AGIOS PHARMACEUTICALS, INC. 10-Q

Item 1. Financial Statements (Unaudited) AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) September 30, 2020 December 31, 2019 Assets Current assets: Cash and cash equivalents $ 104,855 $ 80,931 Marketable securities 500,684 483,946 Accounts receivable, net 18,989 8,952 Collaboration receivable – related party 2,334 1,539 Collaboration receivable – other 1,992 1,928 Royalty receivable – related party — 2,900 Inventory 11,371 7,331 Prepaid expenses and other current assets 28,861 24,177 Total current assets 669,086 611,704 Marketable securities 116,889 152,929 Operating lease assets 86,952 93,643 Property and equipment, net 33,495 31,472 Financing lease assets 677 993 Other assets 1,350 — Total assets $ 908,449 $ 890,741 Liabilities and stockholders’ equity Current liabilities: Accounts payable $ 12,853 $ 21,896 Accrued expenses 49,724 53,142 Deferred revenue – related party — 10,933 Operating lease liabilities 6,881 6,642 Financing lease liabilities 313 273 Total current liabilities 69,771 92,886 Deferred revenue, net of current portion – related party — 50,580 Operating lease liabilities, net of current portion 99,693 106,074 Financing lease liabilities, net of current portion 412 673 Liability related to the sale of future revenue, net of debt issuance costs 258,121 — Total liabilities 427,997 250,213 Stockholders’ equity: Preferred stock, $ 0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at September 30, 2020 and December 31, 2019 — — Common stock, $ 0.001 par value; 125,000,000 shares authorized; 69,198,063 and 68,401,105 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively 69 68 Additional paid-in capital 2,225,538 2,156,363 Accumulated other comprehensive income 663 202 Accumulated deficit ( 1,745,818 ) ( 1,516,105 ) Total stockholders’ equity 480,452 640,528 Total liabilities and stockholders’ equity $ 908,449 $ 890,741 See accompanying Notes to Condensed Consolidated Financial Statements. 1 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, (In thousands, except share and per share data) 2020 2019 2020 2019 Revenues: Product revenue, net $ 31,716 $ 17,422 $ 81,971 $ 40,287 Collaboration revenue – related party 1,206 5,516 67,038 32,414 Collaboration revenue – other 1,101 420 2,786 2,202 Royalty revenue – related party 683 2,666 7,356 7,569 Total revenue 34,706 26,024 159,151 82,472 Cost and expenses: Cost of sales 638 393 1,846 1,030 Research and development 89,555 101,672 271,728 304,646 Selling, general and administrative 34,840 33,019 109,292 97,200 Total cost and expenses 125,033 135,084 382,866 402,876 Loss from operations ( 90,327 ) ( 109,060 ) ( 223,715 ) ( 320,404 ) Interest income, net 1,115 2,887 5,820 11,282 Non-cash interest expense for the sale of future revenue ( 9,767 ) — ( 11,818 ) — Net loss $ ( 98,979 ) $ ( 106,173 ) $ ( 229,713 ) $ ( 309,122 ) Net loss per share – basic and diluted $ ( 1.43 ) $ ( 1.81 ) $ ( 3.33 ) $ ( 5.27 ) Weighted-average number of common shares used in computing net loss per share – basic and diluted 69,144,061 58,803,534 68,905,853 58,661,607 See accompanying Notes to Condensed Consolidated Financial Statements. 2 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Net loss $ ( 98,979 ) $ ( 106,173 ) $ ( 229,713 ) $ ( 309,122 ) Other comprehensive (loss) income Unrealized (loss) gain on available-for-sale securities ( 973 ) ( 26 ) 461 2,635 Comprehensive loss $ ( 99,952 ) $ ( 106,199 ) $ ( 229,252 ) $ ( 306,487 ) See accompanying Notes to Condensed Consolidated Financial Statements. 3 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Stockholders' Equity (Unaudited) Common Stock Additional Paid-In Capital Accumulated Other Comprehensive (Loss) Income Accumulated Deficit Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Balance at December 31, 2019 68,401,105 $ 68 $ 2,156,363 $ 202 $ ( 1,516,105 ) $ 640,528 Common stock issued under stock incentive plan and ESPP 388,820 1 5,464 — — 5,465 Stock-based compensation expense — — 19,690 — — 19,690 Other comprehensive loss — — — ( 128 ) — ( 128 ) Net loss — — — — ( 40,256 ) ( 40,256 ) Balance at March 31, 2020 68,789,925 $ 69 $ 2,181,517 $ 74 $ ( 1,556,361 ) $ 625,299 Common stock issued under stock incentive plan and ESPP 268,771 $ — $ 1,652 $ — $ — $ 1,652 Stock-based compensation expense — — 20,430 — — 20,430 Other comprehensive income — — — 1,562 — 1,562 Net loss — — — — ( 90,478 ) ( 90,478 ) Balance at June 30, 2020 69,058,696 $ 69 $ 2,203,599 $ 1,636 $ ( 1,646,839 ) $ 558,465 Common stock issued under stock incentive plan and ESPP 139,367 $ — $ 3,532 $ — $ — $ 3,532 Stock-based compensation expense — — 18,407 — — 18,407 Other comprehensive loss — — — ( 973 ) — ( 973 ) Net loss — — — — ( 98,979 ) ( 98,979 ) Balance at September 30, 2020 69,198,063 $ 69 $ 2,225,538 $ 663 $ ( 1,745,818 ) $ 480,452 See accompanying Notes to Condensed Consolidated Financial Statements. 4 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Stockholders' Equity (Continued) (Unaudited) Common Stock Additional Paid-In Capital Accumulated Other Comprehensive (Loss) Income Accumulated Deficit Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Balance at December 31, 2018 58,218,653 $ 58 $ 1,794,283 $ ( 2,171 ) $ ( 1,104,633 ) $ 687,537 Common stock issued under stock incentive plan and ESPP 441,168 1 6,002 — — 6,003 Stock-based compensation expense — — 18,108 — — 18,108 Other comprehensive income — — — 1,687 — 1,687 Net loss — — — — ( 93,078 ) ( 93,078 ) Balance at March 31, 2019 58,659,821 $ 59 $ 1,818,393 $ ( 484 ) $ ( 1,197,711 ) $ 620,257 Common stock issued under stock incentive plan and ESPP 89,365 $ — $ 2,770 $ — $ — $ 2,770 Stock-based compensation expense — — 18,547 — — 18,547 Other comprehensive income — — — 974 — 974 Net loss — — — — ( 109,871 ) ( 109,871 ) Balance at June 30, 2019 58,749,186 $ 59 $ 1,839,710 $ 490 $ ( 1,307,582 ) $ 532,677 Common stock issued under stock incentive plan and ESPP 128,505 $ — $ 3,225 $ — $ — $ 3,225 Stock-based compensation expense — — 18,588 — — 18,588 Other comprehensive loss — — — ( 26 ) — ( 26 ) Net loss — — — — ( 106,173 ) ( 106,173 ) Balance at September 30, 2019 58,877,691 $ 59 $ 1,861,523 $ 464 $ ( 1,413,755 ) $ 448,291 See accompanying Notes to Condensed Consolidated Financial Statements. 