Blueprint Medicines (BPMC) 10-Q 5 Nov 19 2019 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - $ / shares	9 Months Ended
	Sep. 30, 2019	Oct. 31, 2019
Document and Entity Information [Abstract]
Entity Central Index Key	0001597264
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2019
Document Transition Report	false
Entity File Number	001-37359
Entity Registrant Name	BLUEPRINT MEDICINES CORPORATION
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	26-3632015
Entity Address, Address Line One	45 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	374-7580
Title of 12(b) Security	Common stock, par value $0.001 per share
Trading Symbol	BPMC
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 Listing, Par Value Per Share	$ 0.001
Entity Common Stock, Shares Outstanding		49,202,122
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Amendment Flag	false

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 89,237	$ 68,064
Investments, available-for-sale	404,205	425,948
Accounts receivable	2,414	64
Unbilled accounts receivable	2,662	151
Prepaid expenses and other current assets	15,208	5,560
Total current assets	513,726	499,787
Investments, available-for-sale	101,017
Property and equipment, net	38,310	29,627
Operating lease right-of-use assets, net	73,967
Restricted cash	5,164	5,154
Other assets	5,741	5,556
Total assets	737,925	540,124
Current liabilities:
Accounts payable	2,203	3,298
Accrued expenses	80,419	51,711
Current portion of operating lease liabilities	6,587
Current portion of deferred revenue	4,933	3,600
Current portion of lease incentive obligation		1,714
Total current liabilities	94,142	60,323
Deferred rent, net of current portion		5,130
Operating lease liabilities, net of current portion	90,921
Deferred revenue, net of current portion	36,398	42,567
Lease incentive obligation, net of current portion		12,903
Other long-term liabilities	120	192
Total liabilities	221,581	121,115
Commitments (Note 12)
Stockholders' equity:
Preferred stock, $0.001 par value; 5,000,000 shares authorized; no shares issued and outstanding
Common stock, $0.001 par value; 120,000,000 shares authorized; 49,175,422 and 44,037,026 shares issued and outstanding at September 30, 2019 and December 31, 2018, respectively	49	44
Additional paid-in capital	1,394,566	1,016,690
Accumulated other comprehensive income (loss)	637	(180)
Accumulated deficit	(878,908)	(597,545)
Total stockholders' equity	516,344	419,009
Total liabilities and stockholders' equity	$ 737,925	$ 540,124

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2019	Dec. 31, 2018
Preferred Stock Disclosures
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	0	0
Preferred stock, shares outstanding (in shares)	0	0
Common Stock Disclosures
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized (in shares)	120,000,000	120,000,000
Common stock, shares issued (in shares)	49,175,442	44,037,026
Common Stock, shares outstanding (in shares)	49,175,422	44,037,026

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Condensed Consolidated Statements of Operations and Comprehensive Loss
Collaboration revenue	$ 9,139	$ 1,095	$ 14,979	$ 43,488
Operating expenses:
Research and development	81,453	64,562	242,804	173,089
General and administrative	25,647	12,041	64,123	34,285
Total operating expenses	107,100	76,603	306,927	207,374
Other income (expense):
Other income (expense), net	3,692	2,799	10,595	7,635
Interest expense	(6)	(14)	(10)	(69)
Total other income	3,686	2,785	10,585	7,566
Net loss	(94,275)	(72,723)	(281,363)	(156,320)
Other comprehensive loss:
Changes in foreign currency translation adjustments	(3)		(10)
Changes in unrealized gain (losses) related to available-for-sale investments	(287)	44	828	(68)
Comprehensive loss	$ (94,565)	$ (72,679)	$ (280,545)	$ (156,388)
Net loss per share - basic and diluted	$ (1.93)	$ (1.66)	$ (5.94)	$ (3.57)
Weighted-average number of common shares used in net loss per share - basic and diluted	48,921,445	43,915,376	47,360,675	43,824,773

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total
Beginning Balance at Dec. 31, 2017	$ 43	$ 979,785	$ (269)	$ (355,589)	$ 623,970
Beginning Balance (in shares) at Dec. 31, 2017	43,577,526
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan	$ 1	3,552			3,553
Issuance of common stock under stock plan (in shares)	243,721
Stock-based compensation expense		5,549			5,549
Adoption of new accounting standard				(5,314)	(5,314)
Unrealized gain (loss) on available-for-sale securities			(322)		(322)
Other		(14)			(14)
Net loss				(56,549)	(56,549)
Ending Balance at Mar. 31, 2018	$ 44	988,872	(591)	(417,452)	570,873
Ending Balance (in shares) at Mar. 31, 2018	43,821,247
Beginning Balance at Dec. 31, 2017	$ 43	979,785	(269)	(355,589)	623,970
Beginning Balance (in shares) at Dec. 31, 2017	43,577,526
Increase (Decrease) in Stockholders' Equity
Net loss					(156,320)
Ending Balance at Sep. 30, 2018	$ 44	1,006,812	(337)	(517,223)	489,296
Ending Balance (in shares) at Sep. 30, 2018	43,945,316
Beginning Balance at Mar. 31, 2018	$ 44	988,872	(591)	(417,452)	570,873
Beginning Balance (in shares) at Mar. 31, 2018	43,821,247
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		742			742
Issuance of common stock under stock plan (in shares)	56,955
Purchase of common stock under ESPP		345			345
Purchase of common stock under ESPP (in shares)	5,572
Stock-based compensation expense		7,762			7,762
Unrealized gain (loss) on available-for-sale securities			210		210
Other		49			49
Net loss				(27,048)	(27,048)
Ending Balance at Jun. 30, 2018	$ 44	997,770	(381)	(444,500)	552,933
Ending Balance (in shares) at Jun. 30, 2018	43,883,774
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		651			651
Issuance of common stock under stock plan (in shares)	61,542
Stock-based compensation expense		8,391			8,391
Unrealized gain (loss) on available-for-sale securities			44		44
Net loss				(72,723)	(72,723)
Ending Balance at Sep. 30, 2018	$ 44	1,006,812	(337)	(517,223)	489,296
Ending Balance (in shares) at Sep. 30, 2018	43,945,316
Beginning Balance at Dec. 31, 2018	$ 44	1,016,690	(180)	(597,545)	$ 419,009
Beginning Balance (in shares) at Dec. 31, 2018	44,037,026				44,037,026
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		2,061			$ 2,061
Issuance of common stock under stock plan (in shares)	134,439
Stock-based compensation expense		10,295			10,295
Cumulative translation adjustment			(15)		(15)
Unrealized gain (loss) on available-for-sale securities			270		270
Net loss				(87,407)	(87,407)
Ending Balance at Mar. 31, 2019	$ 44	1,029,046	75	(684,952)	344,213
Ending Balance (in shares) at Mar. 31, 2019	44,171,465
Beginning Balance at Dec. 31, 2018	$ 44	1,016,690	(180)	(597,545)	$ 419,009
Beginning Balance (in shares) at Dec. 31, 2018	44,037,026				44,037,026
Increase (Decrease) in Stockholders' Equity
Cumulative translation adjustment					$ (10)
Net loss					(281,363)
Ending Balance at Sep. 30, 2019	$ 49	1,394,566	637	(878,908)	$ 516,344
Ending Balance (in shares) at Sep. 30, 2019	49,175,442				49,175,442
Beginning Balance at Mar. 31, 2019	$ 44	1,029,046	75	(684,952)	$ 344,213
Beginning Balance (in shares) at Mar. 31, 2019	44,171,465
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		5,813			5,813
Issuance of common stock under stock plan (in shares)	215,299
Purchase of common stock under ESPP		522			522
Purchase of common stock under ESPP (in shares)	10,718
Stock-based compensation expense		13,666			13,666
Cumulative translation adjustment			7		7
Unrealized gain (loss) on available-for-sale securities			845		845
Initial public offering / Follow on offering, net of issuance costs	$ 5	327,437			327,442
Initial public offering / Follow on offering, net of issuance costs (in shares)	4,662,162
Net loss				(99,681)	(99,681)
Ending Balance at Jun. 30, 2019	$ 49	1,376,484	927	(784,633)	592,827
Ending Balance (in shares) at Jun. 30, 2019	49,059,644
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		3,089			3,089
Issuance of common stock under stock plan (in shares)	115,798
Stock-based compensation expense		14,993			14,993
Cumulative translation adjustment			(3)		(3)
Unrealized gain (loss) on available-for-sale securities			(287)		(287)
Net loss				(94,275)	(94,275)
Ending Balance at Sep. 30, 2019	$ 49	$ 1,394,566	$ 637	$ (878,908)	$ 516,344
Ending Balance (in shares) at Sep. 30, 2019	49,175,442				49,175,442

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Cash flows from operating activities
Net loss	$ (281,363)	$ (156,320)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,334	3,076
Stock-based compensation	38,954	21,702
Accretion of premiums and discounts on investments	(4,366)	(2,934)
Other		10
Changes in assets and liabilities:
Prepaid expenses and other current assets	(7,175)	6,007
Other assets	(58)	(4,265)
Accounts receivable	(2,350)	413
Unbilled accounts receivable	(2,417)	(344)
Accounts payable	(1,095)	244
Accrued expenses	26,408	18,926
Deferred revenue	(4,836)	6,512
Deferred rent		(454)
Operating lease liabilities	(2,156)
Net cash used in operating activities	(233,120)	(107,427)
Cash flows from investing activities
Purchases of property and equipment	(10,122)	(12,252)
Purchases of investments	(597,514)	(648,902)
Maturities of investments	523,434	443,825
Net cash used in investing activities	(84,202)	(217,329)
Cash flows from financing activities
Principal payments on loan payable		(1,250)
Proceeds from public offering of common stock, net of issuance cost	327,466
Net proceeds from stock option exercises and employee stock purchase plan	11,454	5,341
Payment of offering costs		(281)
Other financing activities	(116)	(120)
Net cash provided by financing activities	338,804	3,690
Net increase (decrease) in cash, cash equivalents, and restricted cash	21,482	(321,066)
Cash, cash equivalents and restricted cash at beginning of period	73,429	405,072
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(10)
Cash, cash equivalents and restricted cash at end of period	94,901	84,006
Supplemental cash flow information
Public offering costs incurred but unpaid at period end	25
Property and equipment purchases unpaid at period end	3,225	128
Cash paid for interest	5	61
Cash paid for taxes, net	$ 130	$ 105

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2018
Reconciliation of cash, cash equivalents, and restricted cash
Cash and cash equivalents	$ 89,237	$ 78,641
Restricted cash included in prepaid expenses and other current assets	500	211
Restricted cash	5,164	5,154
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$ 94,901	$ 84,006

Nature of Business

Nature of Business	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Nature of Business	1. Nature of Business Blueprint Medicines Corporation (the Company), a Delaware corporation incorporated on October 14, 2008, is a precision therapy company focused on genomically defined cancers, rare diseases and cancer immunotherapy. The Company’s approach is to leverage its novel target discovery engine to systematically and reproducibly identify kinases that are drivers of diseases and to craft highly selective and potent drug candidates that may provide significant and durable clinical responses for patients without adequate treatment options. The Company is devoting substantially all of its efforts to research and development, initial market development and raising capital. The Company is subject to a number of risks similar to those of other early stage companies, including dependence on key individuals; establishing safety and efficacy in clinical trials for its drug candidates; the need to develop commercially viable drug candidates; competition from other companies, many of which are larger and better capitalized; and the need to obtain adequate additional financing to fund the development of its drug candidates. If the Company is unable to raise capital when needed or on attractive terms, it would be forced to delay, reduce, eliminate or out-license certain of its research and development programs or future commercialization efforts. On April 2, 2019, the Company closed an underwritten public offering of 4,662,162 shares of its common stock at a price to the public of $74.00 per share, including 608,108 shares of common stock sold by the Company pursuant to the exercise in full by the underwriters of their option to purchase additional shares in connection with the offering. The Company received net proceeds of $327.4 million, after deducting underwriting discounts and commissions and offering expenses. As of September 30, 2019, the Company had cash, cash equivalents and investments of $594.5 million. Based on the Company’s current operating plans, the Company believes that its existing cash, cash equivalents and investments, together with the $25.0 million upfront cash payment from Clementia Pharmaceuticals, Inc. (Clementia) and an $8.0 million research milestone achieved in the fourth quarter of 2019 under the collaboration with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. (collectively, Roche), but excluding any additional potential option fees, milestone payments or other payments from Roche, CStone Pharmaceuticals (CStone) or Clementia, will be sufficient to enable it to fund its operating expenses and capital expenditure requirements into the second half of 2021. See Note 13, Subsequent Events

