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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2016	Feb. 24, 2017	Jun. 30, 2016
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	0001070081
Document Type	10-K
Document Period End Date	Dec. 31, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 230,565,407
Entity Common Stock, Shares Outstanding (in shares)		34,556,440
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 58,321	$ 58,022
Marketable securities	173,345	280,903
Prepaid expenses and other current assets	4,691	5,930
Trade receivables, net	24,929	11,094
Total current assets	261,286	355,949
Fixed assets, net	7,429	8,974
Deposits and other assets	630	358
Total assets	269,345	365,281
Current liabilities:
Accounts payable and accrued expenses	48,759	45,247
Deferred revenue	0	139
Other current liabilities	865	0
Total current liabilities	49,624	45,386
Deferred revenue - long-term	1,587	0
Long-term debt	98,216	91,848
Other long-term liabilities	335	2,046
Total liabilities	149,762	139,280
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 34,169,410 shares at December 31, 2016. Authorized 125,000,000 shares; issued and outstanding 33,916,559 shares at December 31, 2015	34	34
Additional paid-in capital	856,142	820,165
Accumulated other comprehensive loss	(1,485)	(1,200)
Accumulated deficit	(735,108)	(592,998)
Total stockholders’ equity	119,583	226,001
Total liabilities and stockholders’ equity	$ 269,345	$ 365,281

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares (in shares)	125,000,000	125,000,000
Common stock, issued shares (in shares)	34,169,410	33,916,559
Common stock, outstanding shares (in shares)	34,169,410	33,916,559

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Revenues:
Net product revenue	$ 81,447	$ 33,696	$ 717
Collaboration and grant revenue	1,258	3,070	24,528
Total revenues	82,705	36,766	25,245
Operating expenses:
Research and development	117,633	121,816	79,838
Selling, general and administrative	97,130	82,080	44,820
Total operating expenses	214,763	203,896	124,658
Loss from operations	(132,058)	(167,130)	(99,413)
Interest (expense) income, net	(8,276)	(2,367)	1,180
Other expense, net	(1,207)	(465)	(213)
Loss from operations before tax (expense) benefit	(141,541)	(169,962)	(98,446)
Income tax (expense) benefit	(569)	(485)	4,693
Net loss attributable to common stockholders	$ (142,110)	$ (170,447)	$ (93,753)
Weighted-average shares outstanding:
Basic and diluted (in shares)	34,044,584	33,626,248	31,565,310
Net loss per share—basic and diluted (in dollars per share)	$ (4.17)	$ (5.07)	$ (2.97)

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Statement of Comprehensive Income [Abstract]
Net loss	$ (142,110)	$ (170,447)	$ (93,753)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities, net of tax	386	(202)	(457)
Foreign currency translation loss	(671)	(261)	(350)
Comprehensive loss	$ (142,395)	$ (170,910)	$ (94,560)

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common stock	Additional paid-in capital	Accumulated other comprehensive income (loss)	Accumulated deficit
Balance at Dec. 31, 2013	$ 136,542	$ 24	$ 465,246	$ 70	$ (328,798)
Balance (in shares) at Dec. 31, 2013		23,803,282
Increase (Decrease) in Stockholders' Equity
Issuance of common stock from public offerings and exercise of over allotment exercise, net of offering costs	235,980	$ 9	235,971
Issuance of common stock from public offerings and exercise of over allotment exercise, net of offering costs (in shares)		8,613,265
Exercise of options	1,195	$ 0	1,195
Exercise of stock options (in shares)		108,645
Restricted stock vesting	0
Restricted stock vesting (in shares)		373,200
Share-based compensation expense	19,310		19,310
Net loss	(93,753)				(93,753)
Comprehensive loss	(807)			(807)
Balance at Dec. 31, 2014	298,467	$ 33	721,722	(737)	(422,551)
Balance (in shares) at Dec. 31, 2014		32,898,392
Increase (Decrease) in Stockholders' Equity
Equity component of the convertible notes issuance, net	55,754		55,754
Exercise of options	8,711	$ 1	8,710
Exercise of stock options (in shares)		656,248
Restricted stock vesting	0
Restricted stock vesting (in shares)		361,919
Share-based compensation expense	33,979		33,979
Net loss	(170,447)				(170,447)
Comprehensive loss	(463)			(463)
Balance at Dec. 31, 2015	226,001	$ 34	820,165	(1,200)	(592,998)
Balance (in shares) at Dec. 31, 2015		33,916,559
Increase (Decrease) in Stockholders' Equity
Exercise of options	968	$ 0	968
Exercise of stock options (in shares)		89,216
Restricted stock vesting	0
Restricted stock vesting (in shares)		163,635
Share-based compensation expense	35,009		35,009
Net loss	(142,110)				(142,110)
Comprehensive loss	(285)			(285)
Balance at Dec. 31, 2016	$ 119,583	$ 34	$ 856,142	$ (1,485)	$ (735,108)
Balance (in shares) at Dec. 31, 2016		34,169,410

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Cash flows from operating activities
Net loss	$ (142,110)	$ (170,447)	$ (93,753)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	3,290	2,876	2,235
Change in valuation of warrant liability	(47)	(140)	130
Amortization of premiums on investments	1,885	2,480	1,607
Amortization of debt issuance costs	302	107	0
Share-based compensation expense	35,009	33,979	19,310
Non-cash interest expense	6,065	2,146	0
Disposal of asset	0	(37)	0
Benefit for deferred income taxes	(199)	0	0
Unrealized foreign currency transaction losses, net	1,202	0	0
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	1,171	(2,107)	(2,286)
Trade receivables, net	(14,842)	(6,907)	(3,487)
Deposits and other assets	(278)	131	(340)
Accounts payable and accrued expenses	4,259	16,981	16,914
Other long-term liabilities	(799)	(92)	(80)
Deferred revenue	1,526	(3,307)	2,476
Net cash used in operating activities	(103,566)	(124,337)	(57,274)
Cash flows from investing activities
Purchases of fixed assets	(1,776)	(2,720)	(4,664)
Purchases of marketable securities	(85,377)	(223,762)	(247,804)
Sale & redemption of marketable securities	191,634	205,671	107,300
Net cash provided by (used in) investing activities	104,481	(20,811)	(145,168)
Cash flows from financing activities
Payments on long-term debt	0	0	(49)
Proceeds from exercise of options	968	8,711	1,196
Net proceeds from public offerings	0	0	235,979
Debt issuance costs related to convertible notes	0	(4,650)	0
Proceeds from issuance of convertible notes	0	150,000	0
Net cash provided by financing activities	968	154,061	237,126
Effect of exchange rate changes on cash	(1,584)	(639)	(350)
Net increase in cash and cash equivalents	299	8,274	34,334
Cash and cash equivalents, beginning of period	58,022	49,748	15,414
Cash and cash equivalents, end of period	58,321	58,022	49,748
Supplemental disclosure of cash information
Cash paid for interest	4,513	0	1
Cash paid for income taxes	943	111	0
Supplemental disclosures of non-cash information related to investing and financing activities
Change in unrealized gain (loss) on marketable securities	$ 386	$ (202)	$ (457)

The Company	12 Months Ended
The Company	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	The Company PTC Therapeutics, Inc. (the Company or PTC) was incorporated as a Delaware corporation on March 31, 1998. PTC is a global biopharmaceutical company focused on the discovery, development and commercialization of orally administered, small molecule therapeutics targeting an area of RNA biology referred to as post-transcriptional control. The letters “PTC” in the corporate name are an acronym for post-transcriptional control processes, which are the regulatory events that occur in cells during and after a messenger RNA is copied from DNA through the transcription process. The Company has discovered all of its compounds currently under development using its proprietary technologies. The Company plans to continue to develop these compounds both on its own and through selective collaboration arrangements with leading pharmaceutical and biotechnology companies. The Company believes that systematically targeting post-transcriptional control processes represents an unexploited approach to drug discovery and development. The Company’s internally discovered pipeline addresses multiple therapeutic areas, including rare disorders and oncology. The Company’s lead product, Translarna™ (ataluren) received marketing authorization from the European Commission in August 2014 for the treatment of nmDMD in ambulatory patients age 5 years and over in the 31 member states of the European Economic Area, or EEA. nmDMD is a rare, life threatening disorder. The Company’s marketing authorization in the EEA is subject to annual review and renewal by the European Commission following reassessment by the European Medicines Agency, or EMA, of the benefit-risk balance of the authorization, which the Company refers to as the annual EMA reassessment. This marketing authorization is further subject to the specific obligation to conduct and submit the results of a multi-center, randomized, double-blind, 18-month, placebo-controlled trial, followed by an 18-month open-label extension, according to an agreed protocol, in order to confirm the efficacy and safety of Translarna in the approved patient population. The final report on the trial and open-label extension is to be submitted by the Company to the EMA by the end of the third quarter of 2021. The Company refers to the trial and open-label extension together as Study 041. The marketing authorization in the EEA was last renewed in January 2017 and is effective, unless extended, through August 5, 2017. The renewal was based on the Company’s commitment to conduct Study 041 and the totality of the clinical data available from its trials and studies of Translarna for the treatment of nmDMD, including the safety and efficacy results of the Phase 2b and Phase 3 clinical trials. The primary efficacy endpoint was not achieved in either trial within the pre-specified level of statistical significance. The Company submitted a marketing authorization renewal request to the EMA in February 2017. In June 2014, the Company initiated reimbursed early access programs, or EAP programs, for Translarna for nmDMD patients in selected territories in the EEA and recorded its first sales of Translarna in the third quarter of 2014 pursuant to an EAP program. In December 2014, the Company recorded its first commercial sales in Germany. As of December 31, 2016, Translarna was available in over 25 countries on a commercial basis or pursuant to the EAP program. The Company expects to expand its launch activities across the EEA pursuant to the marketing authorization granted by the EMA throughout 2017 and future years, subject to continued renewal of its marketing authorization following annual EMA reassessments and successful completion of pricing and reimbursement negotiations. Concurrently, the Company plans to continue to pursue EAP programs in select countries where those mechanisms exist, both within the EEA and in other countries that will reference the marketing authorization in the EEA. Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application, or NDA, over protest with the United States Food and Drug Administration, or FDA. The FDA has granted a standard review for the NDA and has set a target review date under the Prescription Drug User Fee Act, or PDUFA, of October 24, 2017. The PDUFA date is the goal date for the FDA to complete its review of the NDA, however, such date is not binding on the agency and there can be no assurance that the FDA will complete its review of our NDA by the PDUFA goal date. Filing over protest is a procedural path permitted by FDA regulations that allows a company to have its NDA filed and reviewed when there is a disagreement with regulators over the acceptability of the NDA submission. The NDA, which seeks approval of Translarna for the treatment of nmDMD in the United States, was initially submitted by the Company in December 2015. In February 2016, following the initial submission, the Company received a Refuse to File letter from the FDA regarding the NDA. The FDA stated in the Refuse to File letter that the NDA was not sufficiently complete to permit a substantive review. Specifically, the Company was notified in the letter that, in the view of the FDA, both the Phase 2b and Phase 3 ACT DMD trials were negative and do not provide substantial evidence of effectiveness and that the NDA did not contain adequate information regarding the abuse potential of Translarna. Additionally, the FDA stated that the Company had proposed a post-hoc adjustment of ACT DMD that eliminates data from a majority of enrolled patients. During July 2016, the Company appealed the Refuse to File decision via the formal dispute resolution process within FDA’s Center for Drug Evaluation and Research; however, this appeal was denied by the FDA’s Office of Drug Evaluation I in October 2016. On March 2, 2017, the Company announced that the primary and secondary endpoints were not achieved in ACT CF, the Company’s Phase 3 double-blind, placebo-controlled, 48-week clinical trial comparing Translarna to placebo in nonsense mutation cystic fibrosis, or nmCF, patients six years of age or older not receiving chronic inhaled aminoglycosides. The safety profile of Translarna in the ACT CF study was consistent with previous studies and no new safety signals were identified. Based on the results of ACT CF, the Company plans to discontinue its current clinical development of Translarna for nmCF and close ongoing extension studies of Translarna for the treatment of nmCF. The Company has withdrawn its type II variation submission with the EMA, which sought approval of Translarna for the treatment of nmCF in the EEA. During 2016, the Company’s revenues were primarily generated from sales of Translarna in countries in the EEA where pricing and reimbursement approval is obtained at acceptable levels and in other territories where the Company is permitted to distribute Translarna under EAP programs. The Company is subject to a number of risks similar to those of other early stage companies, including dependence on key individuals, the difficulties inherent in the development of commercially usable products, the potential need to obtain additional capital necessary to fund the development of its products, and competition from other companies. As of December 31, 2016, the Company had an accumulated deficit of approximately $735.1 million. The Company has financed its operations to date primarily through the private offering in August 2015 of 3.00% convertible senior notes due 2022 (see Note 6), public offerings of common stock in February 2014 and October 2014, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, convertible debt financings, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates.

Summary of significant accounting policies

12 Months Ended

Dec. 31, 2016

Accounting Policies [Abstract]

Summary of significant accounting policies

Basis of presentation

The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) and include all adjustments necessary for the fair presentation of the Company’s financial position for the periods presented.

Use of estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Consolidation

The consolidated financial statements include the accounts of PTC Therapeutics, Inc. and our wholly owned subsidiaries. All inter-company accounts, transactions, and profits have been eliminated in consolidation.

