Blueprint Medicines (BPMC) 10-Q 9 May 19 2019 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - $ / shares	3 Months Ended
	Mar. 31, 2019	May 06, 2019
Document and Entity Information [Abstract]
Entity Registrant Name	Blueprint Medicines Corp
Entity Central Index Key	0001597264
Document Type	10-Q
Document Period End Date	Mar. 31, 2019
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Listing, Par Value Per Share	$ 0.001
Trading Symbol	BPMC
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Common Stock, Shares Outstanding		48,853,933
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q1

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 79,391	$ 68,064
Investments, available-for-sale	336,465	425,948
Prepaid expenses and other current assets	10,660	5,775
Total current assets	426,516	499,787
Property and equipment, net	30,615	29,627
Operating lease right-of-use assets, net	76,528
Restricted cash	5,159	5,154
Other assets	5,845	5,556
Total assets	544,663	540,124
Current liabilities:
Accounts payable	4,421	3,298
Accrued expenses	50,826	51,711
Current portion of operating lease liabilities	5,278
Current portion of deferred revenue	4,238	3,600
Current portion of lease incentive obligation		1,714
Total current liabilities	64,763	60,323
Deferred rent, net of current portion		5,130
Operating lease liabilities, net of current portion	94,322
Deferred revenue, net of current portion	41,198	42,567
Lease incentive obligation, net of current portion		12,903
Other long-term liabilities	167	192
Total liabilities	200,450	121,115
Commitments and Contingencies (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; 44,171,465 and 44,037,026 shares issued and outstanding at March 31, 2019 and December 31, 2018, respectively	44	44
Additional paid-in capital	1,029,046	1,016,690
Accumulated other comprehensive income (loss)	75	(180)
Accumulated deficit	(684,952)	(597,545)
Total stockholders’ equity	344,213	419,009
Total liabilities and stockholders’ equity	$ 544,663	$ 540,124

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 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)	44,171,465	44,037,026
Common Stock, shares outstanding (in shares)	44,171,465	44,037,026

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Condensed Consolidated Statements of Operations and Comprehensive Loss
Collaboration revenue	$ 730	$ 954
Operating expenses:
Research and development	74,250	49,954
General and administrative	16,553	9,911
Total operating expenses	90,803	59,865
Other income (expense):
Other income (expense), net	2,669	2,394
Interest expense	(3)	(32)
Total other income	2,666	2,362
Net loss	(87,407)	(56,549)
Other comprehensive loss:
Changes in foreign currency translation adjustments	(15)
Changes in unrealized gain (losses) related to available-for-sale investments	270	(323)
Comprehensive loss	$ (87,152)	$ (56,872)
Net loss per share — basic and diluted (in dollars per share)	$ (1.98)	$ (1.29)
Weighted-average number of common shares used in net loss per share — basic and diluted (in shares)	44,097	43,700

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, 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				44,171,465

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Cash flows from operating activities
Net loss	$ (87,407)	$ (56,549)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	2,219	780
Stock-based compensation	10,295	5,549
Accretion of premiums and discounts on investments	(1,332)	(692)
Other		4
Changes in assets and liabilities:
Prepaid expenses and other current assets	(1,923)	3,473
Other assets	(114)	(27)
Accounts payable	982	(482)
Accrued expenses	(1,208)	(525)
Deferred revenue	(731)	(954)
Deferred rent		(140)
Operating lease liabilities	(969)
Net cash used in operating activities	(80,188)	(49,563)
Cash flows from investing activities
Purchases of property and equipment	(1,770)	(6,312)
Purchases of investments	(112,916)	(338,816)
Maturities of investments	204,000	126,000
Net cash provided by (used in) investing activities	89,314	(219,128)
Cash flows from financing activities
Principal payments on loan payable		(417)
Proceeds from issuance of common stock	2,039	3,643
Payment of offering costs		(164)
Other financing activities	(28)
Net cash provided by financing activities	2,011	3,062
Net increase (decrease) in cash, cash equivalents, and restricted cash	11,137	(265,629)
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	(16)
Cash, cash equivalents and restricted cash at end of period	84,550	139,443
Supplemental cash flow information
Public offering costs incurred but unpaid at period end		166
Property and equipment purchases unpaid at period end	1,478	3,126
Cash paid for interest	$ 2	$ 18

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018	Mar. 31, 2018	Dec. 31, 2017
Reconciliation of cash, cash equivalents, and restricted cash
Cash and cash equivalents	$ 79,391	$ 68,064	$ 134,886
Restricted cash	5,159	5,154	4,557
Total cash, cash equivalents, and restricted cash shown in consolidated statements of cash flows	$ 84,550	$ 73,429	$ 139,443	$ 405,072

Nature of Business

Nature of Business	3 Months Ended
	Mar. 31, 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 April 2019 follow-on public offering). The Company received estimated net proceeds of $327.2 million, after deducting underwriting discounts and commissions and estimated offering expenses payable by the Company. As of March 31, 2019, the Company had cash, cash equivalents and investments of $415.9 million. Based on the Company’s current plans, the Company expects that its existing cash, cash equivalents and investments, including the $327.2 million in estimated net proceeds from its April 2019 follow-on public offering but excluding any potential option fees and milestone payments under its existing collaborations with Roche and CStone, will be sufficient to enable it to fund its operating expenses and capital expenditure requirements into the middle of 2021.

