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Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2015	Jun. 10, 2015
Document and Entity Information [Abstract]
Entity Registrant Name	Blueprint Medicines Corp
Entity Central Index Key	0001597264
Document Type	10-Q
Document Period End Date	Mar. 31, 2015
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		27,111,402
Document Fiscal Year Focus	2015
Document Fiscal Period Focus	Q1

Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014
Current assets:
Cash and cash equivalents	$ 50,298	$ 47,240
Restricted cash	119	119
Unbilled accounts receivable	484
Prepaid expenses and other current assets	1,279	915
Total current assets	52,180	48,274
Property and equipment, net	1,295	1,482
Other assets	1,099	99
Restricted cash	1,336	70
Total assets	55,910	49,925
Current liabilities:
Accounts payable	2,334	814
Accrued expenses	4,404	3,810
Deferred rent	98	138
Restricted stock liability	292	298
Current porton of deferred revenue	5,375
Current portion of term loan payable	2,127	1,704
Total current liabilities	14,630	6,764
Restricted stock liability, net of current portion	25	29
Warrant liability	403	365
Deferred revenue, net of current portion	9,457
Term loan, net of current portion	6,525	7,338
Other long term liabilities	147
Commitments
Stockholders' deficit:
Common stock	2	2
Additional paid-in capital	3,691	2,822
Accumulated deficit	(93,778)	(82,206)
Total stockholders' deficit	(90,085)	(79,382)
Total liabilities, convertible preferred stock and stockholders' deficit	55,910	49,925
Series A convertible preferred stock
Current liabilities:
Convertible preferred stock	39,958	39,958
Series B convertible preferred stock
Current liabilities:
Convertible preferred stock	24,985	24,985
Series C convertible preferred stock
Current liabilities:
Convertible preferred stock	$ 49,865	$ 49,868

Balance (Parenthetical) - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014
Common Stock Disclosures
Common stock, par value (in NIS per share)	$ 0.001	$ 0.001
Common stock, shares authorized	110,000,000	110,000,000
Common stock, shares issued	2,223,766	2,218,652
Common Stock, Shares, Outstanding	1,731,437	1,626,738
Series A convertible preferred stock
Temporary Equity Disclosures
Convertible preferred stock, par value (in NIS per share)	$ 0.001	$ 0.001
Convertible preferred stock, shares authorized	40,150,000	40,150,000
Convertible preferred stock, shares issued	40,000,000	40,000,000
Convertible preferred stock, shares outstanding	40,000,000	40,000,000
Convertible preferred stock, liquidation preference (in dollars)	$ 49,027
Series B convertible preferred stock
Temporary Equity Disclosures
Convertible preferred stock, par value (in NIS per share)	$ 0.001	$ 0.001
Convertible preferred stock, shares authorized	20,999,996	20,999,996
Convertible preferred stock, shares issued	20,916,663	20,916,663
Convertible preferred stock, shares outstanding	20,916,663	20,916,663
Convertible preferred stock, liquidation preference (in dollars)	$ 27,570
Series C convertible preferred stock
Temporary Equity Disclosures
Convertible preferred stock, par value (in NIS per share)	$ 0.001	$ 0.001
Convertible preferred stock, shares authorized	24,154,589	24,154,589
Convertible preferred stock, shares issued	24,154,589	24,154,589
Convertible preferred stock, shares outstanding	24,154,589	24,154,589
Convertible preferred stock, liquidation preference (in dollars)	$ 51,578

Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2015	Mar. 31, 2014
Revenues
Collaboration revenue	$ 652
Operating expenses:
Research and development	9,232	$ 5,381
General and administrative	2,770	1,572
Total operating expenses	12,002	6,953
Other income (expense):
Other income (expense), net	(37)	18
Interest expense	(185)	(92)
Total other income (expense)	(222)	(74)
Net loss	(11,572)	(7,027)
Convertible preferred stock dividends	(2,270)	(1,249)
Net loss applicable to common stockholders	$ (13,842)	$ (8,276)
Net loss per share applicable to common stockholders - basic and diluted	$ (8.23)	$ (6.44)
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted (unaudited)	1,681	1,285

Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
Statements of Cash Flows - USD ($) $ in Thousands	Mar. 31, 2015	Mar. 31, 2014
Operating activities
Net loss	$ (11,572)	$ (7,027)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	209	134
Noncash interest expense	29	30
Change in fair value of warrant liability	38	(18)
Stock-based compensation	840	267
Changes in assets and liabilities:
Unbilled accounts receivable	(484)
Prepaid expenses and other current assets	(364)	29
Accounts payable	1,517	(318)
Accrued expenses	(115)	327
Deferred revenue	14,832
Deferred rent	(40)	(34)
Net cash provided by (used in) operating activities	4,890	(6,610)
Investing activities
Purchases of property and equipment	(19)	(94)
Restricted cash	(1,266)
Net cash used in investing activities	(1,285)	(94)
Financing activities
Principal payments on loan payable	(417)
Payment of offering costs	(146)
Proceeds from issuance of common stock	19
Net cash provided by (used in) financing activities	(547)	24,986
Net increase in cash and cash equivalents	3,058	18,282
Cash and cash equivalents at beginning of period	47,240	1,987
Cash and cash equivalents at end of period	50,298	20,269
Supplemental cash flow information
Cash paid for interest	120	39
Public offering costs incurred byt unpaid at period end	805
Series B convertible preferred stock
Financing activities
Proceeds from issuance of convertible preferred stock, net of issuance costs		$ 24,986
Series C convertible preferred stock
Financing activities
Convertible preferred stock issuance costs	$ (3)

Nature of Business	3 Months Ended
Nature of Business	Mar. 31, 2015
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 genomically defined diseases and to craft drug candidates with therapeutic windows that provide significant and durable clinical response to patients. 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 compounds; the need to develop commercially viable drugs; 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 drugs. 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 the sale of 9,367,708 shares of its common stock (inclusive of 1,221,874 shares of common stock sold by the Company pursuant to the full exercise of an option to purchase additional shares granted to the underwriters in connection with the offering) in an initial public offering (IPO) at a price to the public of $18.00 per share, resulting in net proceeds of $154.2 million after deducting underwriting discounts and commissions and estimated offering costs payable by the Company.

Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2015

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation

The unaudited interim condensed 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) and Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB). 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, 2014 and notes thereto, included in the Company’s prospectus filed with the SEC pursuant to Rule 424(b)(4) on April 30, 2015 (the Prospectus).

The unaudited interim condensed financial statements have been prepared on the same basis as the audited financial statements. In the opinion of the Company’s management, the accompanying unaudited interim condensed financial statements contain all adjustments which are necessary to present fairly the Company’s financial position as of March 31, 2015 and the results of its operations and cash flows for the three months ended March 31, 2015 and 2014. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 2015 are not necessarily indicative of the results for the year ending December 31, 2015, 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, 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 were automatically converted into warrants exercisable for 42,423 shares of common stock. Additionally, the Company is now authorized to issue 120,000,000 shares of common stock and 5,000,000 shares of preferred stock. The significant increase in shares outstanding in April 2015 is expected to impact the year-over-year comparability of the Company’s net loss per share calculations over the next year.

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 (the Common Stock); revenue recognition; the valuation of liability‑classified warrants; accrued expenses; and income taxes.

Revenue recognition

The Company recognizes revenue from license and collaboration agreements in accordance with FASB ASC Topic 605, Revenue Recognition (ASC 605). Accordingly, revenue is recognized when all of the following criteria are met:

Persuasive evidence of an arrangement exists;

Delivery has occurred or services have been rendered;

The seller’s price to the buyer is fixed or determinable; and

Collectability is reasonably assured.

Amounts received prior to satisfying the revenue recognition criteria are recognized as deferred revenue in the Company’s balance sheets. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, current portion. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion.

The Company’s revenue is currently generated through its collaboration agreement with Alexion Pharma Holding (Alexion). The terms of this agreement contains multiple elements, or deliverables, including an exclusive license to research, develop, manufacture and commercialize the licensed products and the compounds in the field in the territory, as well as research and development activities to be performed by the Company on behalf of Alexion related to the licensed product candidates. In addition, the terms of this agreement include payments to the Company of one or more of the following: a nonrefundable, upfront payment; contingent milestone payments related to specified pre-clinical milestones, development milestones and sales-based commercial milestones; fees for research and development services rendered; and royalties on commercial sales of licensed product candidates, if any. To date, the Company has received the upfront payment and is due certain research and development service payments but has not received any milestone payments or earned royalty revenue as a result of product sales. See Note 9 for additional information on this agreement.

When evaluating multiple element arrangements, the Company considers whether the deliverables under the arrangement represent separate units of accounting. This evaluation requires subjective determinations and requires management to make judgments about the individual deliverables and whether such deliverables are separable from the other aspects of the contractual relationship. In determining the units of accounting, management evaluates certain criteria, including whether the deliverables have standalone value, based on the consideration of the relevant facts and circumstances for each arrangement. The consideration received is allocated among the separate units of accounting using the relative selling price method, and the applicable revenue recognition criteria are applied to each of the separate units. Deliverables are considered separate units of accounting provided that: (i) the delivered item(s) has value to the customer on a stand-alone basis and (ii) if the arrangement includes a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) is considered probable and substantially in the control of the Company. In assessing whether an item has stand-alone value, the Company considers factors such as the research, manufacturing and commercialization capabilities of the collaboration partner and the availability of the associated expertise in the general marketplace. In addition, the Company considers whether the collaboration partner can use the deliverable(s) for their intended purpose without the receipt of the remaining element(s), whether the value of the deliverable is dependent on the undelivered item(s) and whether there are other vendors that can provide the undelivered element(s). The Company’s collaboration agreement with Alexion does not contain a general right of return relative to the delivered item(s).

Arrangement consideration that is fixed or determinable is allocated among the separate units of accounting using the relative selling price method. Then, the applicable revenue recognition criteria in ASC 605-25 are applied to each of the separate units of accounting in determining the appropriate period and pattern of recognition. The Company determines the selling price of a unit of accounting following the hierarchy of evidence prescribed by ASC 605-25. Accordingly, the Company determines the estimated selling price for units of accounting within each arrangement using vendor-specific objective evidence (VSOE) of selling price, if available, third-party evidence (TPE) of selling price if VSOE is not available, or best estimate of selling price (BESP) if neither VSOE nor TPE is available. The Company typically uses BESP to estimate the selling price, since it generally does not have VSOE or TPE of selling price for its units of accounting. Determining the BESP for a unit of accounting requires significant judgment. In developing the BESP for a unit of accounting, the Company considers applicable market conditions and relevant entity-specific factors, including factors that were contemplated in negotiating the agreement with the customer and estimated costs. The Company validates the BESP for units of accounting by evaluating whether changes in the key assumptions used to determine the BESP will have a significant effect on the allocation of arrangement consideration between multiple units of accounting.

In the event that an element of a multiple element arrangement does not represent a separate unit of accounting, the Company recognizes revenue from the combined element over the period over which it expects to fulfill its performance obligations or as undelivered items are delivered, as appropriate, if all of the other revenue recognition criteria in ASC 605-25 are met. If the pattern of performance in which the service is provided to the customer can be determined and objectively measurable performance measures exist, then the Company recognizes revenue under the arrangement using the proportional performance method. If there is no discernible pattern of performance and/or objectively measurable performance measures do not exist, then the Company recognizes revenue under the arrangement on a straight-line basis over the period the Company is expected to complete its performance obligations. Revenue recognized is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method or proportional performance method, as applicable, as of the period ending date.