Segment and geographic information

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision making group, in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating and reporting segment.

Cash equivalents

The Company considers all highly liquid investments with a maturity of 90 days or less at the time of purchase to be cash equivalents. Cash equivalents are carried at cost which approximates fair value due to their short-term nature.

Marketable securities

The Company considers securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. The Company evaluates securities with unrealized losses to determine whether such losses, if any, are other than temporary.

Fixed assets

Fixed assets are stated at cost. Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows:



Leasehold improvements	Lesser of useful life or lease term
Computer equipment and software	3 years
Furniture, fixtures, and lab equipment	3 to 7 years

Concentration of credit risk

The Company’s financial instruments that are exposed to credit risks consist primarily of cash and cash equivalents, available-for-sale marketable securities and accounts receivable. The Company maintains its cash and cash equivalents in bank accounts, which, at times, exceed federally insured limits. The Company has not experienced any credit losses in these accounts and does not believe it is exposed to any significant credit risk on these funds. The Company’s investment policy includes guidelines on the quality of the financial institutions and financial instruments the Company is allowed to invest in, which the Company believes minimizes the exposure to concentration of credit risk.

The Company is subject to credit risk from its accounts receivable related to its product sales revenue of Translarna. The payment terms are predetermined and the Company evaluates the creditworthiness of each customer or distributor on a regular basis. The Company reserves all uninsured amounts billed directly to a patient until the time of cash receipt as collectability is not reasonably assured at the time the product is received. To date, the Company has not incurred any credit losses.

Inventories and cost of product revenue

In 2014, the Company was notified that the European Commission granted conditional marketing authorization for Translarna for the treatment of nmDMD in ambulatory patients aged five years and older. The conditional marketing authorization allows the Company to market Translarna for the treatment of nmDMD in the 31 member states of the EEA. The launch in these countries is on a country by country basis. This marketing authorization is subject to annual review and renewal by the European Commission following reassessment by the EMA of the risk benefit balance of the authorization, as well as satisfaction of any specific obligation or other requirement placed upon the marketing authorization.

In January 2016, the Company submitted the final clinical study report from ACT DMD report to the EMA in fulfillment of the initial specific obligation placed on the marketing authorization. The primary efficacy endpoint of ACT DMD was not achieved with statistical significance. The Company made this submission as a type II variation request that sought to have this initial specific obligation to the marketing authorization removed and a full marketing authorization granted. In February 2016, the Company also submitted a marketing authorization renewal request with the EMA.

In January 2017, the European Commission renewed the Company’s marketing authorization, subject to the specific obligation to conduct Study 041. Because the EMA did not grant the Company’s request for full marketing authorization, the authorization remains subject to annual EMA reassessment. The last granted marketing authorization renewal is effective, unless extended, through August 5, 2017. The Company submitted a marketing authorization renewal request to the EMA in February 2017. The Company plans to seek to renew the marketing authorization on an annual basis until a marketing authorization that is not subject to any specific obligation is granted, if ever.

If, in any annual renewal cycle, the EMA determines that the balance of benefits and risks of using Translarna for the treatment of nmDMD has changed materially or that the Company has not or is unable to comply with any specific obligation or other requirement that has been or may be placed on the marketing authorization, the European Commission could, at the EMA’s recommendation, vary, suspend, withdraw or refuse to renew the marketing authorization for Translarna or impose other specific obligations or restrictions.

Although there continues to be substantial risk that regulators could, in the future, suspend or not renew the Company’s marketing authorization in the EEA for Translarna for the treatment of nmDMD, the Company has determined that it will capitalize inventory with respect to the Translarna finished product for commercial use effective January 1, 2017 and commence the expensing of cost of goods sold based on the marketing authorization renewal granted by the EC. Had the Company capitalized as inventory all of the Translarna product that is available for commercial sale on hand as of December 31, 2016, the value of that inventory would have been approximately $1.7 million. In addition, had the Company expensed the cost of Translarna product sold as a cost of sales, the gross profit margin would have been greater than 90%, which the Company believes is consistent with the cost of producing small molecule therapeutics for orphan drug diseases in the pharmaceutical industry.

Deferred rent

The Company has an operating lease for office space. Rent expense is recorded on a straight-line basis over the initial lease term. The difference between the actual cash paid and the straight-line rent expense is recorded as deferred rent. Leasehold improvements made related to this lease, subsequent to its inception, are amortized over the remaining lease term.

Accumulated other comprehensive income (loss)

Accumulated other comprehensive income (loss) consists of unrealized gains or losses on marketable securities and foreign currency translation adjustments.

Revenue recognition

The Company recognizes revenue when amounts are realized or realizable and earned. Revenue is considered realizable and earned when the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the price is fixed or determinable; and (4) collection of the amounts due are reasonably assured.

Net Product Sales

The Company’s net product sales have consisted solely of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company began recognizing revenue for payments received under the reimbursed EAPs for Translarna in nmDMD patients in select countries in the third quarter of 2014. The Company has now established a pattern of collectability and, since January 2015, the Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition—Products.

The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and, in some cases, one of the Company’s third-party partner distributors. Revenue is recognized when risk of ownership has transferred. The Company’s third-party distributors act as intermediaries between the Company and end users and do not typically stock significant quantities of Translarna. The ultimate payor for Translarna is typically a government authority or institution or a third-party health insurer.

The Company records revenue net of allowances, including estimated third party discounts and rebates. Allowances are recorded as a reduction of revenue at the time revenues from product sales are recognized. These allowances are adjusted to reflect known changes in factors and may impact such allowances in the quarter those changes are known.

Collaboration and Grant Revenue

The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.

The Company evaluates all contingent consideration earned, such as a milestone payment, using the criteria as provided by the Financial Accounting Standards Board (FASB), guidance on the milestone method of revenue recognition. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from our activities to achieve the milestone; (2) the milestone be related to past performance; and (3) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement. If these criteria are met then the contingent milestones can be considered a substantive milestone and will be recognized as revenue in the period that the milestone is achieved. The Company recognizes royalties as earned in accordance with the terms of various research and collaboration agreements. If not substantive, the contingent consideration is allocated to the existing units of accounting based on relative selling price and recognized following the same basis previously established for the associated unit of accounting.

The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.

Allowance for doubtful accounts

The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends. The allowance for doubtful accounts was $0.7 million as of December 31, 2016 and $0 as of December 31, 2015.

Research and development costs

Research and development expenses include the clinical development costs associated with the Company’s product development programs and research and development costs associated with the Company’s discovery programs. These expenses include internal research and development costs and the costs of research and development conducted on behalf of the Company by third parties, including sponsored university-based research agreements and clinical study vendors. All research and development costs are expensed as incurred. Costs incurred in obtaining technology licenses are charged immediately to research and development expense if the technology licensed has not reached technological feasibility and has no alternative future uses.

Nonrefundable advance payments made for goods and services that will be used in future research and development activities are deferred if the contracted party has not yet performed the related activities. The amount deferred is then recognized as expense when the research and development activities are performed. The deferred research and development advance payments were $0.4 million and $0.6 million as of December 31, 2016 and 2015, respectively.

Fair value of financial instruments

The Company follows the fair value measurement rules, which provides guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority).


•	Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date.

•

Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs).


•	Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available.

Investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments.

Beneficial conversion

When the Company issues a debt or an equity security that is convertible into common stock at a discount from the fair value of the common stock at the date the debt or equity security counterparty is legally committed to purchase such a security (Commitment Date), a beneficial conversion charge is measured and recorded on the Commitment Date for the difference between the fair value of the Company’s common stock and the effective conversion price of the convertible debt or equity security. If the intrinsic value of the beneficial conversion feature is greater than the proceeds allocated to the convertible debt or equity security, the amount of the discount assigned to the beneficial conversion feature is limited to the amount of the proceeds allocated to the convertible debt or equity security.

The amount allocated to the beneficial conversion feature is presented as a discount or reduction to the related debt security or as an immediate charge to earnings available to common shareholders for convertible preferred stock instruments that are convertible by the shareholders at any time.

Warrant liability

Warrants to purchase the Company’s common stock with nonstandard antidilution provisions, regardless of the probability or likelihood that may conditionally obligate the issuer to ultimately transfer assets, are classified as liabilities and are recorded at their estimated fair value at each reporting period. Any change in fair value of these warrants is recorded as gain/(loss) on warrant valuation each reporting period in Other expense, net on the Company’s statement of operations.

Impairment of long-lived assets

The Company monitors its long-lived assets for indicators of impairment. If such indicators are present, the Company assesses the recoverability of affected assets by determining whether the carrying value of such assets is less than the sum of the undiscounted future cash flows of the assets. If such assets are found not to be recoverable, the Company measures the amount of such impairment by comparing the carrying value of the assets to the fair value of the assets, with the fair value generally determined based on the present value of the expected future cash flows associated with the assets. Although current and historical negative cash flows are indicators of impairment, management believes the future cash flows to be received from the long-lived assets and the potential success of the Company’s research programs will exceed the assets’ carrying value, and accordingly, the Company believes that no impairment of long-lived assets exists as of December 31, 2016.

Share-based compensation

The Company measures the cost of employee services received in exchange for an award of equity instruments based on the grant date fair value of the award. Restricted stock awards are measured based on the fair market values of the underlying stock on the dates of grant. For service type awards, share-based compensation expense is recognized on a straight-line basis over the period during which the employee is required to provide service in exchange for the entire award. For awards that vest or begin vesting upon achievement of a performance condition, the Company estimates the likelihood of satisfaction of the performance condition and recognizes compensation expense when achievement of the performance condition is deemed probable using an accelerated attribution model.

The fair value of options is calculated using the Black-Scholes option pricing model to determine the fair value of stock options on the date of grant based on key assumptions such as expected volatility and expected term. As a new public company, the Company does not have sufficient history to estimate the volatility of its common stock price or the expected life of the options. The Company calculates expected volatility based on a historical volatility analysis of peers that were similar with respect to industry, stage of life cycle, size, and financial leverage and will continue to do so until the historical volatility of its common stock is sufficient to measure expected volatility for future option grants. The Company uses the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.

Income taxes

Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized.

The Company recognized a tax benefit of $4.9 million related to the sale of net operating losses in the New Jersey Technology Business Tax Certificate Transfer Program for the year ended December 31, 2014. The Company did not participate in this program during the years ended December 31, 2016 and 2015.

Foreign currency

The functional currencies of the Company’s foreign subsidiaries primarily are the local currencies of the country in which the subsidiary operates. The Company’s asset and liability accounts are translated using the current exchange rate as of the balance sheet date. Stockholders’ equity accounts are translated using historical rates at the balance sheet date. Revenue and expense accounts are translated using a weighted average exchange rate over the period ended on the balance sheet date. Adjustments resulting from the translation of the financial statements of the Company’s foreign subsidiaries into U.S. dollars are accumulated as a separate component of stockholders’ equity within other comprehensive income. Gains or losses resulting from transactions denominated in foreign currencies are included in other income or expense, within the consolidated statements of income.

Net (loss) income per share

Basic net income per share is calculated by dividing the net income attributable to common stockholders by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents. Diluted net income per share is calculated by dividing the net income attributable to common stockholders by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method and the if-converted method. During periods in which the Company incurs net losses, both basic and diluted loss per share is calculated by dividing the net loss by the weighted average shares outstanding—potentially dilutive securities are excluded from the calculation because their effect would be anti-dilutive. Dilutive common stock equivalents are comprised of convertible preferred stock and options outstanding under the Company’s stock option plans.

Recent accounting pronouncements

In May 2014, the FASB issued Accounting Standards Update (ASU) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 will eliminate transaction- and industry-specific revenue recognition guidance under current GAAP and replace it with a principle-based approach for determining revenue recognition. ASU No. 2014-9 includes the required steps to achieve the core principle that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The ASU will also require 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. With the issuance of ASU No. 2015-14 in August 2015, the FASB deferred the effective date of the revenue recognition guidance to reporting periods beginning after December 15, 2017. Early adoption of the standard is permitted but not before the original effective date, which was for reporting periods beginning after December 15, 2016. With the issuance of ASU No. 2016-8 in March 2016 and ASU No. 2016-10 in April 2016, the FASB further amended guidance on recording revenue on a gross versus a net basis and on identifying performance obligations and licensing, respectively. The issuance of ASU No. 2016-20 in December 2016 allows entities not to make quantitative disclosures about remaining performance obligations in certain cases and require entities that use any of the new or previously existing optional exemptions to expand their qualitative disclosures while also making additional technical corrections and improvements to the new revenue standard. The Company expects to adopt this guidance when effective and continues to evaluate the effect that the updated standard, as well as additional amendments, may have on its consolidated financial statements and accompanying notes. The Company’s implementation approach includes performing a detailed review of key contracts representative of the product being sold and services provided and assessing the conformance of historical accounting policies and practices with the standard. Because the standard may impact the Company’s business processes, systems and controls, the Company has initiated the development of a comprehensive change management project plan to guide the implementation.

In August 2014, the FASB issued ASU 2014-15, “Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern”, which defines management’s responsibility to assess an entity’s ability to continue as a going concern, and to provide related footnote disclosures if there is substantial doubt about its ability to continue as a going concern. The pronouncement is effective for annual reporting periods ending after December 15, 2016 with early adoption permitted. The Company adopted the guidance in the fourth quarter of 2016 and performed an assessment to identify any conditions or events that raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date the financial statements are issued and thus require disclosure. The adoption of this guidance did not have an effect on the Company’s consolidated financial statements.

