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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2016	Aug. 08, 2016
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, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Non-accelerated Filer
Entity Common Stock, Shares Outstanding		27,281,750
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q2

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 109,386	$ 162,707
Investments, available-for-sale	63,167
Restricted cash		119
Unbilled accounts receivable	3,351	3,414
Prepaid expenses and other current assets	2,216	4,176
Total current assets	178,120	170,416
Property and equipment, net	6,565	6,661
Other assets	569	555
Restricted cash	1,266	1,266
Total assets	186,520	178,898
Current liabilities:
Accounts payable	2,730	2,455
Accrued expenses	7,607	6,436
Restricted stock liability	3	7
Current portion of deferred revenue	13,803	5,898
Current portion of lease incentive obligation	578	578
Current portion of term loan payable	3,033	3,266
Total current liabilities	27,754	18,640
Deferred rent, net of current portion	894	842
Restricted stock liability, net of current portion		1
Deferred revenue, net of current portion	39,249	7,742
Lease incentive obligation, net of current portion	3,081	3,370
Term loan payable, net of current portion	2,672	4,072
Other long term liabilities	308	252
Commitments (Note 11)
Stockholders' deficit:
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; 27,276,990 and 27,196,053 shares issued at June 30, 2016 and December 31, 2015, respectively, and 27,227,415 and 27,065,558 shares outstanding at June 30, 2016 and December 31, 2015, respectively	27	27
Additional paid-in capital	281,853	278,927
Accumulated other comprehensive income	55
Accumulated deficit	(169,373)	(134,975)
Total stockholders' equity	112,562	143,979
Total liabilities and stockholders' equity	$ 186,520	$ 178,898

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2016	Dec. 31, 2015
Preferred Stock Disclosures
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common Stock Disclosures
Common stock, par value (in NIS dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	120,000,000	120,000,000
Common stock, shares issued	27,276,990	27,196,053
Common Stock, Shares, Outstanding	27,227,415	27,065,558

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Revenues
Collaboration revenue	$ 7,065	$ 2,687	$ 13,921	$ 3,339
Operating expenses:
Research and development	21,273	11,243	38,908	20,476
General and administrative	4,688	3,840	9,334	6,610
Total operating expenses	25,961	15,083	48,242	27,086
Other income (expense):
Other income (expense), net	131	(405)	192	(441)
Interest expense	(129)	(179)	(269)	(364)
Total other income (expense)	2	(584)	(77)	(805)
Net loss	(18,894)	(12,980)	(34,398)	(24,552)
Other comprehensive income (loss):
Unrealized gain on investments	24		55
Comprehensive loss	(18,870)	(12,980)	(34,343)	(24,552)
Reconciliation of net loss applicable to common stockholders:
Net loss	(18,894)	(12,980)	(34,398)	(24,552)
Convertible preferred stock dividends		(883)		(3,153)
Net loss applicable to common stockholders	$ (18,894)	$ (13,863)	$ (34,398)	$ (27,705)
Net loss per share applicable to common stockholders - basic and diluted	$ (0.70)	$ (0.81)	$ (1.27)	$ (2.94)
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted	27,170,423	17,092,989	27,129,171	9,430,462

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Operating activities
Net loss	$ (34,398)	$ (24,552)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	782	411
Noncash interest expense	42	58
Change in fair value of warrant liability		445
Stock-based compensation	2,589	3,014
Accretion of premiums and discounts on investments	110
Changes in assets and liabilities:
Unbilled accounts receivable	63	(1,923)
Prepaid expenses and other current assets	1,943	(639)
Other assets	(17)	(31)
Accounts payable	427	781
Accrued expenses	2,202	456
Deferred revenue	39,412	15,818
Deferred rent	(237)	(3)
Net cash provided by (used in) operating activities	12,918	(6,165)
Investing activities
Purchases of property and equipment	(1,814)	(307)
Restricted cash	119	(1,266)
Purchases of investments	(69,222)
Maturities of investments	6,000
Net cash used in investing activities	(64,917)	(1,573)
Financing activities
Principal payments on loan payable	(1,667)	(833)
Proceeds from IPO, net of commissions and underwriting discounts		156,815
Payment of offering costs		(1,965)
Proceeds from issuance of common stock, net of repurchases	345	68
Net cash (used in) provided by financing activities	(1,322)	154,085
Net (decrease) increase in cash and cash equivalents	(53,321)	146,347
Cash and cash equivalents at beginning of period	162,707	47,240
Cash and cash equivalents at end of period	109,386	193,587
Supplemental cash flow information
Cash paid for interest	180	236
Property and equipment purchases incurred but unpaid at period end	$ 116	15
Conversion of convertible preferred stock into common stock		114,808
Reclassification of warrant liability to additional paid-in-capital		810
Public offering costs incurred but unpaid at period end		$ 28

Nature of Business	6 Months Ended
Nature of Business	Jun. 30, 2016
Nature of Business
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 with therapeutic windows 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, 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, at a price to the public of $18.00 per share. The Company received net proceeds of $154.8 million after deducting underwriting discounts and commissions and offering costs paid by the Company.

