-change income or taxes may be limited. We may experience ownership changes in the future as a result of subsequent shifts in our stock ownership, some of which may be outside of our control. If an ownership change occurs and our ability to use our net operating loss carryforwards or other tax attributes is materially limited, it would harm our future operating results by effectively increasing our future tax obligations. As a result of the Akcea Acquisition, we are subject to the Separate Return Limitation Year, or SRLY, rules. Under SRLY, our utilization of Akcea’s pre-acquisition net operating loss and tax credit carryforwards is limited to the amount of income that Akcea contributes to our consolidated taxable income. The Akcea pre-acquisition tax attributes cannot be used to offset any of the income that Ionis contributes to our consolidated taxable income. In addition, at the state level, there may be periods during which the use of net operating losses is suspended or otherwise limited, which could accelerate or permanently increase state taxes owed.

Our future taxable income could be impacted by changes in tax laws, regulations and treaties.

A change in tax laws, treaties or regulations, or their interpretation, of any country in which we operate could materially affect us.

We could be subject to additional tax liabilities.

We are subject to U.S. federal, state, local and sales taxes in the U.S. and foreign income taxes, withholding taxes and transaction taxes in foreign jurisdictions. Significant judgment is required in evaluating our tax positions and our worldwide provision for taxes. During the ordinary course of business, there are many activities and transactions for which the ultimate tax determination is uncertain. In addition, our tax obligations and effective tax rates could be adversely affected by changes in the relevant tax, accounting and other laws, regulations, principles and interpretations, including those relating to income tax nexus, by recognizing tax losses or lower than anticipated earnings in jurisdictions where we have lower statutory rates and higher than anticipated earnings in jurisdictions where we have higher statutory rates, by changes in foreign currency exchange rates, or by changes in the valuation of our deferred tax assets and liabilities. We may be audited in various jurisdictions, and such jurisdictions may assess additional taxes, sales taxes and value-added taxes against us. Although we believe our tax estimates are reasonable, the final determination of any tax audits or litigation could be materially different from our historical tax provisions and accruals, which could have a material adverse effect on our operating results or cash flows in the period for which a determination is made.

General Risk Factors

If the price of our securities continues to be highly volatile, this could make it harder for you to liquidate your investment and could increase your risk of suffering a loss.*

The market price of our common stock, like that of the securities of many other biopharmaceutical companies, has been and is likely to continue to be highly volatile. These fluctuations in our common stock price may significantly affect the trading price of our securities. During the 12 months preceding March 31, 2020,2021, the market price of our common stock ranged from $64.34$64.37 to $39.32$41.42 per share. Many factors can affect the market price of our securities, including, for example, fluctuations in our operating results, announcements of collaborations, clinical study results, technological innovations or new products being developed by us or our competitors, the commercial success of our approved medicines, governmental regulation, marketing authorizations, changes in payers’ reimbursement policies, developments in patent or other proprietary rights and public concern regarding the safety of our medicines.

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The current COVID-19 Pandemic has caused a significant disruption of global financial markets and has resulted in increased volatility in the trading price of our common stock. Additionally, broad market and industry factors may also materially harm the market price of our common stock irrespective of our operating performance. The stock market in general, and NASDAQ and the market for biotechnology companies in particular, have experienced extreme price and volume fluctuations that have often been unrelated or disproportionate to the operating performance of the particular companies affected. The trading prices and valuations of these stocks, and of ours, may not be predictable. A loss of investor confidence in the market for biotechnology or pharmaceutical stocks or the stocks of other companies which investors perceive to be similar to us, the opportunities in the biotechnology and pharmaceutical market or the stock market in general, could depress our stock price regardless of our business, prospects, financial conditions or results of operations.

Provisions in our certificate of incorporation, convertible notes documents, call spread hedge transaction documents and Delaware law may prevent stockholders from receiving a premium for their shares.

Our certificate of incorporation provides for classified terms for the members of our board of directors. Our certificate also includes a provision that requires at least 66 2/3 percent of our voting stockholders to approve a merger or certain other business transactions with, or proposed by, any holder of 15 percent or more of our voting stock, except in cases where certain directors approve the transaction or certain minimum price criteria and other procedural requirements are met.

