0001439222-19-000017 | 10-Q | XBRL Viewer | Agios Pharmaceuticals INC

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Inventory - Schedule of Inventory (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Inventory Disclosure [Abstract]
Raw materials	$ 180	$ 0
Work-in-process	4,392	788
Finished goods	87	81
Total inventory	$ 4,659	$ 869

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 83,580	$ 70,502
Marketable securities	411,810	514,800
Accounts receivable, net	7,147	5,076
Collaboration receivable – related party	2,524	2,462
Collaboration receivable – other	2,222	670
Royalty receivable – related party	2,700	2,234
Inventory	4,659	869
Prepaid expenses and other current assets	19,063	17,167
Total current assets	533,705	613,780
Marketable securities	128,649	220,119
Operating lease assets	98,500
Property and equipment, net	23,016	24,320
Other non-current assets	0	238
Total assets	783,870	858,457
Current liabilities:
Accounts payable	15,435	17,880
Accrued expenses	49,218	42,147
Deferred revenue – related party	18,454	32,710
Operating lease liabilities	6,397
Deferred rent	0	766
Total current liabilities	89,504	93,503
Deferred revenue, net of current portion – related party	51,616	59,809
Operating lease liabilities, net of current portion	110,073
Deferred rent, net of current portion	0	17,608
Total liabilities	251,193	170,920
Stockholders’ equity:
Preferred stock, $0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at June 30, 2019 and December 31, 2018	0	0
Common stock, $0.001 par value; 125,000,000 shares authorized; 58,749,186 and 58,218,653 shares issued and outstanding at June 30, 2019 and December 31, 2018, respectively	59	58
Additional paid-in capital	1,839,710	1,794,283
Accumulated other comprehensive income (loss)	490	(2,171)
Accumulated deficit	(1,307,582)	(1,104,633)
Total stockholders’ equity	532,677	687,537
Total liabilities and stockholders’ equity	$ 783,870	$ 858,457

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Statement of Comprehensive Income [Abstract]
Net loss	$ (109,871)	$ (68,745)	$ (202,949)	$ (159,570)
Other comprehensive income (loss)
Unrealized gain (loss) on available-for-sale securities	974	245	2,661	(1,009)
Comprehensive loss	$ (108,897)	$ (68,500)	$ (200,288)	$ (160,579)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Collaboration and License Agreements - Schedule of Collaboration Revenue from CStone Agreement (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 26,221	$ 40,414	$ 56,448	$ 49,176
Licenses
Disaggregation of Revenue [Line Items]
Revenue	0	15,000	0	15,000
Licenses \| CStone Agreement
Disaggregation of Revenue [Line Items]
Revenue	0	12,440	0	12,440
Other Services \| CStone Agreement
Disaggregation of Revenue [Line Items]
Revenue	812	0	1,782	0
Collaboration revenue – other
Disaggregation of Revenue [Line Items]
Revenue	812	12,440	1,782	12,440
Collaboration revenue – other \| CStone Agreement
Disaggregation of Revenue [Line Items]
Revenue	$ 812	$ 12,440	$ 1,782	$ 12,440

Overview and Basis of Presentation	6 Months Ended
Overview and Basis of Presentation	Jun. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Overview and Basis of Presentation	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 the fundamental transformation of patients’ lives through scientific leadership in the field of cellular metabolism and adjacent areas of biology, with the goal of making transformative, first- or best-in-class medicines for the treatment of cancer and rare genetic diseases, or RGDs. To address both cancer and RGDs, 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 June 30, 2019, the condensed consolidated statements of operations, comprehensive loss and stockholders' equity for the three and six months ended June 30, 2019 and 2018, and the condensed consolidated statements of cash flows for the six months ended June 30, 2019 and 2018 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 June 30, 2019, our results of operations and stockholders' equity for the three and six months ended June 30, 2019 and 2018, and cash flows for the six months ended June 30, 2019 and 2018. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and six-month periods are also unaudited. The results of operations for the three and six months ended June 30, 2019 are not necessarily indicative of the results to be expected for the year ending December 31, 2019 or for any other future annual or interim period. The year-end condensed consolidated balance sheet data 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. Accordingly, 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, 2018 that was filed with the Securities and Exchange Commission, or the SEC, on February 14, 2019. 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. Liquidity As of June 30, 2019, we had cash, cash equivalents and marketable securities of $624.0 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.

Collaboration and License Agreements - Schedule of Revenues as a Result of Changes in Contract Liabilities (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenue Recognition and Deferred Revenue [Abstract]
Amounts included in the contract liability at the beginning of the period	$ 8,009	$ 9,932	$ 24,419	$ 15,917
Performance obligations satisfied in previous periods	$ 0	$ 220	$ 0	$ 543

Product Revenue

6 Months Ended

Jun. 30, 2019

Revenue from Contract with Customer [Abstract]

Product Revenue

We sell TIBSOVO®, our wholly owned product, to a limited number of specialty distributors and specialty pharmacy providers in the U.S., 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.

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.

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 consist of 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.

Total net product revenue from U.S. sales of TIBSOVO®, which is our only source of product revenue, was $13.7 million and $22.9 million for the three and six months ended June 30, 2019, respectively. We did not record any product revenues during the three and six months ended June 30, 2018. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2019 (in thousands):


	Contractual Adjustments		Government Rebates		Returns		Total
Balance at December 31, 2018	$	592	$	325	$	334	$	1,251
Current provisions relating to sales in the current year	3,145		820		586		4,551
Adjustments relating to prior years	8		—		—		8
Payments/returns relating to sales in the current year	(2,450)		(355)		—		(2,805)
Payments/returns relating to sales in the prior years	(598)		(230)		—		(828)
Balance at June 30, 2019	$	697	$	560	$	920	$	2,177

Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows (in thousands):


	June 30, 2019		December 31, 2018
Reduction of accounts receivable	$	416	$	326
Component of accrued expenses	1,761		925
Total revenue-related reserves	$	2,177	$	1,251

The following table presents changes in our contract assets during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Accounts receivable, net	$	5,076	$	27,395	$	(25,324)	$	7,147

(1) Additions to contract assets relate to amounts billed to Customers for product sales during the reporting period. Deductions to contract assets primarily relate to collection of receivables during the reporting period.

Collaboration and License Agreements - Changes in Contract Assets and Liabilities Under CStone Agreement (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2019 USD ($)
Contract assets
Contract assets, beginning balance	$ 5,076
Deductions	(25,324)
Contract assets, ending balance	7,147
Collaboration receivable - other \| CStone Agreement
Contract assets
Contract assets, beginning balance	670
Additions	1,782
Deductions	(230)
Contract assets, ending balance	$ 2,222

Accrued Expenses (Tables)

6 Months Ended

Jun. 30, 2019

Payables and Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consist of the following (in thousands):


	June 30, 2019		December 31, 2018
Accrued compensation	$	10,541	$	20,843
Accrued research and development costs	30,189		14,777
Accrued professional fees	6,357		5,441
Accrued other	2,131		1,086
Total accrued expenses	$	49,218	$	42,147

Product Revenue - Schedule of Changes in Contract Assets and Liabilities, Product Revenue (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2019 USD ($)
Contract assets
Contract assets, beginning balance	$ 5,076
Additions	27,395
Deductions	(25,324)
Contract assets, ending balance	$ 7,147

Leases (Tables)

6 Months Ended

Jun. 30, 2019

Leases [Abstract]

Schedule of Undiscounted Minimum Rental Commitments Under Topic 842

As of June 30, 2019, undiscounted minimum rental commitments under non-cancelable leases, for each of the next five years and total thereafter were as follows (in thousands):


Remaining 2019	$	5,695
2020	14,015
2021	14,380
2022	16,773
2023	18,126
2024	18,660
Thereafter	63,891
	$	151,540

Schedule of Difference Between Remaining Undiscounted Minimum Rental Commitments and Lease Liability

As of June 30, 2019, the following represents the difference between the remaining undiscounted minimum rental commitments under non-cancelable leases and the operating lease liabilities (in thousands):