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	6 Months Ended
	Jun. 30, 2016
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
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 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, 2015 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015, filed with the Securities and Exchange Commission on March 11, 2016. 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, 2016 and the results of its operations for the three and six months ended June 30, 2016 and 2015 and cash flows for the six months ended June 30, 2016 and 2015. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2016 are not necessarily indicative of the results for the year ending December 31, 2016, or for any future period. In connection with preparing for its IPO, the Company effected a 1‑for‑5.5 reverse stock split of the Company’s common stock. The reverse stock split became effective on April 10, 2015. All share and per share amounts in the financial statements and notes thereto have been retroactively adjusted for all periods presented to give effect to this reverse stock split, including reclassifying an amount equal to the reduction in par value of common stock to additional paid‑in capital. Upon the closing of the IPO in May 2015, all of the Company’s outstanding convertible preferred stock automatically converted into 15,467,479 shares of common stock, and warrants exercisable for convertible preferred stock automatically converted into warrants exercisable for 42,423 shares of common stock. The significant increase in shares outstanding in the three and six months ended June 30, 2016 impacted the year-over-year comparability of the Company’s net loss per share calculations through the second quarter of 2016. 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, including estimating the fair value of the Company’s common stock prior to the IPO; revenue recognition; the valuation of liability‑classified warrants prior to the IPO; 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. Available-for-Sale Investments The Company classifies marketable securities with a remaining maturity when purchased of greater than three months as available-for-sale. Marketable securities with a remaining maturity date greater than one year are classified as non-current. Available-for-sale securities are maintained by an investment manager and may consist of U.S. Treasury securities and U.S. government agency securities. Available-for-sale securities are carried at fair value with the unrealized gains and losses included in other comprehensive income (loss) as a component of stockholders’ equity until realized. Any premium or discount arising at purchase is amortized and/or accreted to interest income and/or expense over the life of the instrument. Realized gains and losses are determined using the specific identification method and are included in other income (expense). If any adjustment to fair value reflects a decline in value of the investment, the Company considers all available evidence to evaluate the extent to which the decline is “other-than-temporary” and, if so, mark the investment to market through a charge to the Company’s statement of operations and comprehensive loss. 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, 2015 related to 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 or retrospectively with the cumulative effect of initially applying this update recognized at the date of initial application. The Company is in the process of evaluating the new guidance and determining the expected effects of the adoption of this standard on its consolidated financial statements. In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern. This new standard is intended to define management’s responsibility to evaluate whether there is substantial doubt about an entity’s ability to continue as a going concern within one year of the date of issuance of the entity’s financial statements and to provide related footnote disclosures. This new accounting guidance is effective for annual reporting periods ending after December 15, 2016, and for interim periods within annual periods beginning after December 15, 2016. Early adoption is permitted. The new accounting standard will impact the disclosure in the Company’s consolidated financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation, 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 amendments are effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2016. Early adoption is permitted. A company that elects early adoption must adopt all of the amendments in the same period. The Company is currently evaluating the potential impact that ASU 2016-09 may have on the Company’s consolidated financial statements In 2016, the FASB issued amended guidance applicable to leases that will be effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2018. Early adoption is permitted. This update requires a company to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on the Company’s consolidated financial statements.

Cash Equivalents and Investments

6 Months Ended

Jun. 30, 2016

Cash Equivalents and Investments

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, 2016 and December 31, 2015 (in thousands):


	Average		Amortized		Unrealized		Unrealized		Fair
June 30, 2016	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	109,386	$	—	$	—	$	109,386
Investments, available-for-sale:
U.S. treasury obligations		270 Days		63,112		55		—		63,167
Total			$	172,498	$	55	$	—	$	172,553

Average

Amortized

Unrealized

Fair

December 31, 2015

Maturity

Cost

Gain

Losses

Value

Cash equivalents:

Money market funds

162,707

—

162,707

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, 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.

Fair Value Of Financial Instruments

6 Months Ended

Jun. 30, 2016

Fair Value of Financial Instruments

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, 2016 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2016		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	109,386	$	109,386	$	—	$	—
Investments, available-for-sale:
U.S Treasury obligations		63,167		63,167		—		—
Total	$	172,553	$	172,553	$	—	$	—

Financial instruments measured at fair value as of December 31, 2015 are classified below based on the fair value hierarchy described above:

Active

Observable

Unobservable

December 31,

Markets

Inputs

Description

2015

(Level 1)

(Level 2)

(Level 3)

Financial Assets

Cash equivalents:

Money market funds

162,707

—

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, 2016
Restricted Cash
Restricted Cash	5. Restricted Cash At June 30, 2016 and December 31, 2015, $1.3 million and $1.4 million, respectively, of the Company’s cash is restricted by a bank. As of June 30, 2016, $1.3 million of restricted cash was included in long-term assets on the Company’s balance sheet related to a security deposit for the lease agreement for the Company’s corporate headquarters.

