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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2017	Jul. 31, 2017
Document and Entity Information [Abstract]
Entity Registrant Name	Blueprint Medicines Corp
Entity Central Index Key	0001597264
Document Type	10-Q
Document Period End Date	Jun. 30, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		39,122,349
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q2

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 91,346	$ 52,069
Investments, available-for-sale	329,668	162,090
Unbilled accounts receivable	3,075	3,577
Prepaid expenses and other current assets	7,239	2,689
Total current assets	431,328	220,425
Investments, available-for-sale		54,059
Property and equipment, net	7,774	6,188
Other assets	852	856
Restricted cash	4,767	1,267
Total assets	444,721	282,795
Current liabilities:
Accounts payable	2,581	2,211
Accrued expenses	17,396	11,746
Current portion of deferred revenue	9,296	11,426
Current portion of lease incentive obligation	1,714	578
Current portion of deferred rent	26
Current portion of term loan payable	1,979	2,551
Total current liabilities	32,992	28,512
Deferred rent, net of current portion	1,659	932
Deferred revenue, net of current portion	32,109	35,809
Lease incentive obligation, net of current portion	3,005	2,792
Term loan payable, net of current portion	692	1,518
Other long term liabilities	175	154
Commitments (Note 10)
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; 39,080,152 and 33,125,479 shares issued at June 30, 2017 and December 31, 2016, respectively, and 39,080,152 and 33,123,354 shares outstanding at June 30, 2017 and December 31, 2016, respectively	39	33
Additional paid-in capital	643,223	420,533
Accumulated other comprehensive loss	(314)	(18)
Accumulated deficit	(268,859)	(207,470)
Total stockholders' equity	374,089	213,078
Total liabilities and stockholders' equity	$ 444,721	$ 282,795

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2017	Dec. 31, 2016
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)	39,080,152	33,125,479
Common Stock, shares outstanding (in shares)	39,080,152	33,123,354

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Revenues
Collaboration revenue	$ 5,890	$ 7,065	$ 11,730	$ 13,921
Operating expenses:
Research and development	33,271	21,273	61,758	38,908
General and administrative	6,833	4,688	12,516	9,334
Total operating expenses	40,104	25,961	74,274	48,242
Other income (expense):
Other income (expense), net	861	131	1,286	192
Interest expense	(59)	(129)	(131)	(269)
Total other income (expense)	802	2	1,155	(77)
Net loss	(33,412)	(18,894)	(61,389)	(34,398)
Other comprehensive loss:
Unrealized (loss) gain on investments	(200)	24	(296)	55
Comprehensive loss	$ (33,612)	$ (18,870)	$ (61,685)	$ (34,343)
Reconciliation of net loss applicable to common stockholders:
Net loss per share applicable to common stockholders - basic and diluted	$ (0.86)	$ (0.70)	$ (1.71)	$ (1.27)
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted	38,775	27,170	35,998	27,129

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Operating activities
Net loss	$ (61,389)	$ (34,398)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	791	782
Noncash interest expense	19	42
Stock-based compensation	5,219	2,589
Accretion of premiums and discounts on investments	76	110
Changes in assets and liabilities:
Unbilled accounts receivable	502	63
Prepaid expenses and other current assets	(2,608)	1,943
Other assets	4	(17)
Accounts payable	297	427
Accrued expenses	3,953	2,202
Deferred revenue	(5,830)	39,412
Deferred rent	369	(237)
Net cash (used in) provided by operating activities	(58,597)	12,918
Investing activities
Purchases of property and equipment	(457)	(1,814)
Restricted cash	(3,500)	119
Purchases of investments	(209,892)	(69,222)
Maturities of investments	96,000	6,000
Net cash (used in) investing activities	(117,849)	(64,917)
Financing activities
Principal payments on loan payable	(1,417)	(1,667)
Payment of offering costs	(716)
Proceeds from public offering of common stock, net of commissions and underwriting discounts	216,200
Proceeds from issuance of common stock, net of repurchases	1,656	345
Net cash provided by (used in) financing activities	215,723	(1,322)
Net increase (decrease) in cash and cash equivalents	39,277	(53,321)
Cash and cash equivalents at beginning of period	52,069	162,707
Cash and cash equivalents at end of period	91,346	109,386
Supplemental cash flow information
Public offering costs incurred but unpaid at period end	306
Property and equipment purchases unpaid at period end	1,920	116
Cash paid for interest	$ 91	$ 180

Nature of Business	6 Months Ended
Nature of Business	Jun. 30, 2017
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 biopharmaceutical company focused on improving the lives of patients with genomically defined diseases driven by abnormal kinase activation. The Company’s approach is to systematically and reproducibly identify kinases that are drivers of diseases in genomically defined patient populations and to craft drug candidates that may provide significant and durable clinical response to 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 May 5, 2015, the Company completed an initial public offering (IPO) of its common stock, which resulted in the sale of 9,367,708 shares of its common stock at a price to the public of $18.00 per share, including 1,221,874 shares of common stock sold by the Company pursuant to the exercise in full by the underwriters of their option to purchase additional shares in connection with the offering. The Company received net proceeds of $154.8 million, after deducting underwriting discounts and commissions and offering expenses paid by the Company. On December 13, 2016, the Company closed a follow-on public offering of 5,750,000 shares of its common stock at a price to the public of $25.00 per share, including 750,000 shares of common stock sold by the Company pursuant to the exercise in full by the underwriters of their option to purchase additional shares in connection with the offering. The Company received net proceeds of $134.5 million, after deducting underwriting discounts and commissions and offering expenses payable by the Company. On April 4, 2017, the Company closed a follow-on public offering of 5,750,000 shares of its common stock at a price to the public of $40.00 per share, including 750,000 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 2017 follow-on public offering). The Company received net proceeds of $215.6 million, after deducting underwriting discounts and commissions and offering expenses payable by the Company. As of June 30, 2017, the Company had cash, cash equivalents and investments of $421.0 million. Based on the Company’s current plans, the Company believes its existing cash, cash equivalents and investments, excluding any potential option fees and milestone payments under its existing collaboration with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. (collectively, Roche), will be sufficient to enable the Company to fund its operating expenses and capital expenditure requirements into the second half of 2019.

