PART I. FINANCIAL INFORMATION [Financial Statements (Unaudited)](index=4&type=section&id=Item%201.%20Financial%20Statements%20(Unaudited)) The unaudited Q1 2019 financial statements reflect significant revenue growth driven by TIBSOVO®, an increased net loss, and balance sheet changes from new lease accounting standards [Condensed Consolidated Balance Sheets](index=4&type=section&id=Condensed%20Consolidated%20Balance%20Sheets) The balance sheet as of March 31, 2019, shows decreased total assets and stockholders' equity, with increased liabilities primarily due to ASC 842 adoption Condensed Consolidated Balance Sheet Highlights (in thousands) | Account | March 31, 2019 | December 31, 2018 | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $103,443 | $70,502 | | Marketable securities (current & non-current) | $604,348 | $734,919 | | Total assets | $822,131 | $858,457 | | **Liabilities & Equity** | | | | Operating lease liabilities (current & non-current) | $75,134 | $0 | | Total liabilities | $201,874 | $170,920 | | Total stockholders' equity | $620,257 | $687,537 | | Total liabilities and stockholders' equity | $822,131 | $858,457 | - The company adopted the new lease accounting standard ASC 842 on January 1, 2019, resulting in the recognition of **$59.9 million** in operating lease assets and **$77.3 million** in operating lease liabilities[22](index=22&type=chunk) [Condensed Consolidated Statements of Operations](index=5&type=section&id=Condensed%20Consolidated%20Statements%20of%20Operations) Q1 2019 statements show total revenue significantly increased to **$30.2 million**, driven by TIBSOVO® sales, while rising expenses led to a **$93.1 million** net loss Consolidated Statements of Operations Highlights (in thousands) | Metric | Three Months Ended March 31, 2019 | Three Months Ended March 31, 2018 | | :--- | :--- | :--- | | Product revenue, net | $9,138 | $0 | | Collaboration revenue | $18,889 | $7,345 | | Royalty revenue | $2,200 | $1,417 | | **Total revenue** | **$30,227** | **$8,762** | | Research and development | $95,585 | $78,224 | | Selling, general and administrative | $31,791 | $24,550 | | **Total cost and expenses** | **$127,710** | **$102,774** | | **Net loss** | **($93,078)** | **($90,825)** | | **Net loss per share** | **($1.59)** | **($1.63)** | [Condensed Consolidated Statements of Cash Flows](index=9&type=section&id=Condensed%20Consolidated%20Statements%20of%20Cash%20Flows) Q1 2019 cash flows show increased cash used in operations, a significant shift to cash provided by investing activities, and a net increase in cash and cash equivalents Cash Flow Summary (in thousands) | Activity | Three Months Ended March 31, 2019 | Three Months Ended March 31, 2018 | | :--- | :--- | :--- | | Net cash used in operating activities | ($103,271) | ($99,000) | | Net cash provided by (used in) investing activities | $131,352 | ($167,532) | | Net cash provided by financing activities | $4,860 | $528,277 | | **Net change in cash and cash equivalents** | **$32,941** | **$261,745** | | **Cash and cash equivalents at end of period** | **$103,443** | **$364,469** | [Notes to Condensed Consolidated Financial Statements](index=10&type=section&id=Notes%20to%20Condensed%20Consolidated%20Financial%20Statements) Notes to financial statements detail accounting policies, the impact of ASC 842, revenue sources like TIBSOVO® and collaborations, and the company's liquidity position - As of March 31, 2019, the company had cash, cash equivalents and marketable securities of **$707.8 million** and expects these funds to be sufficient for operations for at least the next twelve months[20](index=20&type=chunk) - TIBSOVO® was approved by the FDA on July 20, 2018, for treating adult patients with R/R AML with a susceptible IDH1 mutation, marking the beginning of the company's product revenue generation[40](index=40&type=chunk) Collaboration Revenue by Partner (in thousands) | Partner | Three Months Ended March 31, 2019 | Three Months Ended March 31, 2018 | | :--- | :--- | :--- | | Celgene (related party) | $17,919 | $7,345 | | CStone (other) | $970 | $0 | - Total stock-based compensation expense was **$18.1 million** for Q1 2019, an increase from **$14.5 million** in Q1 2018, with the majority (**$10.0 million**) allocated to R&D expenses[71](index=71&type=chunk)[72](index=72&type=chunk) [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=25&type=section&id=Item%202.