The Company’s multiple-element revenue arrangements may include the following

Exclusive Licenses

The deliverables under the Company’s collaboration agreements may include exclusive licenses to research, develop, manufacture and commercialize licensed products. To account for this element of an arrangement, management evaluates whether an exclusive license has stand-alone value from the undelivered elements based on the consideration of the relevant facts and circumstances of the arrangement, including the research and development capabilities of the collaboration partner. The Company may recognize the arrangement consideration allocated to licenses upon delivery of the license if facts and circumstances indicate that the license has stand-alone value from the undelivered elements, which generally include research and development services. The Company defers arrangement consideration allocated to licenses if facts and circumstances indicate that the delivered license does not have stand-alone value from the undelivered elements.

When management believes a license does not have stand-alone value from the other deliverables to be provided in the arrangement, the Company recognizes revenue attributed to the license on a proportional basis over the Company’s contractual or estimated performance period, which is typically the term of the Company’s research and development obligations. If management cannot reasonably estimate when the Company’s performance obligation ends, then revenue is deferred until management can reasonably estimate when the performance obligation ends. The periods over which revenue should be recognized are subject to estimates by management and may change over the course of the research and development and licensing agreement. Such a change could have a material impact on the amount of revenue the Company records in future periods.

Research and Development Services

The deliverables under the Company’s collaboration agreements may include research and development services to be performed by the Company on behalf of the partner. Payments or reimbursements resulting from the Company’s research and development efforts are recognized as the services are performed and presented on a gross basis because the Company is the principal for such efforts, so long as there is persuasive evidence of an arrangement, the fee is fixed or determinable, and collection of the related amount is reasonably assured.

Milestone Revenue

The Company’s collaboration agreements may include contingent milestone payments related to specified pre-clinical milestones, development milestones and sales-based commercial milestones.

At the inception of an arrangement that includes milestone payments, the Company evaluates whether each milestone is substantive and at risk to both parties on the basis of the contingent nature of the milestone. This evaluation includes an assessment of whether:

the consideration is commensurate with either the Company’s performance to achieve the milestone or the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the Company’s performance to achieve the milestone;

the consideration relates solely to past performance; and

the consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.

The Company evaluates factors such as the scientific, clinical, regulatory, commercial and other risks that must be overcome to achieve the respective milestone and the level of effort and investment required to achieve the respective milestone in making this assessment. There is considerable judgment involved in determining whether a milestone satisfies all of the criteria required to conclude that a milestone is substantive. Milestones that are not considered substantive are accounted for as license payments and recognized over the remaining period of performance from the date of achievement of the milestone. Milestones that are considered substantive will be recognized in their entirety upon successful accomplishment of the milestone, assuming all other revenue recognition criteria are met.

Royalty Revenue

The Company will recognize royalty revenue in the period of sale of the related product(s), based on the underlying contract terms, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, assuming all other revenue recognition criteria are met.

Cash Equivalents

Cash equivalents are highly liquid investments that are readily convertible into cash with original maturities of three months or less when purchased. These assets include an investment in a money market fund that invests in U.S. Treasury obligations. Cash equivalents consist of the following at March 31, 2015 and December 31, 2014 (in thousands):


	March 31,		December 31,
	2015		2014
Money market fund	$	50,298	$	47,240

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, 2015, are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	March 31,		Markets		Inputs		Inputs
Description	2015		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	50,298	$	50,298	$	—	$	—
Preferred stock warrants		(403)		—		—		(403)

Financial instruments measured at fair value as of December 31, 2014, are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2014		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	47,240	$	47,240	$	—	$	—
Preferred stock warrants		(365)		—		—		(365)

At March 31, 2015 and December 31, 2014, all of the Company’s cash equivalents comprise of a money market account, the fair value of which is valued using Level 1 inputs. 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. The fair value of the preferred stock warrant liability was determined based on Level 3 inputs and utilizing the Black‑ Scholes option pricing model (Note 5).

Deferred Offering Costs

The Company capitalizes certain legal, accounting and other third-party fees that are directly associated with in-process equity financings as other assets until such financings are consummated. After consummation of the equity financing, these costs are recorded in stockholders’ equity (deficit) as a reduction of additional paid-in capital generated as a result of the offering. As of March 31, 2015 and December 31, 2014, the Company recorded $1,093 and $91, respectively, of deferred offering costs, included in other assets in the accompanying balance sheet, in contemplation of its IPO.

There have been no other material changes to the significant accounting policies previously disclosed in the Company’s Prospectus.

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 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 is expected to 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 has not yet determined the potential effects of the adoption of this standard on its consolidated financial position, results of operations or cash flows.

On April 7, 2015, the FASB, issued ASU 2015-03, Simplifying the Presentation of Debt Issuance Costs (ASU 2015-03),which requires debt issuance costs to be presented in the balance sheet as a direct deduction from the carrying value of the associated debt liability, consistent with the presentation of a debt discount. ASU 2015-03 will be effective for the Company on January 1, 2016, with early adoption permitted. ASU 2015-03 will be applied on a retrospective basis. The Company is currently assessing the potential impact of the adoption of ASU 2015-03 on its 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 periods ending after December 15, 2016. Early adoption is permitted. The Company is in process of evaluating the new guidance and determining the expected effect on its financial statements.

Restricted Cash	3 Months Ended
Restricted Cash	Mar. 31, 2015
Restricted Cash
Restricted Cash	3. Restricted Cash At March 31, 2015 and December 31, 2014, $1.5 million and $0.2 million, respectively, of the Company’s cash is restricted by a bank. As of March 31, 2015, $0.1 million of the restricted cash is included in current assets as collateral for a stand‑by letter of credit issued by the Company to its landlord in connection with the lease of the Company’s corporate headquarters. 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, with a lease term commencing June 15, 2015 and ending on October 31, 2022, assuming occupancy in October 2015. The lease agreement required the Company to pay a security deposit of $1.3 million, which is included in long-term assets on the Company’s balance sheet as of March 31, 2015. In addition, $0.1 million of restricted cash is included in long‑term assets related to the Company’s corporate credit card agreement as of March 31, 2015 and December 31, 2014.