Summary of Significant Accounti

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Summary of Significant Accounting Policies and Recent Accounting Pronouncements	2. Summary of Significant Accounting Policies and Recent Accounting Pronouncements Basis of Presentation The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the United States (GAAP) as found in the Accounting Standards Codification (ASC), Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB) and the rules and regulations of the Securities and Exchange Commission (SEC). Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements as of and for the year ended December 31, 2018 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, filed with the SEC on February 26, 2019 (the 2018 Annual Report on Form 10-K). The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements, and updated, as necessary, in this report. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of September 30, 2019, the results of its operations for the three and nine months ended September 30, 2019 and 2018, stockholder’s equity for the three and nine months ended September 30, 2019 and 2018 and cash flows for the nine months ended September 30, 2019 and 2018. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2019 are not necessarily indicative of the results for the year ending December 31, 2019, or for any future period. The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell and hold securities, Blueprint Medicines (Switzerland) GmbH, Blueprint Medicines (Netherlands) B.V., Blueprint Medicines (UK) Ltd, and Blueprint Medicines (Germany) GmbH. All intercompany transactions and balances have been eliminated. The accompanying condensed consolidated financial statements do not include the account of the Company’s wholly-owned subsidiaries Blueprint Medicines Spain, S.L., which was formed in October 2019, and Blueprint Medicines (France) SAS, which was formed in November 2019. Use of Estimates The preparation of financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies and in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Estimates are used in the following areas, among others: revenue recognition, operating lease right-of-use assets, operating lease liabilities, stock-based compensation expense, accrued expenses, and income taxes. Significant Accounting Policies The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and nine months ended September 30, 2019 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2018 Annual Report on Form 10-K, except as noted below with respect to the Company’s accounting policies related to lease obligations and as noted within this Note 2 under the section titled “—New Accounting Pronouncements.” New Accounting Pronouncements Leases ASU No. 2016-02, Leases (Topic 842) ASU No. 2018-01, Leases (Topic 842): Land Easement Practical Expedient for Transition to Topic 842, ASU No. 2018-10, Codification Improvements to Topic 842, Leases, ASU No. 2018-11, Leases (Topic 842): Targeted Improvements, ASU No. 2018-20, Narrow-Scope Improvement for Lessors, and ASU No. 2019-01, Leases (Topic 842): Codification Improvements. Leases or ASC 840, which did not require the recognition of operating lease liabilities on the balance sheet, and is not comparative. Impact of Adoption of ASC 842 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Impact of ASC 842 Adoption on Consolidated Balance Sheet as of January 1, 2019 (in thousands) ​ Balances without adoption of ASC 842 ​ ASC 842 Adjustment ​ Balances with adoption of ASC 842 Operating lease right-of-use assets, net ​ $ — ​ $ 54,245 ​ $ 54,245 Total assets ​ ​ 540,124 ​ ​ 54,245 ​ ​ 594,369 Accrued expenses ​ ​ 51,711 ​ ​ (125) ​ ​ 51,586 Current portion of operating lease liabilities ​ ​ — ​ ​ 4,730 ​ ​ 4,730 Current portion of lease incentive obligation ​ ​ 1,714 ​ ​ (1,714) ​ ​ — Total current liabilities ​ ​ 60,323 ​ ​ 2,891 ​ ​ 63,214 Deferred rent, net of current portion ​ ​ 5,130 ​ ​ (5,130) ​ ​ — Operating lease liabilities, net of current portion ​ ​ — ​ ​ 69,387 ​ ​ 69,387 Lease incentive obligation, net of current portion ​ ​ 12,903 ​ ​ (12,903) ​ ​ — Total liabilities ​ ​ 121,115 ​ ​ 54,245 ​ ​ 175,360 ​ Leases Accounting Policy For contracts entered into on or after the effective date, at the inception of a contract, the Company assesses whether the contract is, or contains, a lease. The assessment is based on: (1) whether the contract involves the use of a distinct identified asset, (2) whether the Company obtains the right to substantially all the economic benefit from the use of the asset throughout the period, and (3) whether the Company has the right to direct the use of the asset. At inception of a lease, the Company allocates the consideration in the contract to each lease component based on its relative stand-alone price to determine the lease payments. Leases are classified as either finance leases or operating leases. A lease is classified as a finance lease if any one of the following criteria are met: the lease transfers ownership of the asset by the end of the lease term, the lease contains an option to purchase the asset that is reasonably certain to be exercised, the lease term is for a major part of the remaining useful life of the asset or the present value of the lease payments equals or exceeds substantially all of the fair value of the asset. A lease is classified as an operating lease if it does not meet any of these criteria. For all leases at the lease commencement date, a right-of-use asset and a lease liability are recognized. The right-of-use asset represents the right to use the leased asset for the lease term. The lease liability represents the present value of the lease payments under the lease. The right-of-use asset is initially measured at cost, which primarily comprises the initial amount of the lease liability, plus any initial direct costs incurred if any, less any lease incentives received. All right-of-use assets are reviewed for impairment. The lease liability is initially measured at the present value of the lease payments, discounted using the interest rate implicit in the lease or, if that rate cannot be readily determined, the secured incremental borrowing rate for the same term as the underlying lease. For real estate leases, the Company uses its secured incremental borrowing rate. For finance leases, the Company uses the rate implicit in the lease or its secured incremental borrowing rate if the implicit lease rate cannot be determined. Lease payments included in the measurement of the lease liability comprise the following: the fixed noncancelable lease payments, payments for optional renewal periods where it is reasonably certain the renewal period will be exercised, and payments for early termination options unless it is reasonably certain the lease will not be terminated early. Lease cost for operating leases consists of the lease payments plus any initial direct costs, primarily brokerage commissions, and is recognized on a straight-line basis over the lease term. Included in lease cost are any variable lease payments incurred in the period that are not included in the initial lease liability and lease payments incurred in the period for any leases with an initial term of 12 months or less. Lease cost for finance leases consists of the amortization of the right-of-use asset on a straight-line basis over the lease term and interest expense determined on an amortized cost basis. The lease payments are allocated between a reduction of the lease liability and interest expense. Credit Losses ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments Debt Securities In March 2017, the FASB issued ASU No. 2017-08, Receivables - Nonrefundable Fees and Other Costs ( Subtopic 310-20 ): Premium Amortization on Purchased Callable Debt Securities. Fair Value Measurements In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework Changes to the Disclosure Requirements for Fair Value Measurement Collaborative Arrangements In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606. ● Clarifies that certain transactions between collaborative arrangement participants should be accounted for as revenue under ASC 606 , Revenue from Contracts with Customers , when the collaborative arrangement participant is a customer in the context of a unit of account. In those situations, all the guidance in ASC 606 should be applied, including recognition, measurement, presentation and disclosure requirements; ● Adds unit-of-account guidance to ASC 808 , Collaborative Arrangements , to align with the guidance in ASC 606 (that is, a distinct good or service) when an entity is assessing whether the collaborative arrangement or a part of the arrangement is within the scope of ASC 606 ; and ● Requires that in a transaction with a collaborative arrangement participant that is not directly related to sales to third parties, presenting that transaction together with revenue recognized under ASC 606 is precluded if the collaborative arrangement participant is not a customer. Internal-Use Software ​ In August 2018, the FASB issued ASU No. 2018-15, Intangibles-Goodwill and Other-Internal-Use Software ( Subtopic 350-40 ): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract

Cash Equivalents and Investment

Cash Equivalents and Investments	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Cash Equivalents and Investments	3. Cash Equivalents and Investments Cash equivalents and investments, available-for-sale, consisted of the following at September 30, 2019 and December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair September 30, 2019 Cost Gain ​ Losses ​ Value Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 89,237 ​ $ — ​ $ — ​ $ 89,237 Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 504,559 ​ ​ 693 ​ ​ (30) ​ ​ 505,222 Total ​ $ 593,796 ​ $ 693 ​ $ (30) ​ $ 594,459 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair December 31, 2018 Cost Gain ​ Losses ​ Value Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 68,064 ​ $ — ​ $ — ​ $ 68,064 Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 426,112 ​ ​ — ​ ​ (164) ​ ​ 425,948 Total ​ $ 494,176 ​ $ — ​ $ (164) ​ $ 494,012 ​ At September 30, 2019 and December 31, 2018, the Company held eight and 54 debt securities, respectively, that were in an unrealized loss position. The aggregate fair value of debt securities in an unrealized loss position at September 30, 2019 and December 31, 2018 was $55.4 million and $397.5 million, respectively. There were no individual securities that were in a significant unrealized loss position as of September 30, 2019 and December 31, 2018. As of September 30, 2019, there was no securities in an unrealized loss position for more than twelve months. The Company has the intent and ability to hold such securities until recovery, and there was no material change in the credit risk of these investments. As a result, the Company determined it did not hold any investments with an other-than-temporary impairment as of September 30, 2019. As of September 30, 2019, 14 securities with an aggregate fair value of $101.0 million have remaining maturities greater than one year. No available-for-sale securities held as of December 31, 2018 had remaining maturities greater than one year.

Fair Value of Financial Instrum

Fair Value of Financial Instruments	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Fair Value of Financial Instruments	4. Fair Value of Financial Instruments The following table summarizes cash equivalents and marketable securities measured at fair value on a recurring basis as of September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Active Observable Unobservable ​ ​ September 30, ​ Markets ​ Inputs ​ Inputs Description ​ 2019 ​ (Level 1) ​ (Level 2) ​ (Level 3) Financial Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 89,237 ​ $ 89,237 ​ $ — ​ $ — Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 505,222 ​ ​ 505,222 ​ ​ — ​ ​ — Total ​ $ 594,459 ​ $ 594,459 ​ $ — ​ $ — ​ ​ The following table summarizes cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Active Observable Unobservable ​ ​ December 31, ​ Markets ​ Inputs ​ Inputs Description ​ 2018 ​ (Level 1) ​ (Level 2) ​ (Level 3) Financial Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 68,064 ​ $ 68,064 ​ $ — ​ $ — Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 425,948 ​ ​ 425,948 ​ ​ — ​ ​ — Total ​ $ 494,012 ​ $ 494,012 ​ $ — ​ $ — ​

Restricted Cash

Restricted Cash	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Restricted Cash	5. Restricted Cash At September 30, 2019 and December 31, 2018, $5.7 million and $5.4 million, respectively, of the Company’s cash is restricted by a bank primarily related to security deposits for the lease agreements for the Company’s current and former corporate headquarters. For additional information on these security deposits, see Note 11, Leases.

Property and Equipment, Net

Property and Equipment, Net	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Property and Equipment, Net	6. Property and Equipment, Net Property and equipment and related accumulated depreciation are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Estimated ​ ​ ​ ​ ​ ​ ​ ​ Useful Life ​ September 30, ​ ​ December 31, ​ ​ (Years) ​ 2019 ​ 2018 Lab equipment 5 $ 8,370 $ 6,232 ​ Furniture and fixtures 4 ​ 3,491 ​ 2,369 ​ Computer equipment 3 ​ 1,632 ​ 1,805 ​ Leasehold improvements Term of lease ​ 35,513 ​ 26,640 ​ Software 3 ​ 408 ​ 280 ​ Construction-in-progress ​ ​ ​ ​ 1,149 ​ ​ 956 ​ ​ ​ ​ ​ 50,563 ​ 38,282 ​ Less: accumulated depreciation and amortization ​ ​ ​ (12,253) ​ (8,655) ​ Total ​ ​ ​ $ 38,310 ​ $ 29,627 ​ ​ Property, plant and equipment are recorded at historical cost, net of accumulated depreciation. For the three and nine months ended September 30, 2019, depreciation expense totaled $1.3 million and $3.7 million, respectively, compared to $1.2 million and $3.1 million, respectively, for the three and nine months ended September 30, 2018.