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	6 Months Ended
	Jun. 30, 2017
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, 2016 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 9, 2017. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements and include the accounts of the Company and its wholly-owned subsidiary, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell, and hold securities. All intercompany transactions and balances have been eliminated. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments which are necessary to present fairly the Company’s financial position as of June 30, 2017 and the results of its operations for the three and six months ended June 30, 2017 and 2016 and cash flows for the six months ended June 30, 2017 and 2016. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2017 are not necessarily indicative of the results for the year ending December 31, 2017, or for any future period. On December 13, 2016 and April 4, 2017, the Company closed underwritten public offerings of 5,750,000 shares in each offering. The significant increase in shares outstanding is expected to impact the year-over-year comparability of the Company’s net loss per share calculations. 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: stock‑based compensation expense; revenue recognition; accrued expenses; and income taxes. Significant Accounting Policies The Company’s critical accounting policies are those policies that require the most significant judgments and estimates in the preparation of our financial statements. Management has determined that the Company’s most critical accounting policies are those relating to revenue recognition, accrued research and development expenses, available-for-sale investments and stock-based compensation. There have been no significant changes to the Company’s critical accounting policies discussed in its Annual Report on Form 10-K for the year ended December 31, 2016 related to available-for-sale investments, revenue recognition, accrued research and development expenses and stock-based compensation. Recent Accounting Pronouncements In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (ASU 2014-09), which supersedes the revenue recognition requirements in ASC 605-25, Multiple-Element Arrangements and most industry-specific guidance. The new standard requires that an entity recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the company expects to be entitled in exchange for those goods or services. The update also requires additional disclosure about the nature, amount, timing and uncertainty of revenue and cash flows arising from customer contracts, including significant judgments and changes in judgments and assets recognized from costs incurred to obtain or fulfill a contract. This new guidance will be effective for annual reporting periods (including interim reporting periods within those years) beginning January 1, 2018. Early adoption in 2017 is permitted. Companies have the option of applying this new guidance retrospectively to each prior reporting period presented (the full retrospective method) or retrospectively with the cumulative effect of initially applying this update recognized at the date of initial application (the modified retrospective method). The Company currently anticipates adoption of the new standard effective January 1, 2018 under the modified retrospective method. The Company believes there may be a potential impact in the way it recognizes revenue under its agreement with Roche as well as the recognition of milestone revenue prior to achievement. The Company is in the process of determining the impact of the new guidance on its financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (ASU No. 2016-09), which amends ASC Topic 718, Compensation – Stock Compensation. The new standard identifies areas for simplification involving several aspects of accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur, as well as certain classifications on the statement of cash flows. The new standard was effective for the Company on January 1, 2017. The Company applied ASU 2016-09 using a modified retrospective approach and adopted the option to recognize gross stock compensation expense with actual forfeitures recognized as they occur. Given that the application of the estimated forfeiture rate prior to January 1, 2017 resulted in an insignificant reduction in stock-based compensation expense, the cumulative-effect adjustment to retained earnings recognized as of January 1, 2017 was not material to the consolidated financial statements. The adoption of ASU 2016-09 also requires all income tax adjustments to be recognized in the consolidated statements of operations. As the increase in net deferred tax assets is fully offset by a corresponding increase to the deferred tax asset valuation allowance, there was no material impact of the adoption of this standard. The amount of deferred tax assets that had not been previously recognized due to the recognition of excess tax benefits is $1.1 million. In February 2016, the FASB issued ASU No. 2016-02, Leases (ASU No. 2016-02), which will change the way the Company recognizes its leased assets. ASU No. 2016-02 will require organizations that lease assets—referred to as “lessees”—to recognize on the balance sheet the assets and liabilities representing the rights and obligations created by those leases. ASU No. 2016-02 will also require disclosures to help investors and other financial statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2018. Early adoption is permitted. The Company is currently evaluating the methods of adoption allowed by the new standard and the effect that adoption of the standard is expected to have on the Company’s consolidated financial statements and related disclosures. In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows (Topic 230) (ASU No. 2016-15), which simplifies certain elements of cash flow classification. The new guidance is intended to reduce diversity in practice in how certain transactions are classified in the statement of cash flows. ASU No. 2016-15 is effective for annual periods beginning after December 15, 2017. The Company is currently evaluating the impact the adoption of ASU No. 2016-15 will have on its consolidated financial statements. In November 2016, the FASB issued ASU No. 2016-18, Restricted Cash (ASU No. 2016-18). The amendments in ASU No. 2016-18 require an entity to reconcile and explain the period-over-period change in total cash, cash equivalents and restricted cash within its statements of cash flows. ASU No. 2016-18 is effective for fiscal years (including interim reporting periods within those years) beginning after December 15, 2017. Early adoption is permitted. A reporting entity must apply the amendments in ASU No. 2016-18 using a full retrospective approach. The Company believes that the adoption of this guidance will not have a significant impact on its consolidated financial statements and related disclosures.

Cash Equivalents and Investments

6 Months Ended

Jun. 30, 2017

Disclosure Text Block

Cash Equivalents and Investments

3. Cash Equivalents and Investments

Cash equivalents are highly liquid investments that are readily convertible into cash with original maturities of three months or less when purchased. Investments consist of securities with original maturities greater than 90 days when purchased. The Company classifies these investments as available-for-sale and records them at fair value in the accompanying condensed consolidated balance sheets. Unrealized gains or losses are included in accumulated other comprehensive income (loss). Premiums or discounts from par value are amortized to investment income over the life of the underlying investment.

Cash equivalents and investments, available-for-sale, consisted of the following at June 30, 2017 and December 31, 2016 (in thousands):


	Average		Amortized		Unrealized		Unrealized		Fair
June 30, 2017	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	57,397	$	—	$	—	$	57,397
Government agency securities				33,949		—		—		33,949
Investments, available-for-sale:
U.S. treasury obligations		303 Days		317,988		—		(314)		317,674
Government agency securities		91 Days		11,994		—		—		11,994
Total			$	421,328	$	—	$	(314)	$	421,014


	Average		Amortized		Unrealized		Unrealized		Fair
December 31, 2016	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	52,069	$	—	$	—	$	52,069
Investments, available-for-sale:
U.S. treasury obligations		298 Days		216,167		14		(32)		216,149
Total			$	268,236	$	14	$	(32)	$	268,218

Although available to be sold to meet operating needs or otherwise, securities are generally held through maturity. The cost of securities sold is determined based on the specific identification method for purposes of recording realized gains and losses. During the three and six months ended June 30, 2017 and June 30, 2016, there were no realized gains or losses on sales of investments, and no investments were adjusted for other than temporary declines in fair value.

At June 30, 2017, the Company held 50 securities that were in an unrealized loss position. The aggregate fair value of securities held by the Company in an unrealized loss position for less than twelve months as of June 30, 2017 was $318.4 million, and there were no securities held by the Company in an unrealized loss position for more than twelve months. The Company has the intent and ability to hold such securities until recovery. The Company determined that there was no material change in the credit risk of the above investments. As a result, the Company determined it did not hold any investments with an other-than temporary impairment as of June 30, 2017.

Fair Value of Financial Instruments

6 Months Ended

Jun. 30, 2017

Disclosure Text Block

Fair Value of Financial Instruments

4. Fair Value of Financial Instruments

The fair value hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three broad levels as follows:

Level 1 inputs are quoted prices (unadjusted) in active markets for identical assets or liabilities.

Level 2 inputs are inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly.

Level 3 inputs are unobservable inputs that reflect the Company’s own assumptions about the assumptions market participants would use in pricing the asset or liability. Financial assets and liabilities are classified in their entirety based on the lowest level of input that is significant to the fair value measurement.

Financial instruments measured at fair value as of June 30, 2017 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2017		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	57,397	$	57,397	$	—	$	—
Government agency securities		33,949		33,949
Investments, available-for-sale:
U.S Treasury obligations		317,674		317,674		—		—
Government agency securities		11,994		11,994
Total	$	421,014	$	421,014	$	—	$	—

Financial instruments measured at fair value as of December 31, 2016 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2016		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	52,069	$	52,069	$	—	$	—
Investments, available-for-sale:
U.S Treasury obligations		216,149		216,149		—		—
Total	$	268,218	$	268,218	$	—	$	—

The fair value of the Company’s term loan payable is determined using current applicable rates for similar instruments as of the balance sheet date. The carrying value of the Company’s term loan payable approximates fair value because the Company’s interest rate yield approximates current market rates. The Company’s term loan payable is a Level 3 liability within the fair value hierarchy.

- Definition

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

+ References + Details

Restricted Cash	6 Months Ended
Restricted Cash	Jun. 30, 2017
Disclosure Text Block
Restricted Cash	5. Restricted Cash As of June 30, 2017 and December 31, 2016, $4.8 million and $1.3 million of restricted cash was included in long-term assets on the Company’s balance sheet, respectively. As of June 30, 2017, $1.3 million of the restricted cash is related to a security deposit for the lease agreement for the Company’s current corporate headquarters located at 38 Sidney Street in Cambridge, Massachusetts. On April 28, 2017, the Company entered into a lease agreement (the Lease Agreement) with UP 45/75 Sidney Street, LLC (Landlord) for approximately 99,833 rentable square feet of office and laboratory space located at 45 Sidney Street in Cambridge, Massachusetts which the Company gained control over on June 1, 2017. The initial term of the Lease Agreement will be for a 146 month period, which the Company currently anticipates will commence on October 1, 2017. The Lease Agreement requires the Company to maintain a security deposit with the Landlord in the amount of $3.5 million, which is included in restricted cash of June 30, 2017. The security deposit is subject to reduction by up to $1.0 million during the term of the Lease Agreement, subject to the satisfaction of specified terms and conditions.