Summary of Significant Accounti

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	3 Months Ended
	Mar. 31, 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 March 31, 2019, the results of its operations for the three months ended March 31, 2019 and 2018, stockholder’s equity for the three months ended March 31, 2019 and 2018 and cash flows for the three months ended March 31, 2019 and 2018. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 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, and Blueprint Medicines (Netherlands) B.V. All intercompany transactions and balances have been eliminated. 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 months ended March 31, 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 From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards have or may have a material impact on its consolidated financial statements and disclosures. Leases In February 2016, the FASB issued Accounting Standards Update ASU No. 2016-02, Leases (Topic 842) or ASC 842, a new standard issued to increase transparency and comparability among organizations related to their leasing activities. This standard established a right-of-use model that requires all lessees to recognize right-of-use assets and lease liabilities on their balance sheet that arise from leases as well as provide disclosures with respect to certain qualitative and quantitative information related to a company's leasing arrangements to meet the objective of allowing users of financial statements to assess the amount, timing and uncertainty of cash flows arising from leases. The FASB subsequently issued the following amendments to ASU 2016-02 that have the same effective date and transition date: 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. The Company adopted these amendments with ASU 2016-02 (collectively, the new leasing standards, or ASC 842) effective January 1, 2019. As permitted by the new leasing standards, the Company elected to adopt ASC 842 using the modified retrospective transition approach, with no restatement of prior periods or cumulative adjustment to retained earnings, and therefore, the consolidated balance sheet prior to January 1, 2019 continues to be reported under ASC Topic 840, Leases, or ASC 840, which did not require the recognition of operating lease liabilities on the balance sheet, and is not comparative. Upon adoption, the Company elected the package of transition practical expedients, which allowed it to carry forward prior conclusions related to whether any expired or existing contracts are or contain leases, the lease classification for any expired or existing leases and initial direct costs for existing leases. The leases that were classified as operating leases under ASC 840 were classified as operating leases under ASC 842, and the accounting for finance leases (capital leases) was substantially unchanged. The Company elected to apply the practical expedient not to separate lease and non-lease components for new and modified leases commencing after adoption. The Company also made an accounting policy election to not recognize leases with an initial term of 12 months or less within the condensed consolidated balance sheets and to recognize those lease payments on a straight-line basis in the condensed consolidated statements of income over the lease term. Impact of Adoption of ASC 842 Upon adoption of the new leasing standards, the Company recognized an adjustment of $54.2 million and $74.1 million to operating lease right-of-use assets and the related lease liabilities, respectively. The operating lease liabilities are based on the present value of the remaining minimum lease payments discounted using the Company’s secured incremental borrowing rate at the effective date of January 1, 2019. The adoption of the new leasing standards did not have an impact on the Company’s condensed consolidated statements of income. The impact of the adoption of ASC 842 on the condensed consolidated balance sheet was as follows: 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 expense 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 expense 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 expense 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 In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments . This standard requires that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, this standard now requires allowances to be recorded instead of reducing the amortized cost of the investment. This standard will be effective for the Company on January 1, 2020. The Company is currently evaluating the potential impact that this standard may have on its consolidated financial position and results of operations. 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. This standard amends the amortization period for certain purchased callable debt securities held at a premium by shortening the amortization period to the earliest call date. This standard became effective for the Company on January 1, 2019, and was adopted using a modified retrospective transition approach. The adoption of this standard did not result in a significant adjustment to the Company’s marketable 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 . This standard modifies certain disclosure requirements on fair value measurements. This standard will be effective for the Company on January 1, 2020. The Company does not expect that the adoption of this standard will have a material impact on the disclosures. 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. This standard makes targeted improvements for collaborative arrangements as follows: · 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. This standard will be effective for the Company on January 1, 2020; however, early adoption is permitted. A retrospective transition approach is required for either all contracts or only for contracts that are not completed at the date of initial application of ASC 606, with a cumulative adjustment to opening retained earnings. The Company is currently evaluating the potential impact that this standard may have on its consolidated financial position and results of operations. 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 , which clarifies the accounting for implementation costs in cloud computing arrangements. This standard will be effective for the Company on January 1, 2020, however, early adoption is permitted. The Company currently is evaluating the impact the adoption may have on its consolidated financial position and results of operations. Reclassifications Certain items in the prior year’s consolidated financial statements have been reclassified to conform to the current presentation.

Cash Equivalents and Investment

Cash Equivalents and Investments	3 Months Ended
	Mar. 31, 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 March 31, 2019 and December 31, 2018 (in thousands): Amortized Unrealized Unrealized Fair March 31, 2019 Cost Gain Losses Value Cash equivalents: Money market funds $ 79,391 $ — $ — $ 79,391 Investments, available-for-sale: U.S. treasury obligations 336,359 129 (23) 336,465 Total $ 415,750 $ 129 $ (23) $ 415,856 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. treasury obligations 426,112 — (164) 425,948 Total $ 494,176 $ — $ (164) $ 494,012 At March 31, 2019 and December 31, 2018, the Company held 15 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 March 31, 2019 and December 31, 2018 was $94.5 million and $397.5 million, respectively. There were no individual securities that were in a significant unrealized loss position as of March 31, 2019 and December 31, 2018. As of March 31, 2019, there were three securities in a total aggregate fair value of $14.0 million were 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 March 31, 2019. No available-for-sale securities held as of March 31, 2019 or December 31, 2018 had remaining maturities greater than one year.