In April 2015, the FASB issued ASU No. 2015-3, “Interest—Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs topic of the Codification”. This standard provides a simplified presentation of debt issuance costs and requires that debt issuance costs related to a recognized debt liability to be presented on the balance sheet as a direct deduction from the carrying amount of that debt liability, consistent with debt discounts. The standard is effective for public companies for annual periods beginning after December 15, 2015. The Company adopted the guidance on January 1, 2016 on a retrospective basis and reclassed $2.8 million from “Deposits and other assets” to “Long-term debt” on the balance sheet as of December 31, 2015. The Company’s unamortized debt issuance cost at December 31, 2016 was $2.5 million which is included within “Long-term debt” on the consolidated balance sheet.

In November 2015, the FASB issued ASU No. 2015-17, “Income Taxes (Topic 740): Balance Sheet Classification of Deferred Taxes”. This standard requires all deferred tax assets and liabilities to be classified as non-current on the balance sheet instead of separating deferred taxes into current and non-current amounts. In addition, valuation allowance allocations between current and non-current deferred tax assets are no longer required because those allowances also will be classified as non-current. This standard is effective for public companies for annual periods beginning after December 15, 2016. The Company’s deferred tax assets are provided with full valuation allowance as of December 31, 2016. As such, the Company does not expect that this standard will have a significant impact upon adoption.

Fair value of financial instruments and investments

12 Months Ended

Dec. 31, 2016

Fair Value Disclosures [Abstract]

Fair value of financial instruments and investments

Fair value of certain investments is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the year. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices.

The Company reviews its investments on a periodic basis for other-than-temporary impairments. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may have a significant adverse effect on the fair value of the investment.

The following represents the fair value using the hierarchy described in Note 2 for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of December 31, 2016 and 2015:



	December 31, 2016
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	173,345	$	—	$	173,345	$	—
Warrant liability	$	1	—		—		1
Stock appreciation rights liability	$	865	—		—		865



	December 31, 2015
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	280,903	$	—	$	280,903	$	—
Warrant Liability	$	48	—		—		48
Stock appreciation rights liability	$	—	—		—		—

The Company uses the market approach to measure fair value for its financial assets. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The Company’s marketable securities investments classified as Level 2 primarily utilize broker to value these securities. No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the year ended December 31, 2016.

The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2016 and 2015:



	December 31, 2016
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	12,919	$	47	$	—		$	12,966
Corporate debt securities	153,240		52		(103		)	153,189
Government obligations	7,188		2		—			7,190
	$	173,347	$	101	$	(103	)	$	173,345



	December 31, 2015
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	26,877	$	80	$	—		$	26,957
Corporate debt securities	226,959		—		(640		)	226,319
Government obligations	27,656		3		(32		)	27,627
	$	281,492	$	83	$	(672	)	$	280,903

Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. During the year ended December 31, 2016, the Company did not have any realized gains/losses from the sale of marketable securities. The cost of securities sold is based on the specific identification method. The Company evaluates investments with unrealized losses to determine if the losses are other than temporary. At December 31, 2016, the Company held securities with an unrealized loss position that were not considered to be other-than-temporarily impaired as the Company has the ability to hold such investments until recovery of their fair value. In addition, the Company considered the financial condition, credit ratings and near-term prospects of the issuers, and the magnitude of the losses as compared to the cost and the length of time the investments have been in an unrealized loss position when determining if the losses are other than temporary.

Marketable securities on the balance sheet at December 31, 2016 and 2015 mature as follows:



	December 31, 2016
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	12,966	$	—
Corporate debt securities	137,196		15,993
Government obligations	7,190		—
Total Marketable securities	$	157,352	$	15,993



	December 31, 2015
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	26,957	$	—
Corporate debt securities	140,831		85,488
Government obligations	18,994		8,633
Total Marketable securities	$	186,782	$	94,121

The Company classifies all of its securities as current as they are all available for sale and are available for current operations.

Convertible 3.0% senior notes

In August 2015, the Company issued $150.0 million of 3.0% convertible senior notes due August 15, 2022 (the “Convertible Notes”). Interest is payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The Company separately accounted for the liability and equity components of the Convertible Notes by allocating the proceeds between the liability component and equity component, as further discussed in Note 6. The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the Convertible Notes at December 31, 2016 was $85.2 million.

Level 3 valuation

The warrant liability is classified in Other long-term liabilities on the Company’s balance sheet. The warrant liability is marked-to-market each reporting period with the change in fair value recorded as a gain or loss within Other income/(expense) on the Company’s statement of operations until the warrants are exercised, expire or other facts and circumstances lead the warrant liability to be reclassified as an equity instrument. The fair value of the warrant liability is determined at each reporting period by utilizing the Black-Scholes option pricing model.

The stock appreciation rights (SARs) liability is classified in Other liabilities on the Company’s consolidated balance sheets. The SARs liability is marked-to-market each reporting period with the change in fair value recorded as compensation expense on the Company’s consolidated statements of operations until the SARS vest. The fair value of the SARs liability is determined at each reporting period by utilizing the Black-Scholes option pricing model.

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability and SARs liability for the years ended December 31, 2016 and 2015:



	Level 3 liabilities
	Warrants			SARs
Beginning balance as of January 1, 2015	$	188		$	—
Change in fair value	(140		)	—
Ending balance as of December 31, 2015	$	48		$	—
Fair value of issuances	—			140
Change in fair value	(47		)	725
Ending balance as of December 31, 2016	$	1		$	865

Fair value of the warrant liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the preferred stock value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of December 31, 2016 include (i) volatility (62%-67%), (ii) risk free interest rate (0.62%-1.34%), (iii) strike price ($128.00-$2,520.00), (iv) fair value of common stock ($10.91) and (v) expected life (0.4-2.7 years). The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of December 31, 2015 include (i) volatility (62%-70%), (ii) risk free interest rate (0.86%-1.54%), (iii) strike price ($128.00-$2,520.00), (iv) fair value of common stock ($32.40) and (v) expected life (1.5-3.7 years).

- Definition

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

+ References + Details

Fixed assets

12 Months Ended

Dec. 31, 2016

Property, Plant and Equipment [Abstract]

Fixed assets

Fixed assets, net were as follows at December 31, 2016 and 2015:



	December 31,
	2016			2015
Leasehold improvements	$	14,038		$	14,029
Computer equipment and software	4,622			4,102
Furniture, fixtures, and lab equipment	19,343			17,443
Assets in process	353			1,102
	38,356			36,676
Less accumulated depreciation and amortization	(30,927		)	(27,702		)
	$	7,429		$	8,974

Depreciation expense was approximately $3.3 million, $2.9 million, and $2.2 million for the years ended December 31, 2016, 2015 and 2014, respectively.

Accounts payable and accrued expenses

12 Months Ended

Dec. 31, 2016

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2016 and 2015 consist of the following:

5. Accounts payable and accrued expenses (Continued)



	December 31,
	2016		2015
Employee compensation, benefits, and related accruals	$	13,649	$	12,630
Consulting and contracted research	11,505		13,753
Professional fees	1,237		2,523
Sales allowances and other related costs	13,245		4,718
Accounts payable	6,298		5,779
Other	2,825		5,844
	$	48,759	$	45,247

Convertible senior notes

12 Months Ended

Dec. 31, 2016

Debt Disclosure [Abstract]

Convertible senior notes

In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.0% convertible senior notes due 2022. The Convertible Notes bear cash interest at a rate of 3.0% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The Convertible Notes will mature on August 15, 2022, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $145.4 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.

The Convertible Notes are governed by an indenture (the Convertible Notes Indenture) with U.S Bank National Association as trustee (the Convertible Notes Trustee).

Holders may convert their Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding February 15, 2022 only under the following circumstances:

•

during any calendar quarter commencing on or after September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;

•

during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the Convertible Notes Indenture) per $1,000 principal amount of Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;


•	during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or


•	upon the occurrence of specified corporate events.

On or after February 15, 2022, until the close of business on the business day immediately preceding the maturity date, holders may convert their Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay cash up to the aggregate principal amount of the Convertible Notes to be converted and deliver shares of its common stock in respect of the remainder, if any, of its conversion obligation in excess of the aggregate principal amount of Convertible Notes being converted.

The conversion rate for the Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock.

The Company may not redeem the Convertible Notes prior to August 20, 2018. The Company may redeem for cash all or any portion of the Convertible Notes, at its option, on or after August 20, 2018 if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the Convertible Notes, which means that the Company is not required to redeem or retire the Convertible Notes periodically.

If the Company undergoes a “fundamental change” (as defined in the Indenture governing the Convertible Notes Indenture), subject to certain conditions, holders of the Convertible Notes may require the Company to repurchase for cash all or part of their Convertible Notes at a repurchase price equal to 100% of the principal amount of the Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.

The Convertible Notes Indenture contains customary events of default with respect to the Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the Convertible Notes when due and payable) occurring and continuing, the Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the Convertible Notes Trustee at the request of such holders (subject to the provisions of the Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.

The Company accounts for the Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the Convertible Notes, the Company separated the Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven-year term of the Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the Convertible Notes is $57.5 million and was recorded in additional paid-in capital.

In accounting for the transaction costs related to the issuance of the Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year term of the Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the Notes.

The Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2016			2015
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,457		)	(2,760		)
Less: Debt discount, net (1)	(49,327		)	(55,392		)
Net carrying amount	$	98,216		$	91,848


(1)	Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the Convertible Notes using the effective interest rate method.

The fair value of the Convertible Notes was approximately $85.2 million as of December 31, 2016. The Company estimates the fair value of its Convertible Notes utilizing market quotations for debt that have quoted prices in active markets. As of December 31, 2016, the remaining contractual life of the Convertible Notes is approximately 5.6 years.

The following table sets forth total interest expense recognized related to the Convertible Notes:



	Year ended December 31,
	2016			2015
Contractual interest expense	$	4,497		$	1,702
Amortization of debt issuance costs	302			107
Amortization of debt discount	6,065			2,146
Total	$	10,864		$	3,955
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure

12 Months Ended

Dec. 31, 2016

Stockholders' Equity Note [Abstract]

Capital structure

Common stock

As of December 31, 2016, the Company’s number of authorized shares of common stock was 125,000,000.

Public offerings of common stock

In February 2014, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-1, as amended. The Company issued and sold an aggregate of 5,163,265 shares of common stock under the registration statement at a public offering price of $24.50 per share, including 673,469 shares pursuant to the exercise by the underwriters of an over-allotment option. The Company received net proceeds from the follow -on public offering of approximately $118.4 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

On October 16, 2014, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 3,450,000 shares of common stock under the registration statement at a public offering price of $36.25 per share, including 450,000 shares issued upon exercise by the underwriters of their option to purchase additional shares. The Company received net proceeds of approximately $117.6 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

Warrants

All of the Company’s outstanding warrants are classified as liabilities as of December 31, 2016 and 2015 because they contain non-standard antidilution provisions.

The following is a summary of the Company’s outstanding warrants as of December 31, 2016 and 2015:



	Warrant shares	Exercise price		Expiration
Common stock	6,250	$	128.00	2017
Common stock	7,030	$	128.00	2019
Common stock	130	$	2,520.00	2019

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 10
-Section S99
-Paragraph 4
-Subparagraph (SAB Topic 4.E)
-URI http://asc.fasb.org/extlink&oid=27010918&loc=d3e74567-122707

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(29))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21488-112644

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08(e))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(31))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
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-Section S99
-Paragraph 4
-Subparagraph (SAB Topic 4.C)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187143-122770

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(30))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08(d))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 30
-Section 50
-Paragraph 2
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Reference 13: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

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-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
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-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

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-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

+ Details

Earnings per share

12 Months Ended

Dec. 31, 2016

Earnings Per Share [Abstract]

Earnings per share

Basic earnings per share is computed by dividing net loss available to common stockholders by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss available to common stockholders by the weighted-average number of common shares plus the effect of dilutive potential common shares outstanding during the period.

The following table sets forth the computation of basic and diluted earnings per share for common stockholders:

Net loss per share



	Year ended December 31,
	2016				2015				2014
Numerator
Net loss	$	(142,110	)		$	(170,447	)		$	(93,753	)
Denominator
Denominator for basic and diluted net loss per share	34,044,584				33,626,248				31,565,310
Net loss per share:
Basic and diluted	$	(4.17	)	*	$	(5.07	)	*	$	(2.97	)	*

* For the years ended December 31, 2016, 2015, and 2014, the Company experienced a net loss and therefore did not report any dilutive share impact.

The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period.



	As of December 31,
	2016	2015	2014
Stock Options	5,854,316	4,826,477	3,432,972
Unvested restricted stock	271,651	344,335	718,400
Total	6,125,967	5,170,812	4,151,372

Stock award plan

12 Months Ended

Dec. 31, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock award plan

In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases.

On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Board approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan.

In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan.

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of December 31, 2016, awards for 329,022 shares of common stock were available for issuance.

The Board of Directors has the authority to select the individuals to whom options are granted and determine the terms of each option, including (i) the number of shares of common stock subject to the option; (ii) the date on which the option becomes exercisable; (iii) the option exercise price, which, in the case of incentive stock options, must be at least 100% (110% in the case of incentive stock options granted to a stockholder owning in excess of 10% of the Company’s stock) of the fair market value of the common stock as of the date of grant; and (iv) the duration of the option (which, in the case of incentive stock options, may not exceed ten years). Options typically vest over a three- or four-year period.