Collaborations	6 Months Ended
Collaborations	Jun. 30, 2017
Disclosure Text Block
Collaborations	6. Collaborations 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 initiated activities for three of the collaboration programs in 2016, and the parties have agreed to work together to use the Company’s novel target discovery engine and proprietary compound library to select targets for up to two additional collaboration programs. 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. Subject to the terms of the Roche agreement, the Company received an upfront cash payment of $45.0 million and will be eligible to receive up to approximately $965.0 million in contingent option fees and milestone payments related to specified research, pre-clinical, clinical, regulatory and sales-based milestones. Of the total contingent payments, up to approximately $215.0 million are for option fees and milestone payments for research, pre-clinical and clinical development events prior to licensing across all five potential collaboration programs, including contingent milestone payments for initiation of each of the collaboration programs for which the parties will work together to select targets (pre-option exercise milestones). In 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 determined that there were five deliverables under the Roche agreement: (i) a non-transferable, sub-licensable and non-exclusive license to use the Company’s intellectual property and collaboration compounds to conduct research activities;(ii) conducting research and development activities through Phase 1 clinical trials under the research plan; (iii) providing pre-clinical and clinical supply of collaboration compounds; (iv) participation on a joint research committee (JRC) and joint development committee (JDC); and (v) regulatory responsibilities under Phase 1 clinical trials. The Company determined that the license did not have value to Roche on a stand-alone basis due to the specialized nature of the research activities to be provided by the Company that are not available in the marketplace and the fact that the license is to perform research and development only. Therefore, the license has limited value without the performance of the research and development activities and is not separable. The pre-clinical and clinical supply activities are integral to the performance of the research and development activities and can only be used for the performance of such activities, and the regulatory responsibilities are dependent on the research and development activities. The Company determined that the best estimate for the selling price of the JRC and JDC participation was inconsequential. Accordingly, the Company combined the license, pre-clinical and clinical supply, JRC and JDC participation and regulatory responsibilities deliverables with the research and development activities, the last item to be delivered in the arrangement, as one unit of accounting. The Company is recognizing the total allocable arrangement consideration consisting of the upfront payment of $45.0 million as revenue on a straight-line basis over the Company’s best estimate of the period it expects to perform research and development activities. The Company expects the services to be delivered ratably. The Company evaluated whether the option fees that may be received in connection with the Roche agreement are substantive. The Company concluded that the option fees were substantive due to the uncertainty around whether the goals of the collaboration will be achieved, and therefore the options are not a deliverable in the current arrangement. If Roche elects to exercise the options, the exercises and related contingent deliverables would be accounted for as a separate arrangement. The Company evaluated whether the milestones that may be received in connection with the Roche agreement are substantive milestones. Pre-option exercise milestones, of up to $215.0 million, that are expected to be achieved as a result of the Company’s efforts during the performance of the research and development activities are considered substantive and are recognized as revenue upon the achievement of the milestone, assuming all other revenue recognition criteria are met. The development event milestones are not considered substantive because the Company does not contribute effort to the achievement of such milestones as they are expected to be achieved after the performance of the research and development activities. Consideration received with respect to these milestones will be added to the total arrangement consideration that has been allocated to the identified units of accounting. As a result, that amount is recognized as revenue ratably over the period starting from the effective date of the agreement to the date that the Company will complete all of its obligations, with a cumulative catch-up from the effective date through the date of achievement of the milestone. If the consideration is received after the completion of all of the Company’s obligations, the amount will be recognized as revenue immediately. During both the three months ended June 30, 2017 and 2016, the Company recognized revenue under the Roche agreement of $1.4 million, which represents a portion of the $45.0 million upfront payment. During the six months ended June 30, 2017 and 2016, the Company recognized revenue under the Roche agreement of $2.8 million and $1.6 million, respectively, which represents a portion of the $45.0 million upfront payment. Alexion In March 2015, the Company entered into a research, development and commercialization agreement (Alexion agreement) with Alexion to research, develop and commercialize one or more drug candidates targeting the ALK2 kinase for the treatment of fibrodysplasia ossificans progressiva. On July 26, 2017, the Company received written notice from Alexion of its election to terminate for convenience the Alexion agreement. In accordance with the Alexion agreement, the termination will become effective on October 24, 2017, which is 90 days following the date of receipt of the notice by the Company. See Note 11 “Subsequent Event.” Under the terms of the Alexion agreement, the Company was responsible for research and pre‑clinical development activities related to any drug candidates, and Alexion was responsible for all clinical development, manufacturing and commercialization activities related to any drug candidates. In addition, Alexion was responsible for funding 100% of the Company’s research and development costs incurred under the research plan, including pass‑through costs and a negotiated yearly rate per full‑time equivalent for its employees’ time and their associated overhead expenses. The Company received a $15.0 million non‑refundable upfront payment in March 2015 upon execution of the Alexion agreement and was eligible to receive over $250.0 million in payments upon the successful achievement of pre‑specified pre‑clinical, clinical, regulatory and commercial milestones as follows: (i) up to $6.0 million in pre‑clinical milestone payments for the first licensed product, (ii) up to $83.0 million and $61.5 million in development milestone payments for the first and second licensed products, respectively, and (iii) up to $51.0 million in commercial milestone payments for each of the first and second licensed products. Prior to receipt by the Company of the notice of termination, the Company had received an aggregate amount of $3.8 million in pre-clinical milestone payments. The Company will not be entitled to receive payment for additional milestones, if any, achieved after the receipt of the notice of termination of the collaboration. Prior to termination, Alexion was required to pay the Company tiered royalties, ranging from mid‑single to low‑double digit percentages, on a country‑by‑country and licensed-product‑by‑licensed product basis, on worldwide net product sales of licensed products. Prior to termination, the royalty term for each licensed product in each country was the period commencing with first commercial sale of such licensed product in such country and ending on the later of (i) the expiration of the last‑to‑expire valid claim of specified patents covering such licensed product, (ii) the expiration of the applicable regulatory exclusivity period, and (iii) 10 or 15 years from specified commercial sales. There are no refund provisions in the Alexion agreement. The Company determined that there were three deliverables under the Alexion agreement: (i) an exclusive license to research, develop, manufacture and commercialize the licensed products and the compounds in the field in the territory, (ii) conducting research and development activities under the research plan and (iii) participation on a joint steering committee (JSC) and joint project team (JPT). The Company determined that the license did not have value to Alexion on a stand-alone basis due to the specialized nature of the research services to be provided by the Company that are not available in the marketplace. Therefore, the deliverables are not separable and, accordingly, the license, undelivered research and development activities and JSC and JPT participation are a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, the Company bases its revenue recognition model on the final deliverable. Under the Alexion agreement, the last deliverable that was anticipated to be completed was the Company’s research and development activities and participation on the JSC and JPT, which were expected to be delivered over the same performance period. The Company was utilizing a proportional performance model to recognize revenue under the Alexion agreement. As a result of the termination of the Alexion agreement, the Company anticipates recognizing the remaining deferred revenue balance related to the revenue recognized under the collaboration utilizing the proportional performance model over the remaining period of involvement. The Company evaluated whether the milestones that it was eligible to receive in connection with the Alexion agreement were substantive or non-substantive milestones. The Company concluded that the first pre-clinical milestone payment received from Alexion was non-substantive due to the certainty at the date the Alexion agreement was entered into that the milestone event would be achieved. In the second quarter of 2015, the Company achieved the first pre-clinical milestone under the Alexion agreement and received a $1.8 million payment from Alexion. The Company is recognizing revenues from the related milestone payment over the period of performance. As a result of the termination of the Alexion agreement, the Company anticipates recognizing the remaining deferred revenue balance related to the revenue recognized under the collaboration utilizing the proportional performance model over the remaining period of involvement. The remaining non-refundable pre-clinical milestones that the Company was eligible to achieve as a result of the Company’s efforts prior to the notice of termination by Alexion were considered substantive and would have been recognized as revenue upon the achievement of the milestone, assuming all other revenue recognition criteria were met. The Company has recognized and received an aggregate of $2.0 million in substantive milestones through June 30, 2017. Milestones that were expected to be achieved after the period of substantial involvement were not considered substantive because the Company would not contribute effort to the achievement of such milestones. These milestones would have been recognized as revenue upon achievement of the milestone, assuming all other revenue recognition criteria were met, as there would have been no undelivered elements remaining and no continuing performance obligations. During the three and six months ended June 30, 2017, the Company recognized revenue under the Alexion agreement of $4.5 million and $8.9 million, respectively, which represents $3.1 million and $5.9 million, respectively, of reimbursable research and development costs, as well as a portion of the $15.0 million upfront payment and the $1.75 million non-substantive milestone payment previously received. During the three and six months ended June 30, 2016, the Company recognized revenue under the Alexion agreement of $5.7 million and $12.3 million, respectively, which represents $3.4 million and $7.6 million, respectively, of reimbursable research and development costs, the $0.75 million milestone payment recognized in the six months ended June 30, 2016, which was recognized upon achievement, as well as the net portion of the $15.0 million upfront payment and the $1.75 million non-substantive milestone payment previously received. During the six months ended June 30, 2017, the Company received $6.4 million related to reimbursable research and development costs under the Alexion agreement. As of June 30, 2017, the Company has recorded unbilled accounts receivable of $3.1 million related to reimbursable research and development costs under the Alexion agreement for activities performed during the second quarter of 2017.