Collaborations	6 Months Ended
Collaborations	Jun. 30, 2016
Collaborations
Collaborations	6. Collaborations Roche In March 2016, the Company entered into a collaboration and license agreement (as amended, Roche agreement) with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. (collectively, 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 have identified targets for three of the collaboration programs, two of which began in the first half of 2016 and the third of which is expected to begin 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 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 the three months and six months ended June 30, 2016, the Company recognized revenue under the Roche agreement of $1.4 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 Pharma Holding (Alexion) to research, develop and commercialize drug candidates for an undisclosed activated kinase target, which is the cause of a rare genetic disease. Under the terms of the Alexion agreement, the Company is responsible for research and pre‑clinical development activities related to drug candidates and Alexion is responsible for all clinical development, manufacturing and commercialization activities related to drug candidates. Alexion is 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 is 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. Alexion will 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. The royalty term for each licensed product in each country is 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. Alexion has the right to terminate the Alexion agreement if the Company undergoes a change of control or becomes an affiliate of a biotechnology or pharmaceutical company, and may terminate the Alexion agreement at will upon 90 days prior written notice. The Company and Alexion have the right to terminate the Alexion agreement in the event of the other party’s uncured breach or insolvency, and in certain other circumstances agreed to by the parties. 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 to be completed is its research and development activities and participation on the JSC and JPT, which are expected to be delivered over the same performance period. The Company is utilizing a proportional performance model to recognize revenue under the Alexion agreement. The Company evaluated whether the milestones that may be received in connection with the Alexion agreement are substantive or non-substantive milestones. The Company concluded that the first pre-clinical milestone payment in the Alexion agreement is non-substantive due to the certainty at the date the arrangement was entered into that the event will be achieved. In the second quarter of 2015, the Company achieved the first pre-clinical milestone under the Alexion agreement and received a $1.75 million payment from Alexion. The Company is recognizing revenues from the related milestone payment over the period of performance. The remaining non-refundable pre-clinical milestones that are expected to be achieved as a result of the Company's efforts during the period of substantial involvement are considered substantive and are recognized as revenue upon the achievement of the milestone, assuming all other revenue recognition criteria are met. The Company recognized the first substantive milestone of $0.25 million in the fourth quarter of 2015 and received payment from Alexion in the first quarter of 2016. In the first quarter of 2016, the Company recognized and received payment from Alexion for the second substantive milestone of $0.75 million. In the third quarter of 2016, the Company achieved a pre-clinical milestone of $1.0 million, which is expected to be paid during the third quarter of 2016. Milestones that are not considered substantive because the Company does not contribute effort to the achievement of such milestones are generally achieved after the period of substantial involvement and are recognized as revenue upon achievement of the milestone, as there are no undelivered elements remaining and no continuing performance obligations, assuming all other revenue recognition criteria are met. 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 reimbursable research and development costs, the $0.75 million milestone payment in the three months ended March 31, 2016, which was recognized upon achievement, 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 six months ended June 30, 2016, the Company received $7.4 million related to reimbursable research and development costs under the Alexion agreement. As of June 30, 2016, the Company has recorded unbilled accounts receivable of $3.4 million related to reimbursable research and development costs under the Alexion agreement for activities performed during the second quarter of 2016.

Term Loan	6 Months Ended
Term Loan	Jun. 30, 2016
Term Loan
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 $1.8 million, in the aggregate, for the remainder of 2016.

Warrants	6 Months Ended
Warrants	Jun. 30, 2016
Warrants
Warrants	8. Warrants 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). Both warrants were exercisable immediately and have a ten‑year life. The Company initially valued the Series A Warrant and the Series B Warrant at issuance and at the balance sheet dates using the Black‑Scholes option pricing model. The significant assumptions used in estimating the fair value of the warrants include the volatility of the stock underlying the warrant, risk‑free interest rate, estimated fair value of the preferred stock underlying the warrant, and the estimated term of the warrant. The fair value of the preferred stock underlying the warrants was estimated using the implied value from the common stock valuations on those dates. In accordance with ASC 480, the characteristics of these warrants and the rights and privileges of the underlying preferred stock resulted in the classification of these warrants as a liability, and they were re‑measured to the‑then current fair value at each balance sheet date through the completion of the IPO. Re‑measurement gains or losses were recorded in other income (expense) in the condensed consolidated statements of operations and comprehensive loss. Changes in the fair value of the warrants represented a recurring measurement that was classified within Level 3 of the fair value hierarchy wherein fair value is estimated using significant unobservable inputs. The Company recorded $0.4 million of expense associated with the change in fair value of the warrants in the six months ended June 30, 2015. Upon completion of the IPO, the Series A Warrant became exercisable for 27,272 shares of the common stock at an exercise price of $5.50 per share, and the Series B Warrant became exercisable for 15,151 shares of the common stock at an exercise price of $6.60 per share. On the date of the conversion of the warrants, the Company revalued the outstanding warrants using the Black-Scholes option pricing model and reclassified the fair value of the warrants of $0.8 million to additional paid-in capital. 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, 2016 and 2015, respectively.