Inducement stock option awards

Pursuant to the NASDAQ inducement grant exception, during the year ended December 31, 2016, the Company issued options to purchase an aggregate of 155,200 shares of common stock to certain new hire employees at a weighted-average exercise price of $13.67 per share. An aggregate of 255,550 of options previously granted as inducement awards were forfeited during the year ended December 31, 2016 in connection with employee separations from the Company.

A summary of stock option activity is as follows:



	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2013	2,095,592		$	20.24
Granted	1,639,996		$	31.09
Exercised	(108,645	)	$	11.00
Forfeited	(193,971	)	$	32.91
Outstanding at December 31, 2014	3,432,972		$	25.00
Granted	2,201,800		$	50.81
Exercised	(656,248	)	$	13.27
Forfeited	(152,047	)	$	49.58
Outstanding at December 31, 2015	4,826,477		$	37.20
Granted	1,500,645		$	27.90
Exercised	(89,216	)	$	10.85
Forfeited	(383,590	)	$	47.42
Outstanding at December 31, 2016	5,854,316		$	34.71	7.80 years	$	341
Vested or Expected to vest at December 31, 2016	2,792,870		$	35.66	8.36 years	$	249
Exercisable at December 31, 2016	2,903,325		$	33.73	7.22 years	$	72

The fair values of grants made in the years ended December 31, 2016, 2015 and 2014 were contemporaneously estimated on the date of grant using the following assumptions:



	2016	2015	2014
Risk-free interest rate	1.30 - 2.24%	1.48 - 2.18%	0.11 - 2.04%
Expected volatility	67 - 78%	67 - 69%	70 - 91%
Expected term	5.05 - 10.00 years	5.50 - 9.12 years	5.50 - 6.25 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the years ended December 31, 2016, 2015 and 2014 was $17.31, $50.81, and $22.39 per share, respectively.

In 2014, the Company modified the terms of stock options granted to a departing member of the executive team. The Company accounted for the modification to the option grants pursuant to ASC Topic 718-20-35 and recognized approximately $1.9 million as additional compensation that was charged to operations during the year ended December 31, 2014.

Restricted Stock Awards—Restricted stock awards are granted subject to certain restrictions, including in some cases service conditions (restricted stock). The grant-date fair value of restricted stock awards, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.

Restricted Stock Units—Restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock units, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.

The following table summarizes information on the Company’s restricted stock awards and units:



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2015	344,335		$	10.85
Granted	141,185		$	30.86
Vested	(163,635	)	$	10.85
Forfeited	(50,234	)	$	18.93
Unvested at December 31, 2016	271,651		$	19.76

Stock Appreciation Rights—Stock appreciation rights (SARs) entitle the holder to receive, upon exercise, an amount of the Company’s common stock or cash (or a combination thereof) determined by reference to appreciation, from and after the date of grant, in the fair market value of a share of the Company’s common stock over the measurement price based on the exercise date.

In May 2016, a total of 897,290 SARs were granted to non-executive employees (the 2016 SARs). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the period ending December 31, 2016, the Company recorded $0.9 million in compensation expense related to the 2016 SARs.

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (ESPP or the Plan) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Board. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six-month period through payroll withholdings and may purchase, at the end of the six-month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the period ending December 31, 2016, the Company recorded $0.2 million in compensation expense related to the ESPP.

The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows:



	Year ended December 31,
	2016		2015		2014
Research and development	$	16,812	$	16,138	$	9,739
Selling, general and administrative	18,197		17,841		9,571
Total	$	35,009	$	33,979	$	19,310

As of December 31, 2016, there was approximately $60.8 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s Plans. This cost is expected to be recognized as compensation expense over the weighted average remaining service period of approximately 2.17 years.

- Definition

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

+ References + Details

Other comprehensive income (loss) and accumulated other comprehensive items

12 Months Ended

Dec. 31, 2016

Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]

Other comprehensive income (loss) and accumulated other comprehensive items

Other comprehensive income (loss) includes changes in equity that are excluded from net loss, such as unrealized gains and losses on marketable securities.

The following table summarizes other comprehensive income (loss) and the changes in accumulated other comprehensive items, by component, for the years ended December 31, 2016, 2015, and 2014, respectively.



	Unrealized Gains/(Losses) On Marketable Securities			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2013	$	70		$	—		$	70
Other comprehensive loss before reclassifications	(457		)	(350		)	(807		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(457		)	(350		)	(807		)
Balance at December 31, 2014	$	(387	)	$	(350	)	$	(737	)
Other comprehensive loss before reclassifications	(202		)	(261		)	(463		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(202		)	(261		)	(463		)
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income (loss) before reclassifications	386			(671		)	(285		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	386			(671		)	(285		)
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)

- Definition

The entire disclosure for comprehensive income, which includes, but is not limited to, 1) the amount of income tax expense or benefit allocated to each component of other comprehensive income, including reclassification adjustments, 2) the reclassification adjustments for each classification of other comprehensive income and 3) the ending accumulated balances for each component of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e689-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=66004124&loc=SL7669619-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 12
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e640-108580

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
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-Paragraph 17
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e716-108580

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e709-108580

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e637-108580

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 14
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e681-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Reclassification Adjustments
-URI http://asc.fasb.org/extlink&oid=6522872

+ Details

Collaborations and grants	12 Months Ended
Collaborations and grants	Dec. 31, 2016
Collaborations and grants
Collaborations and grants	Collaborations and grants The Company has ongoing collaborations with the Spinal Muscular Atrophy Foundation (SMA Foundation) and F. Hoffman-La Roche Ltd and Hoffman- La Roche Inc. (collectively, Roche) and early stage discovery arrangements with other institutions. The following are the key terms to the Company’s (i) ongoing collaborations and (ii) early stage discovery and development arrangements. Roche and SMA Foundation In November 2011, the Company and the SMA Foundation entered into a licensing and collaboration agreement with Roche for a spinal muscular atrophy program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s spinal muscular atrophy program, which includes three compounds currently in preclinical development, as well as potential back-up compounds. The Company received a nonrefundable upfront cash payment of $30.0 million during the research term, which was terminated effective December 31, 2014, Roche provided us with funding, based on an agreed- upon full-time equivalent rate, for an agreed-upon number of full- time equivalent employees that we contributed to the research program. The Company applied the multiple element revenue recognition guidance in evaluating the accounting treatment of this collaboration agreement. The Company identified two possible significant deliverables in the collaboration agreement, the license and the research activities. The Company evaluated whether these significant deliverables have stand-alone value and determined that the license does not have standalone value without the ongoing research and development services given the unique nature of the technology. As such, both of these elements were combined as a single unit for accounting purposes. As a result, the Company deferred the $30.0 million upfront payment which was recognized over the estimated performance period of two years, which was the contracted research period. For the years ended December 31, 2016, 2015 and 2014, the Company recognized approximately $0.4 million, $0.6 million and $20.2 million respectively, in collaboration revenue. The balance of the remaining deferred upfront payment was fully recognized as of December 31, 2013. Under the agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. The Company considers that each of the potential milestone events under the agreement would be substantive because the applicable criteria of its revenue recognition policy (see Note 2) would be satisfied. In January 2014, the Company announced the initiation of a Phase 1 clinical program in its spinal muscular atrophy collaboration with Roche and the SMA Foundation which triggered a $7.5 million milestone payment from Roche. The Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its spinal muscular atrophy collaboration with Roche and the SMA Foundation which triggered a $10 million payment from Roche. The Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. Early stage collaboration and discovery agreements From time to time, the Company has arrangements with several organizations pursuant to which the Company uses its discovery technologies to help identify potential drug candidates. The Company does not take ownership of the potential compounds, but rather provides research services to the collaborator using its specialized technology platform. Generally, these arrangements are structured such that the collaborator and the Company work together to jointly select targets from which to apply its discovery technologies. The research period for the Company to apply its technology is generally three to four years. The Company will typically receive a nonrefundable, upfront cash payment and the collaborator agrees to provide funding for research activities performed on its behalf. The Company applies multiple element revenue recognition guidance in evaluating the accounting treatment for these arrangements. Generally, the two significant deliverables in these arrangements are the license and the research activities. The Company evaluates whether the deliverables have standalone value. Since the Company’s discovery technologies are highly specialized, the Company has generally determined that the license does not have standalone value without the ongoing research and development services and generally accounts for these arrangements as a single unit of accounting. As a result, the Company had deferred revenue of $1.8 million as of December 31, 2014 related to these arrangements. There was no deferred revenue related to these arrangements as of December 31, 2016 and 2015. For the years ended December 31, 2015 and 2014, the Company recognized approximately $1.8 million and $1.3 million in collaboration revenue, respectively. The Company is eligible to receive additional payments from its early stage discovery research arrangements if the discovery compounds are ultimately developed and commercialized. The aggregate potential payments the Company is eligible for if all products are developed is $143.0 million and up to $252.0 million in sales milestones upon achievement of specified sales events and up to double digit royalties on worldwide annual net sales of the licensed product. The Company considers that each of the potential milestone events under the agreement would be substantive because the applicable criteria of its revenue recognition policy (see Note 2) would be satisfied. Grant revenue The Company receives grant funding from various institutions and governmental bodies. The grants are typically for early discovery research, and typically the grant program lasts from two to five years. The Company records revenue as the research activities are performed. If the granting agency provides for an upfront payment, the amount is deferred and recognized as revenue as the expenditures are incurred.

Income taxes

12 Months Ended

Dec. 31, 2016

Income Tax Disclosure [Abstract]

Income taxes

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2016, 2015, and 2014:



	2016		2015		2014
Domestic	(61,446	)	(50,944	)	(46,501	)
Foreign	(80,095	)	(119,018	)	(51,945	)
Total	(141,541	)	(169,962	)	(98,446	)

The Income Tax Provision consisted of the following for the years ended December 31, 2016, 2015 and 2014:



	2016			2015			2014
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(2		)	(2		)	4,890
Foreign	(766		)	(483		)	(197		)
Deferred:
U.S. Federal	199			—			—
U.S. State and Local	—			—			—
Foreign	—			—			—
Total Tax (Expense) Benefit	$	(569	)	$	(485	)	$	4,693

A reconciliation of the U.S. statutory income tax rate to the Company’s effective tax rate is as follows:



	December 31,
	2016		2015		2014
Federal income tax (benefit) at statutory rate	34.00	%	34.00	%	34.00	%
State income tax benefit, net of federal benefit	3.05		(0.43	)	(1.60	)
Permanent differences	(3.70	)	(6.61	)	(0.93	)
NOL IRC Section 382 Limitations	—		—		(21.53	)
Research and development	16.66		19.50		3.78
Increase to valuation allowance	(30.72	)	(20.87	)	9.17
Foreign tax rate differential	(19.84	)	(24.06	)	(18.14	)
Benefit allocated from other comprehensive income	0.14		—		—
Other	0.01		(1.82	)	0.01
Effective income tax rate	(0.40	)%	(0.29	)%	4.76	%

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2016 and 2015 are as follows:



	2016			2015
Deferred tax assets:
Accrued Expense	$	849		$	848
Amortization	46			57
Depreciation	2,968			2,631
Federal tax credits	74,475			50,850
State tax credits	4,996			3,356
Federal net operating losses	80,061			75,200
State net operating losses	9,672			8,848
Capitalized research and development costs	7,248			8,917
Other	22,125			10,345
Total gross deferred tax assets	202,440			161,052
Less valuation allowance	(183,015		)	(139,584		)
Total deferred tax assets, net of valuation allowance	$	19,425		$	21,468
Deferred tax liabilities:
Convertible debt	$	(19,190	)	$	(21,468	)
Gain on marketable securities	$	(235	)	$	—
Total gross deferred tax assets	(19,425		)	(21,468		)
Net deferred tax assets (liabilities)	$	—		$	—

At December 31, 2016 and 2015, the Company recorded a full valuation allowance against its net deferred tax assets of approximately $183.0 million and $139.6 million, respectively. The change in the valuation allowance during the years ended December 31, 2016 and 2015 was approximately $43.4 million and $16.3 million, respectively. A full valuation allowance has been recorded since, in the judgment of management, these assets are not more likely than not to be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during periods in which those temporary differences and carryforwards become deductible or are utilized. As of December 31, 2016, the Company has approximately $285.8 million and $213.2 million of federal and state net operating loss carryforwards, respectively.

As a result of realization requirements of the guidance issued by the FASB, certain deferred tax assets that arose directly from tax deductions related to equity compensation in excess of compensation recognized for financial reporting are excluded from the total deferred tax assets. As of December 31, 2016, approximately $50.4 million of the federal net operating loss carryforwards are related to the exercise of employee stock options and vesting of restricted stock, and the Company will record a tax benefit of approximately of $17.1 million through capital in excess of par value if such losses are realized.