Term Loan	6 Months Ended
Term Loan	Jun. 30, 2017
Disclosure Text Block
Term Loan	7. Term Loan In May 2013, the Company entered into a loan and security agreement with Silicon Valley Bank (the 2013 Term Loan), which provided for up to $5.0 million in funding, to be made available in three tranches. Loan advances accrue interest at a fixed rate of 2% above the prime rate. In June 2013, the Company drew the first loan advance of $1.0 million under the 2013 Term Loan and was required to make interest‑only payments until April 1, 2014, and consecutive monthly payments of principal, plus accrued interest, over the remaining term through March 2017. In September 2013, the Company drew the second loan advance of $2.0 million under the 2013 Term Loan and was required to make interest‑only payments until April 1, 2014, and consecutive monthly payments of principal, plus accrued interest, over the remaining term through March 2017. In June 2014, the Company drew the remaining $2.0 million advance under the 2013 Term Loan and was required to make interest‑only payments until January 1, 2015, and consecutive monthly payments of principal, plus accrued interest, over the remaining term through December 2017. In November 2014, the Company amended the 2013 Term Loan to allow the Company to borrow an additional $5.0 million (the 2014 Term Loan). The Company accounted for the amendment as a modification to the existing 2013 Term Loan. The Company immediately drew the additional $5.0 million under the 2014 Term Loan and was required to make interest‑only payments until December 1, 2015, and consecutive monthly payments of principal, plus accrued interest, over the remaining term through November 2018. The Company is required to pay a fee of 4% of the total loan advances at the end of the term of each of the 2013 Term Loan and the 2014 Term Loan. The fee is being accreted to interest expense over the term of the 2013 Term Loan and the 2014 Term Loan. In the event of prepayment, the Company is obligated to pay 1% to 2% of the amount of the outstanding principal depending upon the timing of the prepayment. The 2013 Term Loan and 2014 Term Loan are collateralized by a blanket lien on all corporate assets, excluding intellectual property, and by a negative pledge of the Company’s intellectual property. The 2013 Term Loan and 2014 Term Loan contain customary default provisions that include material adverse events, as defined therein. The Company has determined that the risk of subjective acceleration under the material adverse events clause is remote and therefore has classified the outstanding principal in current and long‑term liabilities based on scheduled principal payments. The Company assessed all terms and features of the 2013 Term Loan and the 2014 Term Loan in order to identify any potential embedded features that would require bifurcation. As part of this analysis, the Company assessed the economic characteristics and risks of the term loan, including put and call features. The Company determined that all features of each of the 2013 Term Loan and the 2014 Term Loan are clearly and closely associated with a debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial to the Company’s financial statements. The Company will continue to reassess the features on a quarterly basis to determine if they require separate accounting. Future minimum payments, which include principal and interest due under each of the 2013 Term Loan and the 2014 Term Loan, are $1.2 million, in the aggregate, for the remainder of 2017 and $1.6 million, in the aggregate, in 2018. In connection with the 2013 Term Loan, the Company issued a warrant to Silicon Valley Bank to purchase 150,000 shares of Series A convertible preferred stock at an exercise price of $1.00 per share (the Series A Warrant). In connection with the 2014 Term Loan, the Company issued an additional warrant to Silicon Valley Bank to purchase 83,333 shares of Series B convertible preferred stock at an exercise price of $1.20 per share (the Series B Warrant). On May 13, 2015, Silicon Valley Bank exercised the Series A Warrant and the Series B Warrant pursuant to the cashless exercise feature of the warrants. In connection with the exercise of the Series A Warrant under the 2013 Term Loan, the Company issued 21,281 shares of common stock to Silicon Valley Bank. Warrants to purchase 5,991 shares of common stock were cancelled as payment for the aggregate exercise price of the Series A Warrant to Silicon Valley Bank. In connection with the exercise of the Series B Warrant under the 2014 Term Loan, the Company issued 11,157 shares of common stock. Warrants to purchase 3,994 shares of common stock were cancelled as payment for the aggregate exercise price of the Series B Warrant. The Company recorded a debt discount upon issuance of the warrants, which is being accreted as interest expense over the remaining term of the loan. The Company recorded interest expense related to the Series A Warrant and the Series B Warrant of less than $0.1 million in the three and six months ended June 30, 2017 and 2016, respectively.

Stock Awards

6 Months Ended

Jun. 30, 2017

Disclosure Text Block

Stock Awards

8. Stock Awards

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, 2017, the number of shares reserved for issuance under the 2015 Plan was increased by 1,325,019 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 June 30, 2017, there were 1,905,829 shares available for future grant under the 2015 Plan.

Awards

Options and restricted stock awards granted by the Company generally vest ratably over four years, with a one‑year cliff for new employee awards, and are exercisable from the date of grant for a period of ten years.

A summary of the Company’s unvested restricted stock and related information follows:


		Weighted-Average
		Grant Date
	Shares	Fair Value
Unvested at December 31, 2016	2,125	$	1.25
Vested	(2,125)		1.25
Repurchased	—		—
Unvested at June 30, 2017	—		—

The total fair value of restricted stock that vested during the three months ended June 30, 2017 and 2016 was less than $0.1 million and $0.7 million, respectively. The total fair value of restricted stock that vested during the six months ended June 30, 2017 and 2016 was $0.1 million and $1.4 million, respectively.

A summary of the Company’s stock option activity and related information follows:


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(1)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2016	2,622,741	$	11.67	8.30	$	44,025
Granted	992,572		37.55
Exercised	(196,970)		8.54
Canceled	(21,863)		17.36
Outstanding at June 30, 2017	3,396,480	$	19.38	8.45	$	106,292
Exercisable at June 30, 2017	1,183,056	$	9.73	7.73	$	48,431
Vested and expected to vest at June 30, 2017	3,396,480	$	19.38	8.45	$	106,292

(1)

Intrinsic value represents the amount by which the fair market value as of June 30, 2017 of the underlying common stock exceeds the exercise price of the option.

The fair value of stock options is estimated on the grant date using the Black‑Scholes option‑pricing model based on the following weighted average assumptions:


	Three Months Ended			Six Months Ended
	June 30, 2017		June 30, 2016	June 30, 2017		June 30, 2016
Risk-free interest rate	1.93	%	1.36	2.07	%	1.55	%
Expected dividend yield	—	%	—	—	%	—	%
Expected term (years)	5.9		5.7	6.0		6.0
Expected stock price volatility	74.64	%	75.38	75.23	%	76.52	%

The weighted‑average grant date fair value of options granted in the three months ended June 30, 2017 and 2016 was $27.78 and $12.22, respectively. The total intrinsic value of options exercised in the three months ended June 30, 2017 and 2016 was $2.7 million and $0.6 million, respectively. The weighted‑average grant date fair value of options granted in the six months ended June 30, 2017 and 2016 was $24.91 and $10.61 respectively. The total intrinsic value of options exercised in the six months ended June 30, 2017 and 2016 was $6.1 million and $1.0 million, respectively.

Total stock‑based compensation expense recognized for all stock‑based compensation awards in the condensed consolidated statements of operations and comprehensive loss is as follows (in thousands):


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
Research and development	$	1,498	$	757	$	2,622	$	1,283
General and administrative		1,481		730		2,597		1,306
Total stock-based compensation expense	$	2,979	$	1,487	$	5,219	$	2,589

At June 30, 2017, the Company had $35.0 million of total unrecognized compensation cost related to non-vested stock awards, which is expected to be recognized over a weighted‑average period of 2.65 years. Due to an operating loss, the Company does not record tax benefits associated with stock‑based compensation or option exercises. Tax benefit will be recorded when realized.