Stock Awards

6 Months Ended

Jun. 30, 2016

Stock Awards

Stock Awards

9. 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, 2016, the number of shares reserved for issuance under the 2015 Plan was increased by 1,087,842 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, 2016, there were 1,797,924 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, 2015	130,495	$	0.60
Vested	(79,329)		0.57
Repurchased	(1,591)		0.55
Unvested at June 30, 2016	49,575		0.63

The total fair value of restricted stock that vested during the three months ended June 30, 2016 and 2015 was $0.7 million and $1.4 million, respectively. The total fair value of restricted stock that vested during the six months ended June 30, 2016 and 2015 was $1.4 million and $2.1 million, respectively.

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


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(2)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2015	1,802,802	$	5.88	8.76	$	37,008
Granted	818,363		15.97
Exercised	(63,602)		2.34
Canceled	(94,637)		6.64
Outstanding at June 30, 2016	2,462,926	$	9.29	8.64	$	27,647
Exercisable at June 30, 2016	677,412	$	5.56	7.94	$	10,058
Vested and expected to vest at June 30, 2016(1)	2,402,534	$	9.24	8.63	$	27,108

(1)

Represents the number of vested options as of June 30, 2016, plus the number of unvested options expected to vest as of June 30, 2016 based on a forfeiture rate of 2.5%.

(2)

Intrinsic value represents the amount by which the fair market value as of June 30, 2016 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, 2016		June 30, 2015		June 30, 2016		June 30, 2015
Risk-free interest rate	1.36	%	1.74	%	1.55	%	1.67	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (years)	5.7		6.0		6.0		6.0
Expected stock price volatility	75.38	%	82.68	%	76.52	%	85.71	%

The weighted‑average grant date fair value of options granted in the three months ended June 30, 2016 and 2015 was $12.22 and $16.8 respectively. The total intrinsic value of options exercised in the three months ended June, 2016 and 2015 was $0.6 million and $0.3 million, respectively. The weighted‑average grant date fair value of options granted in the six months ended June 30, 2016 and 2015 was $10.61 and $7.71, respectively. The total intrinsic value of options exercised in the six months ended June, 2016 and 2015 was $1.0 million and $0.4 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,
	2016		2015		2016		2015
Research and development	$	757	$	897	$	1,283	$	1,289
General and administrative		730		1,277		1,306		1,725
Total stock-based compensation expense	$	1,487	$	2,174	$	2,589	$	3,014

At June 30, 2016, the Company had $13.1 million of total unrecognized compensation cost related to non-vested stock awards, which is expected to be recognized over a weighted‑average period of 2.53 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, 2016, the number of shares reserved for issuance under the 2015 ESPP was increased by 271,960 shares. The Company issued 11,426 shares under the ESPP during the six months ended June 30, 2016.

Net Loss per Share

6 Months Ended

Jun. 30, 2016

Net Loss per Share

Net Loss per Share

10. 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. Net loss applicable to common stockholders is calculated by adjusting the net loss of the Company for cumulative preferred stock dividends. 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, convertible preferred stock, warrants, 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,
	2016	2015
Stock options	2,462,926	2,098,499
Unvested restricted stock	49,575	257,049
Total	2,512,501	2,355,548

The weighted average number of common shares used in net loss per share applicable to common stockholders on a basic and diluted basis were 27,170,423 and 17,092,989 for the three months ended June 30, 2016 and 2015, respectively, and 27,129,171 and 9,430,462 for the six months ended June 30, 2016 and 2015, respectively.

Commitments	6 Months Ended
Commitments	Jun. 30, 2016
Commitments.
Commitments	11. Commitments The Company leased its prior corporate headquarters under an operating lease that expired on November 1, 2015. On February 1, 2015, the Company’s option to extend the term of the lease for an additional three-year period expired. The Company did not exercise its option to extend the term of the lease. 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, 2016, 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. For the three months ended June 30, 2016 and 2015, rent expense was $0.5 million and $0.3 million, respectively. For the six months ended June 30, 2016 and 2015, rent expense was $0.9 million and $0.5 million, respectively.