%20Management%27s%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses Q1 2019 financial performance, highlighting significant revenue growth from TIBSOVO® and increased R&D and SG&A expenses to advance its clinical pipeline Results of Operations Comparison (in thousands) | Metric | Q1 2019 | Q1 2018 | $ Change | % Change | | :--- | :--- | :--- | :--- | :--- | | Total revenue | $30,227 | $8,762 | $21,465 | 245% | | Research and development | $95,585 | $78,224 | $17,361 | 22% | | Selling, general and administrative | $31,791 | $24,550 | $7,241 | 29% | | Loss from operations | ($97,483) | ($94,012) | ($3,471) | 4% | | Net loss | ($93,078) | ($90,825) | ($2,253) | 2% | R&D Expense by Program (in thousands) | Program | Q1 2019 | Q1 2018 | % Change | | :--- | :--- | :--- | :--- | | Ivosidenib (IDH1m inhibitor) | $36,072 | $30,507 | 18% | | Mitapivat (PKR activator) | $19,356 | $13,115 | 48% | | Vorasidenib (Brain-penetrant IDHm inhibitor) | $5,347 | $3,681 | 45% | | Other research and platform programs | $23,773 | $22,354 | 6% | | **Total R&D expenses, net** | **$95,585** | **$78,224** | **22%** | - The company expects its existing cash, cash equivalents, and marketable securities, along with anticipated revenues and reimbursements, will fund operations and capital expenditures through at least the end of 2020[101](index=101&type=chunk) - Key clinical milestones include the expected top-line results for the Phase 3 ClarIDHy trial of ivosidenib in cholangiocarcinoma in Q2 2019 and the planned initiation of a Phase 3 study of vorasidenib in low-grade glioma by the end of 2019[90](index=90&type=chunk)[91](index=91&type=chunk) [Quantitative and Qualitative Disclosures About Market Risk](index=35&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) The company's primary market risk is interest rate sensitivity on its investment portfolio, with minimal exposure to foreign currency fluctuations, and no material impact expected from rate changes - The company's main market risk is interest rate sensitivity on its investment portfolio of **$707.8 million** as of March 31, 2019[105](index=105&type=chunk) - Due to the short-term nature of its investments, a **1% (100 basis point)** increase in interest rates is not expected to materially impact the portfolio's fair market value[105](index=105&type=chunk) - The company has minimal exposure to foreign currency risk from contracts with international CROs and does not currently use hedging instruments[105](index=105&type=chunk) [Controls and Procedures](index=35&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded that disclosure controls and procedures were effective as of March 31, 2019, with no material changes to internal control over financial reporting during the quarter - Management concluded that as of March 31, 2019, the company's disclosure controls and procedures were effective at a reasonable assurance level[106](index=106&type=chunk)[107](index=107&type=chunk) - No material changes to the company's internal control over financial reporting occurred during the first quarter of 2019[107](index=107&type=chunk) PART II. OTHER INFORMATION [Risk Factors](index=37&type=section&id=Item%201A.%20Risk%20Factors) The company faces significant risks including a history of losses, funding dependency, reliance on TIBSOVO® and collaborators, clinical trial failures, intense competition, and complex regulatory and intellectual property challenges [Risks Related to Financial Position and Capital Needs](index=37&type=section&id=Risks%20Related%20to%20Our%20Financial%20Position%20and%20Need%20for%20Additional%20Capital) The company's history of significant operating losses and accumulated deficit necessitates substantial additional funding, with failure to secure it risking program delays or termination - The company has incurred significant operating losses since inception, with a net loss of **$93.1 million** for Q1 2019 and an accumulated deficit of **$1.2 billion** as of March 31, 2019[110](index=110&type=chunk) - Substantial additional funding is required to continue operations. The current cash runway is expected to last through at least the end of 2020, but this is based on assumptions that may prove wrong[111](index=111&type=chunk) [Risks Related to Product Discovery, Development, and Commercialization](index=39&type=section&id=Risks%20Related%20to%20the%20Discovery%2C%20Development%2C%20and%20Commercialization%20of%20our%20Product%20Candidates) Success hinges on developing and commercializing product candidates like TIBSOVO®, facing risks from clinical trial failures, patient enrollment challenges, intense competition, and market acceptance hurdles - The company's ability to generate product revenue depends heavily on the successful commercialization of TIBSOVO® and the development of other candidates like enasidenib, vorasidenib, and mitapivat[116](index=116&type=chunk)[118](index=118&type=chunk) - Clinical development is fraught with risk, including potential trial failures, delays, and unforeseen adverse side effects, which could prevent or delay marketing approval[120](index=120&type=chunk)[121](index=121&type=chunk) - The company faces substantial competition