Undiscounted minimum rental commitments	$	151,540
Present value adjustment using incremental borrowing rate	(35,070)
Operating lease liabilities	$	116,470

Schedule of Undiscounted Minimum Rental Commitments Under Topic 840

As of December 31, 2018, minimum rental commitments under non-cancelable leases, for each of the next five years and total thereafter were as follows (in thousands):


2019	$	12,759
2020	13,135
2021	13,473
2022	15,552
2023	17,145
Thereafter	19,223
	$	91,287

Collaboration and License Agreements - Additional Information (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Remaining unsatisfied performance obligation	$ 75,500,000		$ 75,500,000
Milestones achieved	0	$ 0	0	$ 0
2010 Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Potential milestone payment	$ 35,000,000.0		$ 35,000,000.0
Collaboration revenue – related party
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestones achieved		$ 15,000,000.0

Share-Based Payments - Summary of Stock Option Activity (Details) - $ / shares	6 Months Ended
	Jun. 30, 2019
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Number of Stock Options, Outstanding, Beginning balance (in shares)	5,416,069
Number of Stock Options, Granted (in shares)	1,464,728
Number of Stock Options, Exercised (in shares)	(181,010)
Number of Stock Options, Forfeited/Expired (in shares)	(356,493)
Number of Stock Options, Outstanding, Ending balance (in shares)	6,343,294
Number of Stock Options, Exercisable (in shares)	3,414,953
Number of Stock Options, Vested and expected to vest (in shares)	6,343,294
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Abstract]
Weighted-Average Exercise Price, Outstanding, Beginning balance (in usd per share)	$ 60.10
Weighted-Average Exercise Price, Granted (in usd per share)	57.08
Weighted-Average Exercise Price, Exercised (in usd per share)	38.59
Weighted-Average Exercise Price, Forfeited/Expired (in usd per share)	66.38
Weighted-Average Exercise Price, Outstanding, Ending balance (in usd per share)	59.66
Weighted-Average Exercise Price, Exercisable (in usd per share)	58.63
Weighted-Average Exercise Price, Vested and expected to vest (in usd per share)	$ 59.66

Share-Based Payments - Summary of Unvested RSUs Activity (Details) - Restricted stock units	6 Months Ended
	Jun. 30, 2019 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Unvested shares beginning of period (in shares) \| shares	532,144
Granted (in shares) \| shares	408,707
Vested (in shares) \| shares	(150,082)
Forfeited (in shares) \| shares	(53,259)
Unvested shares end of period (in shares) \| shares	737,510
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-average grant date fair value, Unvested shares beginning of period (in usd per share) \| $ / shares	$ 75.45
Weighted-average grant date fair value, Granted (in usd per share) \| $ / shares	58.46
Weighted-average grant date fair value, Vested (in usd per share) \| $ / shares	69.29
Weighted-average grant date fair value, Forfeited (in usd per share) \| $ / shares	72.24
Weighted-average grant date fair value, Unvested shares end of period (in usd per share) \| $ / shares	$ 67.52

Collaboration and License Agreements - Collaboration Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 26,221	$ 40,414	$ 56,448	$ 49,176
Licenses
Disaggregation of Revenue [Line Items]
Revenue	0	15,000	0	15,000
On-going research and development services
Disaggregation of Revenue [Line Items]
Revenue	8,155	9,830	25,220	16,194
Development activities
Disaggregation of Revenue [Line Items]
Revenue	0	590	0	590
Commercialization activities
Disaggregation of Revenue [Line Items]
Revenue	824	981	1,678	1,962
Collaboration revenue – related party
Disaggregation of Revenue [Line Items]
Revenue	$ 8,979	$ 26,401	$ 26,898	$ 33,746

Loss per Share

6 Months Ended

Jun. 30, 2019

Earnings Per Share [Abstract]

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 met, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs and MSUs with performance and market vesting conditions, respectively, that were not met as of June 30, 2019 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 Six Months Ended June 30,
	2019	2018
Stock options	6,343,294	5,706,476
Restricted stock units	737,510	438,892

Employee stock purchase plan	33,064	21,205
Total common stock equivalents	7,113,868	6,166,573

Label	Element	Value
Accounting Standards Update 2014-09 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 39,456,000
Accounting Standards Update 2014-09 [Member] \| Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 39,456,000

Collaboration and License Agreements - Schedule of Changes in Contract Assets and Liabilities (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Contract assets
Contract assets, beginning balance			$ 5,076
Additions			27,395
Deductions			(25,324)
Contract assets, ending balance	$ 7,147		7,147
Contract liabilities
Additions	8,009	$ 9,932	24,419	$ 15,917
Collaboration receivable – related party
Contract assets
Contract assets, beginning balance			2,462
Additions			4,452
Deductions			(4,390)
Contract assets, ending balance	2,524		2,524
Royalty receivable – related party
Contract assets
Contract assets, beginning balance			2,234
Additions			4,900
Deductions			(4,434)
Contract assets, ending balance	2,700		2,700
Deferred revenue – related party, current and net of current portions
Contract liabilities
Contract liabilities, beginning balance			92,519
Additions			3,705
Deductions			(26,154)
Contract liabilities, ending balance	$ 70,070		$ 70,070

Leases

6 Months Ended

Jun. 30, 2019

Leases [Abstract]

Leases

On April 11, 2019, we entered into an agreement to lease approximately 13,000 square feet of office space located at 38 Sidney Street, Cambridge, Massachusetts, or the 38 Sidney Lease, with Thirty-Eight Sidney Street, LLC. The initial term of the 38 Sidney Lease commenced on May 1, 2019 and expires on February 29, 2028. At the end of the lease term, we have the option to extend the 38 Sidney Lease for two consecutive terms of five years at fair market rent at the time of the extension. The 38 Sidney Lease provides us with the right to lease additional space within the 38 Sidney Street building and also includes rent escalation clauses and a tenant improvement allowance of $1.0 million.

In connection with the 38 Sidney Lease, we also amended our existing building leases at 88 Sidney Street, Cambridge, Massachusetts and at 64 Sidney Street, Cambridge, Massachusetts to extend the initial terms of those leases by approximately three years through February 29, 2028. The amendments also provide us with the right to lease additional space at the 64 Sidney Street building. Our existing extension options for the 88 Sidney Street building and 64 Sidney Street building continue as set forth in the existing leases for those buildings.

Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of nine 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 option is not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees. Operating lease costs for the three and six months ended June 30, 2019 were $3.8 million and $6.8 million, respectively, and cash paid for amounts included in the measurement of operating lease liabilities for the three and six months ended June 30, 2019 were $3.2 million and $6.3 million, respectively.

We have not entered into any material short-term leases or financing leases as of June 30, 2019.

As of June 30, 2019, undiscounted minimum rental commitments under non-cancelable leases, for each of the next five years and total thereafter were as follows (in thousands):


Remaining 2019	$	5,695
2020	14,015
2021	14,380
2022	16,773
2023	18,126
2024	18,660
Thereafter	63,891
	$	151,540

In arriving at the operating lease liabilities as of June 30, 2019, we applied the weighted-average incremental borrowing rate of 5.7% over a weighted-average remaining lease term of 8.7 years.