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	6 Months Ended
	Jun. 30, 2016
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
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 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, 2015 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015, filed with the Securities and Exchange Commission on March 11, 2016. 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, 2016 and the results of its operations for the three and six months ended June 30, 2016 and 2015 and cash flows for the six months ended June 30, 2016 and 2015. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2016 are not necessarily indicative of the results for the year ending December 31, 2016, or for any future period. In connection with preparing for its IPO, the Company effected a 1‑for‑5.5 reverse stock split of the Company’s common stock. The reverse stock split became effective on April 10, 2015. All share and per share amounts in the financial statements and notes thereto have been retroactively adjusted for all periods presented to give effect to this reverse stock split, including reclassifying an amount equal to the reduction in par value of common stock to additional paid‑in capital. Upon the closing of the IPO in May 2015, all of the Company’s outstanding convertible preferred stock automatically converted into 15,467,479 shares of common stock, and warrants exercisable for convertible preferred stock automatically converted into warrants exercisable for 42,423 shares of common stock. The significant increase in shares outstanding in the three and six months ended June 30, 2016 impacted the year-over-year comparability of the Company’s net loss per share calculations through the second quarter of 2016.
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, including estimating the fair value of the Company’s common stock prior to the IPO; revenue recognition; the valuation of liability‑classified warrants prior to the IPO; accrued expenses; and income taxes.
Available-for-sale Investments	Available-for-Sale Investments The Company classifies marketable securities with a remaining maturity when purchased of greater than three months as available-for-sale. Marketable securities with a remaining maturity date greater than one year are classified as non-current. Available-for-sale securities are maintained by an investment manager and may consist of U.S. Treasury securities and U.S. government agency securities. Available-for-sale securities are carried at fair value with the unrealized gains and losses included in other comprehensive income (loss) as a component of stockholders’ equity until realized. Any premium or discount arising at purchase is amortized and/or accreted to interest income and/or expense over the life of the instrument. Realized gains and losses are determined using the specific identification method and are included in other income (expense). If any adjustment to fair value reflects a decline in value of the investment, the Company considers all available evidence to evaluate the extent to which the decline is “other-than-temporary” and, if so, mark the investment to market through a charge to the Company’s statement of operations and comprehensive loss.
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 or retrospectively with the cumulative effect of initially applying this update recognized at the date of initial application. The Company is in the process of evaluating the new guidance and determining the expected effects of the adoption of this standard on its consolidated financial statements. In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern. This new standard is intended to define management’s responsibility to evaluate whether there is substantial doubt about an entity’s ability to continue as a going concern within one year of the date of issuance of the entity’s financial statements and to provide related footnote disclosures. This new accounting guidance is effective for annual reporting periods ending after December 15, 2016, and for interim periods within annual periods beginning after December 15, 2016. Early adoption is permitted. The new accounting standard will impact the disclosure in the Company’s consolidated financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation, 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 amendments are effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2016. Early adoption is permitted. A company that elects early adoption must adopt all of the amendments in the same period. The Company is currently evaluating the potential impact that ASU 2016-09 may have on the Company’s consolidated financial statements In 2016, the FASB issued amended guidance applicable to leases that will be effective for annual reporting periods (including interim reporting periods within those years) beginning after December 15, 2018. Early adoption is permitted. This update requires a company to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on the Company’s consolidated financial statements.

Cash Equivalents and Investments (Tables)

6 Months Ended

Jun. 30, 2016

Cash Equivalents and Investments

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

Cash equivalents and investments, available-for-sale, consisted of the following at June 30, 2016 and December 31, 2015 (in thousands):


	Average		Amortized		Unrealized		Unrealized		Fair
June 30, 2016	Maturity		Cost		Gain		Losses		Value
Cash equivalents:
Money market funds			$	109,386	$	—	$	—	$	109,386
Investments, available-for-sale:
U.S. treasury obligations		270 Days		63,112		55		—		63,167
Total			$	172,498	$	55	$	—	$	172,553

Average

Amortized

Unrealized

Fair

December 31, 2015

Maturity

Cost

Gain

Losses

Value

Cash equivalents:

Money market funds

162,707

—

162,707

Fair Value Of Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2016

Fair Value of Financial Instruments

Schedule of financial instruments measured at fair value

Financial instruments measured at fair value as of June 30, 2016 are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2016		(Level 1)		(Level 2)		(Level 3)
Financial Assets
Cash equivalents:
Money market funds	$	109,386	$	109,386	$	—	$	—
Investments, available-for-sale:
U.S Treasury obligations		63,167		63,167		—		—
Total	$	172,553	$	172,553	$	—	$	—

Financial instruments measured at fair value as of December 31, 2015 are classified below based on the fair value hierarchy described above:

Active

Observable

Unobservable

December 31,

Markets

Inputs

Description

2015

(Level 1)

(Level 2)

(Level 3)

Financial Assets

Cash equivalents:

Money market funds

162,707

—

Stock Awards (Tables)

