Blueprint Medicines (BPMC) 10-Q 10 May 16 2016 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2016	May. 06, 2016
Document and Entity Information [Abstract]
Entity Registrant Name	Blueprint Medicines Corp
Entity Central Index Key	1,597,264
Document Type	10-Q
Document Period End Date	Mar. 31, 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		27,238,661
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q1

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 122,289	$ 162,707
Investments, available-for-sale	69,218
Restricted cash		119
Unbilled accounts receivable	4,232	3,414
Prepaid expenses and other current assets	1,928	4,176
Total current assets	197,667	170,416
Property and equipment, net	6,537	6,661
Other assets	540	555
Restricted cash	1,266	1,266
Total assets	206,010	178,898
Current liabilities:
Accounts payable	2,773	2,455
Accrued expenses	5,335	6,436
Restricted stock liability	5	7
Current portion of deferred revenue	11,819	5,898
Current portion of lease incentive obligation	578	578
Current portion of term loan payable	3,272	3,266
Total current liabilities	23,782	18,640
Deferred rent, net of current portion	868	842
Restricted stock liability, net of current portion		1
Deferred revenue, net of current portion	44,948	7,742
Lease incentive obligation, net of current portion	3,226	3,370
Term loan, net of current portion	3,246	4,072
Other long term liabilities	$ 281	$ 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; 27,231,723 and 27,196,053 shares issued at March 31, 2016 and December 31, 2015, respectively, and 27,141,593 and 27,065,558 shares outstanding at March 31, 2016 and December 31, 2015, respectively	$ 27	$ 27
Additional paid-in capital	280,080	278,927
Accumulated other comprehensive income	31
Accumulated deficit	(150,479)	(134,975)
Total stockholders' equity	129,659	143,979
Total liabilities and stockholders' equity	$ 206,010	$ 178,898

Condensed Consolidated Balance3

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 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	27,231,723	27,196,053
Common Stock, Shares, Outstanding	27,141,593	27,065,558

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Revenues
Collaboration revenue	$ 6,856	$ 652
Operating expenses:
Research and development	17,635	9,232
General and administrative	4,646	2,770
Total operating expenses	22,281	12,002
Other income (expense):
Other income (expense), net	61	(37)
Interest expense	(140)	(185)
Total other income (expense)	(79)	(222)
Net loss	(15,504)	(11,572)
Other comprehensive income (loss):
Unrealized gain on investments	31
Comprehensive loss	(15,473)	(11,572)
Reconciliation of net loss applicable to common stockholders:
Net loss	(15,504)	(11,572)
Convertible preferred stock dividends		(2,270)
Net loss applicable to common stockholders	$ (15,504)	$ (13,842)
Net loss per share applicable to common stockholders - basic and diluted	$ (0.57)	$ (8.23)
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted	27,087,919	1,681,236

Condensed Consolidated Stateme5

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Operating activities
Net loss	$ (15,504)	$ (11,572)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	386	209
Noncash interest expense	22	29
Change in fair value of warrant liability		38
Stock-based compensation	1,102	840
Accretion of premiums and discounts on investments	35
Changes in assets and liabilities:
Unbilled accounts receivable	(818)	(484)
Prepaid expenses and other current assets	2,262	(364)
Other assets	11
Accounts payable	567	1,517
Accrued expenses	(321)	(115)
Deferred revenue	43,127	14,832
Deferred rent	(118)	(40)
Net cash provided by operating activities	30,751	4,890
Investing activities
Purchases of property and equipment	(1,262)	(19)
Restricted cash	119	(1,266)
Purchases of investments	(69,222)
Net cash used in investing activities	(70,365)	(1,285)
Financing activities
Principal payments on loan payable	(833)	(417)
Proceeds from issuance of Series C convertible preferred stock, net of issuance costs		(3)
Payment of offering costs		(146)
Proceeds from issuance of common stock, net of repurchases	29	19
Net cash used in financing activities	(804)	(547)
Net (decrease) increase in cash and cash equivalents	(40,418)	3,058
Cash and cash equivalents at beginning of period	162,707	47,240
Cash and cash equivalents at end of period	122,289	50,298
Supplemental cash flow information
Cash paid for interest	95	120
Property and equipment purchases incurred but unpaid at period end	$ 244
Public offering costs incurred but unpaid at period end		$ 805