5 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) Nine Months Ended September 30, (In thousands) 2020 2019 Operating activities Net loss $ ( 229,713 ) $ ( 309,122 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 7,307 6,124 Stock-based compensation expense 58,527 55,243 Net accretion of premium and discounts on investments 1,521 ( 2,772 ) Gain on disposal of property and equipment — 466 Non-cash operating lease expense 6,691 6,341 Non-cash interest expense associated with the sale of future revenue 11,818 — Non-cash royalty revenue ( 4,341 ) — Changes in operating assets and liabilities: Accounts receivable, net ( 10,037 ) ( 2,030 ) Collaboration receivable – related party ( 795 ) 624 Collaboration receivable – other ( 64 ) ( 199 ) Royalty receivable – related party 2,900 ( 366 ) Inventory ( 4,040 ) ( 4,980 ) Prepaid expenses and other current and non-current assets ( 6,033 ) ( 3,552 ) Accounts payable ( 7,640 ) 2,649 Accrued expenses 162 4,602 Deferred revenue – related party ( 61,513 ) ( 25,849 ) Operating lease liabilities ( 6,112 ) ( 4,190 ) Net cash used in operating activities ( 241,362 ) ( 277,011 ) Investing activities Purchases of marketable securities ( 430,624 ) ( 194,822 ) Proceeds from maturities and sales of marketable securities 448,866 476,382 Purchases of property and equipment ( 13,892 ) ( 5,347 ) Net cash provided by investing activities 4,350 276,213 Financing activities Payments on financing lease obligations ( 250 ) — Net proceeds from stock option exercises and employee stock purchase plan 10,649 12,005 Proceeds from the sale of future revenue, net of issuance costs 250,537 — Net cash provided by financing activities 260,936 12,005 Net change in cash and cash equivalents 23,924 11,207 Cash and cash equivalents at beginning of the period 80,931 70,502 Cash and cash equivalents at end of the period $ 104,855 $ 81,709 Supplemental disclosure of non-cash investing and financing transactions Additions to property and equipment in accounts payable and accrued expenses $ 185 $ 2,089 Operating lease liabilities arising from obtaining operating lease assets $ — $ 42,322 See accompanying Notes to Condensed Consolidated Financial Statements. 6 Table of Contents AGIOS PHARMACEUTICALS, INC. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Overview and Basis of Presentation References to Agios Throughout this Quarterly Report on Form 10-Q, “we,” “us,” and “our,” and similar expressions, except where the context requires otherwise, refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries, and “our Board of Directors” refers to the board of directors of Agios Pharmaceuticals, Inc. Overview We are a biopharmaceutical company committed to transforming patients’ lives through scientific leadership in the field of cellular metabolism and adjacent areas of biology, with the goal of creating differentiated, small molecule medicines for patients in the areas of hematologic malignancies, solid tumors and rare genetic diseases, or RGDs. To address these focus areas, we take a systems biology approach to deeply understand disease states, drive the discovery and validation of novel therapeutic targets, and define patient selection strategies, thereby increasing the probability that our experimental medicines will have the desired therapeutic effect. We are located in Cambridge, Massachusetts. Basis of presentation The condensed consolidated balance sheet as of September 30, 2020, the condensed consolidated statements of operations, comprehensive loss and stockholders' equity for the three and nine months ended September 30, 2020 and 2019, and the condensed consolidated statements of cash flows for the nine months ended September 30, 2020 and 2019 are unaudited. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of our management, reflect all adjustments, which include only normal recurring adjustments, necessary to fairly state our financial position as of September 30, 2020, our results of operations and stockholders' equity for the three and nine months ended September 30, 2020 and 2019, and cash flows for the nine months ended September 30, 2020 and 2019. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and nine-month periods are also unaudited. The results of operations for the three and nine months ended September 30, 2020 are not necessarily indicative of the results to be expected for the year ending December 31, 2020 or for any other future annual or interim period. The condensed consolidated balance sheet data as of December 31, 2019 was derived from our audited financial statements, but does not include all disclosures required by U.S. generally accepted accounting principles, or U.S. GAAP. The condensed consolidated interim financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2019 that was filed with the Securities and Exchange Commission, or the SEC, on February 19, 2020. Our condensed consolidated financial statements include our accounts and the accounts of our wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP. Use of estimates The preparation of our condensed consolidated financial statements requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the results of which form the basis for making judgments about the carrying values of assets, liabilities and equity and the amount of revenues and expenses. The full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations and financial condition, including sales, expenses, reserves and allowances, clinical trials, research and development costs and employee-related amounts, will depend on future developments that are highly uncertain, including as a result of new information that may emerge concerning COVID-19 and the actions taken to contain the pandemic or treat COVID-19, as well as the economic impact on local, regional, national and international customers and markets. We have made estimates of the impact of COVID-19 within our financial statements and there may be changes to those estimates in future periods. Actual results may differ from these estimates. Liquidity On June 11, 2020, we sold our tiered, sales-based royalty rights on worldwide net sales of IDHIFA® (enasidenib), as well as our rights to receive up to $ 55.0 million in outstanding regulatory milestone payments from Bristol Myers Squibb, or BMS, to Royalty Pharma, or RPI, for $ 255.0 million. Under the 2010 Agreement, we remain eligible to receive a $ 25.0 million potential 7 Table of Contents milestone payment for the enasidenib program upon achievement of a specified ex-U.S. commercial milestone event, as well as reimbursement for costs incurred for our co-commercialization efforts and development activities. As of September 30, 2020, we had cash, cash equivalents and marketable securities of $ 722.4 million. Although we have incurred recurring losses and expect to continue to incur losses for the foreseeable future, we expect our cash, cash equivalents and marketable securities will be sufficient to fund current operations for at least the next twelve months from the issuance date of these financial statements. 