PTC Therapeutics (PTCT) 10-Q 8 May 17 2017 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2017	May 05, 2017
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	1,070,081
Document Type	10-Q
Document Period End Date	Mar. 31, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		41,244,004
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	Q1

Consolidated Balance Sheets (un

Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 54,106	$ 58,321
Marketable securities	148,471	173,345
Inventory	1,354	0
Prepaid expenses and other current assets	4,623	4,691
Trade receivables, net	32,173	24,929
Total current assets	240,727	261,286
Fixed assets, net	7,059	7,429
Deposits and other assets	859	630
Total assets	248,645	269,345
Current liabilities:
Accounts payable and accrued expenses	45,153	48,759
Other current liabilities	265	865
Total current liabilities	45,418	49,624
Deferred revenue - long-term	2,194	1,587
Long-term debt	99,895	98,216
Other long-term liabilities	311	335
Total liabilities	147,818	149,762
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 34,316,836 shares at March 31, 2017. Authorized 125,000,000 shares; issued and outstanding 34,169,410 shares at December 31, 2016	34	34
Additional paid-in capital	865,834	856,142
Accumulated other comprehensive loss	(876)	(1,485)
Accumulated deficit	(764,165)	(735,108)
Total stockholders’ equity	100,827	119,583
Total liabilities and stockholders’ equity	$ 248,645	$ 269,345

Consolidated Balance Sheets (u3

Consolidated Balance Sheets (unaudited) (Parenthetical) - $ / shares	Mar. 31, 2017	Dec. 31, 2016
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)	34,316,836	34,169,410
Common stock, outstanding shares (in shares)	34,316,836	34,169,410

Consolidated Statements of Oper

Consolidated Statements of Operations (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Revenues:
Net product revenue	$ 26,442	$ 18,878
Collaboration and grant revenue	105	17
Total revenues	26,547	18,895
Operating expenses:
Cost of product sales	39	0
Research and development	27,363	31,399
Selling, general and administrative	25,500	25,938
Total operating expenses	52,902	57,337
Loss from operations	(26,355)	(38,442)
Interest expense, net	(2,219)	(1,956)
Other expense, net	(318)	(721)
Loss before income tax expense	(28,892)	(41,119)
Income tax expense	(165)	(114)
Net loss attributable to common stockholders	$ (29,057)	$ (41,233)
Weighted-average shares outstanding:
Basic and diluted (in shares)	34,305,948	33,919,169
Net loss per share-basic and diluted (in dollars per share)
Net loss per share—basic and diluted (in dollars per share)	$ (0.85)	$ (1.22)

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Statement of Comprehensive Income [Abstract]
Net loss	$ (29,057)	$ (41,233)
Other comprehensive loss:
Unrealized (loss) gain on marketable securities, net of tax	(22)	658
Foreign currency translation gain	631	1,626
Comprehensive loss	$ (28,448)	$ (38,949)

Consolidated Statements of Cash

Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Cash flows from operating activities
Net loss	$ (29,057)	$ (41,233)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	612	849
Change in valuation of warrant liability	0	(47)
Non-cash interest expense	1,600	1,446
Amortization of premiums on investments	208	631
Amortization of debt issuance costs	80	72
Share-based compensation expense	9,029	8,915
Unrealized foreign currency transaction losses, net	820	0
Changes in operating assets and liabilities:
Inventory	(1,350)	0
Prepaid expenses and other current assets	93	702
Trade receivables, net	(6,746)	(10,678)
Deposits and other assets	(226)	(12)
Accounts payable and accrued expenses	(3,923)	(2,452)
Other liabilities	(624)	(23)
Deferred revenue	582	243
Net cash used in operating activities	(28,902)	(41,587)
Cash flows from investing activities
Purchases of fixed assets	(225)	(265)
Purchases of marketable securities	(19,467)	(19,413)
Sale and redemption of marketable securities	44,110	41,795
Net cash provided by investing activities	24,418	22,117
Cash flows from financing activities
Proceeds from exercise of options	106	34
Proceeds from shares issued under employee stock purchase plan	557	0
Net cash provided by financing activities	663	34
Effect of exchange rate changes on cash	(394)	1,579
Net decrease in cash and cash equivalents	(4,215)	(17,857)
Cash and cash equivalents, beginning of period	58,321	58,022
Cash and cash equivalents, end of period	54,106	40,165
Supplemental disclosure of cash information
Cash paid for interest	2,250	2,263
Cash paid for income taxes	28	225
Supplemental disclosures of non-cash information related to investing and financing activities
Change in unrealized (loss) gain on marketable securities, net of tax	$ (22)	$ 658