Fair Value of Financial Instrum

Fair Value of Financial Instruments	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Fair Value of Financial Instruments	4. Fair Value of Financial Instruments The following table summarizes our cash equivalents and marketable securities measured at fair value on a recurring basis as of March 31, 2019 (in thousands): Active Observable Unobservable March 31, Markets Inputs Inputs Description 2019 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ 79,391 $ 79,391 $ — $ — Investments, available-for-sale: U.S Treasury obligations 336,465 336,465 — — Total $ 415,856 $ 415,856 $ — $ — The following table summarizes our 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 Treasury obligations 425,948 425,948 — — Total $ 494,012 $ 494,012 $ — $ —

Restricted Cash

Restricted Cash	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Restricted Cash	5. Restricted Cash At March 31, 2019 and December 31, 2018, $5.2 million and $5.4 million, respectively, of the Company’s cash is restricted by a bank 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	3 Months Ended
	Mar. 31, 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 March 31, December 31, (Years) 2019 2018 Lab equipment 5 $ 6,742 $ 6,232 Furniture and fixtures 4 2,455 2,369 Computer equipment 3 1,554 1,805 Leasehold improvements Term of lease 26,660 26,640 Software 3 408 280 Construction-in-progress 2,542 956 40,361 38,282 Less: accumulated depreciation and amortization (9,746) (8,655) Total $ 30,615 $ 29,627 Property, plant and equipment are recorded at historical cost, net of accumulated depreciation. For the three months ended March 31, 2019, depreciation expense totaled $1.2 million, compared to $0.8 million in the prior year comparative period.

Accrued Expenses

Accrued Expenses	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Accrued Expenses	7. Accrued Expenses Accrued expenses consist of the following (in thousands): March 31, December 31, 2019 2018 External research and development $ 36,641 $ 36,213 Employee compensation 4,545 8,071 Accrued professional fees 5,758 4,423 Property and equipment costs 1,338 912 Other 2,544 2,092 Total $ 50,826 $ 51,711

Collaborations

Collaborations	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Collaborations	8. Collaborations 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 BLU-554, avapritinib and BLU-667, 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 BLU-554 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 BLU-554 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. Accordingly, the Company recorded a reduction of expenses of $0.8 million for the three months ended March 31, 2019. 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 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. There was no adjustment in the transaction price as of March 31, 2019. Because the performance obligations have been satisfied, any addition to the transaction price would be immediately recognized as revenue. 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, and there was no revenue deferred as a contract liability associated with the CStone agreement as of December 31, 2018 and March 31, 2019. 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. The parties are currently conducting activities for up to five programs under the collaboration, including up to two collaboration programs leveraging the Company’s novel target discovery engine and proprietary compound library to select potential targets. Under the Roche agreement, Roche is 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. For up to three of the five collaboration programs, if Roche exercises its option, Roche will receive worldwide, exclusive commercialization rights for the licensed products. For up to two of the five collaboration programs, if Roche exercises its option, the Company will retain commercialization rights in the United States for the licensed products, and Roche will receive commercialization rights outside of the United States for the licensed products. The Company will also retain worldwide rights to any products for which Roche elects not to exercise its applicable option. 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 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 March 31, 2019, there has been no significant changes in the costs expected to be incurred in the future to satisfy the performance obligation, and the Company recognized revenue of $0.7 million under the Roche collaboration, of which $1.0 million was recognized as a result of the change in the contract liability balances as of December 31, 2018. As of March 31, 2019, the Company had revenue deferred as a contract liability related to the Roche agreement of $45.4 million, of which $4.2 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 six years.

Stock-based compensations

Stock-based compensations	3 Months Ended
	Mar. 31, 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 our capitalization. At March 31, 2019, there were 2,244,841 shares available for future grant under the 2015 Plan. Stock options The following table summarizes the stock option activity for the three months ended March 31, 2019: Weighted-Average Shares Exercise Price Outstanding at December 31, 2018 4,557,800 $ 44.64 Granted 1,061,306 85.05 Exercised (134,439) 15.34 Canceled (23,785) 63.18 Outstanding at March 31, 2019 5,460,882 $ 53.13 Exercisable at March 31, 2019 2,199,374 $ 27.46 At March 31, 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 3.0 years. Restricted stock units The following table summarizes the restricted stock units activity for the three months ended March 31, 2019: Weighted-Average Grant Date Shares Fair Value Unvested shares at December 31, 2018 36,868 $ 66.28 Granted 256,124 85.40 Vested — — Forfeited (1,000) 86.60 Unvested shares at March 31, 2019 291,992 $ 82.98 At March 31, 2019, the total unrecognized compensation expense related to unvested restricted stock units was $23.4 million, which is expected to be recognize over a weighted-average period of approximately 3.9 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 IPO 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. No shares were issued under the 2015 ESPP during the three months ended March 31, 2019 and 2018. Stock-based compensation expense The Company recognized stock-based compensation expense totaling $10.3 million and $5.5 million for the three months ended March 31, 2019 and 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 March 31, 2019 2018 Stock options $ 9,579 $ 5,491 Restricted stock units 624 — Employee stock purchase plan 92 58 Total stock-based compensation expense $ 10,295 $ 5,549 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 March 31, 2019 2018 Research and development $ 5,790 $ 3,011 General and administrative 4,505 2,538 Total stock-based compensation expense $ 10,295 $ 5,549