6 Months Ended

Jun. 30, 2016

Stock Awards

Summary of unvested restricted stock


		Weighted-Average
		Grant Date
	Shares	Fair Value
Unvested at December 31, 2015	130,495	$	0.60
Vested	(79,329)		0.57
Repurchased	(1,591)		0.55
Unvested at June 30, 2016	49,575		0.63

Summary of stock option activity


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(2)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2015	1,802,802	$	5.88	8.76	$	37,008
Granted	818,363		15.97
Exercised	(63,602)		2.34
Canceled	(94,637)		6.64
Outstanding at June 30, 2016	2,462,926	$	9.29	8.64	$	27,647
Exercisable at June 30, 2016	677,412	$	5.56	7.94	$	10,058
Vested and expected to vest at June 30, 2016(1)	2,402,534	$	9.24	8.63	$	27,108

(1)

Represents the number of vested options as of June 30, 2016, plus the number of unvested options expected to vest as of June 30, 2016 based on a forfeiture rate of 2.5%.

(2)

Intrinsic value represents the amount by which the fair market value as of June 30, 2016 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, 2016		June 30, 2015		June 30, 2016		June 30, 2015
Risk-free interest rate	1.36	%	1.74	%	1.55	%	1.67	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (years)	5.7		6.0		6.0		6.0
Expected stock price volatility	75.38	%	82.68	%	76.52	%	85.71	%

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


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2016		2015		2016		2015
Research and development	$	757	$	897	$	1,283	$	1,289
General and administrative		730		1,277		1,306		1,725
Total stock-based compensation expense	$	1,487	$	2,174	$	2,589	$	3,014

Net Loss per Share (Tables)

6 Months Ended

Jun. 30, 2016

Net Loss per Share

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


	Six Months Ended
	June 30,
	2016	2015
Stock options	2,462,926	2,098,499
Unvested restricted stock	49,575	257,049
Total	2,512,501	2,355,548

Nature of Business (Details) - USD ($) $ / shares in Units, $ in Thousands		6 Months Ended
	May 05, 2015	Jun. 30, 2015
Initial Public Offering
Proceeds from issuance of IPO shares		$ 156,815
IPO \| Common Stock
Initial Public Offering
Stock sold (in shares)	9,367,708
Shares issued to underwriters in IPO	1,221,874
Share price (in dollars per share)	$ 18.00
Proceeds from issuance of IPO shares	$ 154,800

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Stock Split and Conversion of Stock (Details) - IPO - Common Stock	May 05, 2015 shares	Apr. 10, 2015
Stock Split and Conversion of stock
Reverse stock split ratio		0.1818
Shares issued upon stock conversion (in shares)	15,467,479
Number of shares that can be purchased by the warrants issued	42,423

Cash Equivalents and Investments (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2016	Dec. 31, 2015
Cash Equivalents and Investments
Total, Amortized Cost	$ 172,498	$ 172,498
Available-for-sale, Unrealized Gain	55	55
Total, Fair Value	172,553	172,553
Realized gain (loss) on sales of investments	0	0
Adjustment for other than temporary FV decline	0	$ 0
US Treasury obligations
Cash Equivalents and Investments
Average Maturity		270 days
Available-for-sale, Amortized Cost	63,112	$ 63,112
Available-for-sale, Unrealized Gain	55	55
Available-for-sale, Fair Value	63,167	63,167
Money market fund
Cash Equivalents and Investments
Cash equivalents, Amortized Cost	109,386	109,386	$ 162,707
Cash equivalents, Fair Value	$ 109,386	$ 109,386	$ 162,707

Fair Value of Financial Instruments (Details) - Recurring - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Fair Value of Financial Instruments
Total	$ 172,553
Money market fund
Fair Value of Financial Instruments
Cash equivalents	109,386	$ 162,707
US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	63,167
Active Markets (Level 1)
Fair Value of Financial Instruments
Total	172,553
Active Markets (Level 1) \| Money market fund
Fair Value of Financial Instruments
Cash equivalents	109,386	$ 162,707
Active Markets (Level 1) \| US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	$ 63,167

Restricted Cash (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Restricted Cash
Restricted cash included in long-term assets	$ 1,266	$ 1,266
Corporate Headquarters Lease
Restricted Cash
Restricted cash included in long-term assets	1,300
Restricted by bank
Restricted Cash
Restricted cash, current and noncurrent	$ 1,300	$ 1,400