Our certificate of incorporation also requires that any action required or permitted to be taken by our stockholders must be taken at a duly called annual or special meeting of stockholders and may not be taken by written consent. In addition, only our board of directors, chairman of the board or chief executive officer can call special meetings of our stockholders. We have in the past, and may in the future, implement a stockholders’ rights plan, also called a poison pill, which could make it uneconomical for a third party to acquire our company on a hostile basis. In addition, our board of directors has the authority to fix the rights and preferences of, and issue shares of preferred stock, which may have the effect of delaying or preventing a change in control of our company without action by our stockholders.

The provisions of our convertible senior notes could make it more difficult or more expensive for a third party to acquire us. Upon the occurrence of certain transactions constituting a fundamental change, holders of the notes will have the right, at their option, to require us to repurchase all of their notes or a portion of their notes, which may discourage certain types of transactions in which our stockholders might otherwise receive a premium for their shares over the then current market prices.

In April 2021, we completed a $632.5 million offering of 0% Notes. In December 2019, we entered into privately negotiated exchange and/or subscription agreements with certain new investors and certain holders of our existing 1% Notes to exchange $375.6 million of our 1% Notes for $439.3 million of our 0.125% Notes, and to issue $109.5 million of our 0.125% Notes. Additionally, in connection with the pricing of our 0% Notes and 0.125% Notes, we entered into call spread transactions in which we purchased note hedges and sold warrants. Terminating or unwinding the call spread transactions could require us to make substantial payments to the counterparties under those agreements or may increase our stock price. The costs or any increase in stock price that may arise from terminating or unwinding such agreements could make an acquisition of our company significantly more expensive to the purchaser.

These provisions, as well as Delaware law, including Section 203 of the Delaware General Corporation Law, and other of our agreements, may discourage certain types of transactions in which our stockholders might otherwise receive a premium for their shares over then current market prices, and may limit the ability of our stockholders to approve transactions that they think may be in their best interests.

Future sales of our common stock in the public market could adversely affect the trading price of our securities.

Future sales of substantial amounts of our common stock in the public market, or the perception that such sales could occur, could adversely affect trading prices of our securities. For example, we may issue approximately 18.4 million shares of our common stock upon conversion of our 0% Notes, 0.125% Notes, and 1% Notes, up to 10.9 million shares in connection with the warrant transactions we entered into in connection with the issuance of our 0% Notes, and up to 6.6 million shares in connection with the warrant transactions we entered into in connection with the issuance of our 0.125% Notes, in each case subject to customary anti-dilution adjustments. The addition of any of these shares into the public market may have an adverse effect on the price of our securities.

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In addition, pursuant to the call spread transactions we entered into in connection with the pricing of our 0% Notes and 0.125% Notes, the counterparties are likely to modify their hedge positions from time to time at or prior to the conversion or maturity of the notes by purchasing and selling shares of our common stock, other of our securities, or other instruments, including over-the-counter derivative instruments, that they may wish to use in connection with such hedging, which may have a negative effect on the conversion value of those notes and an adverse impact on the trading price of our common stock. The call spread transactions are expected generally to reduce potential dilution to holders of our common stock upon any conversion of our 0% Notes or 0.125% Notes or offset any cash payments we are required to make in excess of the principal amount of the converted 0% Notes or 0.125% Notes, as the case may be. However, the warrant transactions could separately have a dilutive effect to the extent that the market value per share of our common stock exceeds the applicable strike price of the warrants.

We are exposed to potential product liability claims, and insurance against these claims may not be available to us at a reasonable rate in the future or at all.

Our business exposes us to potential product liability risks that are inherent in the testing, manufacturing, marketing and sale of therapeutic products, including potential product liability claims related to SPINRAZA, TEGSEDI and WAYLIVRA, and our medicines in development. We have clinical study insurance coverage and commercial product liability insurance coverage. However, this insurance coverage may not be adequate to cover claims against us, or be available to us at an acceptable cost, if at all. Regardless of their merit or eventual outcome, product liability claims may result in decreased demand for our medicines, injury to our reputation, withdrawal of clinical study volunteers and loss of revenues. Thus, whether or not we are insured, a product liability claim or product recall may result in losses that could be material.