Net Loss per Share

Net Loss per Share	3 Months Ended
	Mar. 31, 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. Three Months Ended March 31, 2019 2018 Stock options 5,460,882 4,119,870 Restricted stock units 291,992 — ESPP shares 10,275 5,722 Total 5,763,149 4,125,592 The weighted average number of common shares used in net loss per share on a basic and diluted basis were 44,096,806 and 43,700,226 for the three months ended March 31, 2019 and 2018, respectively.

Leases

Leases	3 Months Ended
	Mar. 31, 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 March 31, 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 March 31, 2019, the minimum sublease rental commitment by the sublessee was $5.0 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, which is recorded in restricted cash on the Company’s condensed consolidated balance sheet as of March 31, 2019. 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 date on which the Company will become responsible for paying rent with respect to the expansion space will be the earlier of (i) the date upon which the Company first occupies the expansion premises for business purposes or (ii) July 1, 2019. The Company currently anticipates the rent commencement date for the expansion premises will be 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 March 31, 2019. The components of lease expense for the three months ended March 31, 2019 were as follows: Operating leases: Three Months Ended March 31, 2019 Lease cost $ 3,564 Sublease income (701) Net lease cost 2,863 For the three months ended March 31, 2018, rent expense under ASC 840, net of sublease income, was $2.2 million. Supplemental cash flow information related to leases for the three months ended March 31, 2019 was as follows: Three Months Ended March 31, 2019 Cash paid for amounts included in the measurement of lease liabilities: Operating cash flows from operating leases $ 2,621 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 10 years Weighted Average Discount Rate Future minimum lease payments under non-cancellable leases as of March 31, 2019 were as follows (in thousands): 2019 (excluding the 3 months ended March 31,2019) $ 9,627 2020 14,341 2021 14,764 2022 14,719 2023 12,746 Thereafter 83,471 Total future minimum lease payments (1) 149,668 Less imputed interest (50,068) Total $ 99,600 (1) Minimum lease payments have not been reduced by minimum sublease rentals of $4.6 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	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Commitments	12. Commitments The Company has no other commitments other than the minimum lease payments commitment as disclosed in Note 11, Leases .

Subsequent Event

Subsequent Event	3 Months Ended
	Mar. 31, 2019
Disclosure Text Block
Subsequent Event	13. Subsequent Events

Summary of Significant Accoun_2

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	3 Months Ended
	Mar. 31, 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 March 31, 2019, the results of its operations for the three months ended March 31, 2019 and 2018, stockholder’s equity for the three months ended March 31, 2019 and 2018 and cash flows for the three months ended March 31, 2019 and 2018. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 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, and Blueprint Medicines (Netherlands) B.V. All intercompany transactions and balances have been eliminated.
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 months ended March 31, 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 From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards have or may have a material impact on its consolidated financial statements and disclosures. Leases In February 2016, the FASB issued Accounting Standards Update ASU No. 2016-02, Leases (Topic 842) or ASC 842, a new standard issued to increase transparency and comparability among organizations related to their leasing activities. This standard established a right-of-use model that requires all lessees to recognize right-of-use assets and lease liabilities on their balance sheet that arise from leases as well as provide disclosures with respect to certain qualitative and quantitative information related to a company's leasing arrangements to meet the objective of allowing users of financial statements to assess the amount, timing and uncertainty of cash flows arising from leases. The FASB subsequently issued the following amendments to ASU 2016-02 that have the same effective date and transition date: 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. The Company adopted these amendments with ASU 2016-02 (collectively, the new leasing standards, or ASC 842) effective January 1, 2019. As permitted by the new leasing standards, the Company elected to adopt ASC 842 using the modified retrospective transition approach, with no restatement of prior periods or cumulative adjustment to retained earnings, and therefore, the consolidated balance sheet prior to January 1, 2019 continues to be reported under ASC Topic 840, Leases, or ASC 840, which did not require the recognition of operating lease liabilities on the balance sheet, and is not comparative. Upon adoption, the Company elected the package of transition practical expedients, which allowed it to carry forward prior conclusions related to whether any expired or existing contracts are or contain leases, the lease classification for any expired or existing leases and initial direct costs for existing leases. The leases that were classified as operating leases under ASC 840 were classified as operating leases under ASC 842, and the accounting for finance leases (capital leases) was substantially unchanged. The Company elected to apply the practical expedient not to separate lease and non-lease components for new and modified leases commencing after adoption. The Company also made an accounting policy election to not recognize leases with an initial term of 12 months or less within the condensed consolidated balance sheets and to recognize those lease payments on a straight-line basis in the condensed consolidated statements of income over the lease term. Impact of Adoption of ASC 842 Upon adoption of the new leasing standards, the Company recognized an adjustment of $54.2 million and $74.1 million to operating lease right-of-use assets and the related lease liabilities, respectively. The operating lease liabilities are based on the present value of the remaining minimum lease payments discounted using the Company’s secured incremental borrowing rate at the effective date of January 1, 2019. The adoption of the new leasing standards did not have an impact on the Company’s condensed consolidated statements of income. The impact of the adoption of ASC 842 on the condensed consolidated balance sheet was as follows: 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 expense 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 expense 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 expense 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 In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments . This standard requires that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, this standard now requires allowances to be recorded instead of reducing the amortized cost of the investment. This standard will be effective for the Company on January 1, 2020. The Company is currently evaluating the potential impact that this standard may have on its consolidated financial position and results of operations. 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. This standard amends the amortization period for certain purchased callable debt securities held at a premium by shortening the amortization period to the earliest call date. This standard became effective for the Company on January 1, 2019, and was adopted using a modified retrospective transition approach. The adoption of this standard did not result in a significant adjustment to the Company’s marketable 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 . This standard modifies certain disclosure requirements on fair value measurements. This standard will be effective for the Company on January 1, 2020. The Company does not expect that the adoption of this standard will have a material impact on the disclosures. 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. This standard makes targeted improvements for collaborative arrangements as follows: · 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. This standard will be effective for the Company on January 1, 2020; however, early adoption is permitted. A retrospective transition approach is required for either all contracts or only for contracts that are not completed at the date of initial application of ASC 606, with a cumulative adjustment to opening retained earnings. The Company is currently evaluating the potential impact that this standard may have on its consolidated financial position and results of operations. 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 , which clarifies the accounting for implementation costs in cloud computing arrangements. This standard will be effective for the Company on January 1, 2020, however, early adoption is permitted. The Company currently is evaluating the impact the adoption may have on its consolidated financial position and results of operations
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 expense 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 expense 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 expense 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.
Reclassifications	Reclassifications Certain items in the prior year’s consolidated financial statements have been reclassified to conform to the current presentation.