Undiscounted minimum rental commitments	$	151,540
Present value adjustment using incremental borrowing rate	(35,070)
Operating lease liabilities	$	116,470

As of December 31, 2018, minimum rental commitments under non-cancelable leases, for each of the next five years and total thereafter were as follows (in thousands):


2019	$	12,759
2020	13,135
2021	13,473
2022	15,552
2023	17,145
Thereafter	19,223
	$	91,287

Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2019

Investments, Debt and Equity Securities [Abstract]

Schedule of Marketable Securities

Marketable securities at June 30, 2019 consisted of the following (in thousands):


	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:
Certificates of deposit	$	240	$	—	$	—	$	240
U.S. Treasuries	186,295		211		(57)		186,449
Government securities	54,836		20		(34)		54,822
Corporate debt securities	170,255		148		(104)		170,299
Non-current:


Government securities	32,575		19		(48)		32,546
Corporate debt securities	95,657		491		(45)		96,103
Total marketable securities	$	539,858	$	889	$	(288)	$	540,459

Marketable securities at December 31, 2018 consisted of the following (in thousands):


	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:
Certificates of deposit	$	960	$	—	$	(4)	$	956
U.S. Treasuries	231,101		7		(228)		230,880
Government securities	75,335		—		(121)		75,214
Corporate debt securities	208,233		—		(483)		207,750
Non-current:

U.S. Treasuries	12,202		4		(125)		12,081
Government securities	70,177		10		(188)		69,999
Corporate debt securities	139,082		12		(1,055)		138,039
Total marketable securities	$	737,090	$	33	$	(2,204)	$	734,919

Accrued Expenses

6 Months Ended

Jun. 30, 2019

Payables and Accruals [Abstract]

Accrued Expenses

Accrued expenses consist of the following (in thousands):


	June 30, 2019		December 31, 2018
Accrued compensation	$	10,541	$	20,843
Accrued research and development costs	30,189		14,777
Accrued professional fees	6,357		5,441
Accrued other	2,131		1,086
Total accrued expenses	$	49,218	$	42,147

Share-Based Payments - Additional Information (Details) - USD ($) $ in Millions	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018
Restricted stock units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense related to stock option	$ 37.5
Weighted-average period to recognize compensation expense (in years)	2 years
Market-Based Stock Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense related to stock option	$ 1.3
Weighted-average period to recognize compensation expense (in years)	1 year 2 months 12 days
2007 Plan and 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock reserved for issuance (in shares)	9,475,602
2013 Stock Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance (in shares)	2,194,806
Total unrecognized compensation expense related to stock option	$ 114.6
Weighted-average period to recognize compensation expense (in years)	2 years 9 months 18 days
2013 Stock Incentive Plan \| Performance-Based Stock Units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense related to stock option	$ 9.8
Employee stock purchase plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance (in shares)	128,126
Shares issued under 2013 ESPP (in shares)	32,410	27,377
Opportunity to purchase of common stock (in shares)	327,272

Leases - Schedule of Minimum Rental Commitments Under Topic 840 (Details) $ in Thousands	Dec. 31, 2018 USD ($)
Leases [Abstract]
2019	$ 12,759
2020	13,135
2021	13,473
2022	15,552
2023	17,145
Thereafter	19,223
Total minimum rental commitments due under non-cancelable leases	$ 91,287

Marketable Securities - Summary of Marketable Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 539,858	$ 737,090
Unrealized Gains	889	33
Unrealized Losses	(288)	(2,204)
Fair Value	540,459	734,919
Current \| Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	240	960
Unrealized Gains	0	0
Unrealized Losses	0	(4)
Fair Value	240	956
Current \| U.S. Treasuries
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	186,295	231,101
Unrealized Gains	211	7
Unrealized Losses	(57)	(228)
Fair Value	186,449	230,880
Current \| Government securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	54,836	75,335
Unrealized Gains	20	0
Unrealized Losses	(34)	(121)
Fair Value	54,822	75,214
Current \| Corporate debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	170,255	208,233
Unrealized Gains	148	0
Unrealized Losses	(104)	(483)
Fair Value	170,299	207,750
Non-current \| U.S. Treasuries
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		12,202
Unrealized Gains		4
Unrealized Losses		(125)
Fair Value		12,081
Non-current \| Government securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	32,575	70,177
Unrealized Gains	19	10
Unrealized Losses	(48)	(188)
Fair Value	32,546	69,999
Non-current \| Corporate debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	95,657	139,082
Unrealized Gains	491	12
Unrealized Losses	(45)	(1,055)
Fair Value	$ 96,103	$ 138,039

Product Revenue - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Disaggregation of Revenue [Line Items]
Revenue	$ 26,221	$ 40,414	$ 56,448	$ 49,176
Product revenue, net
Disaggregation of Revenue [Line Items]
Revenue	$ 13,727	$ 0	$ 22,865	$ 0

Cover Page - shares	6 Months Ended
Cover Page - shares	Jun. 30, 2019	Jul. 26, 2019
Cover page.
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 2019
Document Transition Report	false
Entity File Number	001-36014
Entity Registrant Name	AGIOS PHARMACEUTICALS INC
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	26-0662915
Entity Address, Address Line One	88 Sidney Street
Entity Address, City or Town	Cambridge
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02139
City Area Code	617
Local Phone Number	649-8600
Title of 12(b) Security	Common Stock, Par Value $0.001 per share
Trading Symbol	AGIO
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		58,752,886
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Central Index Key	0001439222
Current Fiscal Year End Date	--12-31

Fair Value Measurements - Cash Equivalents and Marketable Securities Measured at Fair Value on a Recurring Basis (Details) - Fair Value, Measurements, Recurring $ in Thousands	Jun. 30, 2019 USD ($)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Cash equivalents	$ 38,007
Total cash equivalents and marketable securities	578,466
Certificates of deposit
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	240
U.S. Treasuries
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	186,449
Government securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	87,368
Corporate debt securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	266,402
Level 1
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Cash equivalents	27,012
Total cash equivalents and marketable securities	27,012
Level 1 \| Certificates of deposit
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 1 \| U.S. Treasuries
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 1 \| Government securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 1 \| Corporate debt securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 2
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Cash equivalents	10,995
Total cash equivalents and marketable securities	551,454
Level 2 \| Certificates of deposit
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	240
Level 2 \| U.S. Treasuries
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	186,449
Level 2 \| Government securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	87,368
Level 2 \| Corporate debt securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	266,402
Level 3
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Cash equivalents	0
Total cash equivalents and marketable securities	0
Level 3 \| Certificates of deposit
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 3 \| U.S. Treasuries
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 3 \| Government securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0
Level 3 \| Corporate debt securities
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	$ 0

Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2019

Fair Value Disclosures [Abstract]

Cash Equivalents and Marketable Securities Measured at Fair Value on a Recurring Basis

The following table summarizes our cash equivalents and marketable securities measured at fair value on a recurring basis as of June 30, 2019 (in thousands):


	Level 1		Level 2		Level 3		Total
Cash equivalents	$	27,012	$	10,995	$	—	$	38,007
Marketable securities:
Certificates of deposit	—		240		—		240
U.S. Treasuries	—		186,449		—		186,449
Government securities	—		87,368		—		87,368
Corporate debt securities	—		266,402		—		266,402
Total cash equivalents and marketable securities	$	27,012	$	551,454	$	—	$	578,466

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Preferred stock, par value (in usd per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized (in shares)	25,000,000	25,000,000
Preferred stock, shares issued (in shares)	0	0
Preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (in usd per share)	$ 0.001	$ 0.001
Common stock, shares authorized (in shares)	125,000,000	125,000,000
Common stock, shares issued (in shares)	58,749,186	58,218,653
Common stock, shares outstanding (in shares)	58,749,186	58,218,653

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018
Operating activities
Net loss	$ (202,949)	$ (159,570)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	4,042	3,464
Stock-based compensation expense	36,655	30,977
Net accretion of premium and discounts on investments	(2,019)	(1,291)
(Gain) loss on disposal of property and equipment	0	(20)
Non-cash operating lease expense	4,208
Changes in operating assets and liabilities:
Accounts receivable, net	(2,071)	0
Collaboration receivable – related party	(62)	(16,878)
Collaboration receivable – other	(1,552)	(440)
Royalty receivable – related party	(466)	(351)
Inventory	(3,790)	0
Prepaid expenses and other current and non-current assets	(2,517)	2,413
Accounts payable	(1,874)	(6,198)
Accrued expenses	7,071	(7,841)
Deferred revenue – related party	(22,449)	(10,644)
Operating lease liabilities	(3,649)
Deferred rent	0	(16)
Net cash used in operating activities	(191,422)	(166,395)
Investing activities
Purchases of marketable securities	(144,231)	(592,664)
Proceeds from maturities and sales of marketable securities	343,372	331,666
Purchases of property and equipment	(3,309)	(2,793)
Net cash provided by (used in) investing activities	195,832	(263,791)
Financing activities
Payment of public offering costs, net of reimbursements	0	(391)
Proceeds from public offering of common stock, net of commissions	0	516,206
Net proceeds from stock option exercises and employee stock purchase plan	8,668	21,970
Net cash provided by financing activities	8,668	537,785
Net change in cash and cash equivalents	13,078	107,599
Cash and cash equivalents at beginning of the period	70,502	102,724
Cash and cash equivalents at end of the period	83,580	210,323
Supplemental disclosure of non-cash investing and financing transactions
Additions to property and equipment in accounts payable and accrued expenses	535	1,365
Proceeds from stock option exercises in other current assets	112	$ 0
Operating lease liabilities arising from obtaining operating lease assets	$ 42,856