As of December 31, 2016, research and development credit carryforwards for federal and state purposes are approximately $14.4 million and $7.3 million, respectively. In addition, the Orphan Drug Credit Carryover available as of December 31, 2016 is approximately $60.1 million. The federal net operating loss carryforwards begin to expire in 2021, while the federal credit carryforwards begin to expire in 2019. State net operating loss carryforwards begin to expire in 2030, and the state credit carryforwards began to expire in 2016. Sections 382 and 383 of the Internal Revenue Code of 1986 subject the future utilization of net operating losses and certain other tax attributes, such as research and development tax credits, to an annual limitation in the event of certain ownership changes, as defined. The Company has undergone an ownership change and has determined that a “change in ownership” as defined by IRC Section 382 of the Internal Revenue Code of 1986, as amended, and the rules and regulations promulgated thereunder, did occur in June of 2013. Accordingly, about $231.5 million of the Company’s NOL carryforwards are limited and the Company can only use $16.7 million for the first five years from the ownership change and $5.7 million per year going forward. Therefore, $169.2 million of the NOL’s will be freed up over the next 20 years and $62.3 million are expected to expire unused which are not included in the deferred tax assets listed above. In summary, there are $285.8 million of NOLs available, out of which $169.2 million are limited by IRC Section 382. At December 31, 2016, there is $175.1 million available for immediate use and an additional $16.7 million will free up in 2017.

The income tax expense and benefit for the years ended December 31, 2016 and 2015 differed from the amounts computed by applying the U.S. federal income tax rate of 34% to loss before tax expense and benefit as a result of foreign taxes, nondeductible expenses, tax credits generated, true up of net operating loss carryforwards, and increases in the Company’s valuation allowance. The Company applies the elements of FASB ASC 740-10 regarding accounting for uncertainty in income taxes. This clarifies the accounting for uncertainty in income taxes recognized in financial statements and required impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. As of December 31, 2016 the Company did not have any unrecognized tax benefits and has not accrued any interest or penalties through 2016. The Company does not expect to have any unrecognized tax benefits within the next twelve months. The Company’s policy is to recognize interest and penalties related to tax matters within the income tax provision. Tax years beginning in 2013 are generally subject to examination by taxing authorities, although net operating losses from all years are subject to examinations and adjustments for at least three years following the year in which the attributes are used. Subsequent to year end, the Company received a notice of examination from the United States Internal Revenue Service for tax year 2014 to commence in 2017. As the examination has not yet begun, the timing and ultimate resolution of is uncertain.

For all years through December 31, 2016, the Company generated research credits but has not conducted a study to document the qualified activities. This study may result in an adjustment to the Company’s research and development credit carryforwards; however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the deferred tax asset established for the research and development credit carryforwards and the valuation allowance.

U.S. federal income taxes have not been provided on undistributed earnings of our international subsidiaries as it is our intention to reinvest any earnings into the respective subsidiaries. It is not practicable to estimate the amount of tax that might be payable if some or all of such earnings were to be repatriated, and the amount of foreign tax credits that would be available to reduce or eliminate the resulting U.S. income tax liability. As of December 31, 2016 and December 31, 2015 there are no undistributed earnings.

Commitments and contingencies

12 Months Ended

Dec. 31, 2016

Commitments and Contingencies Disclosure [Abstract]

Commitments and contingencies

Operating leases

The Company leases office space in South Plainfield, New Jersey for its principal office under a noncancelable operating lease through February 2019 in addition to office space in various countries for international employees primarily through workspace providers. Rent expense was approximately $2.2 million, $1.8 million, and $0.9 million for the years ended December 31, 2016, 2015, and 2014, respectively. The Company also leases certain office equipment under operating leases. Future minimum lease payments as of December 31, 2016 are as follows:



2017	$	1,483
2018	1,214
2019	353
2020	177
2021	59
Thereafter	—
	$	3,286

Other contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited (Wellcome Trust) for the research and development of small molecule compounds in connection with our cancer stem cell and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the cancer steam cell program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company made the first development milestone payment of $0.8 million to Wellcome Trust under the cancel stem cell program funding agreement during the second quarter of 2016. Additional milestone payments up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement.

The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single- digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon our payment to the SMA Foundation of a specified amount.

The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur.

Geographic information

12 Months Ended

Dec. 31, 2016

Segments, Geographical Areas [Abstract]

Geographic information

The Company views its operations and manages its business in one operating segment. The following table presents financial information based on the geographic location of the facilities of the Company as of and for the years ended:



	Year Ended December 31, 2016
	United States		Non-US		Total
Total assets	$	223,098	$	46,247	$	269,345
Property and equipment, net	$	6,439	$	990	$	7,429
Revenue	$	1,206	$	81,499	$	82,705



	Year Ended December 31, 2015
	United States		Non-US		Total
Total assets	$	340,755	$	24,526	$	365,281
Property and equipment, net	$	8,206	$	768	$	8,974
Revenue	$	5,218	$	31,548	$	36,766

- Definition

The entire disclosure for reporting segments including data and tables. Reportable segments include those that meet any of the following quantitative thresholds a) it's reported revenue, including sales to external customers and intersegment sales or transfers is 10 percent or more of the combined revenue, internal and external, of all operating segments b) the absolute amount of its reported profit or loss is 10 percent or more of the greater, in absolute amount of 1) the combined reported profit of all operating segments that did not report a loss or 2) the combined reported loss of all operating segments that did report a loss c) its assets are 10 percent or more of the combined assets of all operating segments.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 34
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8981-108599

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 41
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e9038-108599

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 33
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8971-108599

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 12
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8595-108599

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8380-108599

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 32
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8933-108599

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 26
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8844-108599

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 35
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8984-108599

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 40
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e9031-108599

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 42
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-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
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Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
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-Paragraph 29
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8864-108599

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 31
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8924-108599

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 30
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8906-108599

+ Details

401(k) plan	12 Months Ended
401(k) plan	Dec. 31, 2016
Compensation and Retirement Disclosure [Abstract]
401(k) plan	401(k) plan The Company maintains a 401(k) plan for its employees. Employee contributions are voluntary. The Company may match employee contributions in amounts to be determined at the Company’s sole discretion. The Company provides a 50% matching contribution for up to the first 6% of each contributing employee’s base salary contributions. The Company made matching contributions to the 401(k) plan and recorded expense of approximately $1.1 million, $0.7 million and $0.3 million for the years ended December 31, 2016, 2015 and 2014, respectively.

Restructuring

12 Months Ended

Dec. 31, 2016

Restructuring and Related Activities [Abstract]

Restructuring

In March 2016, the Company commenced implementation of a reorganization of its operations intended to improve efficiency and better align the Company’s costs and employment structure with its strategic plans. The Company completed its reorganization in June 2016 and recorded a one-time charge of $2.5 million for the year ended December 31, 2016. The total $2.5 million in one-time charges is related to work-force reduction, recorded in research and development and selling, general and administrative expenses in the accompanying statement of operations.



	Balance as of January 1, 2016		Expenses, net		Cash Payments			Balance as of December 31, 2016
2016 workforce reduction	$	—	$	2,484	$	(2,462	)	$	22

Subsequent events	12 Months Ended
Subsequent events	Dec. 31, 2016
Subsequent Events [Abstract]
Subsequent events	Subsequent events On March 16, 2017, the Company announced it had entered into an Asset Purchase Agreement (the Asset Purchase Agreement) with Marathon Pharmaceuticals, LLC (Marathon) to acquire all rights to Emflaza™ (deflazacort) (the Transaction). Emflaza is approved in the United States for all Duchenne muscular dystrophy patients aged five years and older, regardless of their genetic mutation. Under the terms of the Asset Purchase Agreement, the Company has agreed to pay Marathon total upfront consideration of $140 million upon closing of the Transaction, comprised of approximately $75 million in cash and approximately $65 million in PTC common stock. The number of shares of the Company’s common stock issuable at closing will be based on the volume weighted average price per share of the Company’s common stock on the NASDAQ Stock Market for the 15 trading day period ending on the third trading day immediately preceding the closing of the Transaction and will be subject to reduction such that the number of shares issuable will not exceed 19.9% of the issued and outstanding shares of the Company’s common stock immediately prior to the closing date, which is expected to be a maximum of approximately 6.9 million shares, with any shortfall to be made whole with additional cash consideration. The Company will also assume certain liabilities with respect to the assets to be acquired. In addition, Marathon will be entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount for such payments. The Company estimates that the contingent payments will, on a blended average basis, range in percentages of net sales between the low to mid-twenties. Further, Marathon may be entitled to receive a single $50 million sales-based milestone. Each of the contingent payments and the milestone payment are subject to the terms and conditions of the Asset Purchase Agreement.

Selected quarterly financial data (Unaudited)

12 Months Ended

Dec. 31, 2016

Quarterly Financial Information Disclosure [Abstract]

Selected quarterly financial data (Unaudited)

The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2016 and 2015 are as follows:



	For the quarters ending
	March 31			June 30			September 30			December 31
2016:
Net product revenue	$	18,878		$	15,437		$	22,013		$	25,119
Collaboration and grant revenue	17			196			973			72
Operating expenses	57,337			52,193			55,050			50,183
Loss from operations	(38,442		)	(36,560		)	(32,064		)	(24,992		)
Net loss	(41,233		)	(38,914		)	(35,167		)	(26,796		)
Basic and diluted net loss per common share(1)	$	(1.22	)	$	(1.14	)	$	(1.03	)	$	(0.78	)
2015:
Net product revenue	$	5,069		$	6,161		$	9,772		$	12,694
Collaboration and grant revenue	2,413			613			4			40
Operating expenses	45,553			45,400			52,008			60,935
Loss from operations	(38,071		)	(38,626		)	(42,232		)	(48,201		)
Net loss	(37,915		)	(38,361		)	(43,223		)	(50,948		)
Basic and diluted net loss per common share(1)	$	(1.15	)	$	(1.14	)	$	(1.27	)	$	(1.50	)


(1)	The amounts were computed independently for each quarter and the sum of the quarters may not total the annual amounts.

Summary of significant accounting policies (Policies)

12 Months Ended

Dec. 31, 2016

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Consolidation

Segment and geographic information

Cash equivalents

Marketable securities

Fixed assets

Fixed assets are stated at cost. Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows:



Leasehold improvements	Lesser of useful life or lease term
Computer equipment and software	3 years
Furniture, fixtures, and lab equipment	3 to 7 years

Concentration of credit risk

Inventories and cost of product revenue

Deferred rent

Accumulated other comprehensive income (loss)

Accumulated other comprehensive income (loss) consists of unrealized gains or losses on marketable securities and foreign currency translation adjustments.

Revenue recognition

Net Product Sales

Collaboration and Grant Revenue

Allowance for doubtful accounts

Research and development costs

Fair value of financial instruments


•	Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date.

•


•	Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available.

Beneficial conversion

Warrant liability

Impairment of long-lived assets

Share-based compensation

Income taxes

Foreign currency

Net (loss) income per share

Recent accounting pronouncements

In January 2016, the FASB issued ASU No. 2016-1, “Financial Instruments - Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities”. This standard enhances the reporting model for financial instruments, which includes amendments to address aspects of recognition, measurement, presentation and disclosure. The new guidance affects all reporting organizations (whether public or private) that hold financial assets or owe financial liabilities. ASU 2016-1 is effective for years beginning after December 15, 2017, including interim periods within those fiscal years. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-1 will have on its consolidated financial statements and accompanying notes.

In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)”. This standard will require organizations that lease assets with lease terms of more than 12 months to recognize assets and liabilities for the rights and obligations created by those leases on their balance sheets. The ASU will also require new qualitative and quantitative disclosures to help investors and other financial statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for public companies for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018, with early adoption permitted. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-2 will have on its consolidated financial statements and accompanying notes.

In March 2016, the FASB issued ASU No. 2016-9, “Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting”. This standard requires the recognition of all income tax effects of awards in the income statement when the awards vest or are settled, with Additional Paid in Capital (APIC) pools to be eliminated. In addition, the standard will increase the amount an employer can withhold to cover income taxes on awards and still qualify for the exception to liability classification for shares used to satisfy the employer’s statutory income tax withholding obligation as well as allowing companies to elect whether to account for forfeitures of share-based payments by recognizing forfeitures of awards as they occur or estimating the number of awards expected to be forfeited and adjusting the estimate when it is likely to change, as is currently required. This standard is effective for public companies for fiscal years beginning after December 15, 2016 and interim periods within those years, with early adoption permitted but only if all of the guidance is adopted in the same period. The Company will adopt this guidance in the first quarter of 2017 and is currently assessing what effect the adoption of ASU No. 2016-9 will have on its consolidated financial statements and accompanying notes.

In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. The Company expects to adopt this guidance when effective and is assessing what effect the adoption of ASU 2016-13 will have on its consolidated financial statements and accompanying notes.

In August 2016, the FASB issued ASU No. 2016-15, “Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments”. This standard clarifies the presentation of certain specific cash flow issues in the Statement of cash flows. The standard is effective for public companies for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2017, with early adoption permitted. The adoption of this guidance is not expected to have a significant impact on the Company’s consolidated financial statements.

In November 2016, the FASB issued ASU No. 2016-18, “Statement of Cash Flows (Topic 230): Restricted Cash”. This standard requires entities to show the changes in the total of cash, cash equivalents, restricted cash and restricted cash equivalents in the statement of cash flows and no longer present transfers between cash and cash equivalents and restricted cash and restricted cash equivalents in the statement of cash flows. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2017, including interim periods within those years, with early adoption permitted. The adoption of this guidance is not expected to have a significant impact on the Company’s consolidated financial statements.