Accrued Expenses

3 Months Ended

Mar. 31, 2015

Accrued Expenses

Accrued Expenses

4. Accrued Expenses

Accrued expenses consist of the following (in thousands):


	March 31,		December 31,
	2015		2014
Employee compensation	$	625	$	623
External research and pre-clinical development		1,597		2,034
Severance		541		330
Consulting		288		216
Interest		40		150
Deferred offering costs		805		71
Other		508		386
	$	4,404	$	3,810

Term Loan

3 Months Ended

Mar. 31, 2015

Term Loan

Term Loan

5. 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 is 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 is 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 $1.7 million, in the aggregate, for the remainder of 2015.

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. No portion of the warrants have been exercised as of March 31, 2015.

The Series A Warrant and the Series B Warrant are classified as a liability and are re‑measured to the‑then current fair value at each balance sheet date. Re‑measurement gains or losses are recorded in other income (expense) in the statements of operations. The following table sets forth a summary of changes in the fair value of the warrants which represents a recurring measurement that is classified within Level 3 of the fair value hierarchy wherein fair value is estimated using significant unobservable inputs (in thousands):


	Year Ended
	Three Months Ended March 31,
	2015		2014
Beginning balance	$	365	$	119
Change in fair value		38		(18)
Ending balance	$	403	$	101

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. The Company used the following weighted‑average assumptions in its Black‑Scholes option pricing model:


	Series A Warrant									Series B Warrant
				March 31,			March 31,						March 31,
	Issuance			2015			2014			Issuance			2015
Fair value of underlying instrument	$	1.00		$	1.93		$	0.83		$	1.97		$	2.03
Expected volatility		80.70	%		91.70	%		86.49	%		87.18	%		88.00	%
Expected term (in years)		10.0			8.15			9.2			10.0			9.6
Risk-free interest rate		2.58	%		1.83	%		2.72	%		2.36	%		1.94	%
Expected dividend yield		—	%		—	%		—	%		—	%		—	%

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 also recorded a warrant liability that is classified as a long‑term liability in the accompanying balance sheets. The Company recorded interest expense related to the Series A Warrant and the Series B Warrant of less than $0.1 million in each of the three months ended March 31, 2015 and 2014.

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 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. Warrants to purchase 5,991 shares of Common Stock were cancelled as payment for the aggregate exercise price of the Series A Warrant. 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.

Stock Awards

3 Months Ended

Mar. 31, 2015

Stock Awards

Stock Awards

6. Stock Awards

The Company grants restricted stock awards, incentive stock options (ISO), and nonstatutory stock options (NSO) under the Blueprint Medicines Corporation 2011 Stock Option and Grant Plan (the Plan), as amended and restated. In February 2015, the Company amended the Blueprint Medicines Corporation 2011 Stock Option and Grant Plan to increase the number of shares available for grant to 3,590,927. At March 31, 2015, there were 190,276 shares available for future grant under the Plan. ISOs may not be granted at less than fair value on the date of the grant. Furthermore, the exercise price of ISOs granted to an employee, who at the time of grant is a 10% shareholder, may not be less than 110% of the fair value on the date of grant.

Terms of restricted stock awards and stock option agreements, including vesting requirements, are determined by the board of directors, subject to the provisions of the Plan. 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. For options and restricted stock awards granted to date, the exercise price equaled the estimated fair value of the Common Stock as determined by the board of directors on the date of grant. The dates of the Company’s contemporaneous valuations have not always coincided with the dates of the stock option grants. For financial reporting purposes, the Company performed common stock valuations with the assistance of a third‑party specialist, as of January 6, 2014, July 30, 2014, November 10, 2014, February 1, 2015 and March 1, 2015 to determine stock‑based compensation expense.

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


		Weighted-Average
		Grant Date
	Shares	Fair Value
Unvested at December 31, 2014	425,279	$	0.46
Granted	—		—
Vested	(82,045)		0.30
Repurchased	(15,434)		0.55
Unvested at March 31, 2015	327,800		0.49

The Company has granted restricted stock to non‑employees which contain both performance‑based and service‑based vesting criteria. Stock‑based compensation expense associated with these performance‑based awards is recognized if the performance condition is considered probable of achievement using management’s best estimates. In the three months ended March 31, 2014 management concluded that the milestones associated with 90,909 shares of performance‑based restricted stock were probable of achievement, and the Company began to record stock‑based compensation expense using the accelerated attribution method, accordingly. The Company recorded $0.1 million of stock‑ based compensation expense for non‑employee performance‑based awards in the three months end March 31, 2014. In the three months ended December 31, 2014, management concluded that the milestones associated with an additional 90,909 shares of performance‑based restricted stock were probable of achievement, and the Company began to record stock‑based compensation expense using the accelerated attribution method accordingly. The Company recorded $0.2 million of stock‑ based compensation expense for non‑employee performance‑based awards in the three months end March 31, 2015 related to both milestone achievements.

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


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(3)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2014(1)	1,501,912	$	2.02	9.42	$	7,704
Granted	572,638		8.92
Exercised	(12,652)		1.81
Canceled	(10,270)		2.47
Outstanding at March 31, 2015(1)	2,051,628	$	3.95	9.37	$	11,312
Exercisable at March 31, 2015	241,376	$	2.06	8.97	$	1,787
Vested and expected to vest at March 31, 2015(2)	1,949,469	$	3.94	9.37	$	10,760

(1)

Includes 164,529 unvested shares of common stock related to early exercises of stock options.

(2)

Represents the number of vested options as of March 31, 2015, plus the number of unvested options expected to vest as of March 31, 2015.

(3)

Intrinsic value represents the amount by which the fair market value as of March 31, 2015 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,		March 31,
	2015		2014
Risk-free interest rate	1.41% - 1.67	%	1.88	%
Expected dividend yield	—	%	—	%
Expected term (years)	6		6
Expected stock price volatility	86.14	%	91.36	%

The weighted‑average grant date fair value of options granted in the three months ended March 31, 2015 and 2014 was $6.45 and $1.41, respectively. The total intrinsic value of options exercised in the three months ended March 31, 2015 was $0.1 million. There were no options exercised in the three months ended March 31, 2014.