Leases - Difference Between Remaining Undiscounted Minimum Rental Commitments and Lease Liability (Details) $ in Thousands	Jun. 30, 2019 USD ($)
Leases [Abstract]
Undiscounted minimum rental commitments	$ 151,540
Present value adjustment using incremental borrowing rate	(35,070)
Operating lease liabilities	$ 116,470

Product Revenue (Tables)

6 Months Ended

Jun. 30, 2019

Revenue from Contract with Customer [Abstract]

Schedule of Product Revenue Allowance and Reserves

The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2019 (in thousands):


	Contractual Adjustments		Government Rebates		Returns		Total
Balance at December 31, 2018	$	592	$	325	$	334	$	1,251
Current provisions relating to sales in the current year	3,145		820		586		4,551
Adjustments relating to prior years	8		—		—		8
Payments/returns relating to sales in the current year	(2,450)		(355)		—		(2,805)
Payments/returns relating to sales in the prior years	(598)		(230)		—		(828)
Balance at June 30, 2019	$	697	$	560	$	920	$	2,177

Schedule of Revenue Related Reserves

Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows (in thousands):


	June 30, 2019		December 31, 2018
Reduction of accounts receivable	$	416	$	326
Component of accrued expenses	1,761		925
Total revenue-related reserves	$	2,177	$	1,251

Schedule of Changes in Contract Assets and Liabilities, Product Revenue

The following table presents changes in our contract assets during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Accounts receivable, net	$	5,076	$	27,395	$	(25,324)	$	7,147

Marketable Securities - Additional Information (Details) $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2019 USD ($) security	Jun. 30, 2018 USD ($)	Jun. 30, 2019 USD ($) security	Jun. 30, 2018 USD ($)	Dec. 31, 2018 USD ($) security
Investments, Debt and Equity Securities [Abstract]
Realized gain (loss) on marketable securities	$ 0.0	$ 0.0	$ 0.0	$ 0.0
Debt securities in an unrealized loss position \| security	79		79		242
Aggregate fair value of debt securities in an unrealized loss position	$ 175.5		$ 175.5		$ 639.3

Share-Based Payments

6 Months Ended

Jun. 30, 2019

Share-based Payment Arrangement [Abstract]

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 stock options and other stock-based awards. Following the adoption of the 2013 Plan, we granted no further stock options or other stock-based awards under the 2007 Stock Incentive Plan, or the 2007 Plan. Any stock options or stock-based awards outstanding under the 2007 Plan at the time of adoption of the 2013 Plan remained outstanding and effective. As of June 30, 2019, the total number of shares reserved under the 2007 Plan and the 2013 Plan was 9,475,602, and we had 2,194,806 shares available for future issuance under the 2013 Plan.

Stock options

The following table presents stock option activity for the six months ended June 30, 2019:


	Number of Stock Options	Weighted-Average Exercise Price
Outstanding at December 31, 2018	5,416,069	$	60.10
Granted	1,464,728	57.08
Exercised	(181,010)	38.59
Forfeited/Expired	(356,493)	66.38
Outstanding at June 30, 2019	6,343,294	$	59.66
Exercisable at June 30, 2019	3,414,953	$	58.63
Vested and expected to vest at June 30, 2019	6,343,294	$	59.66

At June 30, 2019, there was approximately $114.6 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.8 years.

Restricted stock units

The following table presents restricted stock unit, or RSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	532,144	$	75.45
Granted	408,707	58.46
Vested	(150,082)	69.29
Forfeited	(53,259)	72.24
Unvested shares at June 30, 2019	737,510	$	67.52

As of June 30, 2019, there was approximately $37.5 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 2.0 years.

Performance-based stock units

The following table presents performance-based stock unit, or PSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	169,031	$	52.67
Granted	155,297	61.93
Vested	(167,031)	52.36

Unvested shares at June 30, 2019	157,297	$	62.15

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.

As of June 30, 2019, there was approximately $9.8 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are not considered probable of achievement.

Market-based stock units

The following table presents market-based stock unit, or MSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	—	$	—
Granted	42,695	41.50


Unvested shares at June 30, 2019	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 June 30, 2019, there was approximately $1.3 million of total unrecognized compensation expense related to MSUs, which we expect to recognize over the remaining derived service period of 1.2 years.

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 32,410 shares and 27,377 shares during the six months ended June 30, 2019 and 2018, respectively, under the 2013 ESPP. The 2013 ESPP provides participating employees with the opportunity to purchase up to an aggregate of 327,272 shares of our common stock. As of June 30, 2019, we had 128,126 shares 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 (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Stock options	$	12,467	$	13,311	$	25,513	$	25,783
Restricted stock units	5,243		2,805		9,791		4,602
Employee stock purchase plan	392		339		720		592
Other stock awards	445		—		631		—
Total stock-based compensation expense	$	18,547	$	16,455	$	36,655	$	30,977

Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Research and development expense	$	10,067	$	9,667	$	20,109	$	18,307
Selling, general and administrative expense	8,480		6,788		16,546		12,670
Total stock-based compensation expense	$	18,547	$	16,455	$	36,655	$	30,977

Collaboration and License Agreements (Tables)

6 Months Ended

Jun. 30, 2019

Revenue Recognition and Deferred Revenue [Abstract]

Schedule of Collaboration Revenue

During the three and six months ended June 30, 2019 and 2018, we recognized the following collaboration revenue (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Services performed that were considered performance obligations as of the modification dates
Licenses	$	—	$	15,000	$	—	$	15,000
On-going research and development services	8,155		9,830		25,220		16,194

Services performed that were not considered performance obligations as of the modification dates
Development activities	—		590		—		590
Commercialization activities	824		981		1,678		1,962
Total collaboration revenue - related party	$	8,979	$	26,401	$	26,898	$	33,746

Schedule of Changes in Contract Assets and Liabilities

The following table presents changes in our contract assets and liabilities during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Collaboration receivable – related party	$	2,462	$	4,452	$	(4,390)	$	2,524
Royalty receivable – related party	2,234		4,900		(4,434)		2,700
Contract liabilities (2)
Deferred revenue – related party, current and net of current portions	92,519		3,705		(26,154)		70,070

(1) Additions to contract assets relate to amounts billed to Celgene during the reporting period. Deductions to contract assets relate to collection of receivables during the reporting period.

(2) Additions to contract liabilities relate to consideration from Celgene during the reporting period. Deductions to contract liabilities relate to deferred revenue recognized as revenue during the reporting period.

During the three and six months ended June 30, 2019 and 2018, we recognized the following as revenue due to changes in the contract liability balances (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Amounts included in the contract liability at the beginning of the period	$	8,009	$	9,932	$	24,419	$	15,917
Performance obligations satisfied in previous periods	—		220		—		543

Schedule of Royalty Revenue

During the three and six months ended June 30, 2019 and 2018, we recognized the following as royalty revenue (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Royalty revenue – related party	$	2,703	$	1,573	$	4,903	$	2,990

Schedule of Collaboration Revenue Under CStone Agreement

During the three and six months ended June 30, 2019 and 2018, we recognized the following collaboration revenue - other (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Services performed that were considered performance obligations as of the inception date
License	$	—	$	12,440	$	—	$	12,440
Services performed that were not considered performance obligations as of the inception date
Other Services	812		—		1,782		—

Total collaboration revenue - other	$	812	$	12,440	$	1,782	$	12,440

Schedule of Changes in Contract Assets and Liabilities, CStone Agreement

The following table presents changes in our contract assets during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Collaboration receivable - other	$	670	$	1,782	$	(230)	$	2,222

(1) Additions to contract assets relate to amounts receivable from CStone. Deductions to contract assets relate to collection of receivables during the reporting period.