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, 2017, the number of shares reserved for issuance under the 2015 ESPP was increased by 331,254 shares. The Company issued 7,703 shares and 11,426 shares under the ESPP during the six months ended June 30, 2017 and 2016, respectively.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Net Loss per Share

6 Months Ended

Jun. 30, 2017

Disclosure Text Block

Net Loss per Share

9. Net Loss per Share

Basic net loss per share applicable to common stockholders is calculated by dividing net loss applicable to common stockholders by the weighted average shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share applicable to common stockholders 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 applicable to common stockholders calculation, stock options, and unvested restricted stock are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share applicable to common stockholders, as their effect would be anti‑dilutive; therefore, basic and diluted net loss per share applicable to common stockholders 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 applicable to common stockholders for the periods indicated because including them would have had an anti‑dilutive effect.


	Six Months Ended
	June 30,
	2017	2016
Stock options	3,396,480	2,462,926
Unvested restricted stock	—	49,575
Total	3,396,480	2,512,501

The weighted average number of common shares used in net loss per share applicable to common stockholders on a basic and diluted basis were 38,774,591 and 27,170,423 for the three months ended June 30, 2017 and 2016, respectively. The weighted average number of common shares used in net loss per share applicable to common stockholders on a basic and diluted basis were 35,997,572 and 27,129,171 for the six months ended June 30, 2017 and 2016, respectively

Commitments	6 Months Ended
Commitments	Jun. 30, 2017
Disclosure Text Block
Commitments	10. Commitments On February 12, 2015, the Company entered into a lease for approximately 38,500 rentable square feet of office and laboratory space in Cambridge, Massachusetts, which the Company gained control over on June 15, 2015, and occupancy commenced in October 2015. The lease ends on October 31, 2022. 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 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 Company is recording rent expense on a straight-line basis through the end of the lease term. The Company has recorded deferred rent on the condensed consolidated balance sheet at June 30, 2017, accordingly. The lease provides the Company with an allowance for leasehold improvements of $4.3 million. The Company accounts for leasehold improvement incentives as a reduction to rent expense ratably over the lease term. The balance from the leasehold improvement incentives is included in lease incentive obligations on the balance sheets. The lease agreement required the Company to pay a security deposit of $1.3 million, which is recorded in restricted cash on the Company’s balance sheet. 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, which the Company gained control over on June 1, 2017. The initial term of the lease agreement will be for a 146 month period, which the Company currently anticipates will commence on October 1, 2017. The lease agreement also provides the Company with an option to extend the lease for two consecutive five-year periods. 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 rises periodically until it reaches approximately $10.6 million. The Company is recording rent expense on a straight-line basis through the end of the lease term. The Company has recorded deferred rent on the condensed and consolidated balance sheet at June 30, 2017 accordingly. The landlord has also agreed to provide the Company with a tenant improvement allowance of approximately $14.2 million for improvements to be made to the premises. The Company accounts for leasehold improvement incentives as a reduction to rent expense ratably over the lease term. The balance from the leasehold improvement incentives of $1.6 million is included in the lease incentive obligation on the balance sheet as of June 30, 2017. The lease agreements required the Company to pay a security deposit of $3.5 million, which is recorded in restricted cash on the Company’s balance sheet. For the three months ended June 30, 2017 and 2016, rent expense was $1.1 million and $0.5 million, respectively. For the six months ended June 30, 2017 and 2016, rent expense was $1.6 million and $0.9 million, respectively.

Subsequent Event	6 Months Ended
Subsequent Event	Jun. 30, 2017
Disclosure Text Block
Subsequent Event	11. Subsequent Event On July 26, 2017, the Company received written notice from Alexion of its election to terminate for convenience the Alexion agreement. In accordance with the Alexion agreement, the termination will become effective on October 24, 2017, which is 90 days following the date of receipt of the notice by the Company. Under the terms of the Alexion agreement, the Company and Alexion agreed to collaborate to research, develop and commercialize one or more drug candidates targeting the ALK2 kinase for the treatment of fibrodysplasia ossificans progressiva (“FOP”). FOP is a rare genetic disease caused by mutations in the ALK2 gene, ACVR1. Pursuant to the Alexion agreement, the Company was responsible for research and preclinical development activities related to any drug candidates, and Alexion was responsible for all clinical development, manufacturing and commercialization activities related to any drug candidates. In addition, Alexion was responsible for funding 100% of the Company’s research and development costs incurred under the research plan, including pass-through costs and a negotiated yearly rate per full-time equivalent for the Company’s employees’ time and their associated overhead expenses. Effective upon the termination, the Company’s exclusivity obligations under the Alexion agreement will terminate, including without limitation, the Company’s exclusivity obligations with respect to (i) the treatment of FOP, heterotopic ossification or diffuse intrinsic pontine glioma, (ii) ALK2, including both wild type and mutated forms, and (iii) certain molecules related to the foregoing. In addition, the research term and all licenses granted to Alexion will terminate, and certain licenses granted by Alexion to the Company will survive and become perpetual, irrevocable and non-terminable. Alexion will remain responsible for the Company’s non-FTE expenses that were incurred or irrevocably committed up to the date of receipt of the notice of termination by the Company, provided that the Company is obligated to use diligent efforts to mitigate such costs to the extent practicable, and for the Company’s FTE expenses for the three month period following the date of receipt of the notice of termination by the Company for personnel that, despite having used diligent efforts, the Company is not able to reallocate from research plan activities to alternative projects. Prior to receipt by the Company of the notice of termination, the Company had received an aggregate amount of $18.8 million in upfront and milestone payments. The Company will not be entitled to receive payment for milestones, if any, achieved after the receipt of the notice of termination of the collaboration. The Company plans to evaluate opportunities to advance the research program that was the subject of the collaboration with Alexion. Under the terms of the Alexion agreement, the Company has the option to elect to negotiate a transition agreement with Alexion, which under the terms of the Alexion agreement, may cover, among other things, the reversion to the Company of all rights to any compounds that were the subject of the collaboration, the payment by the Company of any fees associated with such reversion, the grant by Alexion of licenses to certain patents, know-how and marks controlled by Alexion and the allocation between the parties of certain wind-down and transfer costs and expenses. As a result of the termination of the Alexion agreement, the Company anticipates recognizing the remaining deferred revenue balance of $3.7 million related to the upfront payment and non-substantive milestone payment previously received under the Alexion collaboration for which revenue was recognized utilizing the proportional performance model over the remaining period of involvement.