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


	Three Months Ended
	March 31,
	2015		2014
Research and development	$	392	$	131
General and administrative		448		136
Total stock-based compensation expense	$	840	$	267

At March 31, 2015, there was $7.5 million of total unrecognized compensation cost related to nonvested stock awards, which is expected to be recognized over a weighted‑average period of 3.17 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.

Net Loss Per Share Applicble to Common Stockholders

3 Months Ended

Mar. 31, 2015

Net Loss Per Share Applicble to Common Stockholders

Net Loss Per Share Applicble to Common Stockholders

7. Net Loss per Share Applicable to Common Stockholders

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. 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,
	2015	2014
Convertible preferred stock	15,467,479	11,075,750
Warrants	42,423	27,272
Stock options	2,051,628	482,156
Unvested restricted stock	327,800	720,276
Total	17,889,330	12,305,454

The weighted average number of common shares used in net loss per share applicable to common stockholders on a basic and diluted basis were 1,681,236 and 1,285,168 for the three months ended March 31, 2015 and 2014, respectively.

Collaboration Agreement	3 Months Ended
Collaboration Agreement	Mar. 31, 2015
Collaboration Agreement
Collaboration Agreement	8. Collaboration Agreement Alexion In March 2015, the Company entered into a research, development and commercialization agreement with 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 this 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 its employees’ time devoted to the research plan at 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 agreement and is eligible to receive over $250 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 royalties, 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 agreement. Alexion has the right to terminate the Alexion agreement if the Company undergoes a change of control or become an affiliate of a biotechnology or pharmaceutical company, and may terminate at‑will upon 90 days, prior written notice. The Company and Alexion have the right to terminate the 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 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 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 agreement. During the three months ended March 31, 2015, the Company recognized revenue of $0.7 million related to the agreement. The Company evaluated whether the milestones that may be received in connection with the agreement are substantive or non-substantive milestones. The Company concluded that the first pre-clinical milestone in the agreement is non-substantive due to the certainty at the date the arrangement was entered into that the event will be achieved. The Company will recognize revenues from the related milestone payment over the period of performance. During May 2015, the Company achieved the first pre-clinical milestone of $1.75 million under the terms of the agreement. 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. 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.

Related-Party Transactions	3 Months Ended
Related-Party Transactions	Mar. 31, 2015
Related-Party Transactions
Related-Party Transactions	9. Related‑Party Transactions The Company has received consulting and management services from one of its investors, Third Rock Ventures LLC (Third Rock Ventures). The Company paid Third Rock Ventures $0.1 million for these services during the three months ended March 31, 2014. The Company did not receive any consulting services from Third Rock Ventures during the three months ended March 31, 2015.

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

+ References + Details

Subsequent Events	3 Months Ended
Subsequent Events	Mar. 31, 2015
Subsequent Events
Subsequent Events	10. Subsequent Events 2015 Stock Option and Incentive Plan On April 8, 2015, the 2015 Stock Option and Incentive Plan was adopted by the board of directors and approved by the stockholders and became effective upon the completion of the IPO. The 2015 Stock Option Plan replaced the 2011 Stock Option Plan. Any options or awards outstanding under the Company’s 2011 Stock Option Plan remained outstanding and effective. The 2015 Stock Option Plan provides the Company flexibility to use various equity‑based incentive and other awards as compensation tools to motivate its workforce. These tools include stock options, stock appreciation rights, restricted stock, restricted stock units, unrestricted stock, performance share awards and cash‑based awards. The Company initially reserved 1,460,084 shares of common stock for the issuance of awards under the 2015 Stock Option Plan, which 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. This number is subject to adjustment in the event of a stock split, stock dividend or other change in our capitalization. 2015 Employee Stock Purchase Plan On April 8, 2015, the Company’s stockholders approved the 2015 Employee Stock Purchase Plan. A total of 243,347 shares of common stock were initially authorized for issuance under this plan. The 2015 Employee Stock Purchase Plan became effective upon the completion of the IPO.

Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2015

Summary of Significant Accounting Policies

Basis of Presentation

Use of Estimates

Revenue recognition

Persuasive evidence of an arrangement exists;

Delivery has occurred or services have been rendered;

The seller’s price to the buyer is fixed or determinable; and

Collectability is reasonably assured.

The Company’s multiple-element revenue arrangements may include the following

Exclusive Licenses

Research and Development Services

Milestone Revenue

The Company’s collaboration agreements may include contingent milestone payments related to specified pre-clinical milestones, development milestones and sales-based commercial milestones.

the consideration relates solely to past performance; and

the consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.

Royalty Revenue

Cash Equivalents


	March 31,		December 31,
	2015		2014
Money market fund	$	50,298	$	47,240

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.

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


			Active		Observable		Unobservable
	March 31,		Markets		Inputs		Inputs
Description	2015		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	50,298	$	50,298	$	—	$	—
Preferred stock warrants		(403)		—		—		(403)

Financial instruments measured at fair value as of December 31, 2014, are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2014		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	47,240	$	47,240	$	—	$	—
Preferred stock warrants		(365)		—		—		(365)

Deferred Offering Costs

There have been no other material changes to the significant accounting policies previously disclosed in the Company’s Prospectus.

Recent Accounting Pronouncements

- Definition

Disclosure of accounting policy for cash and cash equivalents, including the policy for determining which items are treated as cash equivalents. Other information that may be disclosed includes (1) the nature of any restrictions on the entity's use of its cash and cash equivalents, (2) whether the entity's cash and cash equivalents are insured or expose the entity to credit risk, (3) the classification of any negative balance accounts (overdrafts), and (4) the carrying basis of cash equivalents (for example, at cost) and whether the carrying amount of cash equivalents approximates fair value.