Collaboration and License Agreements

6 Months Ended

Jun. 30, 2019

Revenue Recognition and Deferred Revenue [Abstract]

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, 2018, 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, 2018.

Collaboration revenue

On January 1, 2018 we adopted ASC 606, Revenue from Contracts with Customers, under the modified retrospective method. Prior to January 1, 2018, we accounted for collaboration agreements under ASC 605-25, Multiple Element Arrangements. In determining the appropriate amount of revenue to be recognized under ASC 606, 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 not considered probable of being achieved 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 Corporation, or Celgene, 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. Under the remaining terms of the 2010 Agreement, we are eligible to receive up to $80.0 million in potential milestone payments for the enasidenib program. The potential milestone payments are comprised of: (i) up to $55.0 million in milestone payments upon achievement of specified ex-U.S. regulatory milestone events, and (ii) a $25.0 million milestone payment upon achievement of a specified ex-U.S. commercial milestone event, as well as royalties at tiered, low-double digit to mid-teen percentage rates on net sales of IDHIFA®.

•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. The initial four-year research term of the 2016 Agreement may be extended for up to two, or in specified cases, up to four additional one-year terms by paying a $40.0 million per year extension fee. Celgene has designated AG-270, our methionine adenosyltransferase 2a, or MAT2A, inhibitor, as a development candidate under the 2016 Agreement, and has the option, upon payment of an option exercise fee of at least $30.0 million, to participate in a worldwide 50/50 cost and profit share with us for AG-270, under which we are eligible for up to $169.0 million in potential milestone payments for the program, comprised of: (i) a $20.0 million milestone-based payment upon achievement of a specified clinical development event and (ii) up to $149.0 million in milestone-based payments upon achievement of specified regulatory milestone events. We are also eligible to receive designation, option exercise and milestone and royalty payments for other programs that may be designated for further development under the 2016 Agreement.

Collaboration revenue

During the three and six months ended June 30, 2019 and 2018, we recognized the following collaboration revenue (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Services performed that were considered performance obligations as of the modification dates
Licenses	$	—	$	15,000	$	—	$	15,000
On-going research and development services	8,155		9,830		25,220		16,194

Services performed that were not considered performance obligations as of the modification dates
Development activities	—		590		—		590
Commercialization activities	824		981		1,678		1,962
Total collaboration revenue - related party	$	8,979	$	26,401	$	26,898	$	33,746

The following table presents changes in our contract assets and liabilities during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Collaboration receivable – related party	$	2,462	$	4,452	$	(4,390)	$	2,524
Royalty receivable – related party	2,234		4,900		(4,434)		2,700
Contract liabilities (2)
Deferred revenue – related party, current and net of current portions	92,519		3,705		(26,154)		70,070

(1) Additions to contract assets relate to amounts billed to Celgene during the reporting period. Deductions to contract assets relate to collection of receivables during the reporting period.

During the three and six months ended June 30, 2019 and 2018, we recognized the following as revenue due to changes in the contract liability balances (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Amounts included in the contract liability at the beginning of the period	$	8,009	$	9,932	$	24,419	$	15,917
Performance obligations satisfied in previous periods	—		220		—		543

As of June 30, 2019, the aggregate amount of the transaction price allocated to performance obligations that are partially unsatisfied was $75.5 million. This amount is expected to be recognized as performance obligations are satisfied through March 2023.

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 six months ended June 30, 2019 and 2018, we recognized the following as royalty revenue (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Royalty revenue – related party	$	2,703	$	1,573	$	4,903	$	2,990

Milestone revenue

During the three months ended June 30, 2018, Celgene submitted a marketing authorization application, or MAA, to the European Medicines Agency, or EMA, for IDHIFA® for isocitrate dehydrogenase 2, or IDH2, mutant-positive relapsed or

refractory, or R/R, acute myeloid leukemia, or AML. As a result of the filing, we recognized a $15.0 million milestone payment as collaboration revenue - related party. No other milestones were achieved during the three and six months ended June 30, 2019 or 2018. The next potential milestone expected to be achieved under our Collaboration Agreements is the first regulatory approval in any of China, Japan or a major European country, which would result in a milestone payment of $35.0 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. Pursuant to the CStone Agreement, CStone will initially be responsible for the development and commercialization of ivosidenib in 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 $412.0 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 six months ended June 30, 2019 and 2018, we recognized the following collaboration revenue - other (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Services performed that were considered performance obligations as of the inception date
License	$	—	$	12,440	$	—	$	12,440
Services performed that were not considered performance obligations as of the inception date
Other Services	812		—		1,782		—

Total collaboration revenue - other	$	812	$	12,440	$	1,782	$	12,440

The following table presents changes in our contract assets during the six months ended June 30, 2019 (in thousands):


	December 31, 2018		Additions		Deductions		June 30, 2019
Contract assets (1)
Collaboration receivable - other	$	670	$	1,782	$	(230)	$	2,222

(1) Additions to contract assets relate to amounts receivable from CStone. Deductions to contract assets relate to collection of receivables during the reporting period.

As of June 30, 2019, the aggregate amount of the transaction price allocated to performance obligations that are partially unsatisfied was $0.7 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 six months ended June 30, 2019 and 2018. 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 hematological indication in mainland China. Achievement of this event will result in a milestone payment of $5.0 million.

Inventory (Tables)

6 Months Ended

Jun. 30, 2019

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory, which consists of commercial supply of TIBSOVO® (ivosidenib), consists of the following (in thousands):


	June 30, 2019		December 31, 2018
Raw materials	$	180	$	—
Work-in-process	4,392		788
Finished goods	87		81
Total inventory	$	4,659	$	869

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenues:
Total revenue	$ 26,221	$ 40,414	$ 56,448	$ 49,176
Cost and expenses:
Cost of sales	303	0	637	0
Research and development	107,389	86,730	202,974	164,954
Selling, general and administrative	32,390	26,633	64,181	51,183
Total cost and expenses	140,082	113,363	267,792	216,137
Loss from operations	(113,861)	(72,949)	(211,344)	(166,961)
Interest income	3,990	4,204	8,395	7,391
Net loss	$ (109,871)	$ (68,745)	$ (202,949)	$ (159,570)
Net loss per share – basic and diluted (in usd per share)	$ (1.87)	$ (1.19)	$ (3.46)	$ (2.81)
Weighted-average number of common shares used in computing net loss per share – basic and diluted	58,722,244	57,721,786	58,589,167	56,713,795
Product revenue, net
Revenues:
Total revenue	$ 13,727	$ 0	$ 22,865	$ 0
Collaboration revenue – related party
Revenues:
Total revenue	8,979	26,401	26,898	33,746
Collaboration revenue – other
Revenues:
Total revenue	812	12,440	1,782	12,440
Royalty revenue – related party
Revenues:
Total revenue	$ 2,703	$ 1,573	$ 4,903	$ 2,990

Share-Based Payments - Schedule of Stock-Based Compensation Expense by Award Type Included Within the Condensed Consolidated Statements of Operations (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 18,547	$ 16,455	$ 36,655	$ 30,977
Stock options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	12,467	13,311	25,513	25,783
Restricted stock units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	5,243	2,805	9,791	4,602
Employee stock purchase plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	392	339	720	592
Other stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 445	$ 0	$ 631	$ 0