Summary of significant accounting policies (Tables)

12 Months Ended

Dec. 31, 2016

Accounting Policies [Abstract]

Schedule of estimated useful life of related assets

Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows:



Leasehold improvements	Lesser of useful life or lease term
Computer equipment and software	3 years
Furniture, fixtures, and lab equipment	3 to 7 years

Fair value of financial instruments and investments (Tables)

12 Months Ended

Dec. 31, 2016

Fair Value Disclosures [Abstract]

Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis



	December 31, 2016
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	173,345	$	—	$	173,345	$	—
Warrant liability	$	1	—		—		1
Stock appreciation rights liability	$	865	—		—		865



	December 31, 2015
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	280,903	$	—	$	280,903	$	—
Warrant Liability	$	48	—		—		48
Stock appreciation rights liability	$	—	—		—		—

Summary of marketable securities accounted for as available-for-sale securities

The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2016 and 2015:



	December 31, 2016
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	12,919	$	47	$	—		$	12,966
Corporate debt securities	153,240		52		(103		)	153,189
Government obligations	7,188		2		—			7,190
	$	173,347	$	101	$	(103	)	$	173,345



	December 31, 2015
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	26,877	$	80	$	—		$	26,957
Corporate debt securities	226,959		—		(640		)	226,319
Government obligations	27,656		3		(32		)	27,627
	$	281,492	$	83	$	(672	)	$	280,903

Schedule of marketable securities on the balance sheet

Marketable securities on the balance sheet at December 31, 2016 and 2015 mature as follows:



	December 31, 2016
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	12,966	$	—
Corporate debt securities	137,196		15,993
Government obligations	7,190		—
Total Marketable securities	$	157,352	$	15,993



	December 31, 2015
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	26,957	$	—
Corporate debt securities	140,831		85,488
Government obligations	18,994		8,633
Total Marketable securities	$	186,782	$	94,121

Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability and SARs liability for the years ended December 31, 2016 and 2015:



	Level 3 liabilities
	Warrants			SARs
Beginning balance as of January 1, 2015	$	188		$	—
Change in fair value	(140		)	—
Ending balance as of December 31, 2015	$	48		$	—
Fair value of issuances	—			140
Change in fair value	(47		)	725
Ending balance as of December 31, 2016	$	1		$	865

Fixed assets (Tables)

12 Months Ended

Dec. 31, 2016

Property, Plant and Equipment [Abstract]

Schedule of fixed assets, net

Fixed assets, net were as follows at December 31, 2016 and 2015:



	December 31,
	2016			2015
Leasehold improvements	$	14,038		$	14,029
Computer equipment and software	4,622			4,102
Furniture, fixtures, and lab equipment	19,343			17,443
Assets in process	353			1,102
	38,356			36,676
Less accumulated depreciation and amortization	(30,927		)	(27,702		)
	$	7,429		$	8,974

Accounts payable and accrued expenses (Tables)

12 Months Ended

Dec. 31, 2016

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2016 and 2015 consist of the following:

5. Accounts payable and accrued expenses (Continued)



	December 31,
	2016		2015
Employee compensation, benefits, and related accruals	$	13,649	$	12,630
Consulting and contracted research	11,505		13,753
Professional fees	1,237		2,523
Sales allowances and other related costs	13,245		4,718
Accounts payable	6,298		5,779
Other	2,825		5,844
	$	48,759	$	45,247

Convertible senior notes (Tables)

12 Months Ended

Dec. 31, 2016

Debt Disclosure [Abstract]

Summary of convertible notes

The Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2016			2015
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,457		)	(2,760		)
Less: Debt discount, net (1)	(49,327		)	(55,392		)
Net carrying amount	$	98,216		$	91,848


(1)	Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the Convertible Notes using the effective interest rate method.

Summary of interest expense recognized related to the Convertible Notes

The following table sets forth total interest expense recognized related to the Convertible Notes:



	Year ended December 31,
	2016			2015
Contractual interest expense	$	4,497		$	1,702
Amortization of debt issuance costs	302			107
Amortization of debt discount	6,065			2,146
Total	$	10,864		$	3,955
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure (Tables)

12 Months Ended

Dec. 31, 2016

Stockholders' Equity Note [Abstract]

Summary of the Company's outstanding warrants

The following is a summary of the Company’s outstanding warrants as of December 31, 2016 and 2015:



	Warrant shares	Exercise price		Expiration
Common stock	6,250	$	128.00	2017
Common stock	7,030	$	128.00	2019
Common stock	130	$	2,520.00	2019

- Definition

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Earnings per share (Tables)

12 Months Ended

Dec. 31, 2016

Earnings Per Share [Abstract]

Schedule of computation of basic and diluted net loss per share for common stockholders

The following table sets forth the computation of basic and diluted earnings per share for common stockholders:

Net loss per share



	Year ended December 31,
	2016				2015				2014
Numerator
Net loss	$	(142,110	)		$	(170,447	)		$	(93,753	)
Denominator
Denominator for basic and diluted net loss per share	34,044,584				33,626,248				31,565,310
Net loss per share:
Basic and diluted	$	(4.17	)	*	$	(5.07	)	*	$	(2.97	)	*

* For the years ended December 31, 2016, 2015, and 2014, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding



	As of December 31,
	2016	2015	2014
Stock Options	5,854,316	4,826,477	3,432,972
Unvested restricted stock	271,651	344,335	718,400
Total	6,125,967	5,170,812	4,151,372

Stock award plan (Tables)

12 Months Ended

Dec. 31, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Summary of stock option activity

A summary of stock option activity is as follows:



	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2013	2,095,592		$	20.24
Granted	1,639,996		$	31.09
Exercised	(108,645	)	$	11.00
Forfeited	(193,971	)	$	32.91
Outstanding at December 31, 2014	3,432,972		$	25.00
Granted	2,201,800		$	50.81
Exercised	(656,248	)	$	13.27
Forfeited	(152,047	)	$	49.58
Outstanding at December 31, 2015	4,826,477		$	37.20
Granted	1,500,645		$	27.90
Exercised	(89,216	)	$	10.85
Forfeited	(383,590	)	$	47.42
Outstanding at December 31, 2016	5,854,316		$	34.71	7.80 years	$	341
Vested or Expected to vest at December 31, 2016	2,792,870		$	35.66	8.36 years	$	249
Exercisable at December 31, 2016	2,903,325		$	33.73	7.22 years	$	72

Schedule of assumptions used to estimate fair values of grants made on the date of grant

The fair values of grants made in the years ended December 31, 2016, 2015 and 2014 were contemporaneously estimated on the date of grant using the following assumptions:



	2016	2015	2014
Risk-free interest rate	1.30 - 2.24%	1.48 - 2.18%	0.11 - 2.04%
Expected volatility	67 - 78%	67 - 69%	70 - 91%
Expected term	5.05 - 10.00 years	5.50 - 9.12 years	5.50 - 6.25 years

Summary of information on the Company's restricted stock

The following table summarizes information on the Company’s restricted stock awards and units:



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2015	344,335		$	10.85
Granted	141,185		$	30.86
Vested	(163,635	)	$	10.85
Forfeited	(50,234	)	$	18.93
Unvested at December 31, 2016	271,651		$	19.76

Schedule of share-based compensation expense recorded in the statement of operations



	Year ended December 31,
	2016		2015		2014
Research and development	$	16,812	$	16,138	$	9,739
Selling, general and administrative	18,197		17,841		9,571
Total	$	35,009	$	33,979	$	19,310

Other comprehensive income (loss) and accumulated other comprehensive items (Tables)

12 Months Ended

Dec. 31, 2016

Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]

Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items



	Unrealized Gains/(Losses) On Marketable Securities			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2013	$	70		$	—		$	70
Other comprehensive loss before reclassifications	(457		)	(350		)	(807		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(457		)	(350		)	(807		)
Balance at December 31, 2014	$	(387	)	$	(350	)	$	(737	)
Other comprehensive loss before reclassifications	(202		)	(261		)	(463		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(202		)	(261		)	(463		)
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income (loss) before reclassifications	386			(671		)	(285		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	386			(671		)	(285		)
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)

Income taxes (Tables)

12 Months Ended

Dec. 31, 2016

Income Tax Disclosure [Abstract]

Schedule of Income before Income Tax, Domestic and Foreign

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2016, 2015, and 2014:



	2016		2015		2014
Domestic	(61,446	)	(50,944	)	(46,501	)
Foreign	(80,095	)	(119,018	)	(51,945	)
Total	(141,541	)	(169,962	)	(98,446	)

Components of Income Tax Provision

The Income Tax Provision consisted of the following for the years ended December 31, 2016, 2015 and 2014:



	2016			2015			2014
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(2		)	(2		)	4,890
Foreign	(766		)	(483		)	(197		)
Deferred:
U.S. Federal	199			—			—
U.S. State and Local	—			—			—
Foreign	—			—			—
Total Tax (Expense) Benefit	$	(569	)	$	(485	)	$	4,693

Schedule of reconciliation of the U.S. statutory income tax rate to the Company's effective tax rate

A reconciliation of the U.S. statutory income tax rate to the Company’s effective tax rate is as follows:



	December 31,
	2016		2015		2014
Federal income tax (benefit) at statutory rate	34.00	%	34.00	%	34.00	%
State income tax benefit, net of federal benefit	3.05		(0.43	)	(1.60	)
Permanent differences	(3.70	)	(6.61	)	(0.93	)
NOL IRC Section 382 Limitations	—		—		(21.53	)
Research and development	16.66		19.50		3.78
Increase to valuation allowance	(30.72	)	(20.87	)	9.17
Foreign tax rate differential	(19.84	)	(24.06	)	(18.14	)
Benefit allocated from other comprehensive income	0.14		—		—
Other	0.01		(1.82	)	0.01
Effective income tax rate	(0.40	)%	(0.29	)%	4.76	%

Schedule of significant components of the Company's deferred tax assets and liabilities

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2016 and 2015 are as follows:



	2016			2015
Deferred tax assets:
Accrued Expense	$	849		$	848
Amortization	46			57
Depreciation	2,968			2,631
Federal tax credits	74,475			50,850
State tax credits	4,996			3,356
Federal net operating losses	80,061			75,200
State net operating losses	9,672			8,848
Capitalized research and development costs	7,248			8,917
Other	22,125			10,345
Total gross deferred tax assets	202,440			161,052
Less valuation allowance	(183,015		)	(139,584		)
Total deferred tax assets, net of valuation allowance	$	19,425		$	21,468
Deferred tax liabilities:
Convertible debt	$	(19,190	)	$	(21,468	)
Gain on marketable securities	$	(235	)	$	—
Total gross deferred tax assets	(19,425		)	(21,468		)
Net deferred tax assets (liabilities)	$	—		$	—

Commitments and contingencies (Tables)	12 Months Ended
Commitments and contingencies (Tables)	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Schedule of future minimum lease payments	perating leases. Future minimum lease payments as of December 31, 2016

Geographic information (Tables)

12 Months Ended

Dec. 31, 2016

Segments, Geographical Areas [Abstract]

Summary of financial information based on geographical location

The following table presents financial information based on the geographic location of the facilities of the Company as of and for the years ended:



	Year Ended December 31, 2016
	United States		Non-US		Total
Total assets	$	223,098	$	46,247	$	269,345
Property and equipment, net	$	6,439	$	990	$	7,429
Revenue	$	1,206	$	81,499	$	82,705



	Year Ended December 31, 2015
	United States		Non-US		Total
Total assets	$	340,755	$	24,526	$	365,281
Property and equipment, net	$	8,206	$	768	$	8,974
Revenue	$	5,218	$	31,548	$	36,766

Restructuring (Tables)

12 Months Ended

Dec. 31, 2016

Restructuring and Related Activities [Abstract]

Restructuring



	Balance as of January 1, 2016		Expenses, net		Cash Payments			Balance as of December 31, 2016
2016 workforce reduction	$	—	$	2,484	$	(2,462	)	$	22

Selected quarterly financial data (Tables)

12 Months Ended

Dec. 31, 2016

Quarterly Financial Information Disclosure [Abstract]

Summary of quarterly data



	For the quarters ending
	March 31			June 30			September 30			December 31
2016:
Net product revenue	$	18,878		$	15,437		$	22,013		$	25,119
Collaboration and grant revenue	17			196			973			72
Operating expenses	57,337			52,193			55,050			50,183
Loss from operations	(38,442		)	(36,560		)	(32,064		)	(24,992		)
Net loss	(41,233		)	(38,914		)	(35,167		)	(26,796		)
Basic and diluted net loss per common share(1)	$	(1.22	)	$	(1.14	)	$	(1.03	)	$	(0.78	)
2015:
Net product revenue	$	5,069		$	6,161		$	9,772		$	12,694
Collaboration and grant revenue	2,413			613			4			40
Operating expenses	45,553			45,400			52,008			60,935
Loss from operations	(38,071		)	(38,626		)	(42,232		)	(48,201		)
Net loss	(37,915		)	(38,361		)	(43,223		)	(50,948		)
Basic and diluted net loss per common share(1)	$	(1.15	)	$	(1.14	)	$	(1.27	)	$	(1.50	)


(1)	The amounts were computed independently for each quarter and the sum of the quarters may not total the annual amounts.