We are dependent on information technology systems, infrastructure and data, which exposes us to data security risks.*

We are dependent upon our own and third-party information technology systems, infrastructure and data, including mobile technologies, to operate our business. The multitude and complexity of our computer systems may make them vulnerable to service interruption or destruction, disruption of data integrity, malicious intrusion, or random attacks. Likewise, data privacy or security incidents or breaches by employees or others may pose a risk that sensitive data, including our intellectual property, trade secrets or personal information of our employees, patients, customers or other business partners may be exposed to unauthorized persons or to the public. Cyber-attacks are increasing in their frequency, sophistication and intensity, with third-party phishing and social engineering attacks in particular increasing in connection with the COVID-19 Pandemic. Cyber-attacks could include the deployment of harmful malware, denial-of-service, social engineering and other means to affect service reliability and threaten data confidentiality, integrity and availability. Our business partners face similar risks and any security breach of their systems could adversely affect our security posture. A security breach or privacy violation that leads to disclosure or modification of or prevents access to patient information, including personally identifiable information or protected health information, could harm our reputation, compel us to comply with federal and state breach notification laws and foreign law equivalents, subject us to financial penalties and mandatory and costly corrective action, require us to verify the correctness of database contents and otherwise subject us to litigation or other liability under laws and regulations that protect personal data, any of which could disrupt our business and result in increased costs or loss of revenue. Moreover, the prevalent use of mobile devices that access confidential information increases the risk of data security breaches, which could lead to the loss of confidential information, trade secrets or other intellectual property. While we have invested, and continue to invest, in the protection of our data and information technology infrastructure, our efforts may not prevent service interruptions, or identify breaches in our systems, that could adversely affect our business and operations and result in the loss of critical or sensitive information, which could result in financial, legal, business or reputational harm to us. In addition, our liability insurance may not be sufficient in type or amount to cover us against claims related to security breaches, cyber-attacks and other related breaches.

Because we use biological materials, hazardous materials, chemicals and radioactive compounds, if we do not comply with laws regulating the protection of the environment and health and human safety, our business could be adversely affected.

Our research, development and manufacturing activities involve the use of potentially harmful biological materials as well as materials, chemicals and various radioactive compounds that could be hazardous to human health and safety or the environment. We store most of these materials and various wastes resulting from their use at our facilities in Carlsbad, California pending ultimate use and disposal. We cannot completely eliminate the risk of contamination, which could cause:

interruption of our research, development and manufacturing efforts;
injury to our employees and others;
environmental damage resulting in costly clean up; and
liabilities under federal, state and local laws and regulations governing health and human safety, as well as the use, storage, handling and disposal of these materials and resultant waste products.


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In such an event, we may be held liable for any resulting damages, and any liability could exceed our resources. Although we carry insurance in amounts and types that we consider commercially reasonable, we do not have insurance coverage for losses relating to an interruption of our research, development or manufacturing efforts caused by contamination, and the coverage or coverage limits of our insurance policies may not be adequate. If our losses exceed our insurance coverage, our financial condition would be adversely affected.

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If a natural or man-made disaster strikes our research, development or manufacturing facilities or otherwise affects our business, it could delay our progress developing and commercializing our medicines.

We manufacture most of our research and clinical supplies in a manufacturing facility located in Carlsbad, California. We manufacture the finished drug product for TEGSEDI and WAYLIVRA at third-party contract manufacturers. Biogen manufactures the finished drug product for SPINRAZA. The facilities and the equipment we, our partners and our contract manufacturers use to research, develop and manufacture our medicines would be costly to replace and could require substantial lead time to repair or replace. Our facilities or those of our partners or contract manufacturers may be harmed by natural or man-made disasters, including, without limitation, earthquakes, floods, fires, acts of terrorism and pandemics; and if such facilities are affected by a disaster, our development and commercialization efforts would be delayed. Although we possess property damage and business interruption insurance coverage, this insurance may not be sufficient to cover all of our potential losses and may not continue to be available to us on acceptable terms, or at all. In addition, our development and commercialization activities could be harmed or delayed by a shutdown of the U.S. government, including the FDA.