2. Summary of Significant Accounting Policies Significant accounting policies In June 2016, the Financial Accounting Standards Board, or FASB issued Accounting Standards Update, or ASU 2016-13, Financial Instruments - Credit Losses (Topic 326), which introduces new guidance for the accounting for credit losses on instruments within its scope. The new guidance introduces an approach based on expected losses to estimate credit losses on certain types of financial instruments. Credit losses relating to available-for-sale debt securities will also be recorded through an allowance for credit losses rather than as a reduction in the amortized cost basis of the securities. The guidance is effective for fiscal years beginning after December 31, 2019, including interim periods within those years. In the quarter ended March 31, 2020, we adopted ASU 2016-13, which eliminated the concept of other-than-temporary impairments and required credit losses on debt securities to be recorded through an allowance for credit losses instead of as a reduction in the amortized cost basis of the securities. Application of the amendments is through a cumulative-effect adjustment to retained earnings as of the effective date. Based upon our analysis, the adoption of this final rule did not have a material impact on the financial statements. Liability related to sale of future revenue We treat the sale of future revenue to RPI as a debt financing, as we have significant continuing involvement in the generation of the cash flows. As result, we recorded the proceeds from this transaction as a liability related to the sale of future revenue to be amortized to interest expense using the effective interest rate method over the life of the arrangement. The liability related to sale of future revenue and the related interest expense are based on our current estimates of future royalties expected to be paid over the life of the arrangement. We will periodically assess the expected royalty payments using a combination of internal projections and forecasts from external sources. To the extent our future estimates of royalty payments are greater or less than previous estimates or the estimated timing of such payments is materially different than its previous estimates, we will prospectively recognize related non-cash interest expense. For further discussion of the sale of future revenue, refer to Note 10, Sale of Future Revenue . Amortization of issuance costs We treated the liability related to sale of future revenue as a debt financing. As such, the long-term liability is initially recorded at its proceeds, net of deferred costs. Issuance costs, fees directly related to the sale of future revenue, are offset against initial carrying value of the long-term liability and are amortized on a straight-line basis over the remaining patent life of the product to an operating expense. There have been no other material changes to the significant accounting policies previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2019. Recent accounting pronouncements Other accounting standards that have been issued by the FASB or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on our financial statements upon adoption. 3. Fair Value Measurements We record cash equivalents and marketable securities at fair value. Accounting Standards Codification, or ASC 820, Fair Value Measurements and Disclosures , establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and our own assumptions (unobservable inputs). The hierarchy consists of three levels: Level 1 – Unadjusted quoted prices in active markets for identical assets or liabilities. Level 2 – Quoted prices for similar assets and liabilities in active markets, quoted prices in markets that are not active, or inputs which are observable, directly or indirectly, for substantially the full term of the asset or liability. 8 Table of Contents Level 3 – Unobservable inputs that reflect our own assumptions about the assumptions market participants would use in pricing the asset or liability in which there is little, if any, market activity for the asset or liability at the measurement date. The following table summarizes our cash equivalents and marketable securities measured at fair value on a recurring basis as of September 30, 2020: (In thousands) Level 1 Level 2 Level 3 Total Cash equivalents $ 54,494 $ — $ — $ 54,494 Total cash equivalents 54,494 — — 54,494 Marketable securities: U.S. Treasuries — 145,087 — 145,087 Government securities — 155,725 — 155,725 Corporate debt securities — 316,761 — 316,761 Total marketable securities — 617,573 — 617,573 Total cash equivalents and marketable securities $ 54,494 $ 617,573 $ — $ 672,067 Cash equivalents and marketable securities have been initially valued at the transaction price and subsequently, at the end of each reporting period, valued utilizing third-party pricing services or other market observable data. The pricing services utilize industry standard valuation models, including both income and market-based approaches, and observable market inputs to determine value. After completing our validation procedures, we did not adjust or override any fair value measurements provided by the pricing services as of September 30, 2020. There have been no changes to the valuation methods during the nine months ended September 30, 2020. We evaluate transfers between levels at the end of each reporting period. We have no financial assets or liabilities that were classified as Level 3 at any point during the nine months ended September 30, 2020. 