Summary of Significant Accoun_3

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of financial statement impact of the cumulative adjustment	The impact of the adoption of ASC 842 on the condensed consolidated balance sheet was as follows: 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)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of cash equivalents and investments, available-for-sale	Amortized Unrealized Unrealized Fair March 31, 2019 Cost Gain Losses Value Cash equivalents: Money market funds $ 79,391 $ — $ — $ 79,391 Investments, available-for-sale: U.S. treasury obligations 336,359 129 (23) 336,465 Total $ 415,750 $ 129 $ (23) $ 415,856 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. treasury obligations 426,112 — (164) 425,948 Total $ 494,176 $ — $ (164) $ 494,012

Fair Value of Financial Instr_2

Fair Value of Financial Instruments (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of financial instruments measured at fair value	The following table summarizes our cash equivalents and marketable securities measured at fair value on a recurring basis as of March 31, 2019 (in thousands): Active Observable Unobservable March 31, Markets Inputs Inputs Description 2019 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ 79,391 $ 79,391 $ — $ — Investments, available-for-sale: U.S Treasury obligations 336,465 336,465 — — Total $ 415,856 $ 415,856 $ — $ — The following table summarizes our 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 Treasury obligations 425,948 425,948 — — Total $ 494,012 $ 494,012 $ — $ —

Property and Equipment, Net (Ta

Property and Equipment, Net (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of property and equipment	Property and equipment and related accumulated depreciation are as follows (in thousands): Estimated Useful Life March 31, December 31, (Years) 2019 2018 Lab equipment 5 $ 6,742 $ 6,232 Furniture and fixtures 4 2,455 2,369 Computer equipment 3 1,554 1,805 Leasehold improvements Term of lease 26,660 26,640 Software 3 408 280 Construction-in-progress 2,542 956 40,361 38,282 Less: accumulated depreciation and amortization (9,746) (8,655) Total $ 30,615 $ 29,627

Accrued Expenses (Tables)

Accrued Expenses (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of accrued expenses	Accrued expenses consist of the following (in thousands): March 31, December 31, 2019 2018 External research and development $ 36,641 $ 36,213 Employee compensation 4,545 8,071 Accrued professional fees 5,758 4,423 Property and equipment costs 1,338 912 Other 2,544 2,092 Total $ 50,826 $ 51,711

Stock-based compensations (Tabl

Stock-based compensations (Tables)	3 Months Ended
	Mar. 31, 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 1,061,306 85.05 Exercised (134,439) 15.34 Canceled (23,785) 63.18 Outstanding at March 31, 2019 5,460,882 $ 53.13 Exercisable at March 31, 2019 2,199,374 $ 27.46
Summary of restricted stock units activity	Weighted-Average Grant Date Shares Fair Value Unvested shares at December 31, 2018 36,868 $ 66.28 Granted 256,124 85.40 Vested — — Forfeited (1,000) 86.60 Unvested shares at March 31, 2019 291,992 $ 82.98
Summary of Stock-based compensation expense allocation by type of awards	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 March 31, 2019 2018 Stock options $ 9,579 $ 5,491 Restricted stock units 624 — Employee stock purchase plan 92 58 Total stock-based compensation expense $ 10,295 $ 5,549
Summary of stock-based compensation expense recognized in statements of operations	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 March 31, 2019 2018 Research and development $ 5,790 $ 3,011 General and administrative 4,505 2,538 Total stock-based compensation expense $ 10,295 $ 5,549