Nature of Business

Nature of Business	3 Months Ended
	Mar. 31, 2016
Nature of Business
Nature of Business	1. Nature of Business Blueprint Medicines Corporation (the Company), a Delaware corporation formed 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 Accounti

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	3 Months Ended
	Mar. 31, 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 March 31, 2016 and the results of its operations for the three months ended March 31, 2016 and 2015 and cash flows for the three months ended March 31, 2016 and 2015. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 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 months ended March 31, 2016 is expected to impact 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 There have been no other material changes to the significant accounting policies previously disclosed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015. 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 2014, the FASB issued new guidance on management’s responsibility in evaluating whether or not there is substantial doubt about a company’s ability to continue as a going concern within one year from the date the financial statements are issued each reporting period. This new accounting guidance is effective for annual reporting periods (including interim reporting periods within those years) ending 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 Investment

Cash Equivalents and Investments	3 Months Ended
	Mar. 31, 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 March 31, 2016 and December 31, 2015 (in thousands): Average Amortized Unrealized Unrealized Fair March 31, 2016 Maturity Cost Gain Losses Value Cash equivalents: Money market funds $ $ — $ — $ Investments, available-for-sale: U.S. treasury obligations 258 Days — Total $ $ $ — $ Average Amortized Unrealized Unrealized Fair December 31, 2015 Maturity Cost Gain Losses Value Cash equivalents: Money market funds $ $ — $ — $ 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 months ended March 31, 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 Instrum

Fair Value Of Financial Instruments	3 Months Ended
	Mar. 31, 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 March 31, 2016 are classified below based on the fair value hierarchy described above: Active Observable Unobservable March 31, Markets Inputs Inputs Description 2016 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ $ $ — $ — Investments, available-for-sale: U.S Treasury obligations — — Total $ $ $ — $ — 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 Inputs Description 2015 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ $ $ — $ — 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.

Restricted Cash

Restricted Cash	3 Months Ended
	Mar. 31, 2016
Restricted Cash
Restricted Cash	5. Restricted Cash At March 31, 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 March 31, 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

Collaborations	3 Months Ended
	Mar. 31, 2016
Collaborations
Collaborations	6. Collaborations Roche In March 2016, t he Company entered into a collaboration and license agreement (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 agreed to the targets for three of the collaboration programs, all of which are 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 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. P re-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 ended March 31, 2016, the Company recognized revenue under the Roche agreement of $0.2 million, 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 c ertainty 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. 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 months ended March 31, 2016, the Company recognized revenue under the Alexion agreement of $6.6 million, which represents reimburseable research and development costs, the $0.75 million milestone payment, 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. T he Company received $3.2 million related to reimbursable research and development costs under the Alexion agreement for the three months ended March 31, 2016. As of March 31, 2016, the Company has recorded unbilled accounts receivable of $4.2 million related to reimbursable research and development costs under the Alexion agreement for activities performed during the first quarter of 2016.

Term Loan

Term Loan	3 Months Ended
	Mar. 31, 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 $ 2.7 million , in the aggregate, for the remainder of 2016.

Warrants

Warrants	3 Months Ended
	Mar. 31, 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 less than $0.1 million of expense associated with the change in fair value of the warrants in the three months ended March 31, 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 months ended March 31, 2016 and 2015.