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	6 Months Ended
	Jun. 30, 2017
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, 2016 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 9, 2017. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements and include the accounts of the Company and its wholly-owned subsidiary, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell, and hold securities. All intercompany transactions and balances have been eliminated. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments which are necessary to present fairly the Company’s financial position as of June 30, 2017 and the results of its operations for the three and six months ended June 30, 2017 and 2016 and cash flows for the six months ended June 30, 2017 and 2016. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2017 are not necessarily indicative of the results for the year ending December 31, 2017, or for any future period. On December 13, 2016 and April 4, 2017, the Company closed underwritten public offerings of 5,750,000 shares in each offering. The significant increase in shares outstanding is expected to impact the year-over-year comparability of the Company’s net loss per share calculations.
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: stock‑based compensation expense; revenue recognition; accrued expenses; and income taxes.
Significant Accounting Policies	Significant Accounting Policies The Company’s critical accounting policies are those policies that require the most significant judgments and estimates in the preparation of our financial statements. Management has determined that the Company’s most critical accounting policies are those relating to revenue recognition, accrued research and development expenses, available-for-sale investments and stock-based compensation. There have been no significant changes to the Company’s critical accounting policies discussed in its Annual Report on Form 10-K for the year ended December 31, 2016 related to available-for-sale investments, revenue recognition, accrued research and development expenses and stock-based compensation.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (ASU 2014-09), which supersedes the revenue recognition requirements in ASC 605-25, Multiple-Element Arrangements and most industry-specific guidance. The new standard requires that an entity recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the company expects to be entitled in exchange for those goods or services. The update also requires additional disclosure about the nature, amount, timing and uncertainty of revenue and cash flows arising from customer contracts, including significant judgments and changes in judgments and assets recognized from costs incurred to obtain or fulfill a contract. This new guidance will be effective for annual reporting periods (including interim reporting periods within those years) beginning January 1, 2018. Early adoption in 2017 is permitted. Companies have the option of applying this new guidance retrospectively to each prior reporting period presented (the full retrospective method) or retrospectively with the cumulative effect of initially applying this update recognized at the date of initial application (the modified retrospective method). The Company currently anticipates adoption of the new standard effective January 1, 2018 under the modified retrospective method. The Company believes there may be a potential impact in the way it recognizes revenue under its agreement with Roche as well as the recognition of milestone revenue prior to achievement. The Company is in the process of determining the impact of the new guidance on its financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (ASU No. 2016-09), which amends ASC Topic 718, Compensation – Stock Compensation. The new standard identifies areas for simplification involving several aspects of accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur, as well as certain classifications on the statement of cash flows. The new standard was effective for the Company on January 1, 2017. The Company applied ASU 2016-09 using a modified retrospective approach and adopted the option to recognize gross stock compensation expense with actual forfeitures recognized as they occur. Given that the application of the estimated forfeiture rate prior to January 1, 2017 resulted in an insignificant reduction in stock-based compensation expense, the cumulative-effect adjustment to retained earnings recognized as of January 1, 2017 was not material to the consolidated financial statements. The adoption of ASU 2016-09 also requires all income tax adjustments to be recognized in the consolidated statements of operations. As the increase in net deferred tax assets is fully offset by a corresponding increase to the deferred tax asset valuation allowance, there was no material impact of the adoption of this standard. The amount of deferred tax assets that had not been previously recognized due to the recognition of excess tax benefits is $1.1 million. In February 2016, the FASB issued ASU No. 2016-02, Leases (ASU No. 2016-02), which will change the way the Company recognizes its leased assets. ASU No. 2016-02 will require organizations that lease assets—referred to as “lessees”—to recognize on the balance sheet the assets and liabilities representing the rights and obligations created by those leases. ASU No. 2016-02 will also require disclosures to help investors and other financial statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2018. Early adoption is permitted. The Company is currently evaluating the methods of adoption allowed by the new standard and the effect that adoption of the standard is expected to have on the Company’s consolidated financial statements and related disclosures. In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows (Topic 230) (ASU No. 2016-15), which simplifies certain elements of cash flow classification. The new guidance is intended to reduce diversity in practice in how certain transactions are classified in the statement of cash flows. ASU No. 2016-15 is effective for annual periods beginning after December 15, 2017. The Company is currently evaluating the impact the adoption of ASU No. 2016-15 will have on its consolidated financial statements. In November 2016, the FASB issued ASU No. 2016-18, Restricted Cash (ASU No. 2016-18). The amendments in ASU No. 2016-18 require an entity to reconcile and explain the period-over-period change in total cash, cash equivalents and restricted cash within its statements of cash flows. ASU No. 2016-18 is effective for fiscal years (including interim reporting periods within those years) beginning after December 15, 2017. Early adoption is permitted. A reporting entity must apply the amendments in ASU No. 2016-18 using a full retrospective approach. The Company believes that the adoption of this guidance will not have a significant impact on its consolidated financial statements and related disclosures.

Cash Equivalents and Investments (Tables)

6 Months Ended

Jun. 30, 2017

Table Text Blocks

Schedule of cash equivalents and investments, available-for-sale

Cash equivalents and investments, available-for-sale, consisted of the following at June 30, 2017 and December 31, 2016 (in thousands):


	Average		Amortized		Unrealized		Unrealized		Fair
June 30, 2017	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	57,397	$	—	$	—	$	57,397
Government agency securities				33,949		—		—		33,949
Investments, available-for-sale:
U.S. treasury obligations		303 Days		317,988		—		(314)		317,674
Government agency securities		91 Days		11,994		—		—		11,994
Total			$	421,328	$	—	$	(314)	$	421,014


	Average		Amortized		Unrealized		Unrealized		Fair
December 31, 2016	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	52,069	$	—	$	—	$	52,069
Investments, available-for-sale:
U.S. treasury obligations		298 Days		216,167		14		(32)		216,149
Total			$	268,236	$	14	$	(32)	$	268,218

Fair Value of Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2017

Table Text Blocks

Schedule of financial instruments measured at fair value

Financial instruments measured at fair value as of June 30, 2017 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2017		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	57,397	$	57,397	$	—	$	—
Government agency securities		33,949		33,949
Investments, available-for-sale:
U.S Treasury obligations		317,674		317,674		—		—
Government agency securities		11,994		11,994
Total	$	421,014	$	421,014	$	—	$	—

Financial instruments measured at fair value as of December 31, 2016 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2016		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	52,069	$	52,069	$	—	$	—
Investments, available-for-sale:
U.S Treasury obligations		216,149		216,149		—		—
Total	$	268,218	$	268,218	$	—	$	—

- Definition

Tabular disclosure of financial instruments measured at fair value, including those classified in shareholders' equity measured on a recurring or nonrecurring basis. Disclosures include, but are not limited to, fair value measurements recorded and the reasons for the measurements, level within the fair value hierarchy in which the fair value measurements are categorized and transfers between levels 1 and 2. Nonrecurring fair value measurements are those that are required or permitted in the statement of financial position in particular circumstances.

+ References + Details

Stock Awards (Tables)

6 Months Ended

Jun. 30, 2017

Table Text Blocks

Summary of unvested restricted stock


		Weighted-Average
		Grant Date
	Shares	Fair Value
Unvested at December 31, 2016	2,125	$	1.25
Vested	(2,125)		1.25
Repurchased	—		—
Unvested at June 30, 2017	—		—

Summary of stock option activity


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(1)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2016	2,622,741	$	11.67	8.30	$	44,025
Granted	992,572		37.55
Exercised	(196,970)		8.54
Canceled	(21,863)		17.36
Outstanding at June 30, 2017	3,396,480	$	19.38	8.45	$	106,292
Exercisable at June 30, 2017	1,183,056	$	9.73	7.73	$	48,431
Vested and expected to vest at June 30, 2017	3,396,480	$	19.38	8.45	$	106,292

(1)

Intrinsic value represents the amount by which the fair market value as of June 30, 2017 of the underlying common stock exceeds the exercise price of the option.

Assumptions used in estimating fair value of stock options on grant date


	Three Months Ended			Six Months Ended
	June 30, 2017		June 30, 2016	June 30, 2017		June 30, 2016
Risk-free interest rate	1.93	%	1.36	2.07	%	1.55	%
Expected dividend yield	—	%	—	—	%	—	%
Expected term (years)	5.9		5.7	6.0		6.0
Expected stock price volatility	74.64	%	75.38	75.23	%	76.52	%

Summary of stock-based compensation expense recognized in statements of operations


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
Research and development	$	1,498	$	757	$	2,622	$	1,283
General and administrative		1,481		730		2,597		1,306
Total stock-based compensation expense	$	2,979	$	1,487	$	5,219	$	2,589

Net Loss per Share (Tables)

6 Months Ended

Jun. 30, 2017

Table Text Blocks

Schedule of common stock equivalents excluded from calculation of diluted net loss per share applicable to common stockholders


	Six Months Ended
	June 30,
	2017	2016
Stock options	3,396,480	2,462,926
Unvested restricted stock	—	49,575
Total	3,396,480	2,512,501

Nature of Business (Details) - USD ($) $ / shares in Units, $ in Thousands				6 Months Ended
	Apr. 04, 2017	Dec. 13, 2016	May 05, 2015	Jun. 30, 2017	Jun. 30, 2016
Nature of Business
Proceeds from issuance of IPO shares				$ 216,200
Proceeds from issuance of common stock				1,656	$ 345
Cash, cash equivalents and investments				$ 421,000
IPO \| Common Stock
Nature of Business
Stock sold (in shares)			9,367,708
Share price (in dollars per share)			$ 18.00
Proceeds from issuance of IPO shares			$ 154,800
Follow-on Offering
Nature of Business
Proceeds from issuance of common stock		$ 134,500
Follow-on Offering \| Common Stock
Nature of Business
Stock sold (in shares)	5,750,000	5,750,000
Share price (in dollars per share)	$ 40.00	$ 25.00
Proceeds from issuance of common stock	$ 215,600
Underwriters' Option \| Common Stock
Nature of Business
Stock sold (in shares)	750,000	750,000	1,221,874