The Company

The Company	3 Months Ended
	Mar. 31, 2017
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 novel medicines using its expertise in RNA biology. PTC has discovered all of its compounds currently under development using its proprietary technologies. PTC plans to continue to develop these compounds both on its own and through selective collaboration arrangements with leading pharmaceutical and biotechnology companies. PTC’s internally discovered pipeline addresses multiple therapeutic areas, including rare disorders and oncology. The Company’s product, Translarna ™ (ataluren) received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients age five years and older 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 April 2017, the EMA’s Committee for Human Medicinal Products, or CHMP, issued a positive recommendation to this renewal request, which is pending endorsement from the European Commission. If the European Commission endorses the recommendation, the Company expects the renewal would be effective for a period of twelve months. 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 March 31, 2017 , Translarna was available in over 25 countries on a commercial basis or pursuant to an 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 the Company's 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 has discontinued its current clinical development of Translarna for nmCF and has begun to 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. On April 20, 2017, the Company, completed its acquisition of all rights to EMFLAZA™ (deflazacort), or the Transaction. EMFLAZA is approved in the United States for the treatment of Duchenne muscular dystrophy, or DMD, patients five years and older. The Transaction was completed pursuant to an asset purchase agreement, dated March 15, 2017, as amended on April 20, 2017, or the Asset Purchase Agreement, by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The assets acquired by the Company in the Transaction include intellectual property rights related to EMFLAZA, inventories of EMFLAZA, certain contractual rights related to EMFLAZA and certain other assets related to EMFLAZA. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction. Upon the closing of the Transaction, the Company paid to Marathon total upfront consideration of approximately $140 million . The total upfront consideration was comprised of $75 million in cash, funded through cash on hand, and 6,683,598 shares of the Company’s common stock. The number of shares of common stock issued at closing was determined by dividing $65 million by 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. 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, and a single $50 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement. The Company expects that the contingent payments will, on a blended average basis, range in percentages of net sales between the low to mid-twenties. As of March 31, 2017 , the Company had an accumulated deficit of approximately $764.2 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 9), 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 accounti

Summary of significant accounting policies	3 Months Ended
	Mar. 31, 2017
Accounting Policies [Abstract]
Summary of significant accounting policies	Summary of significant accounting policies The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2016 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (SEC) on March 16, 2017 ( 2016 Form 10-K). Basis of presentation The accompanying financial information as of March 31, 2017 and for the three months ended March 31, 2017 and 2016 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States (GAAP) have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2016 and notes thereto included in the 2016 Form 10-K. In the opinion of management, the unaudited financial information as of March 31, 2017 and for the three months ended March 31, 2017 and 2016 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three month periods ended March 31, 2017 are not necessarily indicative of the results to be expected for the year ended December 31, 2017 or for any other interim period or for any other future year. 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, allowance for doubtful accounts, inventory 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. Inventory and cost of product sales In January 2017, the European Commission granted an annual renewal of the Company’s marketing authorization for Translarna for the treatment of nmDMD. Until this renewal, the Company had considered the authorization to be subject to risk and did not capitalize productions costs in inventory as it was not probable that such costs would be recovered. With the renewal, the Company now considers recovery of the costs to be probable and began capitalizing production costs in inventory, effective January 1, 2017. Production costs will be expensed as cost of product sales when the related products are sold. The costs for a portion of the inventory available for sale was expensed as research and development costs prior to the January 2017 annual renewal of the Translarna marketing authorization and as such the cost of products sold and related gross margins are not necessarily indicative of future cost of products sold and gross margin. The product sales in the period ended March 31, 2017 reflects de minimis cost of inventory as the majority was expensed to research and development costs in prior periods. Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Translarna product which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2017 December 31, 2016 Work in progress $ 320 $ — Finished goods 1,034 — Total inventory $ 1,354 $ — The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. Cost of product sales Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, product shipping and handling costs and storage costs. 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 partner 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 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 FASB ASC 605-28, Revenue Recognition—Milestone Method. 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 $0.8 million as of March 31, 2017 and $0.7 million as of December 31, 2016 . Recently issued accounting standards 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 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 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 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. In January 2017, the FASB issued ASU No. 2017-01, "Business Combinations (Topic 805): Clarifying the Definition of a Business". This standard changed the definition of a business to help entities determine whether a set of transferred assets and activities is a business. This standard is effective for public companies for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, with early adoption permitted. The Company expects to adopt this guidance when effective and is assessing what effect the adoption of ASU 2017-01 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements 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 adopted the guidance on January 1, 2017 on a prospective basis. As the Company’s deferred tax assets is provided with full valuation allowance as of March 31, 2017 , adoption of this standard did not have a significant impact on the Company's financial statements.