+ References + Details

- Definition

Disclosure of accounting policy for revenue recognition. If the entity has different policies for different types of revenue transactions, the policy for each material type of transaction is generally disclosed. If a sales transaction has multiple element arrangements (for example, delivery of multiple products, services or the rights to use assets) the disclosure may indicate the accounting policy for each unit of accounting as well as how units of accounting are determined and valued. The disclosure may encompass important judgment as to appropriateness of principles related to recognition of revenue. The disclosure also may indicate the entity's treatment of any unearned or deferred revenue that arises from the transaction.

+ References + Details

Summary of Significant Accounting Policies (Tables)

3 Months Ended

Mar. 31, 2015

Summary of Significant Accounting Policies

Schedule of cash equivalents

Cash equivalents consist of the following at March 31, 2015 and December 31, 2014 (in thousands):


	March 31,		December 31,
	2015		2014
Money market fund	$	50,298	$	47,240

Schedule of financial instruments measured at fair value

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


			Active		Observable		Unobservable
	March 31,		Markets		Inputs		Inputs
Description	2015		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	50,298	$	50,298	$	—	$	—
Preferred stock warrants		(403)		—		—		(403)

Financial instruments measured at fair value as of December 31, 2014, are classified below based on the fair value hierarchy described above:


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2014		(Level 1)		(Level 2)		(Level 3)
Money market funds, included in cash equivalents	$	47,240	$	47,240	$	—	$	—
Preferred stock warrants		(365)		—		—		(365)

Accrued Expenses (Tables)

3 Months Ended

Mar. 31, 2015

Accrued Expenses

Schedule of accrued expenses

Accrued expenses consist of the following (in thousands):


	March 31,		December 31,
	2015		2014
Employee compensation	$	625	$	623
External research and pre-clinical development		1,597		2,034
Severance		541		330
Consulting		288		216
Interest		40		150
Deferred offering costs		805		71
Other		508		386
	$	4,404	$	3,810

Term Loan (Tables)

3 Months Ended

Mar. 31, 2015

Term Loan

Summary of changes in the fair value of the warrants which represents a recurring measurement that is classified within Level 3 of the fair value hierarchy wherein fair value is estimated

The following table sets forth a summary of changes in the fair value of the warrants which represents a recurring measurement that is classified within Level 3 of the fair value hierarchy wherein fair value is estimated using significant unobservable inputs (in thousands):


	Year Ended
	Three Months Ended March 31,
	2015		2014
Beginning balance	$	365	$	119
Change in fair value		38		(18)
Ending balance	$	403	$	101

Schedule of weighted average assumptions of warrants in Black Scholes option pricing model


	Series A Warrant									Series B Warrant
				March 31,			March 31,						March 31,
	Issuance			2015			2014			Issuance			2015
Fair value of underlying instrument	$	1.00		$	1.93		$	0.83		$	1.97		$	2.03
Expected volatility		80.70	%		91.70	%		86.49	%		87.18	%		88.00	%
Expected term (in years)		10.0			8.15			9.2			10.0			9.6
Risk-free interest rate		2.58	%		1.83	%		2.72	%		2.36	%		1.94	%
Expected dividend yield		—	%		—	%		—	%		—	%		—	%

Stock Awards (Tables)

3 Months Ended

Mar. 31, 2015

Stock Awards

Summary of unvested restricted stock


		Weighted-Average
		Grant Date
	Shares	Fair Value
Unvested at December 31, 2014	425,279	$	0.46
Granted	—		—
Vested	(82,045)		0.30
Repurchased	(15,434)		0.55
Unvested at March 31, 2015	327,800		0.49

Summary of stock option activity


		Weighted-		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value(3)
	Shares	Price		(in Years)	(in thousands)
Outstanding at December 31, 2014(1)	1,501,912	$	2.02	9.42	$	7,704
Granted	572,638		8.92
Exercised	(12,652)		1.81
Canceled	(10,270)		2.47
Outstanding at March 31, 2015(1)	2,051,628	$	3.95	9.37	$	11,312
Exercisable at March 31, 2015	241,376	$	2.06	8.97	$	1,787
Vested and expected to vest at March 31, 2015(2)	1,949,469	$	3.94	9.37	$	10,760

(1)

Includes 164,529 unvested shares of common stock related to early exercises of stock options.

(2)

Represents the number of vested options as of March 31, 2015, plus the number of unvested options expected to vest as of March 31, 2015.

Intrinsic value represents the amount by which the fair market value as of March 31, 2015 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,		March 31,
	2015		2014
Risk-free interest rate	1.41% - 1.67	%	1.88	%
Expected dividend yield	—	%	—	%
Expected term (years)	6		6
Expected stock price volatility	86.14	%	91.36	%

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 statements of operations is as follows (in thousands):


	Three Months Ended
	March 31,
	2015		2014
Research and development	$	392	$	131
General and administrative		448		136
Total stock-based compensation expense	$	840	$	267

Net Loss Per Share Applicble to Common Stockholders (Tables)

3 Months Ended

Mar. 31, 2015

Net Loss Per Share Applicble to Common Stockholders

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


	Three Months Ended
	March 31,
	2015	2014
Convertible preferred stock	15,467,479	11,075,750
Warrants	42,423	27,272
Stock options	2,051,628	482,156
Unvested restricted stock	327,800	720,276
Total	17,889,330	12,305,454

Nature of Business (Details) - Subsequent Event - IPO - Common Stock $ / shares in Units, $ in Millions	May 05, 2015 USD ($) $ / shares shares
Initial Public Offering
Stock sold (in shares)	9,367,708
Share price (in dollars per share) \| $ / shares	$ 18.00
Proceeds from issuance of IPO shares \| $	$ 154.2
Shares issued to underwriters in IPO	1,221,874

Summary of Significant Accounting Policies - Stock Split nad Conversion of Stock (Details)	May 05, 2015 shares	Apr. 10, 2015	Mar. 31, 2015 shares	Dec. 31, 2014 shares
Stock Split and Conversion of stock
Common stock, shares authorized			110,000,000	110,000,000
Subsequent Event \| IPO \| Common Stock
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
Common stock, shares authorized	120,000,000
Subsequent Event \| IPO \| Preferred Stock
Stock Split and Conversion of stock
Preferred stock, shares authorized	5,000,000