Summary of Significant Accounting Policies (Policies)	6 Months Ended
Summary of Significant Accounting Policies (Policies)	Jun. 30, 2019
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The condensed consolidated balance sheet as of June 30, 2019, the condensed consolidated statements of operations, comprehensive loss and stockholders' equity for the three and six months ended June 30, 2019 and 2018, and the condensed consolidated statements of cash flows for the six months ended June 30, 2019 and 2018 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 June 30, 2019, our results of operations and stockholders' equity for the three and six months ended June 30, 2019 and 2018, and cash flows for the six months ended June 30, 2019 and 2018. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and six-month periods are also unaudited. The results of operations for the three and six months ended June 30, 2019 are not necessarily indicative of the results to be expected for the year ending December 31, 2019 or for any other future annual or interim period. The year-end condensed consolidated balance sheet data 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. Accordingly, 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, 2018 that was filed with the Securities and Exchange Commission, or the SEC, on February 14, 2019. 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.
Leases	Leases In February 2016, the Financial Accounting Standards Board, or FASB, issued Accounting Standards Update, or ASU, 2016-02, Leases (Topic 842), which was codified as Accounting Standards Codification, or ASC, 842, Leases, and amended through subsequent ASUs. We adopted ASC 842 effective January 1, 2019 using the modified retrospective transition approach and elected the package of practical expedients, both provided for under ASU 2018-11, Leases (Topic 842): Targeted Improvements. The package of practical expedients allows us not to reassess whether contracts are or contain leases, lease classification, and whether initial direct costs qualify for capitalization. Additionally, as an accounting policy, we have chosen not to separate the non-lease components from the lease components for our building leases and, instead, accounted for non-lease and lease components as a single component. Impact of Adoption of ASC 842 Upon adoption of ASC 842 on January 1, 2019, we recorded operating lease assets of $59.9 million and operating lease liabilities of $77.3 million. The adoption of ASC 842 did not have a material impact on our condensed consolidated statements of operations. Prior periods are presented in accordance with ASC 840, Leases. Leases Accounting Policy We determine if an arrangement is a lease at inception. An arrangement is determined to contain a lease if the contract conveys the right to control the use of an identified property, plant, or equipment for a period of time in exchange for consideration. If we can benefit from the various underlying assets of a lease on their own or together with other resources that are readily available, or if the various underlying assets are neither highly dependent on nor highly interrelated with other underlying assets in the arrangement, they are considered to be a separate lease component. In the event multiple underlying assets are identified, the lease consideration is allocated to the various components based on each of the component’s relative fair value. Operating lease assets represent our right to use an underlying asset for the lease term and operating lease liabilities represent our obligation to make lease payments arising from the leasing arrangement. Operating lease assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. As most of our leases do not provide an implicit rate, in determining the operating lease liabilities we use an estimate of our incremental borrowing rate. The incremental borrowing rate is determined using two alternative credit scoring models to estimate our credit rating, adjusted for collateralization. The calculation of the operating lease assets includes any lease payments made and excludes any lease incentives. Our lease terms may include options to extend or terminate the lease when it is reasonably certain that we will exercise that option. For operating leases, we record operating lease assets and liabilities in our consolidated balance sheets. Lease expense for lease payments is recognized on a straight-line basis over the lease term. Short-term leases, or leases that have a lease term of 12 months or less at commencement date, are excluded from this treatment and are recognized on a straight-line basis over the term of the lease.
Recent accounting pronouncements	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.
Fair Value Measurements	We record cash equivalents and marketable securities at fair value. 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. 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.
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, with unrealized gains and losses included as a component of accumulated other comprehensive income (loss) 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. Realized gains and losses are included in investment income on a specific-identification basis.
Product Revenue	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. 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. 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 consist of 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.
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 met, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs and MSUs with performance and market vesting conditions, respectively, that were not met as of June 30, 2019 are not considered to be common stock equivalents.

Loss per Share - Common Stock Excluded from Calculation of Diluted Net Loss Per Share (Details) - shares	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total common stock equivalents excluded from computation of earnings per share (in shares)	7,113,868	6,166,573	7,113,868	6,166,573
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total common stock equivalents excluded from computation of earnings per share (in shares)	6,343,294	5,706,476	6,343,294	5,706,476
Restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total common stock equivalents excluded from computation of earnings per share (in shares)	737,510	438,892	737,510	438,892
Employee stock purchase plan
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total common stock equivalents excluded from computation of earnings per share (in shares)	33,064	21,205	33,064	21,205

Loss per Share (Tables)

6 Months Ended

Jun. 30, 2019

Earnings Per Share [Abstract]

Common Stock Excluded from Calculation of Diluted Earnings Per Share


	Three and Six Months Ended June 30,
	2019	2018
Stock options	6,343,294	5,706,476
Restricted stock units	737,510	438,892

Employee stock purchase plan	33,064	21,205
Total common stock equivalents	7,113,868	6,166,573

Summary of Significant Accounting Policies	6 Months Ended
Summary of Significant Accounting Policies	Jun. 30, 2019
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Leases In February 2016, the Financial Accounting Standards Board, or FASB, issued Accounting Standards Update, or ASU, 2016-02, Leases (Topic 842), which was codified as Accounting Standards Codification, or ASC, 842, Leases, and amended through subsequent ASUs. We adopted ASC 842 effective January 1, 2019 using the modified retrospective transition approach and elected the package of practical expedients, both provided for under ASU 2018-11, Leases (Topic 842): Targeted Improvements. The package of practical expedients allows us not to reassess whether contracts are or contain leases, lease classification, and whether initial direct costs qualify for capitalization. Additionally, as an accounting policy, we have chosen not to separate the non-lease components from the lease components for our building leases and, instead, accounted for non-lease and lease components as a single component. Impact of Adoption of ASC 842 Upon adoption of ASC 842 on January 1, 2019, we recorded operating lease assets of $59.9 million and operating lease liabilities of $77.3 million. The adoption of ASC 842 did not have a material impact on our condensed consolidated statements of operations. Prior periods are presented in accordance with ASC 840, Leases. Leases Accounting Policy We determine if an arrangement is a lease at inception. An arrangement is determined to contain a lease if the contract conveys the right to control the use of an identified property, plant, or equipment for a period of time in exchange for consideration. If we can benefit from the various underlying assets of a lease on their own or together with other resources that are readily available, or if the various underlying assets are neither highly dependent on nor highly interrelated with other underlying assets in the arrangement, they are considered to be a separate lease component. In the event multiple underlying assets are identified, the lease consideration is allocated to the various components based on each of the component’s relative fair value. Operating lease assets represent our right to use an underlying asset for the lease term and operating lease liabilities represent our obligation to make lease payments arising from the leasing arrangement. Operating lease assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. As most of our leases do not provide an implicit rate, in determining the operating lease liabilities we use an estimate of our incremental borrowing rate. The incremental borrowing rate is determined using two alternative credit scoring models to estimate our credit rating, adjusted for collateralization. The calculation of the operating lease assets includes any lease payments made and excludes any lease incentives. Our lease terms may include options to extend or terminate the lease when it is reasonably certain that we will exercise that option. For operating leases, we record operating lease assets and liabilities in our consolidated balance sheets. Lease expense for lease payments is recognized on a straight-line basis over the lease term. Short-term leases, or leases that have a lease term of 12 months or less at commencement date, are excluded from this treatment and are recognized on a straight-line basis over the term of the lease. 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.

Marketable Securities

6 Months Ended

Jun. 30, 2019

Investments, Debt and Equity Securities [Abstract]

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, with unrealized gains and losses included as a component of accumulated other comprehensive income (loss) 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. 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 six months ended June 30, 2019 and 2018.

Marketable securities at June 30, 2019 consisted of the following (in thousands):


	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:
Certificates of deposit	$	240	$	—	$	—	$	240
U.S. Treasuries	186,295		211		(57)		186,449
Government securities	54,836		20		(34)		54,822
Corporate debt securities	170,255		148		(104)		170,299
Non-current:


Government securities	32,575		19		(48)		32,546
Corporate debt securities	95,657		491		(45)		96,103
Total marketable securities	$	539,858	$	889	$	(288)	$	540,459

Marketable securities at December 31, 2018 consisted of the following (in thousands):


	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:
Certificates of deposit	$	960	$	—	$	(4)	$	956
U.S. Treasuries	231,101		7		(228)		230,880
Government securities	75,335		—		(121)		75,214
Corporate debt securities	208,233		—		(483)		207,750
Non-current:

U.S. Treasuries	12,202		4		(125)		12,081
Government securities	70,177		10		(188)		69,999
Corporate debt securities	139,082		12		(1,055)		138,039
Total marketable securities	$	737,090	$	33	$	(2,204)	$	734,919

As of June 30, 2019 and December 31, 2018, 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 June 30, 2019 and December 31, 2018, we held 79 and 242 debt securities, respectively, that were in an unrealized loss position for less than one year. The aggregate fair value of debt securities in an unrealized loss position at June 30, 2019 and December 31, 2018 was $175.5 million and $639.3 million, respectively. There were no individual securities that were in a significant unrealized loss position as of June 30, 2019 and December 31, 2018. 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 other-than-temporarily impaired as of June 30, 2019 and December 31, 2018.