Provisions in our certificate of incorporation, convertible notes documents, call spread hedge transaction documents and Delaware law may prevent stockholders from receiving a premium for their shares.

Our certificate of incorporation provides for classified terms for the members of our board of directors. Our certificate also includes a provision that requires at least 66 2/3 percent of our voting stockholders to approve a merger or certain other business transactions with, or proposed by, any holder of 15 percent or more of our voting stock, except in cases where certain directors approve the transaction or certain minimum price criteria and other procedural requirements are met.

Our certificate of incorporation also requires that any action required or permitted to be taken by our stockholders must be taken at a duly called annual or special meeting of stockholders and may not be taken by written consent. In addition, only our board of directors, chairman of the board or chief executive officer can call special meetings of our stockholders. We have in the past, and may in the future, implement a stockholders’ rights plan, also called a poison pill, which could make it uneconomical for a third party to acquire our company on a hostile basis. In addition, our board of directors has the authority to fix the rights and preferences of, and issue shares of preferred stock, which may have the effect of delaying or preventing a change in control of our company without action by our stockholders.

The provisions of our convertible senior notes could make it more difficult or more expensive for a third party to acquire us. Upon the occurrence of certain transactions constituting a fundamental change, holders of the notes will have the right, at their option, to require us to repurchase all of their notes or a portion of their notes, which may discourage certain types of transactions in which our stockholders might otherwise receive a premium for their shares over the then current market prices.

In December 2019, we entered into privately negotiated exchange and/or subscription agreements with certain new investors and certain holders of our existing 1% Notes to exchange $375.6 million of our 1% Notes for $439.3 million of our 0.125% Notes, and to issue $109.5 million of our 0.125% Notes. Additionally, in connection with the pricing of our 0.125% Notes, we entered into call spread transactions in which we purchased note hedges and sold warrants. Terminating or unwinding the call spread transactions could require us to make substantial payments to the counterparties under those agreements or may increase our stock price. The costs or any increase in stock price that may arise from terminating or unwinding such agreements could make an acquisition of our company significantly more expensive to the purchaser.

These provisions, as well as Delaware law, including Section 203 of the Delaware General Corporation Law, and other of our agreements, may discourage certain types of transactions in which our stockholders might otherwise receive a premium for their shares over then current market prices, and may limit the ability of our stockholders to approve transactions that they think may be in their best interests.

Future sales of our common stock in the public market could adversely affect the trading price of our securities.

Future sales of substantial amounts of our common stock in the public market, or the perception that such sales could occur, could adversely affect trading prices of our securities. For example, we may issue approximately 11.2 million shares of our common stock upon conversion of our convertible senior notes and up to 6.6 million shares may be issued in connection with the warrant transactions we entered into in connection with the issuance of our 0.125% Notes, in each case subject to customary anti-dilution adjustments. The addition of any of these shares into the public market may have an adverse effect on the price of our securities.

In addition, pursuant to the call spread transactions we entered into in connection with the pricing of our 0.125% Notes, the counterparties are likely to modify their hedge positions from time to time at or prior to the conversion or maturity of the notes by purchasing and selling shares of our common stock, other of our securities, or other instruments, including over-the-counter derivative instruments, that they may wish to use in connection with such hedging, which may have a negative effect on the conversion value of those notes and an adverse impact on the trading price of our common stock. The call spread transactions are expected generally to reduce potential dilution to holders of our common stock upon any conversion of our 0.125% Notes or offset any cash payments we are required to make in excess of the principal amount of the converted 0.125% Notes, as the case may be. However, the warrant transactions could separately have a dilutive effect to the extent that the market value per share of our common stock exceeds the applicable strike price of the warrants.