Stock Awards

Stock Awards	3 Months Ended
	Mar. 31, 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 March 31, 2016, there were 1,906,722 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 $ Granted — — Vested Repurchased — — Unvested at March 31, 2016 The total fair value of restricted stock that vested during the three months ended March 31, 2016 and 2015 was $0.7 million and $0.6 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 $ $ Granted Exercised Canceled Outstanding at March 31, 2016 $ $ Exercisable at March 31, 2016 $ $ Vested and expected to vest at March 31, 2016(1) $ $ (1) Represents the number of vested options as of March 31, 2016, plus the number of unvested options expected to vest as of March 31, 2016 based on a forfeiture rate of 2.5% . (2) Intrinsic value represents the amount by which the fair market value as of March 31, 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 March 31, 2016 2015 Risk-free interest rate % % Expected dividend yield — % — % Expected term (years) Expected stock price volatility % % The weighted ‑average grant date fair value of options granted in the three months ended March 31, 2016 and 2015 was $10.29 and $6.45 , respectively. The total intrinsic value of options exercised in the three months ended March 31, 2016 and 2015 was $0.4 million and $0.1 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 March 31, 2016 2015 Research and development $ $ General and administrative Total stock-based compensation expense $ $ At March 31, 2016, the Company had $ 13.0 million of total unrecognized compensation cost related to non-vested stock awards, which is expected to be recognized over a weighted ‑average period of 2.77 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 did not issue any shares under the ESPP during the three months ended March 31, 2016.

Net Loss per Share

Net Loss per Share	3 Months Ended
	Mar. 31, 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. Three Months Ended March 31, 2016 2015 Convertible preferred stock — Warrants — Stock options Unvested restricted stock Total The weighted average number of common shares used in net loss per share applicable to common stockholders on a basic and diluted basis were 27,087,919 and 1,681,236 for the three months ended March 31, 2016 and 2015, respectively.

Commitments

Commitments	3 Months Ended
	Mar. 31, 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 March 31, 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 March 31, 2016 and 2015, rent expense was $0.6 million and $0.2 million, respectively.

Summary of Significant Accoun17

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	3 Months Ended
	Mar. 31, 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 March 31, 2016 and the results of its operations for the three months ended March 31, 2016 and 2015 and cash flows for the three months ended March 31, 2016 and 2015. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 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 months ended March 31, 2016 is expected to impact 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.
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 2014, the FASB issued new guidance on management’s responsibility in evaluating whether or not there is substantial doubt about a company’s ability to continue as a going concern within one year from the date the financial statements are issued each reporting period. This new accounting guidance is effective for annual reporting periods (including interim reporting periods within those years) ending 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 Investme18

Cash Equivalents and Investments (Tables)	3 Months Ended
	Mar. 31, 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 March 31, 2016 and December 31, 2015 (in thousands): Average Amortized Unrealized Unrealized Fair March 31, 2016 Maturity Cost Gain Losses Value Cash equivalents: Money market funds $ $ — $ — $ Investments, available-for-sale: U.S. treasury obligations 258 Days — Total $ $ $ — $ Average Amortized Unrealized Unrealized Fair December 31, 2015 Maturity Cost Gain Losses Value Cash equivalents: Money market funds $ $ — $ — $

Fair Value Of Financial Instr19

Fair Value Of Financial Instruments (Tables)	3 Months Ended
	Mar. 31, 2016
Fair Value of Financial Instruments
Schedule of financial instruments measured at fair value	Financial instruments measured at fair value as of March 31, 2016 are classified below based on the fair value hierarchy described above: Active Observable Unobservable March 31, Markets Inputs Inputs Description 2016 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ $ $ — $ — Investments, available-for-sale: U.S Treasury obligations — — Total $ $ $ — $ — 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 Inputs Description 2015 (Level 1) (Level 2) (Level 3) Financial Assets Cash equivalents: Money market funds $ $ $ — $ —

Stock Awards (Tables)

Stock Awards (Tables)	3 Months Ended
	Mar. 31, 2016
Stock Awards
Summary of unvested restricted stock	Weighted-Average Grant Date Shares Fair Value Unvested at December 31, 2015 $ Granted — — Vested Repurchased — — Unvested at March 31, 2016
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 $ $ Granted Exercised Canceled Outstanding at March 31, 2016 $ $ Exercisable at March 31, 2016 $ $ Vested and expected to vest at March 31, 2016(1) $ $ (1) Represents the number of vested options as of March 31, 2016, plus the number of unvested options expected to vest as of March 31, 2016 based on a forfeiture rate of 2.5% . (2) Intrinsic value represents the amount by which the fair market value as of March 31, 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 March 31, 2016 2015 Risk-free interest rate % % Expected dividend yield — % — % Expected term (years) Expected stock price volatility % %
Summary of stock-based compensation expense recognized in statements of operations	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 March 31, 2016 2015 Research and development $ $ General and administrative Total stock-based compensation expense $ $