Share-Based Payments - Expenses Related to Equity-Based Awards (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 18,547	$ 16,455	$ 36,655	$ 30,977
Research and development expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	10,067	9,667	20,109	18,307
Selling, general and administrative expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 8,480	$ 6,788	$ 16,546	$ 12,670

Collaboration and License Agreements - Celegene Purchase Agreements (Details)	1 Months Ended
	May 31, 2016 USD ($) extension	Jun. 30, 2019 USD ($)	May 17, 2016 USD ($)
2010 Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone-based receivable payments, eligible to be received		$ 80,000,000.0
Milestone payments upon achievement of specified regulatory milestone events		55,000,000.0
Milestone payment upon achievement of a specified commercial milestone event		$ 25,000,000.0
2016 Agreement \| Celgene
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Term of agreements	4 years
Extension period \| extension	2
Number of allowable special case extensions \| extension	4
Special case extension term	1 year
Upfront payment agreement extension fee receivable	$ 40,000,000.0
Option exercise fee receivable			$ 30,000,000.0
2016 Agreement \| Celgene \| Specified clinical development event
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone-based receivable payments, eligible to be received	20,000,000.0
2016 Agreement \| Celgene \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone-based receivable payments, eligible to be received	169,000,000.0
2016 Agreement \| Celgene \| Maximum \| Specified regulatory milestone events
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone-based receivable payments, eligible to be received	$ 149,000,000.0

Overview and Basis of Presentation - Additional Information (Details) $ in Millions	Jun. 30, 2019 USD ($)
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Cash, cash equivalents, and short-term investments	$ 624.0

Share-Based Payments - Schedule of Performance-Based and Market- Based Units (Details)	6 Months Ended
	Jun. 30, 2019 $ / shares shares
Performance-Based Stock Units
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Unvested shares beginning of period (in shares) \| shares	169,031
Granted (in shares) \| shares	155,297
Vested (in shares) \| shares	(167,031)
Unvested shares end of period (in shares) \| shares	157,297
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-average grant date fair value, Unvested shares beginning of period (in usd per share) \| $ / shares	$ 52.67
Weighted-average grant date fair value, Granted (in usd per share) \| $ / shares	61.93
Weighted-average grant date fair value, Vested (in usd per share) \| $ / shares	52.36
Weighted-average grant date fair value, Unvested shares end of period (in usd per share) \| $ / shares	$ 62.15
Market-Based Stock Units
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Unvested shares beginning of period (in shares) \| shares	0
Granted (in shares) \| shares	42,695
Unvested shares end of period (in shares) \| shares	42,695
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-average grant date fair value, Unvested shares beginning of period (in usd per share) \| $ / shares	$ 0
Weighted-average grant date fair value, Granted (in usd per share) \| $ / shares	41.50
Weighted-average grant date fair value, Unvested shares end of period (in usd per share) \| $ / shares	$ 41.50

Share-Based Payments (Tables)

6 Months Ended

Jun. 30, 2019

Share-based Payment Arrangement [Abstract]

Schedule of Company's Stock Option Activity

The following table presents stock option activity for the six months ended June 30, 2019:


	Number of Stock Options	Weighted-Average Exercise Price
Outstanding at December 31, 2018	5,416,069	$	60.10
Granted	1,464,728	57.08
Exercised	(181,010)	38.59
Forfeited/Expired	(356,493)	66.38
Outstanding at June 30, 2019	6,343,294	$	59.66
Exercisable at June 30, 2019	3,414,953	$	58.63
Vested and expected to vest at June 30, 2019	6,343,294	$	59.66

Unvested Stock Unit Activity

The following table presents restricted stock unit, or RSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	532,144	$	75.45
Granted	408,707	58.46
Vested	(150,082)	69.29
Forfeited	(53,259)	72.24
Unvested shares at June 30, 2019	737,510	$	67.52

Schedule of Performance-Based Units

The following table presents performance-based stock unit, or PSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	169,031	$	52.67
Granted	155,297	61.93
Vested	(167,031)	52.36

Unvested shares at June 30, 2019	157,297	$	62.15

Schedule of Market-Based Units Activity

The following table presents market-based stock unit, or MSU, activity for the six months ended June 30, 2019:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2018	—	$	—
Granted	42,695	41.50


Unvested shares at June 30, 2019	42,695	$	41.50

Schedule of Stock-Based Compensation Expense by Award Type Included Within the Condensed Consolidated Statements of Operations

Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Stock options	$	12,467	$	13,311	$	25,513	$	25,783
Restricted stock units	5,243		2,805		9,791		4,602
Employee stock purchase plan	392		339		720		592
Other stock awards	445		—		631		—
Total stock-based compensation expense	$	18,547	$	16,455	$	36,655	$	30,977

Schedule of Allocated Stock-Based Compensation Expense

Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2019		2018		2019		2018
Research and development expense	$	10,067	$	9,667	$	20,109	$	18,307
Selling, general and administrative expense	8,480		6,788		16,546		12,670
Total stock-based compensation expense	$	18,547	$	16,455	$	36,655	$	30,977

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit
Beginning balance (in shares) at Dec. 31, 2017		48,826,153
Beginning balance at Dec. 31, 2017	$ 375,503	$ 49	$ 1,174,904	$ (1,389)	$ (798,061)
Issuance of common stock for follow-on offering (in shares)		8,152,986
Issuance of common stock for follow-on offering	516,206	$ 8	516,198
Common stock issued under stock incentive plan and ESPP (in shares)		562,474
Common stock issued under stock incentive plan and ESPP	12,332	$ 1	12,331
Stock-based compensation expense	14,522		14,522
Other comprehensive income (loss)	(1,254)			(1,254)
Net loss	(90,825)				(90,825)
Other	(346)		(346)
Ending balance (in shares) at Mar. 31, 2018		57,541,613
Ending balance at Mar. 31, 2018	865,594	$ 58	1,717,609	(2,643)	(849,430)
Beginning balance (in shares) at Dec. 31, 2017		48,826,153
Beginning balance at Dec. 31, 2017	375,503	$ 49	1,174,904	(1,389)	(798,061)
Net loss	(159,570)
Ending balance (in shares) at Jun. 30, 2018		57,933,036
Ending balance at Jun. 30, 2018	823,142	$ 58	1,743,657	(2,398)	(918,175)
Beginning balance (in shares) at Mar. 31, 2018		57,541,613
Beginning balance at Mar. 31, 2018	865,594	$ 58	1,717,609	(2,643)	(849,430)
Common stock issued under stock incentive plan and ESPP (in shares)		391,423
Common stock issued under stock incentive plan and ESPP	9,638		9,638
Stock-based compensation expense	16,455		16,455
Other comprehensive income (loss)	245			245
Net loss	(68,745)				(68,745)
Other	(45)		(45)
Ending balance (in shares) at Jun. 30, 2018		57,933,036
Ending balance at Jun. 30, 2018	823,142	$ 58	1,743,657	(2,398)	(918,175)
Beginning balance (in shares) at Dec. 31, 2018		58,218,653
Beginning balance at Dec. 31, 2018	687,537	$ 58	1,794,283	(2,171)	(1,104,633)
Common stock issued under stock incentive plan and ESPP (in shares)		441,168
Common stock issued under stock incentive plan and ESPP	6,003	$ 1	6,002
Stock-based compensation expense	18,108		18,108
Other comprehensive income (loss)	1,687			1,687
Net loss	(93,078)				(93,078)
Ending balance (in shares) at Mar. 31, 2019		58,659,821
Ending balance at Mar. 31, 2019	620,257	$ 59	1,818,393	(484)	(1,197,711)
Beginning balance (in shares) at Dec. 31, 2018		58,218,653
Beginning balance at Dec. 31, 2018	$ 687,537	$ 58	1,794,283	(2,171)	(1,104,633)
Common stock issued under stock incentive plan and ESPP (in shares)	181,010
Net loss	$ (202,949)
Ending balance (in shares) at Jun. 30, 2019		58,749,186
Ending balance at Jun. 30, 2019	532,677	$ 59	1,839,710	490	(1,307,582)
Beginning balance (in shares) at Mar. 31, 2019		58,659,821
Beginning balance at Mar. 31, 2019	620,257	$ 59	1,818,393	(484)	(1,197,711)
Common stock issued under stock incentive plan and ESPP (in shares)		89,365
Common stock issued under stock incentive plan and ESPP	2,770		2,770
Stock-based compensation expense	18,547		18,547
Other comprehensive income (loss)	974			974
Net loss	(109,871)				(109,871)
Ending balance (in shares) at Jun. 30, 2019		58,749,186
Ending balance at Jun. 30, 2019	$ 532,677	$ 59	$ 1,839,710	$ 490	$ (1,307,582)