Fair value of financial instrum

Fair value of financial instruments and marketable securities	3 Months Ended
	Mar. 31, 2017
Fair Value Disclosures [Abstract]
Fair value of financial instruments and marketable securities	Fair value of financial instruments and marketable securities 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. Cash equivalents and investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables, accounts payable and accrued expenses, and debt approximates fair value due to the short-term nature of those instruments. Fair value of certain marketable securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. 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 above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2017 and December 31, 2016 : March 31, 2017 Total Quoted prices Significant Significant Marketable securities $ 148,471 $ — $ 148,471 $ — Warrant liability $ 1 $ — $ — $ 1 Stock appreciation rights liability $ 265 $ — $ — $ 265 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 No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the periods ended March 31, 2017 and December 31, 2016 . The following is a summary of marketable securities accounted for as available-for-sale securities at March 31, 2017 and December 31, 2016 : March 31, 2017 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 19,162 $ 35 $ — $ 19,197 Corporate debt securities 126,134 23 (84 ) 126,073 Government obligations 3,201 — — 3,201 $ 148,497 $ 58 $ (84 ) $ 148,471 December 31, 2016 Amortized Cost Gross Unrealized Fair Value 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 At March 31, 2017 and 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. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. As of March 31, 2017 and December 31, 2016 , the Company did not have any realized gains/losses from the sale of marketable securities. Marketable securities on the balance sheet at March 31, 2017 and December 31, 2016 mature as follows: March 31, 2017 Less Than 12 Months More Than 12 Months Commercial paper $ 19,197 $ — Corporate debt securities 122,077 3,995 Government obligations 3,202 — Total Marketable securities $ 144,476 $ 3,995 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 The Company classifies all of its securities as current as they are all available for sale and are available for current operations. Level 3 valuation The warrant liability is classified in Other long-term liabilities on the Company’s consolidated balance sheets. The warrant liability is marked-to-market each reporting period with the change in fair value recorded as a gain or loss within Other expense, net, on the Company’s consolidated statements 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 long-term 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 valuations for the warrant liability and SARs liability for the period ended March 31, 2017 : Level 3 liabilities Warrants SARs Beginning balance as of December 31, 2016 $ 1 $ 865 Change in fair value — 464 Payments — (1,064 ) Ending balance as of March 31, 2017 $ 1 $ 265 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 stock fair 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 March 31, 2017 include (i) volatility ( 55% — 69% ), (ii) risk free interest rate ( 0.76% — 1.39% ), (iii) strike price ( $128.00 - $2,520.00 ), (iv) fair value of common stock ( $9.84 ), and (v) expected life ( 0.21 — 2.48 years). 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). Fair value of the SARs liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the stock fair value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s SARs as of March 31, 2017 include (i) volatility ( 67% — 69% ), (ii) risk free interest rate ( 0.97% — 1.50% ), (iii) strike price ( $6.76 - $30.86 ), (iv) fair value of common stock ( $9.84 ), and (v) expected life ( 0.8 — 2.8 years).