Net Loss per Share (Tables)

Net Loss per Share (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Schedule of common stock equivalents excluded from calculation of diluted net loss per share applicable to common stockholders	Three Months Ended March 31, 2019 2018 Stock options 5,460,882 4,119,870 Restricted stock units 291,992 — ESPP shares 10,275 5,722 Total 5,763,149 4,125,592

Leases (Tables)

Leases (Tables)	3 Months Ended
	Mar. 31, 2019
Table Text Blocks
Summary of lease expenses and cash flow and weighted average information	The components of lease expense for the three months ended March 31, 2019 were as follows: Operating leases: Three Months Ended March 31, 2019 Lease cost $ 3,564 Sublease income (701) Net lease cost 2,863 For the three months ended March 31, 2018, rent expense under ASC 840, net of sublease income, was $2.2 million. Supplemental cash flow information related to leases for the three months ended March 31, 2019 was as follows: Three Months Ended March 31, 2019 Cash paid for amounts included in the measurement of lease liabilities: Operating cash flows from operating leases $ 2,621 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 10 years Weighted Average Discount Rate
Schedule of future minimum lease payments - ASC 842	2019 (excluding the 3 months ended March 31,2019) $ 9,627 2020 14,341 2021 14,764 2022 14,719 2023 12,746 Thereafter 83,471 Total future minimum lease payments (1) 149,668 Less imputed interest (50,068) Total $ 99,600 (1) Minimum lease payments have not been reduced by minimum sublease rentals of $4.6 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) - Subsequent Event $ / 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 | $	$ 327.2
Underwriters' Option
Nature of Business
Stock sold (in shares)	608,108

Nature of Business - Additional

Nature of Business - Additional Information (Details) $ in Millions	Mar. 31, 2019USD ($)
Cash, cash equivalents and investments
Cash, cash equivalents and investments	$ 415.9

Summary of Significant Accoun_4

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Leases (Details)	3 Months Ended
	Mar. 31, 2019
Leases
Lease, Practical Expedients, Package	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	Mar. 31, 2019	Jan. 01, 2019
Leases
Operating lease right-of-use assets, net	$ 76,528	$ 54,245
Lease liability	$ 99,600
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	Mar. 31, 2019	Jan. 01, 2019	Dec. 31, 2018
Leases
Operating lease right-of-use assets, net	$ 76,528	$ 54,245
Total assets	544,663	594,369	$ 540,124
Accrued expenses	50,826	51,586	51,711
Current portion of operating lease liabilities	5,278	4,730
Current portion of lease incentive obligation			1,714
Total current liabilities	64,763	63,214	60,323
Deferred rent, net of current portion			5,130
Operating lease liabilities, net of current portion	94,322	69,387
Lease Incentive Payable, Noncurrent			12,903
Total liabilities	$ 200,450	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 Payable, Noncurrent		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 Payable, Noncurrent		(12,903)
Total liabilities		$ 54,245

Cash Equivalents and Investme_3

Cash Equivalents and Investments - Tabular Disclosure - Cash Equivalents (Details) - Money market funds - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Cash equivalents:
Cash equivalents, Amortized Cost	$ 79,391	$ 68,064
Cash equivalents	$ 79,391	$ 68,064

Cash Equivalents and Investme_4

Cash Equivalents and Investments - Tabular Disclosure - Investments, Available-for-sale (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Investments, available-for-sale:
Available-for-sale, Amortized Cost	$ 336,359	$ 426,112
Available-for-sale, Unrealized Gain	129
Available-for-sale, Unrealized Losses	(23)	(164)
Investments, available-for-sale	$ 336,465	$ 425,948
Investments, available-for-sale, type	us-gaap:USTreasurySecuritiesMember	us-gaap:USTreasurySecuritiesMember

Cash Equivalents and Investme_5

Cash Equivalents and Investments - Tabular Disclosure - Total (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Cash Equivalents and Investments
Total, Amortized Cost	$ 415,750	$ 494,176
Total, Unrealized Gain	129
Total, Unrealized Losses	(23)	(164)
Total, Fair Value	$ 415,856	$ 494,012

Cash Equivalents and Investme_6

Cash Equivalents and Investments - Unrealized Loss Position (Details) $ in Millions	Mar. 31, 2019USD ($)security	Dec. 31, 2018USD ($)security
Unrealized loss position, number of positions
Number of held securities in an unrealized loss position | security	15	54
Number of held securities in an unrealized loss position for 12 months or longer | security	3
Unrealized loss position, aggregate fair value
Unrealized loss position | $	$ 94.5	$ 397.5
Unrealized loss position for more than 12 months | $	$ 14

Cash Equivalents and Investme_7

Cash Equivalents and Investments - Gains or Losses (Details) $ in Millions	3 Months Ended
	Mar. 31, 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) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Investments, available-for-sale
Investments, available-for-sale	$ 336,465	$ 425,948
Investments, available-for-sale, remaining maturities within one year	$ 336,465	$ 425,948