4. Marketable Securities Our marketable securities are classified as available-for-sale pursuant to ASC 320, Investments – Debt and Equity Securities , and are recorded at fair value. Unrealized gains are included as a component of accumulated other comprehensive income in the condensed consolidated balance sheets and statements of stockholders’ equity and a component of total comprehensive loss in the condensed consolidated statements of comprehensive loss, until realized. Unrealized losses are evaluated for impairment under ASC 326, Financial Instruments - Credit Losses , to determine if the impairment is credit-related or noncredit-related. Credit-related impairment is recognized as an allowance on the balance sheet with a corresponding adjustment to earnings, and noncredit-related impairment is recognized in other comprehensive income, net of taxes. Realized gains and losses are included in investment income on a specific-identification basis. There were no material realized gains or losses on marketable securities for the three and nine months ended September 30, 2020 or 2019. Marketable securities at September 30, 2020 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: U.S. Treasuries $ 139,583 $ 380 $ ( 4 ) $ 139,959 Government securities 94,336 77 ( 11 ) 94,402 Corporate debt securities 265,999 367 ( 43 ) 266,323 Total Current 499,918 824 ( 58 ) 500,684 Non-current: U.S. Treasuries 5,132 — ( 4 ) 5,128 Government securities 61,320 9 ( 6 ) 61,323 Corporate debt securities 50,540 1 ( 103 ) 50,438 Total Non-current 116,992 10 ( 113 ) 116,889 Total marketable securities $ 616,910 $ 834 $ ( 171 ) $ 617,573 9 Table of Contents Marketable securities at December 31, 2019 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: U.S. Treasuries $ 178,721 $ 58 $ ( 38 ) $ 178,741 Government securities 80,228 17 ( 16 ) 80,229 Corporate debt securities 224,928 139 ( 91 ) 224,976 Total Current 483,877 214 ( 145 ) 483,946 Non-current: U.S. Treasuries 35,296 3 ( 13 ) 35,286 Government securities 17,587 14 ( 10 ) 17,591 Corporate debt securities 99,913 239 ( 100 ) 100,052 Total Non-current 152,796 256 ( 123 ) 152,929 Total marketable securities $ 636,673 $ 470 $ ( 268 ) $ 636,875 As of September 30, 2020 and December 31, 2019, we held both current and non-current investments. Investments classified as current have maturities of less than one year. Investments classified as non-current are those that: (i) have a maturity of greater than one year, and (ii) we do not intend to liquidate within the next twelve months, although these funds are available for use and, therefore, are classified as available-for-sale. As of September 30, 2020 and December 31, 2019, we held 74 and 113 debt securities, respectively, that were in an unrealized loss position for less than one year. We did no t record an allowance for credit losses as of September 30, 2020 and December 31, 2019 related to these securities. The aggregate fair value of debt securities in an unrealized loss position at September 30, 2020 and December 31, 2019 was $ 247.7 million and $ 345.7 million, respectively. There were no individual securities that were in a significant unrealized loss position as of September 30, 2020 and December 31, 2019. Given our intent and ability to hold such securities until recovery, and the lack of significant change in the credit risk of these investments, we do not consider these marketable securities to be impaired as of September 30, 2020 and December 31, 2019. 5. Inventory Inventory, which consists of commercial supply of TIBSOVO®, consists of the following: (In thousands) September 30, 2020 December 31, 2019 Raw materials $ 1,406 $ 180 Work-in-process 9,166 6,808 Finished goods 799 343 Total inventory $ 11,371 $ 7,331 6. Leases Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of seven years and contain various clauses for renewal at our option. The renewal options were not included in the calculation of the operating lease assets and the operating lease liabilities as the renewal options are not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees. Operating lease costs for the three and nine months ended September 30, 2020 were $ 3.8 million and $ 11.4 million, respectively, and cash paid for amounts included in the measurement of operating lease liabilities for the three and nine months ended September 30, 2020 were $ 3.5 million and $ 10.9 million, respectively. Operating lease costs for the three and nine months ended September 30, 2019 were $ 3.8 million and $ 10.6 million, respectively, and cash paid for amounts included in the measurement of operating lease liabilities for the three and nine months ended September 30, 2019 were $ 2.2 million and $ 8.5 million, respectively. We have not entered into any material short-term leases or financing leases as of September 30, 2020. 10 Table of Contents As of September 30, 2020, undiscounted minimum rental commitments under non-cancelable leases, for each of the next five years and total thereafter were as follows: (In thousands) Remaining 2020 $ 2,364 2021 14,380 2022 16,773 2023 18,126 2024 18,660 2025 19,507 Thereafter 44,385 Undiscounted minimum rental commitments $ 134,195 Interest ( 27,621 ) Operating lease liabilities $ 106,574 In arriving at the operating lease liabilities as of September 30, 2020 and December 31, 2019, we applied the weighted-average incremental borrowing rate of 5.7 % for both periods over a weighted-average remaining lease term of 7.4 years and 8.2 years, respectively. 7. Accrued Expenses Accrued expenses consist of the following: (In thousands) September 30, 2020 December 31, 2019 Accrued compensation $ 19,044 $ 18,982 Accrued research and development costs 16,188 21,777 Accrued professional fees 3,474 8,335 Accrued revenue-related reserves and other 11,018 4,048 Total accrued expenses $ 49,724 $ 53,142 8. Product Revenue We sell TIBSOVO®, our wholly owned product, to a limited number of specialty distributors and specialty pharmacy providers, or collectively, the Customers. The Customers subsequently resell TIBSOVO® to pharmacies or dispense directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of TIBSOVO®. The performance obligation related to the sale of TIBSOVO® is satisfied and revenue is recognized when the Customer obtains control of the product, which occurs at a point in time, typically upon delivery to the Customer. Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Product revenue, net $ 31,716 $ 17,422 $ 81,971 $ 40,287 Reserves for Variable Consideration Revenues from product sales are recorded at the net sales price, or transaction price, which includes estimates of variable consideration for which reserves are established and result from contractual adjustments, government rebates, returns and other allowances that are offered within the contracts with our Customers, healthcare providers, payors and other indirect customers relating to the sale of our products. 