from major pharmaceutical and biotechnology companies with greater resources, including those with therapies for AML and other cancers[127](index=127&type=chunk)[128](index=128&type=chunk) - Commercial success depends on market acceptance by physicians and payors, and the company faces uncertainty regarding third-party coverage and reimbursement, which are critical for profitability[126](index=126&type=chunk)[129](index=129&type=chunk) [Risks Related to Dependence on Third Parties](index=52&type=section&id=Risks%20Related%20to%20Our%20Dependence%20on%20Third%20Parties) The company's operations and revenue are highly dependent on third parties, including Celgene for IDHIFA® commercialization and CROs for development, with merger uncertainty impacting collaborations - The company is heavily reliant on Celgene for the development and commercialization of IDHIFA®, and its revenue from this product depends on Celgene's performance[132](index=132&type=chunk) - The announced merger between Bristol-Myers Squibb and Celgene creates uncertainty, as BMS could reprioritize or terminate programs post-acquisition[133](index=133&type=chunk)[134](index=134&type=chunk) - The company relies on third-party CROs to conduct clinical trials and on contract manufacturers for product supply, which exposes it to risks of non-performance, delays, and regulatory compliance failures[135](index=135&type=chunk)[136](index=136&type=chunk) [Risks Related to Intellectual Property](index=58&type=section&id=Risks%20Related%20to%20Our%20Intellectual%20Property) Success relies on obtaining and defending intellectual property, facing risks from uncertain patent processes, potential litigation, and challenges in protecting trade secrets for its technology - The company's success is highly dependent on its ability to obtain and maintain patent protection for its products and technology, a process which is expensive, time-consuming, and uncertain[138](index=138&type=chunk) - The company may face costly lawsuits to protect its patents or defend against claims that it infringes on third-party intellectual property, which could divert resources and harm the business[140](index=140&type=chunk) - The company relies on trade secrets, particularly for its cellular metabolism technology platform, which are difficult to protect and could be lost through disclosure or independent discovery by competitors[142](index=142&type=chunk) [Risks Related to Regulatory Approval and Legal Compliance](index=60&type=section&id=Risks%20Related%20to%20Regulatory%20Approval%20of%20Our%20Product%20Candidates%20and%20Other%20Legal%20Compliance%20Matters) The company faces extensive regulatory approval challenges, ongoing compliance burdens including healthcare fraud and data privacy laws, and uncertainties from potential healthcare reform and drug pricing pressures - The regulatory approval process for product candidates is expensive, time-consuming, and uncertain, and failure to obtain approvals will prevent commercialization[143](index=143&type=chunk) - The company is subject to complex healthcare laws, including anti-kickback and false claims statutes, and non-compliance could lead to criminal sanctions, civil penalties, and exclusion from government healthcare programs[147](index=147&type=chunk) - Legislative and regulatory changes, including potential repeal or replacement of the ACA and measures to control drug pricing, could increase costs and negatively affect product prices and reimbursement[150](index=150&type=chunk)[151](index=151&type=chunk)[152](index=152&type=chunk) - Compliance with global data privacy laws like the EU's GDPR imposes significant costs and obligations, with non-compliance carrying the risk of substantial fines[131](index=131&type=chunk)[149](index=149&type=chunk) [Exhibits](index=75&type=section&id=Item%206.%20Exhibits) This section lists exhibits filed with the Form 10-Q, including officer certifications and XBRL Interactive Data Files - Lists exhibits filed with the report, including officer certifications (31.1, 31.2, 32.1, 32.2) and XBRL data files (101 series)[169](index=169&type=chunk) [Signatures](index=76&type=section&id=Signatures) The report was signed on May 2, 2019, by the Chief Executive Officer and Chief Financial Officer of Agios Pharmaceuticals, Inc - The report was signed on May 2, 2019, by the company's Chief Executive Officer and Chief Financial Officer[172](index=172&type=chunk)

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 Form 10-K (Mark One) ☑ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2018 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Commission File Number: 001-36014 AGIOS PHARMACEUTICALS, INC. (Exact name of registrant as specified in its charter) Delaware 26-0662915 (State or other jurisdiction of incorpora ...