Accrued Expenses

Accrued Expenses	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Accrued Expenses	7. Accrued Expenses Accrued expenses consist of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2019 2018 External research and development ​ $ 55,270 ​ $ 36,213 ​ Employee compensation ​ ​ 10,960 ​ ​ 8,071 ​ Accrued professional fees ​ 8,720 ​ 4,423 ​ Property and equipment costs ​ 3,225 ​ 912 ​ Other ​ ​ 2,244 ​ ​ 2,092 ​ Total ​ $ 80,419 ​ $ 51,711 ​ ​

Collaboration Agreements

Collaboration Agreements	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Collaboration Agreements	8. Collaboration Agreements CStone Pharmaceuticals On June 1, 2018, the Company entered into a collaboration and license agreement (the CStone agreement) with CStone pursuant to which the Company granted CStone exclusive rights to develop and commercialize the Company’s drug candidates avapritinib, pralsetinib and fisogatinib, including back-up forms and certain other forms thereof, in Mainland China, Hong Kong, Macau and Taiwan (each, a CStone region and collectively, the CStone territory), either as a monotherapy or as part of a combination therapy. The Company will retain exclusive rights to the licensed products outside the CStone territory. The Company received an upfront cash payment of $40.0 million, and subject to the terms of the CStone agreement, will be eligible to receive up to approximately $346.0 million in milestone payments, including $118.5 million related to development and regulatory milestones and $227.5 million related to sales-based milestones. In addition, CStone will be obligated to pay the Company tiered percentage royalties on a licensed product-by-licensed product basis ranging from the mid-teens to low twenties on annual net sales of each licensed product in the CStone territory, subject to adjustment in specified circumstances. CStone will be responsible for costs related to the development of the licensed products in the CStone territory, other than specified costs related to the development of fisogatinib as a combination therapy in the CStone territory that will be shared by the Company and CStone. Pursuant to the terms of the CStone agreement, CStone will be responsible for conducting all development and commercialization activities in the CStone territory related to the licensed products, and the Company and CStone plan to conduct a proof-of-concept clinical trial in China evaluating fisogatinib in combination with CS1001, a clinical-stage anti-programmed death ligand-1 immunotherapy being developed by CStone, as a first-line therapy for the treatment of patients with hepatocellular carcinoma. The CStone agreement will continue on a licensed product-by-licensed product and CStone region-by-CStone region basis until the later of (i) 12 years after the first commercial sale of a licensed product in a CStone region in the CStone territory and (ii) the date of expiration of the last valid patent claim related to the Company’s patent rights or any joint collaboration patent rights for the licensed product that covers the composition of matter, method of use or method of manufacturing such licensed product in such region. Subject to the terms of the CStone agreement, CStone may terminate the CStone agreement in its entirety or with respect to one or more licensed products for convenience by providing written notice to the Company after June 1, 2019, and CStone may terminate the CStone agreement with respect to a licensed product for convenience at any time by providing written notice to the Company following the occurrence of specified events. In addition, the Company may terminate the CStone agreement under specified circumstances if CStone or certain other parties challenges the Company’s patent rights or any joint collaboration patent rights or if CStone or its affiliates do not conduct any material development or commercialization activities with respect to one or more licensed products for a specified period of time, subject to specified exceptions. Either party may terminate the CStone agreement for the other party’s uncured material breach or insolvency. In certain termination circumstances, the parties are entitled to retain specified licenses to be able to continue to exploit the licensed products, and in the event of termination by CStone for the Company’s uncured material breach, the Company will be obligated to pay CStone a low single digit percentage royalty on a licensed product-by-licensed product basis on annual net sales of such licensed product in the CStone territory, subject to a cap and other specified exceptions. The Company evaluated the CStone agreement to determine whether it is a collaborative arrangement for purposes of ASC 808. The Company determined that there were two material components of the CStone agreement: (i) the CStone territory-specific license and related activities in the CStone territory, and (ii) the parties’ participation in global development of the licensed products. The Company concluded that the CStone territory-specific license and related activities in the CStone territory are not within the scope of ASC 808 because the Company is not exposed to significant risks and rewards. The Company concluded that CStone is a customer with regard to the component that includes the CStone territory-specific license and related activities in CStone territory, which include manufacturing. For the parties’ participation in global development of the licensed products, the Company concluded that the research and development activities and cost-sharing payments related to such activities are within the scope of ASC 808 as both parties are active participants exposed to the risk of the activities under the CStone agreement. The Company concluded that CStone is not a customer with regard to the global development component in the context of the CStone agreement. Therefore, payments received by the Company for global development activities under the CStone agreement, including manufacturing, will be accounted for as a reduction of related expenses. A summary of manufacturing services related to the global development activities during the three and nine months ended September 30, 2019 and 2018 is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Manufacturing services related to global development activities ​ $ 1,275 $ 345 $ 2,403 $ 345 ​ The Company evaluated the CStone territory-specific license and related activities in the CStone territory under ASC 606 as these transactions are considered transactions with a customer. The Company identified the following material promises under the arrangement: (1) the three exclusive licenses granted in the CStone territory to develop, manufacture and commercialize the three licensed products; (2) the initial know-how transfer for each licensed product; (3) manufacturing activities related to development and commercial supply of the licensed products; (4) participation in the joint steering committee (JSC) and joint project teams (JPT); (5) regulatory responsibilities; and (6) manufacturing technology and continuing know-how transfers. The Company determined that each licensed product is distinct from the other licensed products. In addition, the Company determined that the exclusive licenses and initial know-how transfers for each licensed product were not distinct from each other, as each exclusive license has limited value without the corresponding initial know-how transfer. For purposes of ASC 606, the Company determined that that participation on the JSC and JPTs, the regulatory responsibilities and the manufacturing technology and continuing know-how transfers are qualitatively and quantitatively immaterial in the context of the CStone agreement and therefore are excluded from performance obligations. As such, the Company determined that these six material promises, described above, should be combined into one performance obligation for each of the three candidates. The Company evaluated the provision of manufacturing activities related to development and commercial supply of the licensed products as an option for purposes of ASC 606 to determine whether these manufacturing activities provide CStone with any material rights. The Company concluded that the manufacturing activities were not issued at a significant and incremental discount, and therefore do not provide CStone with any material rights. As such, the manufacturing activities are excluded as performance obligations at the outset of the arrangement. Based on these assessments, the Company identified three distinct performance obligations at the outset of the CStone agreement, which consists of the following for each licensed product: (1) the exclusive license and (2) the initial know-how transfer. Under the CStone agreement, in order to evaluate the transaction price for purposes of ASC 606, the Company determined that the upfront amount of $40.0 million constituted the entirety of the consideration to be included in the transaction price as of the outset of the arrangement, which was allocated to the three performance obligations. The potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. The Company satisfied the performance obligations upon delivery of the licenses, initial know-how transfers and product trademark and recognized the upfront payment of $40.0 million as revenue during the second quarter of 2018. The Company will reevaluate the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company will adjust its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal. During the three months ended September 30, 2019, three development and regulatory milestones were either achieved or deemed probable, and the associated aggregate cash consideration of $6.0 million for such milestones was added to the estimated transaction price for the CStone agreement. A summary of revenue recognized under the CStone agreement during the three and nine months ended September 30, 2019 and 2018 is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 License milestone revenue ​ $ 6,000 $ — $ 10,000 $ 40,000 Manufacturing services related to territory-specific activities ​ ​ — ​ ​ — ​ ​ 144 ​ ​ — Total CStone collaboration revenue ​ $ 6,000 ​ $ — ​ $ 10,144 ​ $ 40,000 ​ The following table presents the contract assets associated with the CStone agreement as of September 30, 2019 and December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ ​ December 31, ​ ​ 2019 ​ 2018 Accounts receivables ​ $ 2,414 $ — Unbilled accounts receivables ​ $ 2,662 $ 151 ​ There was no revenue deferred as a contract liability associated with the CStone agreement as of September 30, 2019 and December 31, 2018. Roche In March 2016, the Company entered into a collaboration and license agreement (as amended, Roche agreement) with Roche for the discovery, development and commercialization of up to five small molecule therapeutics targeting kinases believed to be important in cancer immunotherapy, as single products or possibly in combination with other therapeutics. Under the Roche agreement, Roche was granted up to five option rights to obtain an exclusive license to exploit products derived from the collaboration programs in the field of cancer immunotherapy. Such option rights are triggered upon the achievement of Phase 1 proof-of-concept. As a result of an amendment to the Roche agreement in the fourth quarter of 2019, the parties are currently conducting activities for up to four programs under the collaboration. See Note 13, Subsequent Events Prior to Roche’s exercise of an option, the Company will have the lead responsibility for drug discovery and pre-clinical development of all collaboration programs. In addition, the Company will have the lead responsibility for the conduct of all Phase 1 clinical trials other than those Phase 1 clinical trials for any product in combination with Roche’s portfolio of therapeutics, for which Roche will have the right to lead the conduct of such Phase 1 clinical trials. Pursuant to the Roche agreement, the parties will share the costs of Phase 1 development for each collaboration program. In addition, Roche will be responsible for post-Phase 1 development costs for each licensed product for which it retains global commercialization rights, and the Company and Roche will share post-Phase 1 development costs for each licensed product for which the Company retains commercialization rights in the United States. The Company received an upfront cash payment of $45.0 million in March 2016 upon execution of the Roche agreement, and subject to the terms of the Roche agreement, the Company will be eligible to receive up to approximately $965.0 million in contingent option fees and milestone payments related to specified research, pre-clinical, clinical, regulatory and sales-based milestones. Of the total contingent payments, up to approximately $215.0 million are for option fees and milestone payments for research, pre-clinical and clinical development events prior to licensing across all five potential collaboration programs, including contingent milestone payments for initiation of each of the collaboration programs for which the parties will work together to select targets (pre-option exercise milestones). In June 2018, the Company achieved and received a $10.0 million research milestone payment. In addition, for any licensed product for which Roche retains worldwide commercialization rights, the Company will be eligible to receive tiered royalties ranging from low double-digits to high-teens on future net sales of the licensed product. For any licensed product for which the Company retains commercialization rights in the United States, the Company and Roche will be eligible to receive tiered royalties ranging from mid-single-digits to low double-digits on future net sales in the other party’s respective territories in which it commercializes the licensed product. The upfront cash payment and any payments for milestones, option fees and royalties are non-refundable, non-creditable and not subject to set-off. The Roche agreement will continue until the date when no royalty or other payment obligations are or will become due, unless earlier terminated in accordance with the terms of the Roche agreement. Prior to its exercise of its first option, Roche may terminate the Roche agreement at will, in whole or on a collaboration target-by-collaboration target basis, upon 120 days’ prior written notice to the Company. Following its exercise of an option, Roche may terminate the Roche agreement at will, in whole, on a collaboration target-by-collaboration target basis, on a collaboration program-by-collaboration program basis or, if a licensed product has been commercially sold, on a country-by-country basis, (i) upon 120 days’ prior written notice if a licensed product has not been commercially sold or (ii) upon 180 days’ prior written notice if a licensed product has been commercially sold. Either party may terminate the Roche agreement for the other party’s uncured material breach or insolvency and in certain other circumstances agreed to by the parties. In certain termination circumstances, the Company is entitled to retain specified licenses to be able to continue to exploit the licensed products. The Company assessed this arrangement in accordance with ASC 606 upon the adoption of the new standard on January 1, 2018, and concluded that the contract counterparty, Roche, is a customer prior to the exercise, if any, of an option by Roche. The Company identified the following material promises under the arrangement: (1) a non-transferable, sub-licensable and non-exclusive license to use the Company’s intellectual property and collaboration compounds to conduct research activities; (2) research and development activities through Phase 1 clinical trials under the research plan; (3) five option rights for licenses to develop, manufacture, and commercialize the collaboration targets; (4) participation on a joint research committee (JRC) and joint development committee (JDC); and (5) regulatory responsibilities under Phase 1 clinical trials. The Company determined that the license and research and development activities were not distinct from another, as the license has limited value without the performance of the research and development activities. Participation on the JRC and JDC to oversee the research and development activities was determined to be quantitatively and qualitatively immaterial and therefore is excluded from performance obligations. The regulatory responsibilities related to filings and obtaining approvals related to the products that may result from each program do not represent separate performance obligations based on their dependence on the research and development efforts. As such, the Company determined that these promises should be combined into a single performance obligation. The Company evaluated the option rights for licenses to develop, manufacture, and commercialize the collaboration targets to determine whether it provides Roche with any material rights. The Company concluded that the options were not issued at a significant and incremental discount, and therefore do not provide material rights. As such, they are excluded as performance obligations at the outset of the arrangement. Based on these assessments, the Company identified one performance obligation at the outset of the Roche agreement, which consists of: (1) the non-exclusive license; (2) the research and development activities through Phase 1; and (3) regulatory responsibilities under Phase 1 clinical trials. Under the Roche agreement, in order to evaluate the appropriate transaction price, the Company determined that as of January 1, 2018, the upfront amount of $45.0 million constituted the entirety of the consideration to be included in the transaction price as of the outset of the arrangement, which was allocated to the single performance obligation. The option exercise payments that may be received are excluded from the transaction price until each customer option is exercised as it was determined that the options are not material rights. The potential milestone payments that the Company is eligible to receive prior to the exercise of the options were initially excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. The Company will reevaluate the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and, if necessary, adjust its estimate of the transaction price. In June 2018, the Company achieved and received a $10.0 million research milestone payment related to the Roche agreement, and it became probable that a significant reversal of cumulative revenue would not occur for the $10.0 million research milestone achieved. At such time, the associated consideration was added to the estimated transaction price and allocated to the existing performance obligation. The Company recognizes revenue associated with the performance obligation as the research and development services are provided using an input method, according to the costs incurred as related to the research and development activities on each program and the costs expected to be incurred in the future to satisfy the performance obligation. The transfer of control occurs over this time period and, in management’s judgment, is the best measure of progress towards satisfying the performance obligation. The amounts received that have not yet been recognized as revenue are deferred as a contract liability on the Company’s consolidated balance sheet and will be recognized over the remaining research and development period until the performance obligation is satisfied. During the three months ended September 30, 2019, a reduction in the costs expected to be incurred in the future to satisfy certain performance obligations under the collaboration became probable. Accordingly, the Company recorded a cumulative revenue catch-up of $2.0 million during the three months ended September 30, 2019. For additional information, see Note 13, Subsequent Events . A summary of revenue recognized under the Roche agreement during the three and nine months ended September 30, 2019 and 2018 is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Roche collaboration research and development services revenue ​ $ 3,139 $ 1,095 $ 4,836 $ 3,488 ​ During the three and nine months ended September 30, 2019 and 2018, the Company recognized the following revenue due to the changes in the contract liability balances (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Amounts included in the contract liability at the beginning of the period ​ $ 1,149 $ 1,129 $ 3,470 $ 3,240 ​ As of September 30, 2019, the Company had revenue deferred as a contract liability related to the Roche agreement of $41.3 million, of which $4.9 million was included in current liabilities, and the research and development services related to the performance obligation are expected to be performed over a remaining period of approximately 5.5 years.