11 Table of Contents Contractual Adjustments We generally provide Customers with discounts, including prompt pay discounts, and allowances that are explicitly stated in the contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive sales order management, data and distribution services from certain Customers. Chargebacks for fees and discounts represent the estimated obligations resulting from contractual commitments to sell products to qualified healthcare providers at prices lower than the list prices charged to Customers who directly purchase the product from us. Customers charge us for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These reserves are estimated using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated channel mix and are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue. Government Rebates Government rebates include Medicare, TriCare, and Medicaid rebates, which we estimate using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated payor mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue. 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. Returns We estimate the amount of product sales that may be returned by Customers and record this estimate as a reduction of revenue in the period the related product revenue is recognized. We currently estimate product return liabilities using the expected value method, based on available industry data, including our visibility into the inventory remaining in the distribution channel. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the nine months ended September 30, 2020: (In thousands) Contractual Adjustments Government Rebates Returns Total Balance at December 31, 2019 $ 874 $ 1,124 $ 1,798 $ 3,796 Current provisions relating to sales in the current year 10,261 9,299 1,296 20,856 Adjustments relating to prior years ( 3 ) 122 ( 476 ) ( 357 ) Payments/returns relating to sales in the current year ( 8,966 ) ( 2,260 ) — ( 11,226 ) Payments/returns relating to sales in the prior years ( 653 ) ( 677 ) — ( 1,330 ) Balance at September 30, 2020 $ 1,513 $ 7,608 $ 2,618 $ 11,739 Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows: (In thousands) September 30, 2020 December 31, 2019 Reduction of accounts receivable $ 732 $ 540 Component of accrued expenses 11,007 3,256 Total revenue-related reserves $ 11,739 $ 3,796 The following table presents changes in our contract assets during the nine months ended September 30, 2020: (In thousands) December 31, 2019 Additions Deductions September 30, 2020 Contract assets (1) Accounts receivable, net $ 8,952 $ 102,504 $ ( 92,467 ) $ 18,989 (1) Additions to contract assets relate to amounts billed to Customers for product sales and deductions to contract assets primarily relate to collection of receivables during the reporting period. 9. Collaboration and License Agreements Accounting analysis and revenue recognition Our collaboration and license agreements typically involve us granting licenses of our intellectual property and performing research and development services in exchange of upfront fees, milestone payments and royalty payments. Since December 31, 12 Table of Contents 2019, there have been no material changes to the key terms of our collaboration or license agreements. For further information on the terms and conditions of our existing collaboration and license agreements, please see the notes to the consolidated financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2019. Collaboration revenue We recognize revenue when the customer obtains control of promised goods or services, in an amount that reflects the consideration that we expect to receive in exchange for those goods or services . In determining the appropriate amount of revenue to be recognized, we performed the following steps: (i) identified the promised goods or services in the contract; (ii) determined whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measured the transaction price, including the constraint on variable consideration; (iv) allocated the transaction price to the performance obligations; and (v) recognized revenue when (or as) we satisfied each performance obligation. Royalty revenue For arrangements that include sales-based royalties and sales-based milestones and in which the license is deemed to be the predominant item to which the royalties relate, we recognize royalty revenue upon the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). Milestone revenue At each reporting period we evaluate whether milestones are considered probable of being reached and, to the extent that a significant reversal would not occur in future periods, estimate the amount to be included in the transaction price using the most likely amount method. Milestone payments that are not within our control, such as regulatory approvals, are considered constrained and are excluded from the transaction price until those approvals are received. Celgene Corporation We have entered into the following collaboration agreements, or collectively, the Collaboration Agreements, with Celgene, a wholly owned subsidiary of BMS, which is a related party through ownership of our common stock: • In April 2010, we entered into a discovery and development collaboration and license agreement focused on cancer metabolism, or the 2010 Agreement, which was amended in October 2011 and July 2014. The discovery phase of the 2010 Agreement expired in April 2016. On August 15, 2016, we terminated the 2010 Agreement as to the program directed to the isocitrate dehydrogenase 1, or IDH1, target, for which ivosidenib was the lead development candidate. Accordingly, the sole program remaining under the 2010 Agreement is IDHIFA® (enasidenib), a co-commercialized licensed program for which Celgene leads and funds global development and commercialization activities. On June 11, 2020, we sold our tiered, sales-based royalty rights on worldwide net sales of IDHIFA® (enasidenib), as well as our rights to receive up to $ 55.0 million in outstanding regulatory milestone payments from BMS, to RPI for $ 255.0 million. Under the 2010 Agreement, we remain eligible to receive a $ 25.0 million potential milestone payment for the enasidenib program upon achievement of a specified ex-U.S. commercial milestone event, as well as reimbursement for costs incurred for our co-commercialization efforts and development activities. • In April 2015, we entered into a joint worldwide development and profit share collaboration and license agreement with Celgene, and our wholly owned subsidiary, Agios International Sarl, entered into a collaboration and license agreement with Celgene International II Sarl, or collectively, the AG-881 