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Our business is subject to changing regulations for corporate governance and public disclosure that has increased both our costs and the risk of noncompliance.

Each year we are required to evaluate our internal controls systems in order to allow management to report on and our Independent Registered Public Accounting Firm to attest to, our internal controls as required by Section 404 of the Sarbanes-Oxley Act. As a result, we continue to incur additional expenses and divert our management’s time to comply with these regulations. In addition, if we cannot continue to comply with the requirements of Section 404 in a timely manner, we might be subject to sanctions or investigation by regulatory authorities, such as the SEC, the Public Company Accounting Oversight Board, or PCAOB, or The Nasdaq Global Select Market. Any such action could adversely affect our financial results and the market price of our common stock.

The SEC and other regulators have continued to adopt new rules and regulations and make additional changes to existing regulations that require our compliance. On July 21, 2010, the Dodd-Frank Wall Street Reform and Protection Act, or the Dodd-Frank Act, was enacted. There are significant corporate governance and executive compensation-related provisions in the Dodd-Frank Act that require the SEC to adopt, or where the SEC has adopted, additional rules and regulations in these areas such as “say on pay” and proxy access. Stockholder activism, the current political environment and the current high level of government intervention and regulatory reform may lead to substantial new regulations and disclosure obligations, which may lead to additional compliance costs and impact the manner in which we operate our business.

Changes in tax laws, regulations and treaties could affect our future taxable income.

A change in tax laws, treaties or regulations, or their interpretation, of any country in which we operate could materially affect us.

We could be subject to additional tax liabilities.

We are subject to U.S. federal, state, local and sales taxes in the U.S. and foreign income taxes, withholding taxes and transaction taxes in foreign jurisdictions. Significant judgment is required in evaluating our tax positions and our worldwide provision for taxes. During the ordinary course of business, there are many activities and transactions for which the ultimate tax determination is uncertain. In addition, our tax obligations and effective tax rates could be adversely affected by changes in the relevant tax, accounting and other laws, regulations, principles and interpretations, including those relating to income tax nexus, by recognizing tax losses or lower than anticipated earnings in jurisdictions where we have lower statutory rates and higher than anticipated earnings in jurisdictions where we have higher statutory rates, by changes in foreign currency exchange rates, or by changes in the valuation of our deferred tax assets and liabilities. We may be audited in various jurisdictions, and such jurisdictions may assess additional taxes, sales taxes and value-added taxes against us. Although we believe our tax estimates are reasonable, the final determination of any tax audits or litigation could be materially different from our historical tax provisions and accruals, which could have a material adverse effect on our operating results or cash flows in the period for which a determination is made.

Negative conditions in the global credit markets and financial services and other industries may adversely affect our business.*

The global credit markets, the financial services industry, the U.S. capital markets, and the U.S. economy as a whole are currently experiencing substantial turmoil and uncertainty characterized by unprecedented intervention by the U.S. federal government in response to the COVID-19 Pandemic. In the past, the failure, bankruptcy, or sale of various financial and other institutions created similar turmoil and uncertainty in such markets and industries. It is possible that a crisis in the global credit markets, the U.S. capital markets, the financial services industry or the U.S. economy may adversely affect our business, vendors and prospects, as well as our liquidity and financial condition. More specifically, our insurance carriers and insurance policies covering all aspects of our business may become financially unstable or may not be sufficient to cover any or all of our losses and may not continue to be available to us on acceptable terms, or at all.