Stock-based Compensation

Stock-based Compensation	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Stock-based Compensation	9. Stock-based compensation 2015 Stock Option and Incentive Plan In 2015, the Company’s board of directors and stockholders approved the 2015 Stock Option and Incentive Plan (the 2015 Plan), which replaced the Company’s 2011 Stock Option and Grant Plan, as amended (the 2011 Plan). The 2015 Plan includes incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock, restricted stock units, unrestricted stock, performance share awards and cash-based awards. The Company initially reserved a total of 1,460,084 shares of common stock for the issuance of awards under the 2015 Plan. The 2015 Plan provides that the number of shares reserved and available for issuance under the 2015 Plan will be cumulatively increased on January 1 of each calendar year by 4% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors. For the calendar year beginning January 1, 2019, the number of shares reserved for issuance under the 2015 Plan was increased by 1,761,481 shares. In addition, the total number of shares reserved for issuance is subject to adjustment in the event of a stock split, stock dividend or other change in the Company’s capitalization. At September 30, 2019, there were 1,653,349 shares available for future grant under the 2015 Plan. Stock options The following table summarizes the stock option activity for the nine months ended September 30, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-Average ​ ​ ​ Shares ​ ​ Exercise Price ​ Outstanding at December 31, 2018 4,557,800 ​ $ 44.64 ​ Granted 1,673,749 ​ ​ 84.12 ​ ​ Exercised (462,806) ​ 23.69 ​ ​ Canceled (137,266) ​ 68.03 ​ ​ Outstanding at September 30, 2019 5,631,477 ​ $ 57.53 ​ Exercisable at September 30, 2019 2,527,772 ​ $ 36.67 ​ ​ At September 30, 2019, the total unrecognized compensation expense related to unvested stock option awards was $135.3 million, which is expected to be recognized over a weighted-average period of approximately 2.82 years. Restricted stock units The following table summarizes the restricted stock units activity for the nine months ended September 30, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-Average ​ ​ ​ ​ ​ Grant Date ​ Shares Fair Value Unvested shares at December 31, 2018 36,868 ​ $ 66.28 ​ Granted 356,915 ​ 85.30 ​ Vested (2,730) ​ 66.40 ​ Forfeited (9,261) ​ 80.53 ​ Unvested shares at September 30, 2019 381,792 ​ $ 83.72 ​ ​ At September 30, 2019, the total unrecognized compensation expense related to unvested restricted stock units was $27.7 million, which is expected to be recognize over a weighted-average period of approximately 3.39 years. 2015 Employee Stock Purchase Plan In 2015, the Company’s board of directors and stockholders approved the 2015 Employee Stock Purchase Plan (the 2015 ESPP), which became effective upon the closing of the Company’s initial public offering in May 2015. The Company initially reserved a total of 243,347 shares of common stock for issuance under the 2015 ESPP. The 2015 ESPP provides that the number of shares reserved and available for issuance under the 2015 ESPP will be cumulatively increased on January 1 of each calendar year by 1% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors. For the calendar year beginning January 1, 2019, the number of shares reserved for issuance under the 2015 ESPP was increased by 440,370 shares. The Company issued 10,718 and 5,572 shares under the 2015 ESPP during the nine months ended September 30, 2019 and 2018, respectively. Stock-based compensation expense The Company recognized stock-based compensation expense totaling $15.0 million and $39.0 million for the three and nine months ended September 30, 2019, respectively. The Company recognized stock-based compensation expense totaling $8.4 million and $21.7 million for the three and nine months ended September 30, 2018, respectively. Stock-based compensation expense by award type included within the unaudited condensed consolidated statements of operations and comprehensive loss was as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ ​ September 30, ​ ​ 2019 ​ 2018 ​ ​ 2019 ​ 2018 Stock options $ 12,778 ​ $ 8,278 ​ $ 34,373 ​ $ 21,468 Restricted stock units ​ 2,076 ​ ​ 42 ​ ​ 4,243 ​ ​ 42 Employee stock purchase plan ​ 139 ​ ​ 71 ​ ​ 338 ​ ​ 192 Total stock-based compensation expense $ 14,993 ​ $ 8,391 ​ $ 38,954 ​ $ 21,702 ​ Stock-based compensation expense by classification within the unaudited condensed consolidated statements of operations and comprehensive loss is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ ​ September 30, ​ September 30, ​ ​ ​ 2019 2018 ​ 2019 2018 ​ Research and development ​ $ 7,678 $ 4,770 $ 20,971 $ 12,054 ​ General and administrative ​ 7,315 ​ 3,621 ​ 17,983 ​ 9,648 ​ Total stock-based compensation expense ​ $ 14,993 ​ $ 8,391 ​ $ 38,954 ​ $ 21,702 ​ ​

Net Loss per Share

Net Loss per Share	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Net Loss per Share	10. Net 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 weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period. For purposes of the dilutive net loss per share calculation, stock options, unvested restricted stock units and ESPP shares are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share, as their effect would be anti-dilutive; therefore, basic and diluted net loss per share were the same for all periods presented as a result of the Company’s net loss. The following common stock equivalents were excluded from the calculation of diluted net loss per share for the periods indicated because including them would have had an anti-dilutive effect. ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended ​ ​ September 30, ​ 2019 2018 Stock options 5,631,477 ​ 4,458,508 Restricted stock units 381,792 ​ 12,195 ESPP shares ​ 11,641 ​ 5,860 Total 6,024,910 4,476,563 ​ The weighted average number of common shares used in net loss per share on a basic and diluted basis were 48,921,445 and 43,915,376