Agreements, to establish a worldwide collaboration focused on the development and commercialization of vorasidenib products. Under the AG-881 Agreements, we and Celgene split all worldwide development costs for vorasidenib, subject to specified exceptions. The AG-881 Agreements were terminated effective September 4, 2018, upon which we received sole global rights to vorasidenib. In connection with the termination of the AG-881 Agreements, Celgene will be eligible to receive royalties from us at a low single-digit percentage rate on worldwide net sales of products containing vorasidenib. • In May 2016, we entered into a master research and collaboration agreement with Celgene, or the 2016 Agreement, focused on metabolic immuno-oncology, or MIO, a developing field which aims to modulate the activity of relevant immune cells by targeting critical metabolic nodes, thereby enhancing the immune mediated anti-tumor response. The initial four-year research term of the 2016 Agreement ended May 2020. On March 25, 2020 Celgene declined the option to extend the research agreement for up to two , or in specified cases, up to four additional one-year terms which would have required the payment of a $ 40.0 million extension fee. Further, on April 10, 2020 Celgene notified us that they will be declining to elect any program as a continuation program under the 2016 agreement. Celgene had designated AG-270, our inhibitor of methionine adenosyltransferase 2a, or MAT2A, as a development candidate under the 2016 Agreement. On March 25, 2020, Celgene notified us of their decision to decline their option to enter into a Development & Commercialization Agreement with respect to the MAT2A program under the 2016 Agreement which 13 Table of Contents would have required the payment of a $ 30.0 million fee. As a result of the decisions, the research services were fully satisfied as of May 17, 2020, no additional performance obligations remain under the 2016 Agreement and we are no longer eligible for any milestone payments for the 2016 Agreement. Collaboration revenue During the three and nine months ended September 30, 2020 and 2019, we recognized the following collaboration revenue: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Services performed that were considered performance obligations as of the modification dates On-going research and development services $ 199 $ 4,695 $ 64,133 $ 29,915 Services performed that were not considered performance obligations as of the modification dates Commercialization activities 1,007 821 2,905 2,499 Total collaboration revenue - related party $ 1,206 $ 5,516 $ 67,038 $ 32,414 The following table presents changes in our contract assets and liabilities during the nine months ended September 30, 2020: (In thousands) December 31, 2019 Additions Deductions September 30, 2020 Contract assets Collaboration receivable – related party (1) $ 1,539 $ 4,228 $ ( 4,693 ) $ 1,074 Unbilled receivable - related party (2) — 1,606 ( 346 ) 1,260 Royalty receivable – related party (3) 2,900 5,015 ( 7,915 ) — Contract liabilities Deferred revenue – related party, current and net of current portions (4) 61,513 2,421 ( 63,934 ) — (1) Additions to collaboration receivables - related party relate to amounts billed to Celgene for reimbursable costs incurred by us during the reporting period. Deductions to receivables relate to collection of receivables during the reporting period. (2) Unbilled receivables - related party amounts relate to future reimbursable costs to Celgene. (3) Additions to royalty receivables - related party relate to amounts billed to Celgene during the reporting period. Deductions to receivables relate to collection of receivables during the reporting period. (4) Additions to deferred revenue - related party relate to consideration from Celgene during the reporting period. Deductions relate to deferred revenue recognized as revenue during the reporting period. The change in collaboration revenue from on-going research and development services during the three and nine months ended September 30, 2020 is primarily due to our updated estimate of the future costs that would be incurred from on-going research and development services to complete one of our performance obligations under the 2016 Agreement that is recognized over time using an input method, due to Celgene’s decision to decline extending the research term in the first quarter of 2020. During the three and nine months ended September 30, 2020 and 2019, we recognized the following as revenue due to changes in the contract liability balances: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Amounts included in the contract liability at the beginning of the period $ — $ 4,404 $ 61,513 $ 28,823 Performance obligations satisfied in previous periods — — — — As of September 30, 2020, the aggregate amount of the transaction price allocated to performance obligations that are partially unsatisfied was $ 4.5 million. This amount is expected to be recognized as performance obligations are satisfied through September 2023. 14 Table of Contents Royalty revenue As the underlying performance obligation, or delivery of the enasidenib license, had been satisfied as of June 2014, royalty revenue is recognized as the related sales occur. During the three and nine months ended September 30, 2020 and 2019, we recognized the following as royalty revenue: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Royalty revenue – related party $ 683 $ 2,666 $ 7,356 $ 7,569 On June 11, 2020, we sold our tiered, sales-based royalty rights on worldwide net sales of IDHIFA® (enasidenib), as well as our rights to receive up to $ 55.0 million in outstanding regulatory milestone payments from BMS, to RPI for $ 255.0 million. For further discussion of the sale of future revenue, refer to Note 10, Sale of Future Revenue . Milestone revenue No milestones were achieved during the three and nine months ended September 30, 2020 or 2019. The next potential milestone expected to be achieved under the remaining terms of our Collaboration Agreements is the achievement of a specified ex-U.S. commercial milestone event, which would result in a milestone payment of $ 25.0 million under the 2010 Agreement. CStone Pharmaceuticals In June 2018, we and CStone Pharmaceuticals, or CStone, entered into an exclusive license agreement, or the CStone Agreement, to grant CStone specified intellectual property licenses to enable CStone to develop and commercialize certain products containing