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Basis of Presentation (Details) - shares	Apr. 04, 2017	Dec. 13, 2016
Follow-on Offering \| Common Stock
Basis of Presentation
Stock sold (in shares)	5,750,000	5,750,000

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Recent Accounting Pronouncements (Details) $ in Millions	Jun. 30, 2017 USD ($)
Accounting Standards Update 2016-09
Recent Accounting Pronouncements
Deferred tax assets	$ 1.1

Cash Equivalents and Investments - Tabular Disclosure - Total (Details) - USD ($) $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2017	Dec. 31, 2016
Cash Equivalents and Investments
Total, Amortized Cost	$ 421,328	$ 268,236
Total, Unrealized Gain		14
Total, Unrealized Losses	(314)	(32)
Total, Fair Value	$ 421,014	$ 268,218
US Treasury obligations
Cash Equivalents and Investments
Average Maturity	303 days	298 days
Available-for-sale, Amortized Cost	$ 317,988	$ 216,167
Available-for-sale, Unrealized Gain		14
Available-for-sale, Unrealized Losses	(314)	(32)
Available-for-sale, Fair Value	$ 317,674	216,149
Government agency securities
Cash Equivalents and Investments
Average Maturity	91 days
Available-for-sale, Amortized Cost	$ 11,994
Available-for-sale, Fair Value	11,994
Money market fund
Cash Equivalents and Investments
Cash equivalents, Amortized Cost	57,397	52,069
Cash equivalents, Fair Value	57,397	$ 52,069
Government agency securities
Cash Equivalents and Investments
Cash equivalents, Amortized Cost	33,949
Cash equivalents, Fair Value	$ 33,949

Cash Equivalents and Investments - Additional Information (Details) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017 USD ($) security	Jun. 30, 2016 USD ($)	Jun. 30, 2017 USD ($) security	Jun. 30, 2016 USD ($)
Unrealized loss position
Unrealized loss position for less than 12 months			$ 318,400
Unrealized loss position for more than 12 months			$ 0
Number of held securities in an unrealized loss position \| security	50		50
Realized gain (loss) on sales of investments
Realized gain (loss) on sales of investments	$ 0	$ 0	$ 0	$ 0
Adjustment for other than temporary fair value decline
Adjustment for other than temporary fair value decline	$ 0	$ 0	$ 0	$ 0

Fair Value of Financial Instruments (Details) - Recurring - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Fair Value of Financial Instruments
Total	$ 421,014	$ 268,218
Money market fund
Fair Value of Financial Instruments
Cash equivalents, Fair Value	57,397	52,069
Government agency securities
Fair Value of Financial Instruments
Cash equivalents, Fair Value	33,949
US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	317,674	216,149
Government agency securities
Fair Value of Financial Instruments
Investments, available-for-sale	11,994
Active Markets (Level 1)
Fair Value of Financial Instruments
Total	421,014	268,218
Active Markets (Level 1) \| Money market fund
Fair Value of Financial Instruments
Cash equivalents, Fair Value	57,397	52,069
Active Markets (Level 1) \| Government agency securities
Fair Value of Financial Instruments
Cash equivalents, Fair Value	33,949
Active Markets (Level 1) \| US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	317,674	$ 216,149
Active Markets (Level 1) \| Government agency securities
Fair Value of Financial Instruments
Investments, available-for-sale	$ 11,994

Restricted Cash (Details) $ in Thousands	Apr. 28, 2017 USD ($) ft²	Feb. 12, 2015 USD ($) ft²	Jun. 30, 2017 USD ($)	Dec. 31, 2016 USD ($)
Restricted Cash
Restricted cash included in long-term assets			$ 4,767	$ 1,267
Corporate Headquarters Lease
Restricted Cash
Restricted cash included in long-term assets			4,800	$ 1,300
Area leased (in square feet) \| ft²	99,833	38,500
Lease term	146 months	7 years
Security deposit included in restricted cash	$ 3,500	$ 1,300
Reduction in security deposit	$ 1,000
Restricted by bank \| Corporate Headquarters Lease
Restricted Cash
Restricted cash included in long-term assets			$ 1,300

Collaborations (Details) $ in Thousands		1 Months Ended		3 Months Ended				6 Months Ended
Collaborations (Details) $ in Thousands	Jul. 26, 2017 USD ($)	Mar. 31, 2016 USD ($) item	Mar. 31, 2015 USD ($) item	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Jun. 30, 2015 USD ($)	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Dec. 31, 2016 USD ($)
Collaborations
Collaboration revenue				$ 5,890	$ 7,065			$ 11,730	$ 13,921
Unbilled accounts receivable for reimbursable research and development costs				3,075				3,075		$ 3,577
Roche Agreement
Collaborations
Non-refundable upfront payment received		$ 45,000		45,000	45,000			45,000	45,000
Number of deliverables \| item		5
Collaboration revenue				1,400	1,400			2,800	1,600
Number of collaboration programs with agreed upon targets \| item		3
Roche Agreement \| Maximum
Collaborations
Number of potential collaboration programs \| item		5
Number of collaboration programs to select targets \| item		2
Total eligible contingent option fees and milestone payments		$ 965,000				$ 965,000
Eligible option fees and milestones prior to licensing for all potential collaboration programs		$ 215,000
Roche Agreement \| Exercise Of License Right Option \| Maximum
Collaborations
Number of collaboration programs with specified commercial rights for each party \| item		2
Roche Agreement \| Roche
Collaborations
Number of option rights to obtain exclusive license \| item		5
Roche Agreement \| Roche \| Prior To Exercise License Right Option
Collaborations
Written termination notice period		120 days
Roche Agreement \| Roche \| Exercise Of License Right Option \| Maximum
Collaborations
Number of collaboration programs with exclusive commercialization rights for licensed products \| item		3
Roche Agreement \| Roche \| Exercise Of License Option Product Not Commercially Sold
Collaborations
Written termination notice period		120 days
Roche Agreement \| Roche \| Exercise Of License Option Product Commercially Sold
Collaborations
Written termination notice period		180 days
Alexion
Collaborations
Collaborative partner's funding responsibility of research and development costs incurred under the research plan (as a percent)			100.00%
Non-refundable upfront payment received			$ 15,000	15,000	15,000			15,000	15,000
Payment receivable upon achievement of milestone			$ 250,000
Royalty term from first commercial sale, option 1			10 years
Royalty term from first commercial sale, option 2			15 years
Number of deliverables \| item			3
Non-substantive milestone payment previously				1,750	1,750			1,750	1,750
Collaboration revenue				4,500	5,700			8,900	12,300
Reimbursable research and development costs recognized				3,100	$ 3,400			5,900	$ 7,600
Reimbursable research and development costs received								6,400
Unbilled accounts receivable for reimbursable research and development costs				$ 3,100				3,100
Alexion \| Subsequent Event
Collaborations
Collaborative partner's funding responsibility of research and development costs incurred under the research plan (as a percent)	100.00%
Written termination notice period	90 days
Revenue recognized from milestone	$ 18,800
Alexion \| Pre-clinical milestone for first licensed product
Collaborations
Achieved milestone payment received which will be recognized over period of performance							$ 1,800
Achieved milestone payment received which will be recognized upon achievement						$ 750
Revenue recognized from milestone			$ 3,800					$ 2,000
Alexion \| Pre-clinical milestone for first licensed product \| Maximum
Collaborations
Payment receivable upon achievement of milestone			6,000
Alexion \| Development milestone for first licensed product \| Maximum
Collaborations
Payment receivable upon achievement of milestone			83,000
Alexion \| Development milestone for second licensed product \| Maximum
Collaborations
Payment receivable upon achievement of milestone			61,500
Alexion \| Commercial milestone
Collaborations
Payment receivable upon achievement of milestone			$ 51,000