Leases

Leases	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Leases	11. Leases 38 Sidney Street On February 12, 2015, the Company entered into a lease for approximately 38,500 rentable square feet of office and laboratory space at 38 Sidney Street in Cambridge, Massachusetts, which the Company gained control over on June 15, 2015, and occupancy commenced in October 2015. The initial term of the lease agreement will expire on October 31, 2022, unless terminated sooner. The Company has an option to extend the lease for five additional years. The lease has a total commitment of $17.8 million over the initial seven-year term. The Company has agreed to pay an initial annual base rent of approximately $2.3 million, which rises periodically until it reaches approximately $2.8 million. The lease provided the Company with an allowance for leasehold improvements of $4.3 million. Prior to adoption of ASC 842, the Company recorded rent expense on a straight-line basis through the end of the lease term and the associated deferred rent on the consolidated balance sheet. The Company also recorded the leasehold improvement incentives as a reduction to rent expense ratably over the lease term, and the balance from the leasehold improvement incentives was included in lease incentive obligations on the consolidated balance sheet as of December 31, 2018. The lease agreement required the Company to pay a security deposit of $1.3 million, of which $0.2 million was released in February 2018 and February 2019, respectively. The remaining $0.9 million is recorded in restricted cash on the Company’s condensed consolidated balance sheet as of September 30, 2019. In the first quarter of 2018, the Company subleased its former corporate headquarters at 38 Sidney Street, Cambridge, Massachusetts through October 31, 2020. Subject to the terms of the sublease agreement and the master lease agreement, including a right of recapture by the Company, the sublessee has the option to extend the sublease through October 31, 2022. The sublease includes a total commitment by the sublessee of $8.2 million over the 32 month term of the sublease agreement. During the 32 month term, the Company will be responsible for total rental payments of $6.9 million and an additional $0.7 million in total payments related to the Company’s profit on the sublease income which are payable by the Company to the landlord. As of September 30, 2019, the remaining minimum sublease rental commitment by the sublessee was $3.4 million. 45 Sidney Street On April 28, 2017, the Company entered into a lease agreement for approximately 99,833 rentable square feet of office and laboratory space located at 45 Sidney Street in Cambridge, Massachusetts. The initial term of the lease agreement commenced on October 1, 2017 and will expire on November 30, 2029, unless terminated sooner. The lease agreement also provides the Company with an option to extend the lease agreement for two consecutive five-year periods at the then fair market annual rent, as defined in the lease agreement. During the initial term of the lease agreement, the Company has agreed to pay an initial annual base rent of approximately $7.7 million, which increases annually until it reaches approximately $10.6 million in the last year of the initial term. The lease provided the Company with a tenant improvement allowance of approximately $14.2 million for improvements to be made to the premises. Prior to adoption of ASC 842, the Company recorded rent expense on a straight-line basis through the end of the lease term and the associated deferred rent on the consolidated balance sheet. The Company also recorded the leasehold improvement incentives as a reduction to rent expense ratably over the lease term, and the balance from the leasehold improvement incentives was included in lease incentive obligations on the consolidated balance sheet as of December 31, 2018. The lease agreement required the Company to pay a security deposit of $3.5 million, of which $3.0 million is recorded in restricted cash on the Company’s condensed consolidated balance sheet as of September 30, 2019, and an additional $0.5 million is due to be released in October 2019 in accordance with the terms of the lease agreement. On September 19, 2018, the Company entered into an amendment to the lease agreement for its office and laboratory space located at 45 Sidney Street in Cambridge, Massachusetts to expand the rentable square footage from approximately 99,833 square feet to approximately 139,216 square feet. The initial term of the lease with respect to the expansion premises commenced on March 1, 2019 and will expire on November 30, 2029, unless terminated sooner. Pursuant to the lease amendment, the rent commencement date for the expansion premises was July 1, 2019. The Company has agreed to pay an initial annual base rent of approximately $3.2 million for the expansion premises, which increases annually until it reaches approximately $4.2 million in the last year of the initial term for the expansion premises. Pursuant to the lease amendment, the landlord has also agreed to provide the Company with a tenant improvement allowance of approximately $3.2 million for improvements to be made to the expansion premises. The lease amendment required the Company to pay an additional security deposit of $0.8 million to the landlord for the expansion premises, which is recorded in restricted cash on the Company’s condensed consolidated balance sheet as of September 30, 2019. The lease agreements do not contain residual value guarantees and t ​ ​ ​ ​ ​ ​ ​ Operating leases: Three Months Ended September 30, 2019 ​ Nine Months Ended September 30, 2019 Lease cost $ 4,167 ​ $ 11,906 Sublease income ​ (708) ​ ​ (2,117) Net lease cost $ 3,459 ​ $ 9,789 ​ ​ ​ ​ ​ ​ ​ ​ For the three and nine months ended September 30, 2018, rent expenses under ASC 840, net of sublease income, was $1.7 million and $5.6 million, respectively. The Company has not entered into any material short-term leases or financing leases as of September 30, 2019. Supplemental cash flow information related to leases for the three and nine months ended September 30, 2019 was as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, 2019 ​ Nine Months Ended September 30, 2019 ​ ​ ​ ​ ​ ​ Cash paid for amounts included in the measurement of lease liabilities: $ 3,485 ​ $ 8,727 ​ ​ ​ ​ ​ ​ Lease liabilities arising from obtaining right-of-use assets: ​ ​ ​ ​ ​ Operating leases $ - ​ $ 23,300 ​ ​ The weighted average remaining lease term and weighted average discount rate of the operating leases are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating leases Weighted average remaining lease term in years ​ ​ ​ ​ 9.50 Weighted average discount rate ​ ​ ​ ​ 8.2% ​ ​ Future minimum lease payments under non-cancellable leases as of September 30, 2019 were as follows (in thousands): ​ ​ ​ ​ ​ 2019 (excluding the 9 months ended September 30, 2019) ​ $ 3,521 2020 ​ ​ 14,341 2021 ​ ​ 14,764 2022 ​ ​ 14,719 2023 ​ ​ 12,746 Thereafter ​ ​ 83,471 Total future minimum lease payments (1) ​ ​ 143,562 Less imputed interest ​ ​ (46,054) Total ​ $ 97,508 ​ (1) Minimum lease payments have not been reduced by minimum sublease rentals of $3.1 million due in the future under the Company’s non-cancelable sublease for the office and laboratory space located at 38 Sidney Street, Cambridge, Massachusetts. The minimum lease payments above do not include any related common area maintenance charges or real estate taxes. ​ ​ Under the prior lease guidance minimum rental commitments under non-cancelable leases for each of the next five years and total thereafter as of December 31, 2018, were as follows (in thousands): ​ ​ ​ ​ ​ 2019 ​ $ 12,247 2020 ​ ​ 14,341 2021 ​ ​ 14,764 2022 ​ ​ 14,719 2023 ​ ​ 12,746 Thereafter ​ ​ 83,471 Total minimum lease payments (1) ​ $ 152,288 ​ (1) Minimum lease payments have not been reduced by minimum sublease rentals of $5.3 million due in the future under the Company’s non-cancelable sublease for the office and laboratory space located at 38 Sidney Street, Cambridge, Massachusetts. The minimum lease payments above do not include any related common area maintenance charges or real estate taxes. ​

Commitments

Commitments	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Commitments	12. Commitments Leases

Subsequent Events

Subsequent Events	9 Months Ended
	Sep. 30, 2019
Disclosure Text Block
Subsequent Events	13. Subsequent Events License Agreement with Clementia On October 15, 2019, the Company entered into a license agreement (the Clementia a greement) with Clementia, a wholly-owned subsidiary of Ipsen S.A. Under the Clementia a greement, the Company granted an exclusive, worldwide, royalty-bearing license to Clementia to develop and commercialize BLU-782, the Company’s oral, highly selective investigational ALK2 inhibitor in Phase 1 clinical development for the treatment of fibrodysplasia ossificans progressiva, as well as specified other compounds related to the BLU-782 program. Subject to the terms of the Clementia a greement, the Company will be eligible to receive up to $535.0 million in upfront, milestone and other payments, including an upfront cash payment of $25.0 million , a $20.0 million cash milestone payment due in the third quarter of 2020 and up to $490.0 million in other payments and potential development, regulatory and sales-based milestone payments for licensed products. In addition, Clementia is obligated to pay to the Company royalties on aggregate annual worldwide net sales of l icensed p roducts at tiered percentage rates ranging from the low- to mid-teens, subject to adjustment in specified circumstances under the Clementia a greement, and to purchase specified manufacturing inventory from the Company. The Company is currently evaluating the revenue recognized under the Clementia agreement and expects to recognize revenue during the fourth quarter of 2019 related to a majority of the $25.0 million upfront cash payment and the $20.0 million cash milestone payment anticipated in the third quarter of 2020 . Collaboration with Roche In the fourth quarter of 2019, the Company achieved an $8.0 million research milestone under the Roche agreement . On November 1, 2019, the Company entered into a sixth amendment to the Roche agreement

Summary of Significant Accoun_2

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	9 Months Ended
	Sep. 30, 2019
Policy Text Blocks
Basis of Presentation	Basis of Presentation The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the United States (GAAP) as found in the Accounting Standards Codification (ASC), Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB) and the rules and regulations of the Securities and Exchange Commission (SEC). Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements as of and for the year ended December 31, 2018 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, filed with the SEC on February 26, 2019 (the 2018 Annual Report on Form 10-K). The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements, and updated, as necessary, in this report. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of September 30, 2019, the results of its operations for the three and nine months ended September 30, 2019 and 2018, stockholder’s equity for the three and nine months ended September 30, 2019 and 2018 and cash flows for the nine months ended September 30, 2019 and 2018. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2019 are not necessarily indicative of the results for the year ending December 31, 2019, or for any future period. The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell and hold securities, Blueprint Medicines (Switzerland) GmbH, Blueprint Medicines (Netherlands) B.V., Blueprint Medicines (UK) Ltd, and Blueprint Medicines (Germany) GmbH. All intercompany transactions and balances have been eliminated. The accompanying condensed consolidated financial statements do not include the account of the Company’s wholly-owned subsidiaries Blueprint Medicines Spain, S.L., which was formed in October 2019, and Blueprint Medicines (France) SAS, which was formed in November 2019.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies and in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Estimates are used in the following areas, among others: revenue recognition, operating lease right-of-use assets, operating lease liabilities, stock-based compensation expense, accrued expenses, and income taxes.
Significant Accounting Policies	Significant Accounting Policies The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and nine months ended September 30, 2019 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2018 Annual Report on Form 10-K, except as noted below with respect to the Company’s accounting policies related to lease obligations and as noted within this Note 2 under the section titled “—New Accounting Pronouncements.”
New Accounting Pronouncements	New Accounting Pronouncements Leases ASU No. 2016-02, Leases (Topic 842) ASU No. 2018-01, Leases (Topic 842): Land Easement Practical Expedient for Transition to Topic 842, ASU No. 2018-10, Codification Improvements to Topic 842, Leases, ASU No. 2018-11, Leases (Topic 842): Targeted Improvements, ASU No. 2018-20, Narrow-Scope Improvement for Lessors, and ASU No. 2019-01, Leases (Topic 842): Codification Improvements. Leases or ASC 840, which did not require the recognition of operating lease liabilities on the balance sheet, and is not comparative. Impact of Adoption of ASC 842 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Impact of ASC 842 Adoption on Consolidated Balance Sheet as of January 1, 2019 (in thousands) ​ Balances without adoption of ASC 842 ​ ASC 842 Adjustment ​ Balances with adoption of ASC 842 Operating lease right-of-use assets, net ​ $ — ​ $ 54,245 ​ $ 54,245 Total assets ​ ​ 540,124 ​ ​ 54,245 ​ ​ 594,369 Accrued expenses ​ ​ 51,711 ​ ​ (125) ​ ​ 51,586 Current portion of operating lease liabilities ​ ​ — ​ ​ 4,730 ​ ​ 4,730 Current portion of lease incentive obligation ​ ​ 1,714 ​ ​ (1,714) ​ ​ — Total current liabilities ​ ​ 60,323 ​ ​ 2,891 ​ ​ 63,214 Deferred rent, net of current portion ​ ​ 5,130 ​ ​ (5,130) ​ ​ — Operating lease liabilities, net of current portion ​ ​ — ​ ​ 69,387 ​ ​ 69,387 Lease incentive obligation, net of current portion ​ ​ 12,903 ​ ​ (12,903) ​ ​ — Total liabilities ​ ​ 121,115 ​ ​ 54,245 ​ ​ 175,360 ​ Leases Accounting Policy For contracts entered into on or after the effective date, at the inception of a contract, the Company assesses whether the contract is, or contains, a lease. The assessment is based on: (1) whether the contract involves the use of a distinct identified asset, (2) whether the Company obtains the right to substantially all the economic benefit from the use of the asset throughout the period, and (3) whether the Company has the right to direct the use of the asset. At inception of a lease, the Company allocates the consideration in the contract to each lease component based on its relative stand-alone price to determine the lease payments. Leases are classified as either finance leases or operating leases. A lease is classified as a finance lease if any one of the following criteria are met: the lease transfers ownership of the asset by the end of the lease term, the lease contains an option to purchase the asset that is reasonably certain to be exercised, the lease term is for a major part of the remaining useful life of the asset or the present value of the lease payments equals or exceeds substantially all of the fair value of the asset. A lease is classified as an operating lease if it does not meet any of these criteria. For all leases at the lease commencement date, a right-of-use asset and a lease liability are recognized. The right-of-use asset represents the right to use the leased asset for the lease term. The lease liability represents the present value of the lease payments under the lease. The right-of-use asset is initially measured at cost, which primarily comprises the initial amount of the lease liability, plus any initial direct costs incurred if any, less any lease incentives received. All right-of-use assets are reviewed for impairment. The lease liability is initially measured at the present value of the lease payments, discounted using the interest rate implicit in the lease or, if that rate cannot be readily determined, the secured incremental borrowing rate for the same term as the underlying lease. For real estate leases, the Company uses its secured incremental borrowing rate. For finance leases, the Company uses the rate implicit in the lease or its secured incremental borrowing rate if the implicit lease rate cannot be determined. Lease payments included in the measurement of the lease liability comprise the following: the fixed noncancelable lease payments, payments for optional renewal periods where it is reasonably certain the renewal period will be exercised, and payments for early termination options unless it is reasonably certain the lease will not be terminated early. Lease cost for operating leases consists of the lease payments plus any initial direct costs, primarily brokerage commissions, and is recognized on a straight-line basis over the lease term. Included in lease cost are any variable lease payments incurred in the period that are not included in the initial lease liability and lease payments incurred in the period for any leases with an initial term of 12 months or less. Lease cost for finance leases consists of the amortization of the right-of-use asset on a straight-line basis over the lease term and interest expense determined on an amortized cost basis. The lease payments are allocated between a reduction of the lease liability and interest expense. Credit Losses ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments Debt Securities In March 2017, the FASB issued ASU No. 2017-08, Receivables - Nonrefundable Fees and Other Costs ( Subtopic 310-20 ): Premium Amortization on Purchased Callable Debt Securities. Fair Value Measurements In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework Changes to the Disclosure Requirements for Fair Value Measurement Collaborative Arrangements In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606. ● Clarifies that certain transactions between collaborative arrangement participants should be accounted for as revenue under ASC 606 , Revenue from Contracts with Customers , when the collaborative arrangement participant is a customer in the context of a unit of account. In those situations, all the guidance in ASC 606 should be applied, including recognition, measurement, presentation and disclosure requirements; ● Adds unit-of-account guidance to ASC 808 , Collaborative Arrangements , to align with the guidance in ASC 606 (that is, a distinct good or service) when an entity is assessing whether the collaborative arrangement or a part of the arrangement is within the scope of ASC 606 ; and ● Requires that in a transaction with a collaborative arrangement participant that is not directly related to sales to third parties, presenting that transaction together with revenue recognized under ASC 606 is precluded if the collaborative arrangement participant is not a customer. Internal-Use Software ​ In August 2018, the FASB issued ASU No. 2018-15, Intangibles-Goodwill and Other-Internal-Use Software ( Subtopic 350-40 ): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract
Leases	Leases Accounting Policy For contracts entered into on or after the effective date, at the inception of a contract, the Company assesses whether the contract is, or contains, a lease. The assessment is based on: (1) whether the contract involves the use of a distinct identified asset, (2) whether the Company obtains the right to substantially all the economic benefit from the use of the asset throughout the period, and (3) whether the Company has the right to direct the use of the asset. At inception of a lease, the Company allocates the consideration in the contract to each lease component based on its relative stand-alone price to determine the lease payments. Leases are classified as either finance leases or operating leases. A lease is classified as a finance lease if any one of the following criteria are met: the lease transfers ownership of the asset by the end of the lease term, the lease contains an option to purchase the asset that is reasonably certain to be exercised, the lease term is for a major part of the remaining useful life of the asset or the present value of the lease payments equals or exceeds substantially all of the fair value of the asset. A lease is classified as an operating lease if it does not meet any of these criteria. For all leases at the lease commencement date, a right-of-use asset and a lease liability are recognized. The right-of-use asset represents the right to use the leased asset for the lease term. The lease liability represents the present value of the lease payments under the lease. The right-of-use asset is initially measured at cost, which primarily comprises the initial amount of the lease liability, plus any initial direct costs incurred if any, less any lease incentives received. All right-of-use assets are reviewed for impairment. The lease liability is initially measured at the present value of the lease payments, discounted using the interest rate implicit in the lease or, if that rate cannot be readily determined, the secured incremental borrowing rate for the same term as the underlying lease. For real estate leases, the Company uses its secured incremental borrowing rate. For finance leases, the Company uses the rate implicit in the lease or its secured incremental borrowing rate if the implicit lease rate cannot be determined. Lease payments included in the measurement of the lease liability comprise the following: the fixed noncancelable lease payments, payments for optional renewal periods where it is reasonably certain the renewal period will be exercised, and payments for early termination options unless it is reasonably certain the lease will not be terminated early. Lease cost for operating leases consists of the lease payments plus any initial direct costs, primarily brokerage commissions, and is recognized on a straight-line basis over the lease term. Included in lease cost are any variable lease payments incurred in the period that are not included in the initial lease liability and lease payments incurred in the period for any leases with an initial term of 12 months or less. Lease cost for finance leases consists of the amortization of the right-of-use asset on a straight-line basis over the lease term and interest expense determined on an amortized cost basis. The lease payments are allocated between a reduction of the lease liability and interest expense.