The Company (Details) $ in Thousands	1 Months Ended	12 Months Ended
The Company (Details) $ in Thousands	Aug. 31, 2014 state	Dec. 31, 2016 USD ($) country	Dec. 31, 2014	Dec. 31, 2015 USD ($)	Aug. 31, 2015
Minimum age of ambulatory patient	5 years		5 years
Number of States In European Economic Area \| state	31
Number of countries made availability of Translama on a commercial basis \| country		25
Accumulated deficit \| $		$ (735,108)		$ (592,998)
3.00% Convertible senior notes due 2022 \| Convertible debt
Interest rate					3.00%

Summary of significant accounting policies (Details) - 12 months ended Dec. 31, 2016	Total	item	segment
Segment and geographic information
Number of operating segments		1	1
Computer equipment and software
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, and lab equipment \| Minimum
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, and lab equipment \| Maximum
Fixed assets
Estimated useful life	7 years

Summary of significant accounting policies (Details 2)	1 Months Ended	12 Months Ended
Summary of significant accounting policies (Details 2)	Aug. 31, 2014	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($) state
Summary
Capitalized inventory		$ 1,700,000
Number of states \| state				31
Minimum age of ambulatory patient	5 years			5 years
Allowance for doubtful accounts		700,000	$ 0
Research and development costs
Deferred research and development advance payments		400,000	600,000
Impairment of long-lived assets
Impairment of long-lived assets		0
Income Tax Expense (Benefit), Continuing Operations [Abstract]
Income tax (expense) benefit		569,000	485,000	$ (4,693,000)
Recent accounting pronouncements
Unamortized debt issuance cost		2,500,000
New Jersey
Income Tax Expense (Benefit), Continuing Operations [Abstract]
Income tax (expense) benefit		$ 0	0	$ 4,900,000
Long-term Debt \| Accounting Standards Update 2015-03
Recent accounting pronouncements
Unamortized debt issuance cost			2,800,000
Deposits and Other Assets \| Accounting Standards Update 2015-03
Recent accounting pronouncements
Unamortized debt issuance cost			$ (2,800,000)
Minimum
Summary
Gross profit margin (as percent)		90.00%

Fair value of financial instruments and marketable securities (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 173,345	$ 280,903
Recurring basis \| Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	173,345	280,903
Warrant liability	1	48
Stock appreciation rights liability	865	0
Recurring basis \| Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	0
Warrant liability	0	0
Stock appreciation rights liability	0	0
Recurring basis \| Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	173,345	280,903
Warrant liability	0	0
Stock appreciation rights liability	0	0
Recurring basis \| Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	0
Warrant liability	1	48
Stock appreciation rights liability	$ 865	$ 0

Fair value of financial instruments and marketable securities (Details 2) - USD ($)	Dec. 31, 2016	Dec. 31, 2015
Marketable securities accounted for as available-for-sale securities
Transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy	$ 0
Amortized Cost	173,347,000	$ 281,492,000
Gross Unrealized Gains	101,000	83,000
Gross Unrealized Losses	(103,000)	(672,000)
Fair Value	173,345,000	280,903,000
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	12,919,000	26,877,000
Gross Unrealized Gains	47,000	80,000
Gross Unrealized Losses	0	0
Fair Value	12,966,000	26,957,000
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	153,240,000	226,959,000
Gross Unrealized Gains	52,000	0
Gross Unrealized Losses	(103,000)	(640,000)
Fair Value	153,189,000	226,319,000
Government obligations
Marketable securities accounted for as available-for-sale securities
Amortized Cost	7,188,000	27,656,000
Gross Unrealized Gains	2,000	3,000
Gross Unrealized Losses	0	(32,000)
Fair Value	$ 7,190,000	$ 27,627,000

Fair value of financial instruments and marketable securities (Details 3) - USD ($)	Dec. 31, 2016	Dec. 31, 2015	Aug. 31, 2015
Marketable securities on the balance sheet
Less Than 12 Months	$ 157,352,000	$ 186,782,000
More Than 12 Months	15,993,000	94,121,000
Commercial paper
Marketable securities on the balance sheet
Less Than 12 Months	12,966,000	26,957,000
More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Less Than 12 Months	137,196,000	140,831,000
More Than 12 Months	15,993,000	85,488,000
Government obligations
Marketable securities on the balance sheet
Less Than 12 Months	7,190,000	18,994,000
More Than 12 Months	0	8,633,000
3.00% Convertible senior notes due 2022 \| Convertible debt
Marketable securities on the balance sheet
Principal	150,000,000	$ 150,000,000	$ 150,000,000
Interest rate			3.00%
Debt instrument	$ 85,200,000

Fair value of financial instruments and marketable securities (Details 4) - USD ($) $ / shares in Units, $ in Thousands	7 Months Ended	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2016	Dec. 31, 2015
Warrants
Changes in the fair value of warrant liability
Beginning balance		$ 48	$ 188
Change in fair value		(47)	(140)
Ending balance	$ 1	$ 1	$ 48
Warrants \| Minimum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)		62.00%	62.00%
Risk-free interest rate (as a percent)		0.62%	0.86%
Strike price (in dollars per share)	$ 128.00	$ 128.00	$ 128.00
Expected life		5 months 12 days	1 year 6 months
Warrants \| Maximum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)		67.00%	70.00%
Risk-free interest rate (as a percent)		1.34%	1.54%
Strike price (in dollars per share)	2,520.00	$ 2,520.00	$ 2,520.00
Expected life		2 years 8 months 19 days	3 years 8 months 12 days
Warrants \| Common stock
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 10.91	$ 10.91	$ 32.4
Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	$ 140
Change in fair value	725
Ending balance	$ 865	$ 865
Stock Appreciation Rights (SARs) \| Minimum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)		48.00%
Risk-free interest rate (as a percent)		0.44%
Strike price (in dollars per share)	$ 6.76	$ 6.76
Expected life			4 days
Stock Appreciation Rights (SARs) \| Maximum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)		71.00%
Risk-free interest rate (as a percent)		1.47%
Strike price (in dollars per share)			$ 30.86
Expected life			3 years 4 days
Stock Appreciation Rights (SARs) \| Common stock
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 10.91	$ 10.91

Fixed assets (Details) - USD ($) $ in Thousands	12 Months Ended
Fixed assets (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Fixed assets
Gross fixed assets	$ 38,356	$ 36,676
Less accumulated depreciation and amortization	(30,927)	(27,702)
Net fixed assets	7,429	8,974
Depreciation expense	3,290	2,876	$ 2,235
Leasehold improvements
Fixed assets
Gross fixed assets	14,038	14,029
Computer equipment and software
Fixed assets
Gross fixed assets	4,622	4,102
Furniture, fixtures, and lab equipment
Fixed assets
Gross fixed assets	19,343	17,443
Assets in process
Fixed assets
Gross fixed assets	$ 353	$ 1,102

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 13,649	$ 12,630
Consulting and contracted research	11,505	13,753
Professional fees	1,237	2,523
Sales allowances and other related costs	13,245	4,718
Accounts payable	6,298	5,779
Other	2,825	5,844
Accounts payable and accrued expenses	$ 48,759	$ 45,247

Convertible senior notes, 2015 Convertible Notes (Details)	1 Months Ended	12 Months Ended
	Aug. 31, 2015 USD ($) item $ / shares	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Long-term debt
Additional paid-in capital		$ 856,142,000	$ 820,165,000
Remaining amortization period		5 years 7 months 13 days
3.00% Convertible senior notes due 2022 \| Convertible debt
Long-term debt
Debt instrument	$ 150,000,000	$ 150,000,000	$ 150,000,000
Interest rate	3.00%
Net proceeds from issuance of convertible notes	$ 145,400,000
Trading days, number \| item	20
Consecutive trading days, period	30 days
Stock price trigger (as a percent)	130.00%
Business days, period	5 days
Consecutive trading-day period	5 days
Common stock per principal amount	$ 1,000
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day (as a percent)	98.00%
Conversion ratio	17.7487
Conversion price per share \| $ / shares	$ 56.34
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default (as a percent)	25.00%
Convertible instruments principal And unpaid interest payable upon events of default	100.00%
Term of the convertible notes	7 years
Additional paid-in capital		57,500,000
Net deferred tax liability in connection with convertible notes	$ 22,300,000
Debt instrument		$ 85,200,000
3.00% Convertible senior notes due 2022 \| Convertible debt \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| item	19
Consecutive trading days, period	30 days
Stock price trigger (as a percent)	130.00%
Redemption price (as a percent)	100.00%

Convertible senior notes, 2015 Convertible Notes (Details 2) - USD ($)	Dec. 31, 2016	Dec. 31, 2015	Aug. 31, 2015
Long-term debt
Less: Debt issuance costs	$ (2,500,000)
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Principal	150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(2,457,000)	(2,760,000)
Less: Debt discount, net	(49,327,000)	(55,392,000)
Net carrying amount	$ 98,216,000	$ 91,848,000

Convertible senior notes, 2015 Convertible Notes Interest Expense (Details 3) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Long-term debt
Amortization of debt issuance costs	$ 302	$ 107	$ 0
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	4,497	1,702
Amortization of debt issuance costs	302	107
Amortization of debt discount	6,065	2,146
Total	$ 10,864	$ 3,955
Effective interest rate of the liability component	11.00%	11.00%

Capital structure (Details) - USD ($) $ / shares in Units, $ in Millions		1 Months Ended
	Oct. 16, 2014	Feb. 28, 2014	Dec. 31, 2016	Dec. 31, 2015	May 31, 2013
Capital structure
Common stock, authorized shares (in shares)			125,000,000	125,000,000
Common stock
Capital structure
Common stock, authorized shares (in shares)					125,000,000
Shares issued and sold (in shares)	3,450,000	5,163,265
Public offering price (in dollars per share)	$ 36.25	$ 24.50
Common stock shares issuable pursuant to the exercise by the underwriters of an over-allotment option (in shares)	450,000	673,469
Net proceeds from public offerings	$ 117.6	$ 118.4

Capital structure (Details 2) - Common stock - $ / shares	Dec. 31, 2016	Dec. 31, 2015
2017
Warrants
Warrant shares (in shares)	6,250	6,250
Exercise price (in dollars per share)	$ 128.00	$ 128.00
2018
Warrants
Warrant shares (in shares)	7,030	7,030
Exercise price (in dollars per share)	$ 128.00	$ 128.00
2019
Warrants
Warrant shares (in shares)	130	130
Exercise price (in dollars per share)	$ 2,520.00	$ 2,520.00

Earnings per share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Numerator
Net loss	$ (26,796)	$ (35,167)	$ (38,914)	$ (41,233)	$ (50,948)	$ (43,223)	$ (38,361)	$ (37,915)	$ (142,110)	$ (170,447)	$ (93,753)
Denominator
Denominator for basic and diluted net loss per share (in shares)									34,044,584	33,626,248	31,565,310
Net loss per share:
Basic and diluted (in dollars per share)	$ (0.78)	$ (1.03)	$ (1.14)	$ (1.22)	$ (1.50)	$ (1.27)	$ (1.14)	$ (1.15)	$ (4.17)	$ (5.07)	$ (2.97)
Total shares excluded from calculation (in shares)									6,125,967	5,170,812	4,151,372
Stock Options
Net loss per share:
Total shares excluded from calculation (in shares)									5,854,316	4,826,477	3,432,972
Unvested restricted stock
Net loss per share:
Total shares excluded from calculation (in shares)									271,651	344,335	718,400

Stock award plan Stock award plan (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended			12 Months Ended
	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Stock option plan
Options granted (in shares)					141,185
Additional compensation recognized due to modifications to the options granted							$ 1,900
Share-based compensation expense					$ 35,009	$ 33,979	$ 19,310
Unrecognized compensation cost					$ 60,800
Weighted average remaining service period for recognition of unrecognized compensation cost					2 years 2 months 1 day
Stock option
Stock option plan
Granted (in shares)					1,500,645	2,201,800	1,639,996
Forfeited (in shares)					383,590	152,047	193,971
Expected dividend yield (as a percent)					0.00%	0.00%	0.00%
Weighted average grant date fair value (in dollars per share)					$ 17.31	$ 50.81	$ 22.39
Stock option \| Maximum
Stock option plan
Vesting period					4 years
Stock option \| Minimum
Stock option plan
Vesting period					3 years
Stock Appreciation Rights (SARs)
Stock option plan
Granted (in shares)			897,290
Vesting period			4 years
Share-based compensation expense					$ 900
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares authorized	739,937
2013 Stock Incentive Plan \| Unvested restricted stock
Stock option plan
Options granted (in shares)	735,324
2013 Stock Incentive Plan \| Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)				0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan \| Stock option \| Maximum
Stock option plan
Expiration period					10 years
2009 Equity and Long Term Incentive Plan \| Stock option \| Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date					100.00%
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date					110.00%
Stockholder's specified ownership percentage					10.00%
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)				122,296
2013 Long Term Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)					329,022
Annual increase in the number of shares outstanding on the first day of the fiscal year (as a percent)				4.00%
2013 Long Term Incentive Plan \| Common stock \| Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)				3,040,444
2013 Long Term Incentive Plan \| Common stock \| Minimum
Stock option plan
Annual increase in the number of shares on the first day of the fiscal year (in shares)				2,500,000
Inducement grant plan \| Stock option
Stock option plan
Granted (in shares)					155,200
Granted (in dollars per share)					$ 13.67
Forfeited (in shares)					255,550
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized		1,000,000
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit, percent		5.00%
Share-based compensation expense					$ 200