Other comprehensive income (los

Other comprehensive income (loss) and accumulated other comprehensive items	3 Months Ended
	Mar. 31, 2017
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Other comprehensive income (loss) and accumulated other comprehensive items	Other comprehensive income (loss) and accumulated other comprehensive items Other comprehensive income (loss) includes changes in equity that are excluded from net income (loss), such as unrealized gains and losses on marketable securities. The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three months ended March 31, 2017 : Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2016 $ (203 ) $ (1,282 ) $ (1,485 ) Other comprehensive (loss) income before reclassifications (22 ) 631 609 Amounts reclassified from other comprehensive items — — — Other comprehensive (loss) income (22 ) 631 609 Balance at March 31, 2017 $ (225 ) $ (651 ) $ (876 )

Accounts payable and accrued ex

Accounts payable and accrued expenses	3 Months Ended
	Mar. 31, 2017
Payables and Accruals [Abstract]
Accounts payable and accrued expenses	Accounts payable and accrued expenses Accounts payable and accrued expenses at March 31, 2017 and December 31, 2016 consist of the following: March 31, December 31, Employee compensation, benefits, and related accruals $ 7,605 $ 13,649 Consulting and contracted research 8,827 11,505 Professional fees 2,298 1,237 Sales allowance and other costs 19,088 13,245 Accounts payable 3,579 6,298 Other 3,756 2,825 $ 45,153 $ 48,759

Warrants

Warrants	3 Months Ended
	Mar. 31, 2017
Stockholders' Equity Note [Abstract]
Warrants	Warrants All of the Company’s outstanding warrants were classified as liabilities as of March 31, 2017 and December 31, 2016 because they contained non-standard antidilution provisions. The following is a summary of the Company’s outstanding warrants as of March 31, 2017 and December 31, 2016 : 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

Net loss per share

Net loss per share	3 Months Ended
	Mar. 31, 2017
Earnings Per Share [Abstract]
Net loss per share	Net loss per share Basic earnings per share is computed by dividing net income (loss) by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net income (loss) by the weighted-average number of common shares plus the effect of dilutive potential common shares outstanding during the period. The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended March 31, 2017 2016 Numerator Net loss $ (29,057 ) $ (41,233 ) Denominator Denominator for basic and diluted net loss per share 34,305,948 33,919,169 Net loss per share: Basic and diluted $ (0.85 ) * $ (1.22 ) * *In the three months ended March 31, 2017 and 2016 , 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 March 31, 2017 2016 Stock Options 7,007,290 6,034,918 Unvested restricted stock awards and units 566,594 453,441 Total 7,573,884 6,488,359

Stock award plan

Stock award plan	3 Months Ended
	Mar. 31, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock award plan	Stock award plan 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 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. 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 March 31, 2017 , awards for 236,792 shares of common stock are available for issuance. From January 1, 2017 through March 31, 2017 , the Company issued a total of 1,244,723 stock options to various employees. Of those, 54,900 were inducement grants for non-statutory stock options. The inducement grant awards were made pursuant to the NASDAQ inducement grant exception as a material component of the Company's new hires’ employment compensation and not under the 2013 Long Term Incentive Plan. A summary of stock option activity is as follows: Number of Weighted- Weighted- Aggregate (in Outstanding at December 31, 2016 5,854,316 $ 34.71 Granted 1,244,723 $ 11.32 Exercised (9,766 ) $ 10.85 Forfeited/Cancelled (81,983 ) $ 35.64 Outstanding at March 31, 2017 7,007,290 $ 30.56 7.87 years $ 179 Vested or Expected to vest at March 31, 2017 3,296,281 $ 28.16 8.68 years $ 144 Exercisable at March 31, 2017 3,478,720 $ 33.28 7.03 years $ 25 The fair value of grants made in the three months ended March 31, 2017 was contemporaneously estimated on the date of grant using the following assumptions: Three months ended Risk-free interest rate 1.94% — 2.45% Expected volatility 76%—81% Expected term 5.04– 10.00 years The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the three -month period ended March 31, 2017 was $7.76 per share. 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 expected volatility of share options was estimated based on a historical volatility analysis of peers that were similar to the Company with respect to industry, stage of life cycle, size, and financial leverage. 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. Restricted Stock Awards —Restricted stock awards are granted subject to certain restrictions, including in some cases service or time 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 Weighted January 1, 2017 271,651 $ 19.76 Granted 328,194 $ 11.23 Vested (30,161 ) $ 30.86 Forfeited (3,090 ) $ 13.98 Unvested at March 31, 2017 566,594 $ 14.26 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 March 31, 2017 , a total of 213,197 SARs vested and the Company recorded $0.2 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 March 31, 2017 , the Company issued 107,499 shares of common stock and 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: Three Months Ended March 31, 2017 2016 Research and development $ 4,467 $ 4,328 Selling, general and administrative 4,562 4,587 Total $ 9,029 $ 8,915 As of March 31, 2017 , there was approximately $63.2 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the 2009 Equity and Long Term Incentive Plan, the 2013 Long Term Incentive Plan and equity awards made pursuant to the NASDAQ inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 2.26 years.