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A variety of risks associated with operating our business and marketing our medicines internationally could adversely affect our business.
In addition to our U.S. operations, we are commercializing TEGSEDI in the EU, Canada, Latin America and certain Caribbean countries, and WAYLIVRA in the EU, Latin America and certain Caribbean countries. We face risks associated with our international operations, including possible unfavorable regulatory, pricing and reimbursement, political, tax and labor conditions, which could harm our business. Because we have international operations we are subject to numerous risks associated with international business activities, including:
compliance with differing or unexpected regulatory requirements for our medicines and foreign employees;
complexities associated with managing multiple payer reimbursement regimes, government payers or patient self-pay systems;
difficulties in staffing and managing foreign operations;
in certain circumstances, increased dependence on the commercialization efforts and regulatory compliance of third-party distributors or strategic partners;
foreign government taxes, regulations and permit requirements;
U.S. and foreign government tariffs, trade restrictions, price and exchange controls and other regulatory requirements;
anti-corruption laws, including the Foreign Corrupt Practices Act, or the FCPA, and its equivalent in foreign jurisdictions;
economic weakness, including inflation, natural disasters, war, events of terrorism, political instability or public health issues or pandemics, such as the current COVID-19 Pandemic, in particular foreign countries or globally;
fluctuations in currency exchange rates, which could result in increased operating expenses and reduced revenue, and other obligations related to doing business in another country;
compliance with tax, employment, privacy, immigration and labor laws, regulations and restrictions for employees living or traveling abroad;
workforce uncertainty in countries where labor unrest is more common than in the U.S.; and
changes in diplomatic and trade relationships.

The United Kingdom’s exit from the E.U. could increase these risks.

Our business activities outside of the U.S. are subject to the FCPA and similar anti-bribery or anti-corruption laws, regulations or rules of other countries in which we operate, including the United Kingdom’s Bribery Act 2010. In many other countries, the healthcare providers who prescribe pharmaceuticals are employed by their government, and the purchasers of pharmaceuticals are government entities; therefore, any dealings with these prescribers and purchasers may be subject to regulation under the FCPA. There is no certainty that all employees and third-party business partners (including our distributors, wholesalers, agents, contractors and other partners) will comply with anti-bribery laws. In particular, we do not control the actions of manufacturers and other third-party agents, although we may be liable for their actions. Violation of these laws may result in civil or criminal sanctions, which could include monetary fines, criminal penalties, and disgorgement of past profits, which could have an adverse impact on our business and financial condition.

The impact on us of the vote by the United Kingdom to leave the European Union cannot be predicted.*

On June 23, 2016,The withdrawal of the United Kingdom, orUK from the U.K., voted to leave the E.U. in an advisory referendum, which is generallyEU, commonly referred to as Brexit. In January 2020,“Brexit,” may adversely impact our ability to obtain regulatory approvals of our medicines in the U.K.EU, result in restrictions or imposition of taxes and duties for importing our medicines into the E.U. entered intoEU, and may require us to incur additional expenses in order to develop, manufacture and commercialize our medicines in the EU.

Following the result of a withdrawal agreement pursuant to whichreferendum in 2016, the U.K. formally withdrew fromUK left the E.U.EU on January 31, 2020. Following suchPursuant to the formal withdrawal arrangements agreed between the U.K. entered intoUK and the EU, the UK was subject to a transition period scheduled to end onthat ended December 31, 2020, or the Transition Period. DuringPeriod, during which EU rules continued to apply. A trade and cooperation agreement, or the Transition Period, negotiations are expected to continue in relation toTrade and Cooperation Agreement, that outlines the customs andfuture trading relationship between the U.K.UK and the E.U. following the expiryEU was agreed in December 2020.

Since a significant proportion of the Transition Period. Dueregulatory framework in the UK applicable to our business and our medicines is derived from EU directives and regulations, Brexit has had, and may continue to have, a material impact upon the COVID-19 Pandemic, negotiations between the U.K. and the E.U. scheduled for March were not held, and there is an increased likelihood that the Transition Period may need to be extended beyond December 31, 2020 (although it remains the position of the U.K. government that it will not be extended).