Collaborations (Details) $ in Thousands	1 Months Ended		3 Months Ended					6 Months Ended
Collaborations (Details) $ in Thousands	Mar. 31, 2016 USD ($) item	Mar. 31, 2015 USD ($) item	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Jun. 30, 2015 USD ($)	Jun. 30, 2016 USD ($) item	Jun. 30, 2015 USD ($)
Collaboration Agreement
Collaboration revenue				$ 7,065			$ 2,687	$ 13,921	$ 3,339
Unbilled accounts receivable for reimbursable research and development costs				3,351		$ 3,414		3,351
Roche Agreement
Collaboration Agreement
Non-refundable upfront payment received	$ 45,000
Number of deliverables \| item	5
Collaboration revenue				1,400				$ 1,600
Number of collaboration programs with agreed upon targets \| item	3
Number of collaboration programs that began during first half of 2016 \| item								2
Roche Agreement \| Maximum
Collaboration Agreement
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
Collaboration Agreement
Number of collaboration program with specified commercial rights for each party \| item	2
Roche Agreement \| Roche
Collaboration Agreement
Number of option rights to obtain exclusive license \| item	5
Roche Agreement \| Roche \| Prior To Exercise License Right Option
Collaboration Agreement
Written termination notice period	120 days
Roche Agreement \| Roche \| Exercise Of License Right Option \| Maximum
Collaboration Agreement
Number of collaborations programs with exclusive commercialization rights for licensed products \| item	3
Roche Agreement \| Roche \| Exercise Of License Option Product Not Commercially Sold
Collaboration Agreement
Written termination notice period	120 days
Roche Agreement \| Roche \| Exercise Of License Option Product Commercially Sold
Collaboration Agreement
Written termination notice period	180 days
Alexion
Collaboration Agreement
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
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
Written termination notice period		90 days
Number of deliverables \| item		3
Refund provisions		$ 0
Collaboration revenue				5,700				$ 12,300
Reimbursable research and development costs								7,400
Unbilled accounts receivable for reimbursable research and development costs				$ 3,400				3,400
Alexion \| Pre-clinical milestone for first licensed product
Collaboration Agreement
Achieved milestone payment received which will be recognized over period of performance							$ 1,750
Revenue recognized from milestone			$ 1,000		$ 750	$ 250		$ 750
Alexion \| Pre-clinical milestone for first licensed product \| Maximum
Collaboration Agreement
Payment receivable upon achievement of milestone		6,000
Alexion \| Development milestone for first licensed product \| Maximum
Collaboration Agreement
Payment receivable upon achievement of milestone		83,000
Alexion \| Development milestone for second licensed product \| Maximum
Collaboration Agreement
Payment receivable upon achievement of milestone		61,500
Alexion \| Commercial milestone
Collaboration Agreement
Payment receivable upon achievement of milestone		$ 51,000

Term Loan (Details) - Loan and Security Agreement $ 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 ($) item	Jun. 30, 2016 USD ($)
Term Loan
Maximum borrowing capacity					$ 5.0
Number of tranches \| item					3
Increase in maximum borrowing capacity	$ 5.0
Percentage fee payable on total loan advances at end of loan						4.00%
Percentage fee payable on outstanding principal in event of prepayment of loan advances, option 1						1.00%
Percentage fee payable on outstanding principal in event of prepayment of loan advances, option 2.						2.00%
Future minimum payments for remainder of year						$ 1.8
2013 Term Loan
Term Loan
Proceeds from bank debt		$ 2.0	$ 2.0	$ 1.0
2013 Term Loan \| Prime Rate
Term Loan
Fixed rate based on percentage points added to base rate					2.00%
2014 Term Loan
Term Loan
Proceeds from bank debt	$ 5.0

Warrants - Warrants (Details) - USD ($) $ / shares in Units, $ in Thousands			3 Months Ended		6 Months Ended
	May 13, 2015	May 05, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Nov. 30, 2014	May 31, 2013
Warrants
Change in fair value of warrant liability						$ 445
Reclassification of warrant liability to additional paid-in-capital						810
Series A and Series B Warrants
Warrants
Reclassification of warrant liability to additional paid-in-capital		$ 800
Series A and Series B Warrants \| Maximum
Warrants
Interest expense			$ 100	$ 100	$ 100	100
Series A Warrants
Warrants
Exercise price of warrants issued (in dollars per share)		$ 5.50
Number of common shares that became exercisable from warrants		27,272
Series B Warrants
Warrants
Exercise price of warrants issued (in dollars per share)		$ 6.60
Number of common shares that became exercisable from warrants		15,151
Loan and Security Agreement \| Series A and Series B Warrants
Warrants
Warrants life					10 years
Loan and Security Agreement \| 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
Stock issued upon exercise of warrants	21,281
Number of warrants cancelled	5,991
Loan and Security Agreement \| 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
Stock issued upon exercise of warrants	11,157
Number of warrants cancelled	3,994
Other expense \| Series A and Series B Warrants
Warrants
Change in fair value of warrant liability				$ 400		$ 400

Stock Awards - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares		6 Months Ended	12 Months Ended
	Jan. 01, 2016	Jun. 30, 2016	Dec. 31, 2015
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	1,087,842
Number of shares available for grant		1,797,924
Award vesting period		4 years
Cliff vesting period for new employees		1 year
Award expiration period		10 years