Summary of Significant Accounting Policies - Cash Equivalents (Details) - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014
Money market fund
Cash Equivalents
Cash equivalents	$ 50,298	$ 47,240

Summary of Significant Accounting Policies - Fair Value Measurements (Details) - Recurring - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014	Mar. 31, 2014	Dec. 31, 2013
Fair Value of Financial Instruments
Preferred stock warrants	$ (403)	$ (365)
Money market fund
Fair Value of Financial Instruments
Cash equivalents	50,298	47,240
Active Markets (Level 1) \| Money market fund
Fair Value of Financial Instruments
Cash equivalents	50,298	47,240
Unobservable Inputs (Level 3)
Fair Value of Financial Instruments
Preferred stock warrants	$ (403)	$ (365)	$ (101)	$ (119)

Summary of Significant Accounting Policies - Deferred Offering Costs (Details) - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014
Summary of Significant Accounting Policies
Deferred Offering Costs	$ 1,093	$ 91

Restricted Cash (Details) $ in Thousands	Feb. 12, 2015 ft²	Mar. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)
Restricted Cash
Restricted cash included in current assets		$ 119	$ 119
Restricted cash included in long-term assets		1,336	70
Corporate Headquarters Lease
Restricted Cash
Lease rentable square footage \| ft²	38,500
Security deposit		1,300
Restricted by bank
Restricted Cash
Restricted cash, current and noncurrent		1,500	200
Stand-by letter of credit to landlord in connection with lease \| Corporate Headquarters Lease
Restricted Cash
Restricted cash included in current assets		100
Restricted cash related to corporate credit card agreement
Restricted Cash
Restricted cash included in long-term assets		$ 100	$ 100

Accrued Expenses (Details) - USD ($) $ in Thousands	Mar. 31, 2015	Dec. 31, 2014
Accrued Expenses
Employee compensation	$ 625	$ 623
External research and pre-clinical development	1,597	2,034
Severance	541	330
Consulting	288	216
Interest	40	150
Deferred offering costs	805	71
Other	508	386
Total accrued expenses	$ 4,404	$ 3,810

Term Loan (Details) - Loan and Security Agreement - USD ($) $ in Millions	1 Months Ended					3 Months Ended
	Nov. 30, 2014	Jun. 30, 2014	Sep. 30, 2013	Jun. 30, 2013	May 31, 2013	Mar. 31, 2015
Term Loan
Maximum borrowing capacity					$ 5.0
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 2015						$ 1.7
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

Term Loan - Warrants (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended		3 Months Ended
	Nov. 30, 2014	May 31, 2013	Mar. 31, 2015	Mar. 31, 2014
Fair value liabilities measured on recurring basis unobservable input reconciliation
Change in fair value of warrant liability			$ 38	$ (18)
Series A And Series B Warrants \| Maximum
Weighted-average assumptions
Interest expense			$ 100	$ 100
Series A Warrants
Weighted-average assumptions
Fair value of underlying instrument		$ 1.00	$ 1.93	$ 0.83
Expected volatility		80.70%	91.70%	86.49%
Expected term		10 years	8 years 1 month 24 days	9 years 2 months 12 days
Risk-free interest rate		2.58%	1.83%	2.72%
Series B Warrants
Weighted-average assumptions
Fair value of underlying instrument	$ 1.97		$ 2.03
Expected volatility	87.18%		88.00%
Expected term	10 years		9 years 7 months 6 days
Risk-free interest rate	2.36%		1.94%
Loan and Security Agreement \| Series A And Series B Warrants
Term Loan
Warrants life			10 years
Warrants exercised			$ 0
Loan and Security Agreement \| 2013 Term Loan \| Series A Warrants
Term Loan
Number of shares that can be purchased by the warrants issued		150,000
Exercise price of warrants issued (in dollars per share)		$ 1.00
Loan and Security Agreement \| 2014 Term Loan \| Series B Warrants
Term Loan
Number of shares that can be purchased by the warrants issued	83,333
Exercise price of warrants issued (in dollars per share)	$ 1.20
Recurring
Fair value liabilities measured on recurring basis unobservable input reconciliation
Beginning balance			365
Ending balance			403
Unobservable Inputs (Level 3) \| Recurring
Fair value liabilities measured on recurring basis unobservable input reconciliation
Beginning balance			365	$ 119
Change in fair value of warrant liability			38	(18)
Ending balance			$ 403	$ 101

Term Loan - Warrants Activity (Details) - $ / shares	May 13, 2015	May 05, 2015	Nov. 30, 2014	May 31, 2013
Series A Warrants \| Subsequent Event
Warrant activity
Number of common shares that became exercisable from warrants		27,272
Exercise price of warrants issued (in dollars per share)		$ 5.50
Series B Warrants \| Subsequent Event
Warrant activity
Number of common shares that became exercisable from warrants		15,151
Exercise price of warrants issued (in dollars per share)		$ 6.60
Loan and Security Agreement \| 2013 Term Loan \| Series A Warrants
Warrant activity
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
Warrant activity
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

Stock Awards - Unvested Restricted Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		12 Months Ended
	Feb. 28, 2015	Mar. 31, 2015	Mar. 31, 2014	Dec. 31, 2014
Nonvested stock awards, Weighted-Average Grant Date Fair Value
Share-based compensation expense recorded		$ 840	$ 267
Restricted Stock
Unvested restricted stock rollforward
Unvested at beginning of period (in shares)		425,279
Vested ( in shares)		(82,045)
Repurchased (in shares)		(15,434)
Unvested at end of period (in shares)		327,800
Nonvested stock awards, Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share)		$ 0.46
Vested (in dollars per share)		$ 0.3
Repurchased (in dollars per share)		0.55
Unvested at end of period (in dollars per share)		$ 0.49		$ 0.46
Shares for which performace condition considered probable of achievement (in shares)			90,909	90,909
Non-employee performance-based restricted stock
Nonvested stock awards, Weighted-Average Grant Date Fair Value
Share-based compensation expense recorded		$ 200	$ 100
2011 Stock Option and Grant Plan
Stock Awards
Increase in number of shares available for grant	3,590,927
Number of shares available for grant		190,276
Minimum percentage of fair value on grant date that the exercise price is required to be for employee shareholders for which restrictions apply		10.00%
Minimum percentage of fair value on grant date that the exercise price is required to be for employee shareholders for which restrictions apply		110.00%
Award vesting period		4 years
Cliff vesting period for new employees		1 year
Award expiration period		10 years