Convertible Senior Notes

Convertible Senior Notes	3 Months Ended
	Mar. 31, 2017
Debt Disclosure [Abstract]
Convertible Senior Notes	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). 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: Liability component March 31, 2017 December 31, 2016 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (2,378 ) (2,457 ) Less: Debt discount, net(1) (47,727 ) (49,327 ) Net carrying amount $ 99,895 $ 98,216 (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 $95.9 million as of March 31, 2017 . The Company estimates the fair value of its Convertible Notes utilizing market quotations for debt that have quoted prices in active markets. As of March 31, 2017 , the remaining contractual life of the Convertible Notes is approximately 5.4 years. The following table sets forth total interest expense recognized related to the Convertible Notes: Three Months Ended March 31, 2017 2016 Contractual interest expense $ 1,110 $ 1,116 Amortization of debt issuance costs 80 72 Amortization of debt discount 1,600 1,446 Total $ 2,790 $ 2,634 Effective interest rate of the liability component 11 % 11 %

Restructuring

Restructuring	3 Months Ended
	Mar. 31, 2017
Restructuring Charges [Abstract]
Restructuring	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 Expenses, Cash payments Balance as of 2016 workforce reduction $ 22 $ — $ (22 ) $ —

Commitments and contingencies

Commitments and contingencies	3 Months Ended
	Mar. 31, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and 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 the Company's 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’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of 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.

Subsequent events

Subsequent events	3 Months Ended
	Mar. 31, 2017
Subsequent Events [Abstract]
Subsequent events	Subsequent events On April 20, 2017, the Company completed its previously announced acquisition of all rights to EMFLAZA™ (deflazacort) pursuant to an asset purchase agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. Upon the closing of the acquisition of EMFLAZA, the Company paid to Marathon total upfront consideration of approximately $140 million , comprised of $75 million in cash, funded through cash on hand, and 6,683,598 shares of the Company's common stock. Marathon is also 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, which the Company expects will range as a percentage of net sales between the low to mid-20s on a blended average basis. In addition, Marathon has the opportunity to receive a single $50 million sales-based milestone. Additional information concerning the EMFLAZA acquisition is discussed in Note 1. The Company is currently assessing the accounting related to the EMFLAZA acquisition. On May 5, 2017, the Company entered into a credit and security agreement with MidCap Financial Trust a Delaware statutory trust, or MidCap Financial, as administrative agent and MidCap Financial and other certain institutions as lenders thereto, or the Credit Agreement, that provides for a $60 million term loan facility, of which $40 million was drawn by the Company at close. The remaining $20 million under the senior secured term loan facility would become available to the Company upon demonstration (prior to December 31, 2018) of net product revenue equaling or exceeding $120 million for the trailing twelve month period. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier. Borrowings under the Credit Agreement bear interest at a rate per annum equal to LIBOR (with a floor rate of 1.00% ) plus 6.15% . The Company is obligated to make only interest payments (payable monthly, in arrears) through April 30, 2019. Commencing on May 1, 2019 and continuing for the remaining twenty-four months of the facility, the Company will be required to make monthly interest payments and monthly principal payments based on the straight-line amortization schedule in the Credit Agreement. The Credit Agreement requires the Company to not have less than $100 million of net revenue (raised to $120 million if the additional $20 million term loan is issued) for the prior twelve months to be measured on the last day of each fiscal quarter beginning on December 31, 2017. The Company is currently assessing the accounting related to the Credit Agreement.