ivosidenib in mainland China, Hong Kong, Macau and Taiwan, or the CStone Territory. We retain development and commercialization rights for the rest of the world. On March 2, 2020, we amended the CStone Agreement to include Singapore as part of the CStone Territory. Pursuant to the CStone Agreement, CStone will initially be responsible for the development and commercialization of ivosidenib in acute myeloid leukemia, or AML, cholangiocarcinoma, and, at our discretion, brain cancer indications. CStone is responsible for all costs it incurs in developing, obtaining regulatory approval of, and commercializing ivosidenib in the CStone Territory, as well as certain costs incurred by us. Pursuant to the CStone Agreement, we received an initial upfront payment in the amount of $ 12.0 million and are entitled to receive up to an additional $ 407.0 million in milestone payments upon the achievement of certain development, regulatory and sales milestone events. We will also be entitled to receive tiered royalties, ranging from 15 % to 19 % percent, on annual net sales, if any, of ivosidenib in the CStone Territory. Collaboration revenue During the three and nine months ended September 30, 2020 and 2019, we recognized the following collaboration revenue -other: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Services performed that were considered performance obligations as of the inception date License and other services $ — $ ( 103 ) $ 192 $ ( 103 ) Services performed that were not considered performance obligations as of the inception date Other services 1,101 523 2,594 2,305 Total collaboration revenue - other $ 1,101 $ 420 $ 2,786 $ 2,202 The following table presents changes in our contract assets during the nine months ended September 30, 2020: (In thousands) December 31, 2019 Additions Deductions September 30, 2020 Contract assets (1) Collaboration receivable - other $ 1,928 $ 2,786 $ ( 2,722 ) $ 1,992 (1) Additions to contract assets relate to amounts receivable from CStone. Deductions to contract assets relate to collection of receivables during the reporting period. 15 Table of Contents As of September 30, 2020, the aggregate amount of the transaction price allocated to performance obligations that are partially unsatisfied was $ 0.5 million. Royalty revenue The license was determined to be the predominant item to which sales-based royalties and sales-based milestones relate. As the license was delivered in June 2018, we will recognize royalty revenue when the related sales occur. To date, no royalties have been received under the CStone Agreement. Milestone revenue No milestones were earned during the three and nine months ended September 30, 2020 and 2019. The next potential milestone expected to be achieved under the CStone Agreement is the dosing of the first patient in a local study in a solid tumor indication in mainland China. Achievement of this event will result in a milestone payment of $ 5.0 million. 10. Sale of Future Revenue On June 11, 2020, we sold our tiered, sales-based royalty rights on worldwide net sales of IDHIFA® (enasidenib), as well as our rights to receive up to $ 55.0 million in outstanding regulatory milestone payments from BMS, to RPI for $ 255.0 million. The gross proceeds of $ 255.0 million approximate the fair value of the liability related to the sale of future revenue based on a discounted cash flow model. The fair value for the liability related to the sale of future revenue at the time of the transaction was based on our current estimates of future royalties expected to be paid to RPI over the remaining patent life of the product, which are considered level 3 inputs. Under the terms of the Purchase Agreement, although we sold all of our rights to receive royalties on worldwide net sales of IDHIFA® and future regulatory milestone payments, we continue to co-promote IDHIFA® and are therefore involved in the generation of these royalties. Due to our continuing involvement, we will continue to account for any royalties earned as revenue. We recorded the net proceeds from this transaction as a liability related to sale of future revenue, or Royalty Obligation, that will be amortized using the effective interest method over the remaining patent life. As royalties are remitted to RPI from BMS, the balance of the Royalty Obligation will be effectively repaid over the life of the BMS license agreement. In order to determine the amortization of the Royalty Obligation, we are required to estimate the total amount of future royalty payments to RPI over the life of the BMS license agreement. The $ 255.0 million recorded will be accreted to the total of these royalty payments as interest expense over the life of the Royalty Obligation. At execution, our estimate of this total interest expense resulted in an effective annual interest rate of approximately 16.4 %. This estimate contains significant assumptions that impact both the amount recorded at execution and the interest expense that will be recognized over the royalty period. We will periodically assess the estimated royalty payments to RPI from BMS and to the extent the amount or timing of such payments is materially different than the original estimates, an adjustment will be recorded prospectively to increase or decrease interest expense. There are a number of factors that could materially affect the amount and timing of royalty payments to RPI from BMS, and correspondingly, the amount of interest expense recorded by us, most of which are not within our control. Such factors include, but are not limited to, delays or discontinuation of development of enasidenib, regulatory approval, changing standards of care, the introduction of competing products, manufacturing or other delays, generic competition, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of the drug products, significant changes in foreign exchange rates as the royalties remitted to RPI are made in U.S. dollars (USD) while the underlying sales of enasidenib will be made in currencies other than USD, and other events or circumstances that are not currently foreseen. Changes to any of these factors could result in increases or decreases to both royalty revenues and interest expense. The following table shows the activity of the Royalty Obligation since the transaction inception through September 30, 2020: (in thousands) September 30, 2020 Proceeds from the sale of future revenue $ 255,000 Issuance costs ( 4,463 ) Non-cash royalty related to the sale of future revenue ( 4,341 ) Non-cash interest expense associated with the sale of future revenue 11,818 Amortization of issuance costs 107 Liability related to the sale of future revenue $ 258,121 During the three and nine months ended September 30, 2020, $ 2.7 million and $ 4.3 million of non-cash royalty revenue from net sales of IDHIFA® were recognized, respectively . 