Term Loan - General Information (Details) - Secured Debt $ in Millions	1 Months Ended					6 Months Ended
	Nov. 30, 2014 USD ($)	Jun. 30, 2014 USD ($)	Sep. 30, 2013 USD ($)	Jun. 30, 2013 USD ($)	May 31, 2013 USD ($) item	Jun. 30, 2017
Term Loan
Percentage fee payable on total loan advances at end of loan (as a percent)						4.00%
Percentage fee payable on outstanding principal in event of prepayment of loan advances, low end of range (as a percent)						1.00%
Percentage fee payable on outstanding principal in event of prepayment of loan advances, high end of range (as a percent)						2.00%
2013 Term Loan
Term Loan
Maximum borrowing capacity					$ 5.0
Number of tranches \| item					3
Proceeds from term loan		$ 2.0	$ 2.0	$ 1.0
2013 Term Loan \| Prime Rate
Term Loan
Fixed rate based on percentage points added to base rate (as a percent)					2.00%
2014 Term Loan
Term Loan
Maximum borrowing capacity	$ 5.0
Proceeds from term loan	$ 5.0

Term Loan - Future Minimum Payments (Details) $ in Millions	Jun. 30, 2017 USD ($)
Future minimum payments
Future minimum payments for remainder of year	$ 1.2
Thereafter	$ 1.6

Term Loan - Warrants (Details) - USD ($) $ / shares in Units, $ in Millions		3 Months Ended		6 Months Ended
	May 13, 2015	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Nov. 30, 2014	May 31, 2013
Series A and Series B Warrants \| Maximum
Warrants
Interest expense		$ 0.1	$ 0.1	$ 0.1	$ 0.1
2013 Term Loan \| Series A Warrants
Warrants
Number of shares that can be purchased by the warrants issued							150,000
Exercise price of warrants issued (in dollars per share)							$ 1.00
Number of warrants cancelled	5,991
Stock issued upon exercise of warrants	21,281
2014 Term Loan \| Series B Warrants
Warrants
Number of shares that can be purchased by the warrants issued						83,333
Exercise price of warrants issued (in dollars per share)						$ 1.20
Number of warrants cancelled	3,994
Stock issued upon exercise of warrants	11,157

Stock Awards - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares		12 Months Ended
	Jan. 01, 2017	Dec. 31, 2016	Jun. 30, 2017
Stock Awards
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	1,325,019
Number of shares available for grant			1,905,829

Stock Awards - Awards - General Information (Details)	6 Months Ended
Stock Awards - Awards - General Information (Details)	Jun. 30, 2017
Employee Stock Options
Stock Awards
Award vesting period	4 years
Cliff vesting period for new employees	1 year
Award expiration period	10 years
Restricted Stock
Stock Awards
Award vesting period	4 years
Cliff vesting period for new employees	1 year
Award expiration period	10 years

Stock Awards - Summary of Unvested Restricted Stock Activity (Details) - Restricted Stock - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Shares
Unvested at beginning of period (in shares)			2,125
Vested (in shares)			(2,125)
Unvested at end of period (in shares)	0		0
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share)			$ 1.25
Vested (in dollars per share)			1.25
Unvested at end of period (in dollars per share)	$ 0.00		$ 0.00
Total fair value of restricted stock that vested	$ 0.1	$ 0.7	$ 0.1	$ 1.4

Stock Awards - Summary of Stock Option Activity (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2017	Dec. 31, 2016
Shares
Outstanding at beginning of period (in shares)	2,622,741
Granted (in shares)	992,572
Exercised (in shares)	(196,970)
Canceled (in shares)	(21,863)
Outstanding at end of period (in shares)	3,396,480	2,622,741
Weighted-Average Exercise Price
Outstanding at beginning of period (in dollars per share)	$ 11.67
Granted (in dollars per share)	37.55
Exercised (in dollars per share)	8.54
Canceled (in dollars per share)	17.36
Outstanding at end of period (in dollars per share)	$ 19.38	$ 11.67
Additional disclosures
Shares - Exercisable (in shares)	1,183,056
Shares - Vested and expected to vest (in shares)	3,396,480
Weighted-Average Exercise Price - Exercisable (in dollars per share)	$ 9.73
Weighted-Average Exercise Price - Vested and expected to vest (in dollars per share)	$ 19.38
Remaining Contractual Life - Outstanding	8 years 5 months 12 days	8 years 3 months 18 days
Remaining Contractual Life - Exercisable	7 years 8 months 23 days
Remaining Contractual Life - Vested and expected to vest	8 years 5 months 12 days
Aggregate Intrinsic Value - Outstanding	$ 106,292	$ 44,025
Aggregate Intrinsic Value - Exercisable	48,431
Aggregate Intrinsic Value - Vested and expected to vest	$ 106,292

Stock Awards - Weighted Average Assumptions (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Assumptions used in estimating the fair value of stock options granted
Risk-free interest rate	1.93%	1.36%	2.07%	1.55%
Expected term (in years)	5 years 10 months 24 days	5 years 8 months 12 days	6 years	6 years
Expected stock price volatility	74.64%	75.38%	75.23%	76.52%
Additional disclosures
Weighted-average grant date fair value of options granted	$ 27.78	$ 12.22	$ 24.91	$ 10.61
Total intrinsic value of options exercised	$ 2.7	$ 0.6	$ 6.1	$ 1.0

Stock Awards - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Total stock based compensation expense
Total stock-based compensation expense	$ 2,979	$ 1,487	$ 5,219	$ 2,589
Research and development
Total stock based compensation expense
Total stock-based compensation expense	1,498	757	2,622	1,283
General and administrative
Total stock based compensation expense
Total stock-based compensation expense	$ 1,481	$ 730	$ 2,597	$ 1,306

Stock Awards - Unrecognized Compensation Costs (Details) - Restricted Stock $ in Millions	6 Months Ended
	Jun. 30, 2017 USD ($)
Stock Awards
Total unrecognized compensation cost related to non-vested stock awards	$ 35.0
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 7 months 24 days

Stock Awards - Employee Stock Purchase Plan (Details) - Employee Stock - 2015 Employee Stock Purchase Plan - shares	1 Months Ended	6 Months Ended
	May 31, 2015	Jun. 30, 2017	Jun. 30, 2016	Jan. 01, 2017
Stock Awards
Number of common shares reserved for future issuance	243,347
Annual increase for common stock for issuance (as a percent)	1.00%
Increase of common shares reserved for future issuance				331,254
ESPP shares issued during period		7,703	11,426

Net Loss per Share - Anti-dilutive Securities (Details) - shares	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	3,396,480	2,512,501
Stock options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	3,396,480	2,462,926
Restricted Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share		49,575

Net Loss per Share - Weighted Average Number of Common Shares (Details) - shares	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Net Loss per Share
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic	38,774,591	27,170,423	35,997,572	27,129,171
Weighted-average number of common shares used in net loss per share applicable to common stockholders - diluted	38,774,591	27,170,423	35,997,572	27,129,171

Commitments (Details) - Corporate Headquarters Lease $ in Millions			3 Months Ended		6 Months Ended
	Apr. 28, 2017 USD ($) ft²	Feb. 12, 2015 USD ($) ft²	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)
Operating Leases
Area leased (in square feet) \| ft²	99,833	38,500
Extension period of lease term	5 years	5 years
Total commitment under the operating lease		$ 17.8
Lease term	146 months	7 years
Base annual rent, initial	$ 7.7	$ 2.3
Base annual rent, maximum	10.6	2.8
Allowance for leasehold improvements		4.3
Tenant improvement allowance	14.2
Balance from the leasehold improvement incentives, included in lease incentive obligation			$ 1.6		$ 1.6
Security deposit included in restricted cash	$ 3.5	$ 1.3
Rent expense			$ 1.1	$ 0.5	$ 1.6	$ 0.9

Subsequent Event (Details) - Alexion - USD ($) $ in Millions		1 Months Ended
	Jul. 26, 2017	Mar. 31, 2015
Subsequent Event
Collaborative partner's funding responsibility of research and development costs incurred under the research plan (as a percent)		100.00%
Subsequent Event
Subsequent Event
Written termination notice period	90 days
Collaborative partner's funding responsibility of research and development costs incurred under the research plan (as a percent)	100.00%
Upfront and milestone payments received	$ 18.8
Subsequent Event \| Forecast
Subsequent Event
Achieved milestone payment received which will be recognized over period of performance	$ 3.7