In addition, as a result of Brexit, the EMA, formerly situated in London, relocated to Amsterdam. Following the Transition Period, there is a risk that the relocation will interrupt current administrative routines and occupy resources, which may generally adversely affect our dealings with the EMA. Further, there is considerable uncertainty resulting from a lack of precedent and the complexity of the U.K. and E.U.’s intertwined legal regimes as to how Brexit (following the Transition Period) will impact the life sciences industry in Europe, including our company, includingregulatory regime with respect to ongoingthe development, manufacture, importation, approval and commercialization of our medicines in the UK or future clinical trials. The impact will largely depend on the model and means by which the U.K.’s relationship with the E.U. is governed post-Brexit.EU. For example, following the Transition Period, the U.K. willGreat Britain is no longer be covered by the centralized procedures for obtaining E.U.-wideEU-wide marketing authorization from the EMA, and unless a specific agreement is entered into, a separate process formarketing authorization of drug products, including our product candidates, will be required to market our medicines in Great Britain. It is currently unclear whether the Medicines & Healthcare products Regulatory Agency in the UK is sufficiently prepared to handle the potential process for whichincreased volume of marketing authorization applications that it is currently unclear.likely to receive. Any delay in obtaining, or an inability to obtain, any marketing approvals, as a result of Brexit may adversely affect andor otherwise, would delay or prevent us from commercializing our ability to commercialize, market and sell our product candidatesmedicines in the U.K.UK or the EU.

While the Trade and Cooperation Agreement provides for the tariff-free trade of medicinal products between the UK and the EU, there may be additional non-tariff costs to such trade which did not exist prior to the end of the Transition Period. Further, should the UK diverge from the EU from a regulatory perspective in relation to medicinal products, tariffs could be put into place in the future. We could therefore, both now and in the future, face significant additional expenses (when compared to the position prior to the end of the Transition Period) to operate our business.

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ITEM 2.UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

Not applicable.

In September 2019, our board of directors approved an initial share repurchase program of up to $125 million of our common stock. All of our repurchases were made under a 10b5-1 plan. In 2019, we repurchased 535,000 shares for $34.4 million. In the first quarter of 2020, we repurchased an additional 1.5 million shares for $90.6 million as follows (in thousands, except per share amounts):

 
Total
Number of
Shares Purchased
  
Average
Price Paid
Per Share (1)
 
January 2020  1,478  $61.27 
Total  1,478     

(1)Average Price Paid Per Share excludes cash paid for commissions.

ITEM 3.DEFAULT UPON SENIOR SECURITIES

Not applicable.

ITEM 4.MINE SAFETY DISCLOSURES

Not applicable.

ITEM 5.OTHER INFORMATION

Not applicable.

ITEM 6.EXHIBITS

a.Exhibits

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Exhibit Number Description of Document
Amended and Restated Bylaws, filed as an exhibit to Registrant’s Form 8-K filed with the SEC on March 29, 2021 and incorporated herein by reference.
10.1Letter agreement dated October 21, 2020 to the License Agreement by and among Akcea Therapeutics, Inc. and Pfizer Inc. dated October 4, 2019. Portions of this exhibit have been omitted because they are both (i) not material and (ii) would be competitively harmful if publicly disclosed.
10.2Board Compensation Policy.
   
Code of Ethics, filed as an exhibit to Registrant’s Form 8-K filed with the SEC on March 29, 2021 and incorporated herein by reference.
31.1 Certification by Chief Executive Officer pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as amended.
   
 Certification by Chief Financial Officer pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as amended.
   
32.1* Certification Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
   
101 
The following financial statements from the Ionis Pharmaceuticals, Inc. Quarterly Report on Form 10-Q for the quarter ended March 31, 2020,2021, formatted in Inline Extensible Business Reporting Language (iXBRL): (i) condensed consolidated balance sheets, (ii) condensed consolidated statements of operations, (iii) condensed consolidated statements of comprehensive income (loss), (iv) condensed consolidated statements of stockholders'stockholders’ equity, (v) condensed consolidated statements of cash flows and (vi) notes to condensed consolidated financial statements (detail tagged).
   
104 Cover Page Interactive Data File (formatted in iXBRL and included in exhibit 101).

*This certification is deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended.


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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

Signatures Title Date
     
/s/ BRETT P. MONIA Director and Chief Executive Officer  
Brett P. Monia, Ph.D.(Principal executive officer)May 6, 20205, 2021
     
/s/ ELIZABETH L. HOUGEN Executive Vice President, Finance and Chief Financial Officer  
Elizabeth L. Hougen(Principal financial and accounting officer)May 6, 20205, 2021

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