Accrued Expenses - Summary of Accrued Expenses (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Payables and Accruals [Abstract]
Accrued compensation	$ 10,541	$ 20,843
Accrued research and development costs	30,189	14,777
Accrued professional fees	6,357	5,441
Accrued other	2,131	1,086
Total accrued expenses	$ 49,218	$ 42,147

Fair Value Measurements - Additional Information (Details)	Jun. 30, 2019 USD ($)
Fair Value, Measurements, Recurring \| Level 3
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of assets (liabilities)	$ 0

Product Revenue - Schedule of Product Revenue Allowance and Reserves (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2019	Dec. 31, 2018
Contractual Adjustments [Roll Forward]
Contract adjustments, beginning balance	$ 592
Contractual adjustments, current provisions relating to sales in the current year	3,145
Contractual adjustments, adjustments relating to prior year	8
Contractual adjustments, payments/returns relating to sales in the current year	(2,450)
Contractual adjustments, payments/returns relating to sales in the prior year	(598)
Contract adjustments, ending balance	697
Government Rebates [Roll Forward]
Government rebates, beginning balance	325
Government rebates, current provisions relating to sales in the current year	820
Government rebates, adjustments relating to prior years	0
Government rebates, payments/returns relating to sales in the current year	(355)
Government rebates, payments/returns relating to sales in the prior years	(230)
Government rebates, ending balance	560
Product Returns [Roll Forward]
Returns, beginning balance	334
Returns, current provisions relating to sales in the current year	586
Returns, adjustments relating to prior years	0
Returns, payments/returns relating to sales in the current year	0
Returns, payments/returns relating to sales in the prior years	0
Returns, ending balance	920
Allowance for Doubtful Accounts Receivable [Roll Forward]
Total revenue-related reserves	2,177	$ 1,251
Total allowances and reserves, current provisions relating to sales in the current year	4,551
Total allowances and reserves, adjustments relating to prior years	8
Total allowances and reserves, payments/returns relating to sales in the current year	(2,805)
Total allowances and reserves, payments/returns relating to sales in the prior years	$ (828)

Leases - Additional Information (Details) ft² in Thousands, $ in Millions		3 Months Ended	6 Months Ended
	Apr. 11, 2019 USD ($) ft² lease_term	Jun. 30, 2019 USD ($)	Jun. 30, 2019 USD ($)
Lessee, Lease, Description [Line Items]
Remaining lease terms			9 years
Operating lease cost		$ 3.8	$ 6.8
Cash paid for amounts included in measurement of lease liabilities		$ 3.2	$ 6.3
Weighted-average incremental borrowing rate		5.70%	5.70%
Weighted-average remaining lease term		8 years 8 months 12 days	8 years 8 months 12 days
38 Sidney Street Lease
Lessee, Lease, Description [Line Items]
Number of square feet of office space (in square feet) \| ft²	13
Number of optional terms available at end of current lease term (in lease terms) \| lease_term	2
Term of optional lease (in years)	5 years
Tenant improvement allowance	$ 1.0
64 Sidney Street Lease
Lessee, Lease, Description [Line Items]
Term for extension of operating lease (in years)	3 years

Collaboration and License Agreements - CStone Pharmaceuticals Purchase Agreement (Details) - USD ($)	1 Months Ended	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Remaining unsatisfied performance obligation		$ 75,500,000		$ 75,500,000
Revenue		26,221,000	$ 40,414,000	56,448,000	$ 49,176,000
Milestones achieved		0	0	0	0
Collaboration revenue – related party
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenue		8,979,000	26,401,000	26,898,000	33,746,000
Milestones achieved			15,000,000.0
Royalty revenue – related party
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenue		2,703,000	$ 1,573,000	4,903,000	$ 2,990,000
CStone Pharmaceuticals \| CStone Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Initial payment received	$ 12,000,000.0
Potential future milestone payments		5,000,000.0		5,000,000.0
Remaining unsatisfied performance obligation		700,000		700,000
Milestones achieved		0
CStone Pharmaceuticals \| CStone Agreement \| Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty percentage	15.00%
CStone Pharmaceuticals \| CStone Agreement \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Potential future milestone payments		$ 412,000,000.0		412,000,000.0
Royalty percentage	19.00%
CStone Pharmaceuticals \| CStone Agreement \| Royalty revenue – related party
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenue				$ 0

Fair Value Measurements

6 Months Ended

Jun. 30, 2019

Fair Value Disclosures [Abstract]

Fair Value Measurements

We record cash equivalents and marketable securities at fair value. 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.

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 June 30, 2019 (in thousands):


	Level 1		Level 2		Level 3		Total
Cash equivalents	$	27,012	$	10,995	$	—	$	38,007
Marketable securities:
Certificates of deposit	—		240		—		240
U.S. Treasuries	—		186,449		—		186,449
Government securities	—		87,368		—		87,368
Corporate debt securities	—		266,402		—		266,402
Total cash equivalents and marketable securities	$	27,012	$	551,454	$	—	$	578,466

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 June 30, 2019.

There have been no changes to the valuation methods during the six months ended June 30, 2019. We evaluate transfers between levels at the end of each reporting period. There were no transfers between Level 1 and Level 2 during the six months ended June 30, 2019. We have no financial assets or liabilities that were classified as Level 3 at any point during the six months ended June 30, 2019.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Leases - Schedule of Undiscounted Minimum Rental Commitments Under Topic 842 (Details) $ in Thousands	Jun. 30, 2019 USD ($)
Leases [Abstract]
Remaining 2019	$ 5,695
2020	14,015
2021	14,380
2022	16,773
2023	18,126
2024	18,660
Thereafter	63,891
Undiscounted minimum rental commitments	$ 151,540

Summary of Significant Accounting Policies (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Jan. 01, 2019
Schedule of Significant Accounting Policies [Line Items]
Operating lease assets	$ 98,500
Operating lease liabilities	$ 116,470
ASU 2016-02
Schedule of Significant Accounting Policies [Line Items]
Operating lease assets		$ 59,900
Operating lease liabilities		$ 77,300

Inventory

6 Months Ended

Jun. 30, 2019

Inventory Disclosure [Abstract]

Inventory

Inventory, which consists of commercial supply of TIBSOVO® (ivosidenib), consists of the following (in thousands):


	June 30, 2019		December 31, 2018
Raw materials	$	180	$	—
Work-in-process	4,392		788
Finished goods	87		81
Total inventory	$	4,659	$	869

Product Revenue - Schedule of Revenue-Related Reserves (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Reduction of accounts receivable	$ 416	$ 326
Component of accrued expenses	1,761	925
Total revenue-related reserves	$ 2,177	$ 1,251