Stock Awards - Stock Options (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2015	Dec. 31, 2014
Stock option rollforward
Outstanding at beginning of period (in shares)	1,501,912
Granted (in shares)	572,638
Exercised ( in shares)	(12,652)
Cancelled ( in shares)	(10,270)
Outstanding at end of period (in shares)	2,051,628	1,501,912
Exercisable at end of period (in shares)	241,376
Vested and expected to vest at end of period (in shares)	1,949,469
Weighted average exercise price
Outstanding at beginning of period (in dollars per share)	$ 2.02
Granted (in dollars per share)	8.92
Exercised ( in dolalrs per share)	1.81
Cancelled ( in dollars per share)	2.47
Outstanding at end of period (in dollars per share)	3.95	$ 2.02
Exercisable at end of period (in dollars per share)	2.06
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest, Outstanding, Weighted Average Exercise Price	$ 3.94
Other disclosures
SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2	9 years 4 months 13 days	9 years 5 months 1 day
SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2	9 years 4 months 13 days	9 years 5 months 1 day
Remaining contratual life, exercisable at end of period	8 years 11 months 19 days
Remaining contractual life, vested and expected to vest at end of period	9 years 4 months 13 days
Aggregate instrinsic value, outstanding at beginning of period	$ 7,704
Aggregate instrinsic value, outstanding at end of period	11,312	$ 7,704
Aggregate instrinsic value, exercisable at end of period	1,787
Aggregate instrinsic value, vested and expected to vest at end of period	$ 10,760
Unvested shares of common stock related to early exercises of stock options included in outstanding stock options at end of period (in shares)	164,529

Stock Awards - Weighted Average Assumptions (Details) - Employee Stock Options - USD ($) $ / shares in Units, $ in Millions	3 Months Ended
	Mar. 31, 2015	Mar. 31, 2014
Assumptions used in estimating the fair value of sotck options granted
Minimum risk-free interest rate	1.41%
Maximum risk-free interest rate	1.67%
Risk-free interest rate		1.88%
Expected term (in years)	6 years	6 years
Expected stock price volatility	86.14%	91.36%
Other disclosures
Weighted-average grant date fair value of options granted	$ 6.45	$ 1.41
Total intrinsic value of options exercised	$ 0.1
Options exercised	12,652

Stock Awards - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2015	Mar. 31, 2014
Stock-based compensation
Allocated Share-based Compensation Expense	$ 840	$ 267
Total unrecognized compensation cost related to non-vested stock option awards	$ 7,500
Weighted-average period over which unrecognized compensation cost will be recognized	3 years 2 months 1 day
Research and development
Stock-based compensation
Allocated Share-based Compensation Expense	$ 392	131
General and administrative
Stock-based compensation
Allocated Share-based Compensation Expense	$ 448	$ 136

Net Loss Per Share Applicble to Common Stockholders (Details) - shares	3 Months Ended
	Mar. 31, 2015	Mar. 31, 2014
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	17,889,330	12,305,454
Weighted-average number of common shares used in net loss per share applicable to common stockholders - basic and diluted (unaudited)	1,681,000	1,285,000
Convertible preferred stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	15,467,479	11,075,750
Warrants
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	42,423	27,272
Stock options
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	2,051,628	482,156
Restricted Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	327,800	720,276

Collaboration Agreement (Details) $ in Thousands	3 Months Ended
Collaboration Agreement (Details) $ in Thousands	Mar. 31, 2015 USD ($) item
Collaboration Agreement
Collaboration revenue	$ 652
Alexion
Collaboration Agreement
Collaborative partner's funding responsbility 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 commerical sale, option 1	10 years
Royalty term from first commerical sale, option 2	15 years
Written termination notice period	90 days
Number of deliverables \| item	3
Collaboration revenue	$ 700
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

Related-Party Transactions (Details) - USD ($)	3 Months Ended
Related-Party Transactions (Details) - USD ($)	Mar. 31, 2015	Mar. 31, 2014
Third Rock Ventures LLC
Related-Party Transactions
Purchases from related party	$ 0	$ 100,000

Subsequent Events - Share Based Compensation (Details) - Subsequent Event	Apr. 08, 2015 shares
2015 Stock Option Plan
Stock Option Plan and Employee Stock Purchase Plan
Number of common shares reserved for future issuance of awards	1,460,084
Annual cumulative increase of number of shares of common stock issued and outstanding which will be reserved for future issuance (as a percent)	4.00%
2015 Employee Stock Purchase Plan
Stock Option Plan and Employee Stock Purchase Plan
Number of shares authorized for issuance	243,347

Subsequent Events - Initial Public Offering (Details) - Subsequent Event - IPO - Common Stock $ / shares in Units, $ in Millions	May 05, 2015 USD ($) $ / shares shares
Subsequent Events
Stock sold (in shares) \| shares	9,367,708
Share price (in dollars per share) \| $ / shares	$ 18.00
Proceeds from issuance of IPO shares \| $	$ 154.2

Subsequent Events - Warrant Exercise and Collaboration Agreement (Details) - Alexion - USD ($) $ in Thousands	1 Months Ended	3 Months Ended
	May 31, 2015	Mar. 31, 2015
Subsequent Event [Line Items]
Payment receivable upon achievement of milestone		$ 250,000
Subsequent Event \| Pre-clinical milestone for first licensed product
Subsequent Event [Line Items]
Payment receivable upon achievement of milestone	$ 1,750