Summary of significant accoun19

Summary of significant accounting policies (Policies)	3 Months Ended
	Mar. 31, 2017
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The accompanying financial information as of March 31, 2017 and for the three months ended March 31, 2017 and 2016 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States (GAAP) have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2016 and notes thereto included in the 2016 Form 10-K. In the opinion of management, the unaudited financial information as of March 31, 2017 and for the three months ended March 31, 2017 and 2016 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three month periods ended March 31, 2017 are not necessarily indicative of the results to be expected for the year ended December 31, 2017 or for any other interim period or for any other future year.
Use of estimates	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, allowance for doubtful accounts, inventory 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.
Inventories and cost of product sales	Inventory and cost of product sales In January 2017, the European Commission granted an annual renewal of the Company’s marketing authorization for Translarna for the treatment of nmDMD. Until this renewal, the Company had considered the authorization to be subject to risk and did not capitalize productions costs in inventory as it was not probable that such costs would be recovered. With the renewal, the Company now considers recovery of the costs to be probable and began capitalizing production costs in inventory, effective January 1, 2017. Production costs will be expensed as cost of product sales when the related products are sold. The costs for a portion of the inventory available for sale was expensed as research and development costs prior to the January 2017 annual renewal of the Translarna marketing authorization and as such the cost of products sold and related gross margins are not necessarily indicative of future cost of products sold and gross margin. The product sales in the period ended March 31, 2017 reflects de minimis cost of inventory as the majority was expensed to research and development costs in prior periods. Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Translarna product which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2017 December 31, 2016 Work in progress $ 320 $ — Finished goods 1,034 — Total inventory $ 1,354 $ — The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. Cost of product sales Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, product shipping and handling costs and storage costs.
Revenue recognition	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 partner 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 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 FASB ASC 605-28, Revenue Recognition—Milestone Method. 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	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.
Recently issued accounting standards	Recently issued accounting standards 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 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 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 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. In January 2017, the FASB issued ASU No. 2017-01, "Business Combinations (Topic 805): Clarifying the Definition of a Business". This standard changed the definition of a business to help entities determine whether a set of transferred assets and activities is a business. This standard is effective for public companies for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, with early adoption permitted. The Company expects to adopt this guidance when effective and is assessing what effect the adoption of ASU 2017-01 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements 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 adopted the guidance on January 1, 2017 on a prospective basis. As the Company’s deferred tax assets is provided with full valuation allowance as of March 31, 2017 , adoption of this standard did not have a significant impact on the Company's financial statements. 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. The Company adopted the guidance on January 1, 2017 and on a prospective basis, the Company will record all excess tax benefits and deficiencies as income tax expense or benefit. Due to the Company's history of operating losses, the adoption did not result in changes to the Company's Net loss or Retained earnings. In connection with the adoption of ASU 2016-9, the Company made a policy election to continue its methodology for the development and application of its forfeiture rate.

Summary of significant accoun20

Summary of significant accounting policies (Tables)	3 Months Ended
	Mar. 31, 2017
Accounting Policies [Abstract]
Schedule of Inventory	The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2017 December 31, 2016 Work in progress $ 320 $ — Finished goods 1,034 — Total inventory $ 1,354 $ —

Fair value of financial instr21

Fair value of financial instruments and marketable securities (Tables)	3 Months Ended
	Mar. 31, 2017
Fair Value Disclosures [Abstract]
Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis	The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2017 and December 31, 2016 : March 31, 2017 Total Quoted prices Significant Significant Marketable securities $ 148,471 $ — $ 148,471 $ — Warrant liability $ 1 $ — $ — $ 1 Stock appreciation rights liability $ 265 $ — $ — $ 265 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
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 March 31, 2017 and December 31, 2016 : March 31, 2017 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 19,162 $ 35 $ — $ 19,197 Corporate debt securities 126,134 23 (84 ) 126,073 Government obligations 3,201 — — 3,201 $ 148,497 $ 58 $ (84 ) $ 148,471 December 31, 2016 Amortized Cost Gross Unrealized Fair Value 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
Schedule of marketable securities on the balance sheet	Marketable securities on the balance sheet at March 31, 2017 and December 31, 2016 mature as follows: March 31, 2017 Less Than 12 Months More Than 12 Months Commercial paper $ 19,197 $ — Corporate debt securities 122,077 3,995 Government obligations 3,202 — Total Marketable securities $ 144,476 $ 3,995 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
Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability and SARs liability	The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the warrant liability and SARs liability for the period ended March 31, 2017 : Level 3 liabilities Warrants SARs Beginning balance as of December 31, 2016 $ 1 $ 865 Change in fair value — 464 Payments — (1,064 ) Ending balance as of March 31, 2017 $ 1 $ 265