Summary of Significant Accoun_3

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of financial statement impact of the cumulative adjustment	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Impact of ASC 842 Adoption on Consolidated Balance Sheet as of January 1, 2019 (in thousands) ​ Balances without adoption of ASC 842 ​ ASC 842 Adjustment ​ Balances with adoption of ASC 842 Operating lease right-of-use assets, net ​ $ — ​ $ 54,245 ​ $ 54,245 Total assets ​ ​ 540,124 ​ ​ 54,245 ​ ​ 594,369 Accrued expenses ​ ​ 51,711 ​ ​ (125) ​ ​ 51,586 Current portion of operating lease liabilities ​ ​ — ​ ​ 4,730 ​ ​ 4,730 Current portion of lease incentive obligation ​ ​ 1,714 ​ ​ (1,714) ​ ​ — Total current liabilities ​ ​ 60,323 ​ ​ 2,891 ​ ​ 63,214 Deferred rent, net of current portion ​ ​ 5,130 ​ ​ (5,130) ​ ​ — Operating lease liabilities, net of current portion ​ ​ — ​ ​ 69,387 ​ ​ 69,387 Lease incentive obligation, net of current portion ​ ​ 12,903 ​ ​ (12,903) ​ ​ — Total liabilities ​ ​ 121,115 ​ ​ 54,245 ​ ​ 175,360

Cash Equivalents and Investme_2

Cash Equivalents and Investments (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of cash equivalents and investments, available-for-sale	Cash equivalents and investments, available-for-sale, consisted of the following at September 30, 2019 and December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair September 30, 2019 Cost Gain ​ Losses ​ Value Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 89,237 ​ $ — ​ $ — ​ $ 89,237 Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 504,559 ​ ​ 693 ​ ​ (30) ​ ​ 505,222 Total ​ $ 593,796 ​ $ 693 ​ $ (30) ​ $ 594,459 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair December 31, 2018 Cost Gain ​ Losses ​ Value Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 68,064 ​ $ — ​ $ — ​ $ 68,064 Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 426,112 ​ ​ — ​ ​ (164) ​ ​ 425,948 Total ​ $ 494,176 ​ $ — ​ $ (164) ​ $ 494,012

Fair Value of Financial Instr_2

Fair Value of Financial Instruments (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of financial instruments measured at fair value	The following table summarizes cash equivalents and marketable securities measured at fair value on a recurring basis as of September 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Active Observable Unobservable ​ ​ September 30, ​ Markets ​ Inputs ​ Inputs Description ​ 2019 ​ (Level 1) ​ (Level 2) ​ (Level 3) Financial Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 89,237 ​ $ 89,237 ​ $ — ​ $ — Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 505,222 ​ ​ 505,222 ​ ​ — ​ ​ — Total ​ $ 594,459 ​ $ 594,459 ​ $ — ​ $ — ​ ​ The following table summarizes cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Active Observable Unobservable ​ ​ December 31, ​ Markets ​ Inputs ​ Inputs Description ​ 2018 ​ (Level 1) ​ (Level 2) ​ (Level 3) Financial Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 68,064 ​ $ 68,064 ​ $ — ​ $ — Investments, available-for-sale: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. government agency securities and treasuries ​ ​ 425,948 ​ ​ 425,948 ​ ​ — ​ ​ — Total ​ $ 494,012 ​ $ 494,012 ​ $ — ​ $ —

Property and Equipment, Net (Ta

Property and Equipment, Net (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of property and equipment	Property and equipment and related accumulated depreciation are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Estimated ​ ​ ​ ​ ​ ​ ​ ​ Useful Life ​ September 30, ​ ​ December 31, ​ ​ (Years) ​ 2019 ​ 2018 Lab equipment 5 $ 8,370 $ 6,232 ​ Furniture and fixtures 4 ​ 3,491 ​ 2,369 ​ Computer equipment 3 ​ 1,632 ​ 1,805 ​ Leasehold improvements Term of lease ​ 35,513 ​ 26,640 ​ Software 3 ​ 408 ​ 280 ​ Construction-in-progress ​ ​ ​ ​ 1,149 ​ ​ 956 ​ ​ ​ ​ ​ 50,563 ​ 38,282 ​ Less: accumulated depreciation and amortization ​ ​ ​ (12,253) ​ (8,655) ​ Total ​ ​ ​ $ 38,310 ​ $ 29,627 ​

Accrued Expenses (Tables)

Accrued Expenses (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of accrued expenses	Accrued expenses consist of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2019 2018 External research and development ​ $ 55,270 ​ $ 36,213 ​ Employee compensation ​ ​ 10,960 ​ ​ 8,071 ​ Accrued professional fees ​ 8,720 ​ 4,423 ​ Property and equipment costs ​ 3,225 ​ 912 ​ Other ​ ​ 2,244 ​ ​ 2,092 ​ Total ​ $ 80,419 ​ $ 51,711 ​

Collaboration Agreements (Table

Collaboration Agreements (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Summary of manufacturing services related to the global development activities	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Manufacturing services related to global development activities ​ $ 1,275 $ 345 $ 2,403 $ 345 ​
Summary of revenue recognized	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 License milestone revenue ​ $ 6,000 $ — $ 10,000 $ 40,000 Manufacturing services related to territory-specific activities ​ ​ — ​ ​ — ​ ​ 144 ​ ​ — Total CStone collaboration revenue ​ $ 6,000 ​ $ — ​ $ 10,144 ​ $ 40,000 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Roche collaboration research and development services revenue ​ $ 3,139 $ 1,095 $ 4,836 $ 3,488 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ ​ 2019 2018 ​ 2019 2018 Amounts included in the contract liability at the beginning of the period ​ $ 1,149 $ 1,129 $ 3,470 $ 3,240
Summary of contract assets	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ ​ December 31, ​ ​ 2019 ​ 2018 Accounts receivables ​ $ 2,414 $ — Unbilled accounts receivables ​ $ 2,662 $ 151

Stock-based Compensation (Table

Stock-based Compensation (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Summary of stock option activity	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-Average ​ ​ ​ Shares ​ ​ Exercise Price ​ Outstanding at December 31, 2018 4,557,800 ​ $ 44.64 ​ Granted 1,673,749 ​ ​ 84.12 ​ ​ Exercised (462,806) ​ 23.69 ​ ​ Canceled (137,266) ​ 68.03 ​ ​ Outstanding at September 30, 2019 5,631,477 ​ $ 57.53 ​ Exercisable at September 30, 2019 2,527,772 ​ $ 36.67 ​
Summary of restricted stock units activity	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-Average ​ ​ ​ ​ ​ Grant Date ​ Shares Fair Value Unvested shares at December 31, 2018 36,868 ​ $ 66.28 ​ Granted 356,915 ​ 85.30 ​ Vested (2,730) ​ 66.40 ​ Forfeited (9,261) ​ 80.53 ​ Unvested shares at September 30, 2019 381,792 ​ $ 83.72 ​
Summary of stock-based compensation expense, allocation by type of awards and recognition in statements of operations	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ ​ September 30, ​ ​ 2019 ​ 2018 ​ ​ 2019 ​ 2018 Stock options $ 12,778 ​ $ 8,278 ​ $ 34,373 ​ $ 21,468 Restricted stock units ​ 2,076 ​ ​ 42 ​ ​ 4,243 ​ ​ 42 Employee stock purchase plan ​ 139 ​ ​ 71 ​ ​ 338 ​ ​ 192 Total stock-based compensation expense $ 14,993 ​ $ 8,391 ​ $ 38,954 ​ $ 21,702 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ ​ September 30, ​ September 30, ​ ​ ​ 2019 2018 ​ 2019 2018 ​ Research and development ​ $ 7,678 $ 4,770 $ 20,971 $ 12,054 ​ General and administrative ​ 7,315 ​ 3,621 ​ 17,983 ​ 9,648 ​ Total stock-based compensation expense ​ $ 14,993 ​ $ 8,391 ​ $ 38,954 ​ $ 21,702 ​

Net Loss per Share (Tables)

Net Loss per Share (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Schedule of common stock equivalents excluded from calculation of diluted net loss per share applicable to common stockholders	​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended ​ ​ September 30, ​ 2019 2018 Stock options 5,631,477 ​ 4,458,508 Restricted stock units 381,792 ​ 12,195 ESPP shares ​ 11,641 ​ 5,860 Total 6,024,910 4,476,563

Leases (Tables)

Leases (Tables)	9 Months Ended
	Sep. 30, 2019
Table Text Blocks
Summary of lease expenses and cash flow and weighted average information	​ ​ ​ ​ ​ ​ ​ Operating leases: Three Months Ended September 30, 2019 ​ Nine Months Ended September 30, 2019 Lease cost $ 4,167 ​ $ 11,906 Sublease income ​ (708) ​ ​ (2,117) Net lease cost $ 3,459 ​ $ 9,789 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, 2019 ​ Nine Months Ended September 30, 2019 ​ ​ ​ ​ ​ ​ Cash paid for amounts included in the measurement of lease liabilities: $ 3,485 ​ $ 8,727 ​ ​ ​ ​ ​ ​ Lease liabilities arising from obtaining right-of-use assets: ​ ​ ​ ​ ​ Operating leases $ - ​ $ 23,300 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating leases Weighted average remaining lease term in years ​ ​ ​ ​ 9.50 Weighted average discount rate ​ ​ ​ ​ 8.2% ​
Schedule of future minimum lease payments - ASC 842	​ ​ ​ ​ ​ 2019 (excluding the 9 months ended September 30, 2019) ​ $ 3,521 2020 ​ ​ 14,341 2021 ​ ​ 14,764 2022 ​ ​ 14,719 2023 ​ ​ 12,746 Thereafter ​ ​ 83,471 Total future minimum lease payments (1) ​ ​ 143,562 Less imputed interest ​ ​ (46,054) Total ​ $ 97,508 ​ (1) Minimum lease payments have not been reduced by minimum sublease rentals of $3.1 million due in the future under the Company’s non-cancelable sublease for the office and laboratory space located at 38 Sidney Street, Cambridge, Massachusetts. The minimum lease payments above do not include any related common area maintenance charges or real estate taxes. ​
Schedule of future minimum lease payments - ASC 840	​ ​ ​ ​ ​ 2019 ​ $ 12,247 2020 ​ ​ 14,341 2021 ​ ​ 14,764 2022 ​ ​ 14,719 2023 ​ ​ 12,746 Thereafter ​ ​ 83,471 Total minimum lease payments (1) ​ $ 152,288 ​ (1) Minimum lease payments have not been reduced by minimum sublease rentals of $5.3 million due in the future under the Company’s non-cancelable sublease for the office and laboratory space located at 38 Sidney Street, Cambridge, Massachusetts. The minimum lease payments above do not include any related common area maintenance charges or real estate taxes.