Fair Value of Financial Instr_3

Fair Value of Financial Instruments (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Fair Value of Financial Instruments
Investments, available-for-sale	$ 336,465	$ 425,948
Investments, available-for-sale, type	us-gaap:USTreasurySecuritiesMember	us-gaap:USTreasurySecuritiesMember
Money market funds
Fair Value of Financial Instruments
Cash equivalents	$ 79,391	$ 68,064
Recurring
Fair Value of Financial Instruments
Investments, available-for-sale	336,465	425,948
Total	415,856	494,012
Recurring | Money market funds
Fair Value of Financial Instruments
Cash equivalents	79,391	68,064
Recurring | Active Markets (Level 1)
Fair Value of Financial Instruments
Investments, available-for-sale	336,465	425,948
Total	415,856	494,012
Recurring | Active Markets (Level 1) | Money market funds
Fair Value of Financial Instruments
Cash equivalents	$ 79,391	$ 68,064

Restricted Cash (Details)

Restricted Cash (Details) - USD ($) $ in Millions	Mar. 31, 2019	Dec. 31, 2018
Restricted Cash
Restricted cash	$ 5.2	$ 5.4

Property and Equipment, Net - E

Property and Equipment, Net - Estimated Useful Lives (Details)	3 Months Ended
	Mar. 31, 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	Mar. 31, 2019	Dec. 31, 2018
Property and Equipment, Net
Gross property and equipment	$ 40,361	$ 38,282
Less: accumulated depreciation and amortization	(9,746)	(8,655)
Total	30,615	29,627
Lab equipment
Property and Equipment, Net
Gross property and equipment	6,742	6,232
Furniture and fixtures
Property and Equipment, Net
Gross property and equipment	2,455	2,369
Computer equipment
Property and Equipment, Net
Gross property and equipment	1,554	1,805
Leasehold improvements
Property and Equipment, Net
Gross property and equipment	26,660	26,640
Software
Property and Equipment, Net
Gross property and equipment	408	280
Construction-in-progress
Property and Equipment, Net
Gross property and equipment	$ 2,542	$ 956

Property and Equipment, Net - D

Property and Equipment, Net - Depreciation Expense (Details) - USD ($) $ in Millions	3 Months Ended	12 Months Ended
	Mar. 31, 2019	Dec. 31, 2018
Depreciation expense
Depreciation expense	$ 1.2	$ 0.8

Accrued Expenses (Details)

Accrued Expenses (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Jan. 01, 2019	Dec. 31, 2018
Accrued Expenses
External research and development	$ 36,641		$ 36,213
Employee compensation	4,545		8,071
Accrued professional fees	5,758		4,423
Property and equipment costs	1,338		912
Other	2,544		2,092
Total	$ 50,826	$ 51,586	$ 51,711

Collaborations (Details)

Collaborations (Details) $ in Thousands	Jun. 01, 2018USD ($)item	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Mar. 31, 2016USD ($)item	Mar. 31, 2019USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Dec. 31, 2018USD ($)
Collaborations
Collaboration revenue					$ 730		$ 954
Current portion of deferred revenue					4,238			$ 3,600
Roche
Collaborations
Collaboration revenue					$ 700
Revenue recognized, change in contract liability								$ 1,000
Roche | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-04-01
Collaborations
Research and development services, performance period					6 years
Collaboration | C Stone
Collaborations
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
Reduced from total operating expenses					$ 800
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						$ 40,000
Deferred revenue			$ 0		0		$ 0
Collaboration | C Stone | Development and regulatory milestones
Collaborations
Eligible milestone payments	118,500
Collaboration | C Stone | Sales-based milestones
Collaborations
Eligible milestone payments	$ 227,500
Collaboration | Roche
Collaborations
Non-refundable upfront payment received				$ 45,000
Number of option rights to obtain exclusive license | item				5
Number of potential collaboration programs | item				5
Initial cash payment			$ 45,000	$ 45,000
Deferred revenue					45,400
Reversal of cumulative milestone revenue not occur for developmental milestone		$ 10,000
Number of collaboration programs with agreed upon targets | item				2
Total eligible contingent option fees and milestone payments				$ 965,000
Eligible option fees and milestones prior to licensing for all potential collaboration programs				$ 215,000
Current portion of deferred revenue					$ 4,200
Achieved research milestone payment received which will be recognized over period of performance		$ 10,000
Collaboration | Roche | Prior To Exercise License Right Option
Collaborations
Written termination notice period				120 days
Collaboration | Roche | Exercise Of License Right Option
Collaborations
Number of collaboration programs with exclusive commercialization rights for licensed products | item				3
Number of collaboration programs with specified commercial rights for each party | item				2
Collaboration | Roche | Exercise Of License Option Product Not Commercially Sold
Collaborations
Written termination notice period				120 days
Collaboration | Roche | Exercise Of License Option Product Commercially Sold
Collaborations
Written termination notice period				180 days

Stock-based compensations - 201

Stock-based compensations - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares	Jan. 01, 2019	Mar. 31, 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		2,244,841