Other comprehensive income (l22

Other comprehensive income (loss) and accumulated other comprehensive items (Tables)	3 Months Ended
	Mar. 31, 2017
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items	The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three months ended March 31, 2017 : Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2016 $ (203 ) $ (1,282 ) $ (1,485 ) Other comprehensive (loss) income before reclassifications (22 ) 631 609 Amounts reclassified from other comprehensive items — — — Other comprehensive (loss) income (22 ) 631 609 Balance at March 31, 2017 $ (225 ) $ (651 ) $ (876 )

Accounts payable and accrued 23

Accounts payable and accrued expenses (Tables)	3 Months Ended
	Mar. 31, 2017
Payables and Accruals [Abstract]
Schedule of components of accounts payable and accrued expenses	Accounts payable and accrued expenses at March 31, 2017 and December 31, 2016 consist of the following: March 31, December 31, Employee compensation, benefits, and related accruals $ 7,605 $ 13,649 Consulting and contracted research 8,827 11,505 Professional fees 2,298 1,237 Sales allowance and other costs 19,088 13,245 Accounts payable 3,579 6,298 Other 3,756 2,825 $ 45,153 $ 48,759

Warrants (Tables)

Warrants (Tables)	3 Months Ended
	Mar. 31, 2017
Stockholders' Equity Note [Abstract]
Summary of the Company's outstanding warrants	The following is a summary of the Company’s outstanding warrants as of March 31, 2017 and December 31, 2016 : 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

Net loss per share (Tables)

Net loss per share (Tables)	3 Months Ended
	Mar. 31, 2017
Earnings Per Share [Abstract]
Schedule of computation of basic and diluted net loss available to common stockholders	The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended March 31, 2017 2016 Numerator Net loss $ (29,057 ) $ (41,233 ) Denominator Denominator for basic and diluted net loss per share 34,305,948 33,919,169 Net loss per share: Basic and diluted $ (0.85 ) * $ (1.22 ) * *In the three months ended March 31, 2017 and 2016 , the Company experienced a net loss and therefore did not report any dilutive share impact.
Schedule of historical dilutive common share equivalents outstanding	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 March 31, 2017 2016 Stock Options 7,007,290 6,034,918 Unvested restricted stock awards and units 566,594 453,441 Total 7,573,884 6,488,359

Stock award plan (Tables)

Stock award plan (Tables)	3 Months Ended
	Mar. 31, 2017
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 Weighted- Weighted- Aggregate (in Outstanding at December 31, 2016 5,854,316 $ 34.71 Granted 1,244,723 $ 11.32 Exercised (9,766 ) $ 10.85 Forfeited/Cancelled (81,983 ) $ 35.64 Outstanding at March 31, 2017 7,007,290 $ 30.56 7.87 years $ 179 Vested or Expected to vest at March 31, 2017 3,296,281 $ 28.16 8.68 years $ 144 Exercisable at March 31, 2017 3,478,720 $ 33.28 7.03 years $ 25
Schedule of assumptions used to estimate fair values of grants made on the date of grant	The fair value of grants made in the three months ended March 31, 2017 was contemporaneously estimated on the date of grant using the following assumptions: Three months ended Risk-free interest rate 1.94% — 2.45% Expected volatility 76%—81% Expected term 5.04– 10.00 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 Weighted January 1, 2017 271,651 $ 19.76 Granted 328,194 $ 11.23 Vested (30,161 ) $ 30.86 Forfeited (3,090 ) $ 13.98 Unvested at March 31, 2017 566,594 $ 14.26
Schedule of share-based compensation expense recorded in the statement of operations	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: Three Months Ended March 31, 2017 2016 Research and development $ 4,467 $ 4,328 Selling, general and administrative 4,562 4,587 Total $ 9,029 $ 8,915