16 Table of Contents 11. Share-Based Payments 2013 Stock Incentive Plan In June 2013, our Board of Directors adopted and, in July 2013 our stockholders approved, the 2013 Stock Incentive Plan, or the 2013 Plan. The 2013 Plan became effective upon the closing of our initial public offering and provides for the grant of incentive stock options, non-qualified stock options, stock appreciation rights, restricted stock awards, restricted stock units, or RSUs, performance-based stock units, or PSUs, and other stock-based awards to employees, non-employees and non-employee directors. Following the adoption of the 2013 Plan, we granted no further stock options or other awards under the 2007 Stock Incentive Plan, or the 2007 Plan. Any options or awards outstanding under the 2007 Plan at the time of adoption of the 2013 Plan remain outstanding and effective. As of September 30, 2020, the total number of shares reserved under the 2007 Plan and the 2013 Plan was 10,680,089 , and we had 2,919,442 shares available for future issuance under the 2013 Plan. Stock options The following table presents stock option activity for the nine months ended September 30, 2020: Number of Stock Options Weighted-Average Exercise Price Outstanding at December 31, 2019 6,201,485 $ 58.61 Granted 956,945 49.84 Exercised ( 339,284 ) 19.51 Forfeited/Expired ( 448,901 ) 65.98 Outstanding at September 30, 2020 6,370,245 $ 58.85 Exercisable at September 30, 2020 4,067,553 $ 61.23 Vested and expected to vest at September 30, 2020 6,370,245 $ 58.85 At September 30, 2020, there was approximately $ 77.4 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.4 years. Restricted stock units The following table presents RSU activity for the nine months ended September 30, 2020: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2019 766,953 $ 63.44 Granted 829,791 50.33 Vested ( 258,461 ) 69.12 Forfeited ( 132,805 ) 58.31 Unvested shares at September 30, 2020 1,205,478 $ 53.77 As of September 30, 2020, there was approximately $ 41.7 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 1.9 years. Performance-based stock units The following table presents PSU activity for the nine months ended September 30, 2020: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2019 218,143 $ 55.64 Granted 20,622 48.49 Vested ( 78,920 ) 54.82 Forfeited ( 17,616 ) 61.93 Unvested shares at September 30, 2020 142,229 $ 54.28 Stock-based compensation expense associated with these PSUs is recognized if the underlying performance condition is considered probable of achievement using our management’s best estimates. 17 Table of Contents As of September 30, 2020, there was no unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered probable of achievement, and $ 5.9 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered not probable of achievement. Market-based stock units The following table presents market-based stock unit, or MSU, activity for the nine months ended September 30, 2020: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2019 42,695 $ 41.50 Granted — — Unvested shares at September 30, 2020 42,695 $ 41.50 The fair value of MSUs are estimated using a Monte Carlo simulation model. Assumptions and estimates utilized in the model include the risk-free interest rate, dividend yield, expected stock volatility and the estimated period to achievement of the market condition. As of September 30, 2020, there was no remaining unrecognized compensation expense related to MSUs. 2013 Employee Stock Purchase Plan In June 2013, our Board of Directors adopted, and in July 2013 our stockholders approved, the 2013 Employee Stock Purchase Plan, or the 2013 ESPP. We issued and sold 120,293 and 77,981 shares of common stock during the nine months ended September 30, 2020 and 2019, respectively, under the 2013 ESPP. The 2013 ESPP provides participating employees with the opportunity to purchase up to an aggregate of 836,363 shares of our common stock. As of September 30, 2020, we had 471,353 shares of common stock available for future issuance under the 2013 ESPP. Stock-based compensation expense Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Stock options $ 11,289 $ 11,552 $ 34,395 $ 37,065 Restricted stock units 6,538 4,917 20,450 14,708 Performance-based stock units — 1,495 1,866 1,681 Employee stock purchase plan 339 350 1,035 1,070 Other stock awards 241 274 781 719 Total stock-based compensation expense $ 18,407 $ 18,588 $ 58,527 $ 55,243 Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations: Three Months Ended September 30, Nine Months Ended September 30, (In thousands) 2020 2019 2020 2019 Research and development expense $ 8,742 $ 9,860 $ 28,464 $ 29,969 Selling, general and administrative expense 9,665 8,728 30,063 25,274 Total stock-based compensation expense $ 18,407 $ 18,588 $ 58,527 $ 55,243 12. Loss per Share Basic net loss per share is calculated by dividing net loss by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury stock method. For purposes of the dilutive net loss per share calculation, stock options, RSUs, PSUs and MSUs for which the performance and market vesting conditions, respectively, have been deemed probable, and 2013 ESPP shares are considered to 18 Table of Contents be common stock equivalents, while PSUs and MSUs with performance and market vesting conditions, respectively, that were not deemed probable as of September 30, 2020 are not considered to be common stock equivalents. Since we had a net loss for all periods presented, the effect of all potentially dilutive securities is anti-dilutive. Accordingly, basic and diluted net loss per share was the same for all periods presented. The following common stock equivalents were excluded from the calculation of diluted net loss per share applicable to common stockholders for the periods indicated because including them would have had an anti-dilutive effect: Three and Nine Months Ended September 30, 2020 2019 Stock options 6,370,245 6,185,935 Restricted stock units 1,205,478 733,100 Performance-based stock units — — Employee stock purchase plan shares 13,201 13,754 Total common stock equivalents 7,588,924 6,932,789 19 Table of Contents