Nature of Business - Sale of St

Nature of Business - Sale of Stock (Details) $ / shares in Units, $ in Millions	Apr. 02, 2019USD ($)$ / sharesshares
April 2019 follow-on public offering
Nature of Business
Stock sold (in shares)	4,662,162
Share price (in dollars per share) | $ / shares	$ 74
Proceeds from issuance of common stock, net of underwriting discounts and commissions and estimated offering expenses | $	$ 327.4
Underwriters' Option
Nature of Business
Stock sold (in shares)	608,108

Nature of Business - Cash, Cash

Nature of Business - Cash, Cash Equivalents and Investments (Details) $ in Millions	Sep. 30, 2019USD ($)
Cash, cash equivalents and investments
Cash, cash equivalents and investments	$ 594.5

Nature of Business - Collaborat

Nature of Business - Collaboration Agreements (Details) - Collaboration - USD ($) $ in Millions	Oct. 15, 2019	Nov. 05, 2019	Mar. 31, 2016
Roche
Collaboration Agreements
Upfront cash payment			$ 45
Subsequent Event | Clementia Pharmaceuticals, Inc.
Collaboration Agreements
Upfront cash payment	$ 25
Subsequent Event | Roche
Collaboration Agreements
Research milestone acheived		$ 8

Summary of Significant Accoun_4

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Leases (Details)	9 Months Ended
	Sep. 30, 2019
Leases
Lease, Practical Expedients, Package	true
Lease, Practical Expedient, Lessor Single Lease Component	true

Summary of Significant Accoun_5

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Impact of Adoption of ASC 842 - General Information (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019
Leases
Operating lease right-of-use assets, net	$ 73,967	$ 54,245
Lease liability	$ 97,508
Accounting Standards Update 2016-02 | Restatement Adjustment
Leases
Operating lease right-of-use assets, net		54,245
Lease liability		$ 74,100

Summary of Significant Accoun_6

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Impact of Adoption of ASC 842 - Consolidated Balance Sheet (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Leases
Operating lease right-of-use assets, net	$ 73,967	$ 54,245
Total assets	737,925	594,369	$ 540,124
Accrued expenses	80,419	51,586	51,711
Current portion of operating lease liabilities	6,587	4,730
Current portion of lease incentive obligation			1,714
Total current liabilities	94,142	63,214	60,323
Deferred rent, net of current portion			5,130
Operating lease liabilities, net of current portion	90,921	69,387
Lease incentive obligation, net of current portion			12,903
Total liabilities	$ 221,581	175,360	$ 121,115
Previously Reported
Leases
Total assets		540,124
Accrued expenses		51,711
Current portion of lease incentive obligation		1,714
Total current liabilities		60,323
Deferred rent, net of current portion		5,130
Lease incentive obligation, net of current portion		12,903
Total liabilities		121,115
Accounting Standards Update 2016-02 | Restatement Adjustment
Leases
Operating lease right-of-use assets, net		54,245
Total assets		54,245
Accrued expenses		(125)
Current portion of operating lease liabilities		4,730
Current portion of lease incentive obligation		(1,714)
Total current liabilities		2,891
Deferred rent, net of current portion		(5,130)
Operating lease liabilities, net of current portion		69,387
Lease incentive obligation, net of current portion		(12,903)
Total liabilities		$ 54,245

Summary of Significant Accoun_7

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Impact of Adoption of ASC 842 - New Accounting Pronouncements (Details)	9 Months Ended
	Sep. 30, 2019
Accounting Standards Update 2016-02
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 1, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Change in Accounting Principle, Accounting Standards Update, Transition Option Elected	Modified Retrospective
New Accounting Pronouncement or Change in Accounting Principle, Prior Period Not Restated	true
Accounting Standards Update 2016-13
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Accounting Standards Update 2017-08
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 1, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Change in Accounting Principle, Accounting Standards Update, Transition Option Elected	Modified Retrospective
Accounting Standards Update 2018-13
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Accounting Standards Update 2018-18
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-15
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false

Cash Equivalents and Investme_3

Cash Equivalents and Investments - Tabular Disclosure - Cash Equivalents (Details) - Money market funds - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Cash equivalents:
Cash equivalents, Amortized Cost	$ 89,237	$ 68,064
Cash equivalents	$ 89,237	$ 68,064

Cash Equivalents and Investme_4

Cash Equivalents and Investments - Tabular Disclosure - Investments, Available-for-sale (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Investments, available-for-sale:
Available-for-sale, Amortized Cost	$ 504,559	$ 426,112
Available-for-sale, Unrealized Gain	693
Available-for-sale, Unrealized Losses	(30)	(164)
Investments, available-for-sale	$ 505,222	$ 425,948
Investments, available-for-sale, type	us-gaap:USTreasuryAndGovernmentMember	us-gaap:USTreasuryAndGovernmentMember

Cash Equivalents and Investme_5

Cash Equivalents and Investments - Tabular Disclosure - Total (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Cash Equivalents and Investments
Total, Amortized Cost	$ 593,796	$ 494,176
Total, Unrealized Gain	693
Total, Unrealized Losses	(30)	(164)
Total, Fair Value	$ 594,459	$ 494,012

Cash Equivalents and Investme_6

Cash Equivalents and Investments - Unrealized Loss Position (Details) $ in Millions	Sep. 30, 2019USD ($)security	Dec. 31, 2018USD ($)security
Unrealized loss position, number of positions
Number of held securities in an unrealized loss position	8	54
Number of held securities in an unrealized loss position for less than 12 months	0
Number of held securities in an unrealized loss position for 12 months or longer	0
Unrealized loss position, aggregate fair value
Unrealized loss position | $	$ 55.4	$ 397.5

Cash Equivalents and Investme_7

Cash Equivalents and Investments - Gains or Losses (Details) $ in Millions	9 Months Ended
	Sep. 30, 2019USD ($)
Adjustment for other than temporary fair value decline
Adjustment for other than temporary fair value decline	$ 0

Cash Equivalents and Investme_8

Cash Equivalents and Investments - Remaining Maturities (Details) $ in Millions	Sep. 30, 2019USD ($)security	Dec. 31, 2018USD ($)
Investments, available-for-sale
Securities with remaining maturities greater than one year | security	14
Aggregate fair value with remaining maturities greater than one year | $	$ 101	$ 0

Fair Value of Financial Instr_3

Fair Value of Financial Instruments (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Fair Value of Financial Instruments
Investments, available-for-sale	$ 505,222	$ 425,948
Investments, available-for-sale, type	us-gaap:USTreasuryAndGovernmentMember	us-gaap:USTreasuryAndGovernmentMember
Money market funds
Fair Value of Financial Instruments
Cash equivalents	$ 89,237	$ 68,064
Recurring
Fair Value of Financial Instruments
Investments, available-for-sale	505,222	425,948
Total	594,459	494,012
Recurring | Money market funds
Fair Value of Financial Instruments
Cash equivalents	89,237	68,064
Recurring | Active Markets (Level 1)
Fair Value of Financial Instruments
Investments, available-for-sale	505,222	425,948
Total	594,459	494,012
Recurring | Active Markets (Level 1) | Money market funds
Fair Value of Financial Instruments
Cash equivalents	$ 89,237	$ 68,064

Restricted Cash (Details)

Restricted Cash (Details) - USD ($) $ in Millions	Sep. 30, 2019	Dec. 31, 2018
Restricted Cash
Restricted cash	$ 5.7	$ 5.4

Property and Equipment, Net - E

Property and Equipment, Net - Estimated Useful Lives (Details)	9 Months Ended
	Sep. 30, 2019
Lab equipment
Property and Equipment, Net
Estimated Useful Life (Years)	5 years
Furniture and fixtures
Property and Equipment, Net
Estimated Useful Life (Years)	4 years
Computer equipment
Property and Equipment, Net
Estimated Useful Life (Years)	3 years
Leasehold improvements
Property and Equipment, Net
Estimated Useful Life	Term of lease
Software
Property and Equipment, Net
Estimated Useful Life (Years)	3 years

Property and Equipment, Net - P

Property and Equipment, Net - Property and Equipment and Related Accumulated Depreciation (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Property and Equipment, Net
Gross property and equipment	$ 50,563	$ 38,282
Less: accumulated depreciation and amortization	(12,253)	(8,655)
Total	38,310	29,627
Lab equipment
Property and Equipment, Net
Gross property and equipment	8,370	6,232
Furniture and fixtures
Property and Equipment, Net
Gross property and equipment	3,491	2,369
Computer equipment
Property and Equipment, Net
Gross property and equipment	1,632	1,805
Leasehold improvements
Property and Equipment, Net
Gross property and equipment	35,513	26,640
Software
Property and Equipment, Net
Gross property and equipment	408	280
Construction-in-progress
Property and Equipment, Net
Gross property and equipment	$ 1,149	$ 956

Property and Equipment, Net - D

Property and Equipment, Net - Depreciation Expense (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Depreciation expense
Depreciation expense	$ 1.3	$ 1.2	$ 3.7	$ 3.1

Accrued Expenses (Details)

Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Accrued Expenses
External research and development	$ 55,270		$ 36,213
Employee compensation	10,960		8,071
Accrued professional fees	8,720		4,423
Property and equipment costs	3,225		912
Other	2,244		2,092
Total	$ 80,419	$ 51,586	$ 51,711