Stock-based compensations - Sto

Stock-based compensations - Stock Options - Activity (Details) - Stock Options	3 Months Ended
	Mar. 31, 2019$ / sharesshares
Shares
Outstanding at beginning of period (in shares) | shares	4,557,800
Granted (in shares) | shares	1,061,306
Exercised (in shares) | shares	(134,439)
Cancelled (in shares) | shares	(23,785)
Outstanding at end of period (in shares) | shares	5,460,882
Weighted-Average Exercise Price
Outstanding at beginning of period (in dollars per share) | $ / shares	$ 44.64
Granted (in dollars per share) | $ / shares	85.05
Exercised (in dollars per share) | $ / shares	15.34
Cancelled (in dollars per share) | $ / shares	63.18
Outstanding at end of period (in dollars per share) | $ / shares	$ 53.13
Additional disclosures
Shares - Exercisable (in shares) | shares	2,199,374
Weighted-Average Exercise Price - Exercisable (in dollars per share) | $ / shares	$ 27.46

Stock-based compensations - Unv

Stock-based compensations - Unvested Restricted Stock - Activity (Details) - Restricted stock units	3 Months Ended
	Mar. 31, 2019$ / sharesshares
Shares
Unvested at beginning of period (in shares) | shares	36,868
Granted (in shares) | shares	256,124
Forfeited (in shares) | shares	(1,000)
Unvested at end of period (in shares) | shares	291,992
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) | $ / shares	$ 66.28
Granted (in dollars per share) | $ / shares	85.40
Forfeited (in dollars per share) | $ / shares	86.60
Unvested at end of period (in dollars per share) | $ / shares	$ 82.98

Stock-based compensations - Unr

Stock-based compensations - Unrecognized Compensation Costs (Details) $ in Millions	Mar. 31, 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	3 years
Restricted stock units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 23.4
Weighted-average period over which unrecognized compensation cost will be recognized	3 years 10 months 24 days

Stock-based compensations - Emp

Stock-based compensations - Employee Stock Purchase Plan (Details) - Employee Stock - shares	1 Months Ended	3 Months Ended
	May 31, 2015	Mar. 31, 2019	Mar. 31, 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)		0	0

Stock-based compensations - S_2

Stock-based compensations - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Total stock based compensation expense
Total stock-based compensation expense	$ 10,295	$ 5,549
Research and development
Total stock based compensation expense
Total stock-based compensation expense	5,790	3,011
General and administrative
Total stock based compensation expense
Total stock-based compensation expense	4,505	2,538
Stock Options
Total stock based compensation expense
Total stock-based compensation expense	9,579	5,491
Restricted stock units
Total stock based compensation expense
Total stock-based compensation expense	624
Employee Stock
Total stock based compensation expense
Total stock-based compensation expense	$ 92	$ 58

Net Loss per Share - Anti-dilut

Net Loss per Share - Anti-dilutive Securities (Details) - shares	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	5,763,149	4,125,592
Stock Options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	5,460,882	4,119,870
Restricted stock units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	291,992
Employee Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	10,275	5,722

Net Loss per Share - Weighted A

Net Loss per Share - Weighted Average Number of Common Shares (Details) - shares	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Net Loss per Share
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic	44,096,806	43,700,226
Weighted-average number of common shares used in net loss per share applicable to common stockholders - diluted	44,096,806	43,700,226

Leases - General Information (D

Leases - General Information (Details) $ in Thousands	Sep. 19, 2018USD ($)ft²	Mar. 31, 2018USD ($)	Apr. 28, 2017USD ($)ft²	Feb. 12, 2015USD ($)ft²	Feb. 28, 2019USD ($)	Feb. 28, 2018USD ($)	Mar. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Sep. 18, 2018ft²
Leases
Initial lease commitments							$ 149,668
Total commitment in sublease							4,600	$ 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 included in restricted cash				$ 1,300			900
Security deposit released					$ 200	$ 200
Total commitment in sublease		$ 8,200					5,000
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 included in restricted cash							3,500
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 included in restricted cash							$ 800

Leases - Components of Lease Ex

Leases - Components of Lease Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Operating leases cost:
Lease cost	$ 3,564
Sublease income	(701)
Net lease cost	$ 2,863
Net rent expenses		$ 2,200

Leases - Cash Flow Information

Leases - Cash Flow Information (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2019USD ($)
Leases
Cash paid for amounts included in the measurement of lease liabilities, operating cash flows from operating leases	$ 2,621
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)	Mar. 31, 2019
Leases
Weighted Average Remaining Lease Term	10 years
Weighted Average Discount Rate	8.20%

Leases - Future Minimum Lease P

Leases - Future Minimum Lease Payments - ASC 842 (Details) $ in Thousands	Mar. 31, 2019USD ($)
Future minimum lease payments
2019 (excluding the 3 months ended March 31,2019)	$ 9,627
2020	14,341
2021	14,764
2022	14,719
2023	12,746
Thereafter	83,471
Total future minimum lease payments	$ 149,668

Leases - Total Lease Liability

Leases - Total Lease Liability (Details) $ in Thousands	Mar. 31, 2019USD ($)
Leases
Total future minimum lease payments	$ 149,668
Less imputed interest	(50,068)
Total	$ 99,600

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	Mar. 31, 2019	Dec. 31, 2018
Leases
Sublease rentals	$ 4.6	$ 5.3

Subsequent Events (Details)

Subsequent Events (Details) - Subsequent Event $ / shares in Units, $ in Millions	Apr. 02, 2019USD ($)$ / sharesshares
April 2019 follow-on public offering
Subsequent Events
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 | $	$ 327.2
Underwriters' Option
Subsequent Events
Stock sold (in shares)	608,108