Stock Awards - Unvested Restricted Stock (Details) - Restricted Stock - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Unvested restricted stock rollforward
Unvested at beginning of period (in shares)			130,495
Vested ( in shares)			(79,329)
Repurchased (in shares)			(1,591)
Unvested at end of period (in shares)	49,575		49,575
Nonvested stock awards, Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share)			$ 0.60
Vested (in dollars per share)			$ 0.57
Repurchased (in dollars per share)			0.55
Unvested at end of period (in dollars per share)	$ 0.63		$ 0.63
Total fair value of restricted stock that vested	$ 0.7	$ 1.4	$ 1.4	$ 2.1

Stock Awards - Stock Options (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2016	Dec. 31, 2015
Stock option rollforward
Outstanding at beginning of period (in shares)	1,802,802
Granted (in shares)	818,363
Exercised ( in shares)	(63,602)
Canceled ( in shares)	(94,637)
Outstanding at end of period (in shares)	2,462,926	1,802,802
Exercisable at end of period (in shares)	677,412
Vested and expected to vest at end of period (in shares)	2,402,534
Weighted average exercise price
Outstanding at beginning of period (in dollars per share)	$ 5.88
Granted (in dollars per share)	15.97
Exercised ( in dollars per share)	2.34
Cancelled ( in dollars per share)	6.64
Outstanding at end of period (in dollars per share)	9.29	$ 5.88
Exercisable at end of period (in dollars per share)	5.56
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Exercise Price	$ 9.24
Other disclosures
Remaining contractual life outstanding	8 years 7 months 21 days	8 years 9 months 4 days
Remaining contractual life, exercisable at end of period	7 years 11 months 9 days
Remaining contractual life, vested and expected to vest at end of period	8 years 7 months 17 days
Aggregate intrinsic value, outstanding at beginning of period	$ 37,008
Aggregate intrinsic value, outstanding at end of period	27,647	$ 37,008
Aggregate intrinsic value, exercisable at end of period	10,058
Aggregate intrinsic value, vested and expected to vest at end of period	$ 27,108
Forfeiture rate (as a percent)	2.50%

Stock Awards - Weighted Average Assumptions (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Assumptions used in estimating the fair value of stock options granted
Risk-free interest rate	1.36%	1.74%	1.55%	1.67%
Expected term (in years)	5 years 8 months 12 days	6 years	6 years	6 years
Expected stock price volatility	75.38%	82.68%	76.52%	85.71%
Other disclosures
Weighted-average grant date fair value of options granted	$ 12.22	$ 16.8	$ 10.61	$ 7.71
Total intrinsic value of options exercised	$ 0.6	$ 0.3	$ 1.0	$ 0.4

Stock Awards - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Stock-based compensation
Allocated Share-based Compensation Expense	$ 1,487	$ 2,174	$ 2,589	$ 3,014
Total unrecognized compensation cost related to non-vested stock awards	13,100		$ 13,100
Weighted-average period over which unrecognized compensation cost will be recognized			2 years 6 months 11 days
Research and development
Stock-based compensation
Allocated Share-based Compensation Expense	757	897	$ 1,283	1,289
General and administrative
Stock-based compensation
Allocated Share-based Compensation Expense	$ 730	$ 1,277	$ 1,306	$ 1,725

Stock Awards - Employee Stock Purchase Plan (Details) - 2015 Employee Stock Purchase Plan - shares	1 Months Ended	6 Months Ended
	May 31, 2015	Jun. 30, 2016	Jan. 01, 2016
Stock Awards
Number of common shares reserved for future issuance of awards	243,347
Annual increase for common stock for issuance (as a percent)	1.00%
Increase of common shares reserved for future issuance			271,960
ESPP shares issued during period		11,426

Net Loss per Share (Details) - shares	3 Months Ended		6 Months Ended
Net Loss per Share (Details) - shares	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share			2,512,501	2,355,548
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted	27,170,423	17,092,989	27,129,171	9,430,462
Stock options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share			2,462,926	2,098,499
Restricted Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share			49,575	257,049

Commitments (Details) - Corporate Headquarters Lease $ in Millions			3 Months Ended		6 Months Ended
	Feb. 12, 2015 USD ($) ft²	Feb. 01, 2015	Jun. 30, 2016 USD ($)	Jun. 30, 2015 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2015 USD ($)
Operating Leases
Prior lease extension period		3 years
Area leased (in square feet) \| ft²	38,500
Extension period of lease term	5 years
Total commitment under the operating lease	$ 17.8
Lease term	7 years
Base annual rent, initial	$ 2.3
Base annual rent, maximum	2.8
Allowance for leasehold improvements	4.3
Security deposit included in restricted cash	$ 1.3
Rent expense			$ 0.5	$ 0.3	$ 0.9	$ 0.5