Net Loss per Share (Tables)

Net Loss per Share (Tables)	3 Months Ended
	Mar. 31, 2016
Net Loss per Share
Schedule of common stock equivalents excluded from calculation of diluted net loss per share applicable to common stockholders	Three Months Ended March 31, 2016 2015 Convertible preferred stock — Warrants — Stock options Unvested restricted stock Total

Nature of Business (Details)

Nature of Business (Details) - IPO - Common Stock $ / shares in Units, $ in Millions	May. 05, 2015USD ($)$ / sharesshares
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) | $ / shares	$ 18
Proceeds from issuance of IPO shares | $	$ 154.8

Summary of Significant Accoun23

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Stock Split and Conversion of Stock (Details) - IPO - Common Stock	May. 05, 2015shares	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 Investme24

Cash Equivalents and Investments (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Dec. 31, 2015
Cash Equivalents and Investments
Total, Amortized Cost	$ 191,476
Available-for-sale, Unrealized Gain	31
Total, Fair Value	191,507
Realized gain (loss) on sales of investments	0
Adjustment for other than temporary FV decline	$ 0
US Treasury obligations
Cash Equivalents and Investments
Average Maturity	258 days
Available-for-sale, Amortized Cost	$ 69,187
Available-for-sale, Unrealized Gain	31
Available-for-sale, Fair Value	69,218
Money market fund
Cash Equivalents and Investments
Cash equivalents, Amortized Cost	122,289	$ 162,707
Cash equivalents, Fair Value	$ 122,289	$ 162,707

Fair Value of Financial Instr25

Fair Value of Financial Instruments (Details) - Recurring - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Fair Value of Financial Instruments
Total	$ 191,507
Money market fund
Fair Value of Financial Instruments
Cash equivalents	122,289	$ 162,707
US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	69,218
Active Markets (Level 1)
Fair Value of Financial Instruments
Total	191,507
Active Markets (Level 1) | Money market fund
Fair Value of Financial Instruments
Cash equivalents	122,289	$ 162,707
Active Markets (Level 1) | US Treasury obligations
Fair Value of Financial Instruments
Investments, available-for-sale	$ 69,218

Restricted Cash (Details)

Restricted Cash (Details) - USD ($) $ in Thousands	Mar. 31, 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)

Collaborations (Details) $ in Thousands	1 Months Ended		3 Months Ended
	Mar. 31, 2016USD ($)item	Mar. 31, 2015USD ($)item	Mar. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Jun. 30, 2015USD ($)	Mar. 31, 2015USD ($)
Collaboration Agreement
Collaboration revenue			$ 6,856			$ 652
Unbilled accounts receivable for reimbursable research and development costs	$ 4,232		4,232	$ 3,414
Roche Agreement
Collaboration Agreement
Non-refundable upfront payment received	$ 45,000
Number of deliverables | item	5
Collaboration revenue			200
Number of collaboration programs with agreed upon targets | item	3
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
Collaboration revenue			6,600
Reimbursable research and development costs			3,200
Unbilled accounts receivable for reimbursable research and development costs	$ 4,200		4,200
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			$ 750	$ 250
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)

Term Loan (Details) - Loan and Security Agreement $ in Millions	1 Months Ended					3 Months Ended
	Nov. 30, 2014USD ($)	Jun. 30, 2014USD ($)	Sep. 30, 2013USD ($)	Jun. 30, 2013USD ($)	May. 31, 2013USD ($)item	Mar. 31, 2016USD ($)
Term Loan
Maximum borrowing capacity					$ 5
Number of tranches | item					3
Increase in maximum borrowing capacity	$ 5
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						$ 2.7
2013 Term Loan
Term Loan
Proceeds from bank debt		$ 2	$ 2	$ 1
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

Warrants - Warrants (Details)