Collaboration Agreements - Gene

Collaboration Agreements - General Information (Details) $ in Thousands	Jun. 01, 2018USD ($)item	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Mar. 31, 2016USD ($)item	Sep. 30, 2019USD ($)item	Sep. 30, 2018USD ($)	Mar. 31, 2016USD ($)item	Sep. 30, 2019USD ($)	Sep. 30, 2018USD ($)	Dec. 31, 2018USD ($)
Collaboration Agreements
Collaboration revenue					$ 9,139	$ 1,095		$ 14,979	$ 43,488
Revenue					9,139	1,095		14,979	43,488
Current portion of deferred revenue					$ 4,933			$ 4,933		$ 3,600
Roche | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-07-01
Collaboration Agreements
Research and development services, performance period					5 years 6 months			5 years 6 months
Collaboration | C Stone
Collaboration Agreements
Non-refundable upfront payment received	$ 40,000
Eligible milestone payments	$ 346,000
Licensed product term from first commercial sale	12 years
Number of materials components | item	2
Number of option rights to obtain exclusive license | item	3
Number of potential collaboration programs | item	3
Number of material promises | item	6
Number of collaboration programs with exclusive commercialization rights for licensed products | item	3
Initial cash payment	$ 40,000
Collaboration revenue					$ 6,000			$ 10,144	40,000
Revenue					6,000			10,144	40,000
Deferred revenue					$ 0			0		$ 0
Revenue recognized, change in contract liability						40,000
Collaboration | C Stone | Development and regulatory milestones
Collaboration Agreements
Eligible milestone payments	118,500
Number of potential collaboration programs | item					3
Collaboration revenue					$ 6,000
Revenue					6,000
Collaboration | C Stone | Sales-based milestones
Collaboration Agreements
Eligible milestone payments	$ 227,500
Collaboration | Roche
Collaboration Agreements
Non-refundable upfront payment received				$ 45,000
Number of option rights to obtain exclusive license | item							5
Initial cash payment			$ 45,000	45,000
Collaboration revenue					3,139	1,095		4,836	3,488
Revenue					3,139	1,095		4,836	3,488
Deferred revenue					41,300			41,300
Reversal of cumulative milestone revenue not occur for developmental milestone		$ 10,000
Total eligible contingent option fees and milestone payments				965,000			$ 965,000
Eligible option fees and milestones prior to licensing for all potential collaboration programs				$ 215,000
Current portion of deferred revenue					4,900			4,900
Achieved research milestone payment received which will be recognized over period of performance		$ 10,000
Revenue recognized, change in contract liability					1,149	$ 1,129		$ 3,470	$ 3,240
Cumulative revenue catch-up					$ 2,000
Collaboration | Roche | Prior To Exercise License Right Option
Collaboration Agreements
Written termination notice period				120 days
Collaboration | Roche | Exercise Of License Right Option
Collaboration Agreements
Number of collaboration programs with exclusive commercialization rights for licensed products | item				2
Number of collaboration programs with specified commercial rights for each party | item				2
Collaboration | Roche | Exercise Of License Option Product Not Commercially Sold
Collaboration Agreements
Written termination notice period				120 days
Collaboration | Roche | Exercise Of License Option Product Commercially Sold
Collaboration Agreements
Written termination notice period				180 days

Collaboration Agreements - Manu

Collaboration Agreements - Manufacturing Services (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Global development of the licensed product | C Stone
Collaboration Agreements
Manufacturing services related to global development activities	$ 1,275	$ 345	$ 2,403	$ 345

Collaboration Agreements - Reve

Collaboration Agreements - Revenue Recognized - CStone (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Collaboration Agreements
Total CStone collaboration revenue	$ 9,139	$ 1,095	$ 14,979	$ 43,488
Collaboration | C Stone
Collaboration Agreements
License milestone revenue	6,000		10,000	40,000
Total CStone collaboration revenue	$ 6,000		10,144	$ 40,000
Territory-specific license and related activities | C Stone
Collaboration Agreements
Manufacturing services related to territory-specific activities			$ 144

Collaboration Agreements - Cont

Collaboration Agreements - Contract Assets - CStone (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Collaboration Agreements
Accounts receivable	$ 2,414	$ 64
Unbilled accounts receivable	2,662	151
C Stone
Collaboration Agreements
Accounts receivable	2,414
Unbilled accounts receivable	$ 2,662	$ 151

Collaboration Agreements - Re_2

Collaboration Agreements - Revenue Recognized - Roche (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Collaboration Agreements
Revenue	$ 9,139	$ 1,095	$ 14,979	$ 43,488
Collaboration | Roche
Collaboration Agreements
Revenue	3,139	1,095	4,836	3,488
Amounts included in the contact liability at the beginning of the period	$ 1,149	$ 1,129	$ 3,470	$ 3,240

Stock-based Compensation - 2015

Stock-based Compensation - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares	Jan. 01, 2019	Sep. 30, 2019	Apr. 08, 2015
Stock-based compensation
Initial shares of common stock authorized for issuance of stock awards			1,460,084
Increase in number of shares available for grant (as a percent)		4.00%
Increase in number of shares available for grant	1,761,481
Number of shares available for grant		1,653,349

Stock-based Compensation - Stoc

Stock-based Compensation - Stock Options - Activity (Details) - Stock Options	9 Months Ended
	Sep. 30, 2019$ / sharesshares
Shares
Outstanding at beginning of period (in shares) | shares	4,557,800
Granted (in shares) | shares	1,673,749
Exercised (in shares) | shares	(462,806)
Cancelled (in shares) | shares	(137,266)
Outstanding at end of period (in shares) | shares	5,631,477
Weighted-Average Exercise Price
Outstanding at beginning of period (in dollars per share) | $ / shares	$ 44.64
Granted (in dollars per share) | $ / shares	84.12
Exercised (in dollars per share) | $ / shares	23.69
Cancelled (in dollars per share) | $ / shares	68.03
Outstanding at end of period (in dollars per share) | $ / shares	$ 57.53
Additional disclosures
Shares - Exercisable (in shares) | shares	2,527,772
Weighted-Average Exercise Price - Exercisable (in dollars per share) | $ / shares	$ 36.67

Stock-based Compensation - Unve

Stock-based Compensation - Unvested Restricted Stock - Activity (Details) - Restricted stock units	9 Months Ended
	Sep. 30, 2019$ / sharesshares
Shares
Unvested at beginning of period (in shares) | shares	36,868
Granted (in shares) | shares	356,915
Vested (in shares) | shares	(2,730)
Forfeited (in shares) | shares	(9,261)
Unvested at end of period (in shares) | shares	381,792
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) | $ / shares	$ 66.28
Granted (in dollars per share) | $ / shares	85.30
Vested (in dollars per share) | $ / shares	66.40
Forfeited (in dollars per share) | $ / shares	80.53
Unvested at end of period (in dollars per share) | $ / shares	$ 83.72

Stock-based Compensation - Unre

Stock-based Compensation - Unrecognized Compensation Costs (Details) $ in Millions	Sep. 30, 2019USD ($)
Stock Options
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock option awards	$ 135.3
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 9 months 25 days
Restricted stock units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 27.7
Weighted-average period over which unrecognized compensation cost will be recognized	3 years 4 months 20 days

Stock-based Compensation - Empl

Stock-based Compensation - Employee Stock Purchase Plan (Details) - Employee Stock - shares	1 Months Ended	9 Months Ended
	May 31, 2015	Sep. 30, 2019	Sep. 30, 2018	Jan. 01, 2019
Stock-based compensation
Number of common shares reserved for future issuance (in shares)	243,347
Annual increase for common stock for issuance (as a percent)	1.00%
Increase of common shares reserved for future issuance (in shares)				440,370
ESPP shares issued during period (in shares)		10,718	5,572

Stock-based Compensation - St_2

Stock-based Compensation - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Total stock based compensation expense
Total stock-based compensation expense	$ 14,993	$ 8,391	$ 38,954	$ 21,702
Research and development
Total stock based compensation expense
Total stock-based compensation expense	7,678	4,770	20,971	12,054
General and administrative
Total stock based compensation expense
Total stock-based compensation expense	7,315	3,621	17,983	9,648
Stock Options
Total stock based compensation expense
Total stock-based compensation expense	12,778	8,278	34,373	21,468
Restricted stock units
Total stock based compensation expense
Total stock-based compensation expense	2,076	42	4,243	42
Employee Stock
Total stock based compensation expense
Total stock-based compensation expense	$ 139	$ 71	$ 338	$ 192

Net Loss per Share - Anti-dilut

Net Loss per Share - Anti-dilutive Securities (Details) - shares	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	6,024,910	4,476,563
Stock Options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	5,631,477	4,458,508
Restricted stock units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	381,792	12,195
Employee Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	11,641	5,860

Net Loss per Share - Weighted A

Net Loss per Share - Weighted Average Number of Common Shares (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Net Loss per Share
Weighted-average number of common shares used in net loss per share - basic and diluted	48,921,445	43,915,376	47,360,675	43,824,773

Leases - General Information (D

Leases - General Information (Details) $ in Thousands	Sep. 19, 2018USD ($)ft²	Apr. 28, 2017USD ($)ft²	Feb. 12, 2015USD ($)ft²	Feb. 28, 2019USD ($)	Feb. 28, 2018USD ($)	Mar. 31, 2018USD ($)	Sep. 30, 2019USD ($)	Dec. 31, 2018USD ($)	Sep. 18, 2018ft²
Leases
Initial lease commitments							$ 143,562
Restricted cash							5,700	$ 5,400
Total commitment in sublease							3,100	$ 5,300
Corporate Headquarters Lease
Leases
Area leased (in square feet) | ft²			38,500
Extension period of lease term			5 years
Lessee, Operating Lease, Existence of Option to Extend			true
Initial lease commitments			$ 17,800
Initial lease term			7 years
Base annual rent, initial			$ 2,300
Base annual rent, maximum			2,800
Allowance for leasehold improvements			4,300
Security deposit			$ 1,300				900
Security deposit released				$ 200	$ 200
Total commitment in sublease						$ 8,200	3,400
Sublease term						32 months
Sublease payable						$ 6,900
Additional sublease payments on share of profits						$ 700
Office and Laboratory Space in Cambridge Massachusetts, 45 Sidney Street
Leases
Area leased (in square feet) | ft²	139,216	99,833							99,833
Extension period of lease term		5 years
Lessee, Operating Lease, Existence of Option to Extend		true
Base annual rent, initial		$ 7,700
Base annual rent, maximum		10,600
Allowance for leasehold improvements		$ 14,200
Security deposit							3,500
Restricted cash							3,000
Security deposit to be released							500
Office and Laboratory Space in Cambridge, Massachusetts, 45 Sidney Street, Expansion Premises
Leases
Base annual rent, initial	$ 3,200
Base annual rent, maximum	4,200
Allowance for leasehold improvements	$ 3,200
Security deposit							$ 800

Leases - Components of Lease Ex

Leases - Components of Lease Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Operating leases cost:
Lease cost	$ 4,167		$ 11,906
Sublease income	(708)		(2,117)
Net lease cost	$ 3,459		$ 9,789
Net rent expenses		$ 1,700		$ 5,600

Leases - Cash Flow Information

Leases - Cash Flow Information (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Leases
Cash paid for amounts included in the measurement of lease liabilities, operating cash flows from operating leases	$ 3,485	$ 8,727
Lease liabilities arising from obtaining right-of-use assets, operating leases		$ 23,300

Leases - Weighted Average Remai

Leases - Weighted Average Remaining Lease-term and Weighted Average Discount Rate (Details)	Sep. 30, 2019
Leases
Weighted average remaining lease term in years	9 years 6 months
Weighted average discount rate	8.20%

Leases - Future Minimum Lease P

Leases - Future Minimum Lease Payments - ASC 842 (Details) $ in Thousands	Sep. 30, 2019USD ($)
Future minimum lease payments
2019 (excluding the 9 months ended September 30,2019)	$ 3,521
2020	14,341
2021	14,764
2022	14,719
2023	12,746
Thereafter	83,471
Total future minimum lease payments	$ 143,562

Leases - Total Lease Liability

Leases - Total Lease Liability (Details) $ in Thousands	Sep. 30, 2019USD ($)
Leases
Total future minimum lease payments	$ 143,562
Less imputed interest	(46,054)
Total	$ 97,508

Leases - Future Minimum Lease_2

Leases - Future Minimum Lease Payments - ASC 840 - Tabular Disclosure (Details) $ in Thousands	Dec. 31, 2018USD ($)
Future minimum lease payments
2019	$ 12,247
2020	14,341
2021	14,764
2022	14,719
2023	12,746
Thereafter	83,471
Total	$ 152,288

Leases - Sublease Rentals (Deta

Leases - Sublease Rentals (Details) - USD ($) $ in Millions	Sep. 30, 2019	Dec. 31, 2018
Leases
Sublease rentals	$ 3.1	$ 5.3

Subsequent Events (Details)

Subsequent Events (Details) - Collaboration - USD ($) $ in Millions	Oct. 15, 2019	Nov. 05, 2019	Mar. 31, 2016
Roche
Subsequent Events
Upfront cash payment			$ 45
Subsequent Event | Clementia Pharmaceuticals, Inc.
Subsequent Events
Upfront, milestone and other payments eligible to receive	$ 535
Upfront cash payment	25
Additional cash payment eligible to receive	20
Milestone and other payments eligible to receive	$ 490
Subsequent Event | Roche
Subsequent Events
Research milestone acheived		$ 8