Stock award plan (Details 2) - Stock option - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Number of options
Outstanding at the beginning of the period (in shares)	4,826,477	3,432,972	2,095,592
Granted (in shares)	1,500,645	2,201,800	1,639,996
Exercised (in shares)	(89,216)	(656,248)	(108,645)
Forfeited (in shares)	(383,590)	(152,047)	(193,971)
Outstanding at the end of the period (in shares)	5,854,316	4,826,477	3,432,972
Vested or expected to vest at the end of the period (in shares)	2,792,870
Exercisable at the end of the period (in shares)	2,903,325
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 37.20	$ 25.00	$ 20.24
Granted (in dollars per share)	27.90	50.81	31.09
Exercised (in dollars per share)	10.85	13.27	11.00
Forfeited (in dollars per share)	47.42	49.58	32.91
Outstanding at the end of the period (in dollars per share)	34.71	$ 37.20	$ 25.00
Vested or expected to vest at the end of the period (in dollars per share)	35.66
Exercisable at the end of the period (in dollars per share)	$ 33.73
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 9 months 18 days
Vested or expected to vest at the end of the period	8 years 4 months 10 days
Exercisable at the end of the period	7 years 2 months 19 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars)	$ 341
Vested or expected to vest at the end of the period (in dollars)	249
Exercisable at the end of the period (in dollars)	$ 72

Stock award plan (Details 3) - Stock option	12 Months Ended
Stock award plan (Details 3) - Stock option	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	1.30%	1.48%	0.11%
Expected volatility (as a percent)	67.00%	67.00%	70.00%
Expected term	5 years 18 days	5 years 6 months	5 years 6 months
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	2.24%	2.18%	2.04%
Expected volatility (as a percent)	78.00%	69.00%	91.00%
Expected term	10 years	9 years 1 month 13 days	6 years 3 months

Stock award plan (Details 4)	12 Months Ended
Stock award plan (Details 4)	Dec. 31, 2016 $ / shares shares
Number of Shares
Granted (in shares) \| shares	141,185
Weighted Average Grant Date Fair Value
Granted (in dollars per share) \| $ / shares	$ 30.86
Unvested restricted stock
Number of Shares
Balance at the beginning of the period (in shares) \| shares	344,335
Vested (in shares) \| shares	(163,635)
Forfeited (in shares) \| shares	(50,234)
Balance at the end of the period (in shares) \| shares	271,651
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 10.85
Vested (in dollars per share) \| $ / shares	10.85
Forfeited (in dollars per share) \| $ / shares	18.93
Balance at the end of the period (in dollars per share) \| $ / shares	$ 19.76

Stock award plan (Details 5) - USD ($) $ in Thousands	12 Months Ended
Stock award plan (Details 5) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 35,009	$ 33,979	$ 19,310
Research and development
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	16,812	16,138	9,739
Total
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 18,197	$ 17,841	$ 9,571

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	$ (1,200)
Balance at the end of the period	(1,485)	$ (1,200)
Unrealized Gains/(Losses) On Marketable Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(589)	(387)	$ 70
Other comprehensive income (loss) before reclassifications	386	(202)	(457)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	386	(202)	(457)
Balance at the end of the period	(203)	(589)	(387)
Foreign Currency Translation
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(611)	(350)	0
Other comprehensive income (loss) before reclassifications	(671)	(261)	(350)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(671)	(261)	(350)
Balance at the end of the period	(1,282)	(611)	(350)
Accumulated other comprehensive income (loss)
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(1,200)	(737)	70
Other comprehensive income (loss) before reclassifications	(285)	(463)	(807)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(285)	(463)	(807)
Balance at the end of the period	$ (1,485)	$ (1,200)	$ (737)

Collaborations and grants (Details)		1 Months Ended			12 Months Ended
Collaborations and grants (Details)	Jan. 02, 2011 item	Nov. 30, 2014 USD ($)	Jan. 31, 2014 USD ($)	Nov. 30, 2011 USD ($) item	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)
Minimum
Grant revenue
Term of grant program					2 years
Maximum
Grant revenue
Term of grant program					5 years
Collaboration agreement \| Development event milestones
Collaborations and grants
Collaboration revenue recognized		$ 10,000,000	$ 7,500,000
Collaboration agreement \| Roche and SMA Foundation [Member]
Collaborations and grants
Number of compounds in preclinical development \| item				3
Deferred revenue				$ 30,000,000
Number of significant deliverables \| item				2
Research period for applying technology				2 years
Collaboration revenue recognized					$ 400,000	$ 600,000	$ 20,200,000
Collaboration agreement \| Roche and SMA Foundation [Member] \| Development event milestones \| Maximum
Collaborations and grants
Additional consideration receivable upon achievement of specified events					135,000,000
Collaboration agreement \| Roche and SMA Foundation [Member] \| Sales milestones \| Maximum
Collaborations and grants
Additional consideration receivable upon achievement of specified events					325,000,000
Early stage collaboration and discovery agreements
Collaborations and grants
Deferred revenue					$ 0	0	1,800,000
Number of significant deliverables \| item	2
Collaboration revenue recognized						$ 1,800,000	$ 1,300,000
Early stage collaboration and discovery agreements \| Minimum
Collaborations and grants
Research period for applying technology					3 years
Early stage collaboration and discovery agreements \| Maximum
Collaborations and grants
Research period for applying technology					4 years
Early stage collaboration and discovery agreements \| Development event milestones
Collaborations and grants
Additional consideration receivable upon achievement of specified events					$ 143,000,000
Early stage collaboration and discovery agreements \| Sales milestones \| Maximum
Collaborations and grants
Additional consideration receivable upon achievement of specified events					$ 252,000,000

Income taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating loss carryforwards
Loss from operations before tax (expense) benefit	$ (141,541)	$ (169,962)	$ (98,446)
United States
Operating loss carryforwards
Loss from operations before tax (expense) benefit	(61,446)	(50,944)	(46,501)
Non-US
Operating loss carryforwards
Loss from operations before tax (expense) benefit	$ (80,095)	$ (119,018)	$ (51,945)

Income taxes (Details 2) - USD ($) $ in Thousands	12 Months Ended
Income taxes (Details 2) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Current:
U.S. Federal	$ 0	$ 0	$ 0
U.S. State and Local	(2)	(2)	4,890
Foreign	(766)	(483)	(197)
Deferred:
U.S. Federal	199	0	0
U.S. State and Local	0	0	0
Foreign	0	0	0
Total Tax (Expense) Benefit	$ (569)	$ (485)	$ 4,693

Income taxes (Details 3)	12 Months Ended
Income taxes (Details 3)	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Reconciliation of the U.S. statutory income tax rate to the entity's effective tax rate
Federal income tax (benefit) at statutory rate (as a percent)	34.00%	34.00%	34.00%
State income tax benefit, net of federal benefit (as a percent)	3.05%	(0.43%)	(1.60%)
Permanent differences (as a percent)	(3.70%)	(6.61%)	(0.93%)
NOL IRC Section 382 Limitations (as a percent)	0.00%	0.00%	(21.53%)
Research and development (as a percent)	16.66%	19.50%	3.78%
Increase to valuation allowance (as a percent)	(30.72%)	(20.87%)	9.17%
Foreign tax rate differential (as a percent)	(19.84%)	(24.06%)	(18.14%)
Benefit allocated from other comprehensive income (as a percent)	0.14%	0.00%	0.00%
Other (as a percent)	0.01%	(1.82%)	0.01%
Effective income tax rate (as a percent)	(0.40%)	(0.29%)	4.76%

Income taxes (Details 4) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Deferred tax assets:
Accrued Expense	$ 849	$ 848
Amortization	46	57
Depreciation	2,968	2,631
Federal tax credits	74,475	50,850
State tax credits	4,996	3,356
Federal net operating losses	80,061	75,200
State net operating losses	9,672	8,848
Capitalized research and development costs	7,248	8,917
Other	22,125	10,345
Total gross deferred tax assets	202,440	161,052
Less valuation allowance	(183,015)	(139,584)
Total deferred tax assets, net of valuation allowance	19,425	21,468
Deferred tax liabilities:
Convertible debt	(19,190)	(21,468)
Gain on marketable securities	(235)	0
Total gross deferred tax assets	(19,425)	(21,468)
Net deferred tax assets (liabilities)	$ 0	$ 0

Income taxes (Details 5) - USD ($) $ in Thousands	12 Months Ended
Income taxes (Details 5) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating loss carryforwards
Valuation allowance	$ 183,015	$ 139,584
Valuation allowance, deferred tax asset, increase (decrease)	(43,400)	$ 16,300
Orphan drug credit carryover	60,100
Limited NOL carryforwards	231,500
Operating loss carryforwards, not subject to expiration	$ 169,200
NOL carryforward period	20 years
Operating loss carryforwards, subject to expiration	$ 62,300
Operating loss carryforwards for immediate use	175,100
Operating loss carryforwards in next twelve months	$ 16,700
Federal income tax (benefit) at statutory rate (as a percent)	34.00%	34.00%	34.00%
Uncertain tax position	$ 0
First five years from ownership change
Operating loss carryforwards
Net operating loss carryforwards	16,700
After five years
Operating loss carryforwards
Net operating loss carryforwards	5,700
Federal
Operating loss carryforwards
Net operating loss carryforwards	285,800
Operating loss carryforwards associated to exercise of stock options and vesting of restricted stock	50,400
Tax benefit related to operating loss carryforwards	17,100
Research and development credit carryforwards	14,400
State
Operating loss carryforwards
Net operating loss carryforwards	213,200
Research and development credit carryforwards	$ 7,300

Commitments and contingencies (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Jan. 31, 2017	Jun. 30, 2016
Other contingencies
Operating leases, rent expense	$ 2.2	$ 1.8	$ 0.9
Funding agreement \| Wellcome trust limited
Other contingencies
Development and regulatory milestone payments which the entity may be obligated to pay					$ 0.8
Subsequent Event \| Funding agreement \| Maximum \| Wellcome trust limited
Other contingencies
Development and regulatory milestone payments which the entity may be obligated to pay				$ 22.4

Commitments and contingencies (Details 1) $ in Thousands	Dec. 31, 2016 USD ($)
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2017	$ 1,483
2018	1,214
2019	353
2020	177
2021	59
Thereafter	0
Total future minimum lease payments	$ 3,286

Geographic information (Details) - 12 months ended Dec. 31, 2016	item	segment
Segments, Geographical Areas [Abstract]
Number of operating segments	1	1

Geographic information (Details 2) - USD ($) $ in Thousands	12 Months Ended
Geographic information (Details 2) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Segment Reporting Information [Line Items]
Total assets	$ 269,345	$ 365,281
Property and equipment, net	7,429	8,974
Revenue	82,705	36,766	$ 25,245
United States
Segment Reporting Information [Line Items]
Total assets	223,098	340,755
Property and equipment, net	6,439	8,206
Revenue	1,206	5,218
Non-US
Segment Reporting Information [Line Items]
Total assets	46,247	24,526
Property and equipment, net	990	768
Revenue	$ 81,499	$ 31,548

401(k) plan (Details) - USD ($) $ in Millions	12 Months Ended
401(k) plan (Details) - USD ($) $ in Millions	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Compensation and Retirement Disclosure [Abstract]
Matching contribution up to the first 6% of employee's base salary (as a percent)	50.00%
Percentage of employee's base salary, matched by employer	6.00%
Expense recorded	$ 1.1	$ 0.7	$ 0.3

Restructuring (Details) $ in Millions	Dec. 31, 2016 USD ($)
Employee Severance \| 2016 workforce reduction
Restructuring Cost and Reserve [Line Items]
Work-force reduction charges	$ 2.5

Restructuring (Details 2) - Employee Severance - 2016 workforce reduction $ in Thousands	12 Months Ended
	Dec. 31, 2016 USD ($)
Restructuring Reserve [Roll Forward]
January 1, 2016	$ 0
Expenses, net	2,484
Cash Payments	(2,462)
December 31, 2016	$ 22

Subsequent events (Details) - Arrangement - Marathon Pharmaceuticals, LLC shares in Millions, $ in Millions	Mar. 16, 2017 USD ($) shares
Subsequent Event
Subsequent Event [Line Items]
Acquisition price	$ 140
Payments to acquire	75
Equity interest issued or issuable	$ 65
Trading day period	15 days
Threshold	19.90%
Equity interest issued or issuable, number of shares (in shares) \| shares	6.9
Scenario, Forecast
Subsequent Event [Line Items]
Development and regulatory milestone payments which the entity may be obligated to pay	$ 50

Selected quarterly financial data (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Quarterly Financial Information Disclosure [Abstract]
Net product revenue	$ 25,119	$ 22,013	$ 15,437	$ 18,878	$ 12,694	$ 9,772	$ 6,161	$ 5,069	$ 81,447	$ 33,696	$ 717
Collaboration and grant revenue	72	973	196	17	40	4	613	2,413	1,258	3,070	24,528
Operating expenses	50,183	55,050	52,193	57,337	60,935	52,008	45,400	45,553	214,763	203,896	124,658
Loss from operations	(24,992)	(32,064)	(36,560)	(38,442)	(48,201)	(42,232)	(38,626)	(38,071)	(132,058)	(167,130)	(99,413)
Net loss	$ (26,796)	$ (35,167)	$ (38,914)	$ (41,233)	$ (50,948)	$ (43,223)	$ (38,361)	$ (37,915)	$ (142,110)	$ (170,447)	$ (93,753)
Net loss per share—basic and diluted (in dollars per share)	$ (0.78)	$ (1.03)	$ (1.14)	$ (1.22)	$ (1.50)	$ (1.27)	$ (1.14)	$ (1.15)	$ (4.17)	$ (5.07)	$ (2.97)