Warrants - Warrants (Details) - USD ($) $ / shares in Units, $ in Thousands	May. 13, 2015	May. 05, 2015	Mar. 31, 2016	Mar. 31, 2015	Nov. 30, 2014	May. 31, 2013
Warrants
Change in fair value of warrant liability				$ 38
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
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
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 | Maximum
Warrants
Change in fair value of warrant liability				$ 100

Stock Awards - 2015 Stock Optio

Stock Awards - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares	Jan. 01, 2016	Mar. 31, 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		1,906,722
Award vesting period		4 years
Cliff vesting period for new employees		1 year
Award expiration period		10 years

Stock Awards - Unvested Restric

Stock Awards - Unvested Restricted Stock (Details) - Restricted Stock - USD ($) $ / shares in Units, $ in Millions	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Unvested restricted stock rollforward
Unvested at beginning of period (in shares)	130,495
Vested ( in shares)	(40,365)
Unvested at end of period (in shares)	90,130
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
Unvested at end of period (in dollars per share)	$ 0.61
Total fair value of restricted stock that vested	$ 0.7	$ 0.6

Stock Awards - Stock Options (D

Stock Awards - Stock Options (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2016	Dec. 31, 2015
Stock option rollforward
Outstanding at beginning of period (in shares)	1,802,802
Granted (in shares)	682,943
Exercised ( in shares)	(62,106)
Canceled ( in shares)	(28,170)
Outstanding at end of period (in shares)	2,395,469	1,802,802
Exercisable at end of period (in shares)	566,574
Vested and expected to vest at end of period (in shares)	2,327,302
Weighted average exercise price
Outstanding at beginning of period (in dollars per share)	$ 5.88
Granted (in dollars per share)	15.37
Exercised ( in dollars per share)	4.34
Cancelled ( in dollars per share)	1.73
Outstanding at end of period (in dollars per share)	8.67	$ 5.88
Exercisable at end of period (in dollars per share)	4.39
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Exercise Price	$ 8.61
Other disclosures
Remaining contractual life outstanding	8 years 9 months 4 days	8 years 9 months 4 days
Remaining contractual life, exercisable at end of period	7 years 9 months 22 days
Remaining contractual life, vested and expected to vest at end of period	8 years 9 months
Aggregate intrinsic value, outstanding at beginning of period	$ 37,008
Aggregate intrinsic value, outstanding at end of period	23,394	$ 37,008
Aggregate intrinsic value, exercisable at end of period	7,797
Aggregate intrinsic value, vested and expected to vest at end of period	$ 22,876
Forfeiture rate (as a percent)	2.50%

Stock Awards - Weighted Average

Stock Awards - Weighted Average Assumptions (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Millions	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Assumptions used in estimating the fair value of stock options granted
Risk-free interest rate	1.59%	1.65%
Expected term (in years)	6 years	6 years
Expected stock price volatility	76.74%	86.14%
Other disclosures
Weighted-average grant date fair value of options granted	$ 10.29	$ 6.45
Total intrinsic value of options exercised	$ 0.4	$ 0.1

Stock Awards - Stock-based Comp

Stock Awards - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Stock-based compensation
Allocated Share-based Compensation Expense	$ 1,102	$ 840
Total unrecognized compensation cost related to non-vested stock awards	$ 13,000
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 9 months 7 days
Research and development
Stock-based compensation
Allocated Share-based Compensation Expense	$ 526	392
General and administrative
Stock-based compensation
Allocated Share-based Compensation Expense	$ 576	$ 448

Stock Awards - Employee Stock P

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

Net Loss per Share (Details)

Net Loss per Share (Details) - shares	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	2,485,599	17,889,330
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted	27,087,919	1,681,236
Convertible preferred stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share		15,467,479
Warrant
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share		42,423
Stock options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	2,395,469	2,051,628
Restricted Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	90,130	327,800

Commitments (Details)

Commitments (Details) - Corporate Headquarters Lease $ in Millions	Feb. 12, 2015USD ($)ft²	Feb. 01, 2015	Mar. 31, 2016USD ($)	Mar. 31, 2015USD ($)
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			$ 0.6	$ 0.2