Convertible Senior Notes (Table

Convertible Senior Notes (Tables)	3 Months Ended
	Mar. 31, 2017
Debt Disclosure [Abstract]
Summary of convertible notes	The Convertible Notes consist of the following: Liability component March 31, 2017 December 31, 2016 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (2,378 ) (2,457 ) Less: Debt discount, net(1) (47,727 ) (49,327 ) Net carrying amount $ 99,895 $ 98,216 (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: Three Months Ended March 31, 2017 2016 Contractual interest expense $ 1,110 $ 1,116 Amortization of debt issuance costs 80 72 Amortization of debt discount 1,600 1,446 Total $ 2,790 $ 2,634 Effective interest rate of the liability component 11 % 11 %

Restructuring (Tables)

Restructuring (Tables)	3 Months Ended
	Mar. 31, 2017
Restructuring Charges [Abstract]
Schedule of restructuring charges related to work-force reduction	Balance as of Expenses, Cash payments Balance as of 2016 workforce reduction $ 22 $ — $ (22 ) $ —

The Company (Details)

The Company (Details) $ in Thousands	Apr. 20, 2017USD ($)shares	Aug. 31, 2014state	Dec. 31, 2016USD ($)country	Mar. 31, 2017USD ($)	Aug. 31, 2015
Long-term debt
Minimum age of ambulatory patient		5 years
Number of member states of the European Economic Area | state		31
Number of countries | country			25
Accumulated deficit			$ (735,108)	$ (764,165)
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Interest rate					3.00%
Non-collaborative Arrangement Transactions | Subsequent Event | Marathon Pharmaceuticals, LLC
Long-term debt
Consideration transferred	$ 140,000
Payments to acquire businesses	75,000
Equity interest issued or issuable, value assigned	$ 65,000
Equity Interest Issued, number of shares (in shares) | shares	6,683,598
Trading day period	15 days
Scenario, Forecast | Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Long-term debt
Development and regulatory milestone payments which the entity may be obligated to pay	$ 50,000

Summary of significant accoun30

Summary of significant accounting policies Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Work in progress	$ 320	$ 0
Finished goods	1,034	0
Inventory, Net	$ 1,354	$ 0

Summary of significant accoun31

Summary of significant accounting policies (Details) - USD ($) $ in Millions	Mar. 31, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Allowance for doubtful accounts receivable	$ 0.8	$ 0.7

Fair value of financial instr32

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 148,471	$ 173,345
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	148,471	173,345
Warrant Liability	1	1
Stock appreciation rights liability	265	865
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	148,471	173,345
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	1
Stock appreciation rights liability	$ 265	$ 865

Fair value of financial instr33

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($)	Mar. 31, 2017	Dec. 31, 2016
Marketable securities accounted for as available-for-sale securities
Amortized Cost	$ 148,497,000	$ 173,347,000
Gross Unrealized Gains	58,000	101,000
Gross Unrealized Losses	(84,000)	(103,000)
Fair Value	148,471,000	173,345,000
Transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy	0	0
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	19,162,000	12,919,000
Gross Unrealized Gains	35,000	47,000
Gross Unrealized Losses	0	0
Fair Value	19,197,000	12,966,000
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	126,134,000	153,240,000
Gross Unrealized Gains	23,000	52,000
Gross Unrealized Losses	(84,000)	(103,000)
Fair Value	126,073,000	153,189,000
Government obligations
Marketable securities accounted for as available-for-sale securities
Amortized Cost	3,201,000	7,188,000
Gross Unrealized Gains	0	2,000
Gross Unrealized Losses	0	0
Fair Value	$ 3,201,000	$ 7,190,000

Fair value of financial instr34

Fair value of financial instruments and marketable securities - Balance Sheet (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 144,476	$ 157,352
Total Marketable securities, More Than 12 Months	3,995	15,993
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	19,197	12,966
Total Marketable securities, More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	122,077	137,196
Total Marketable securities, More Than 12 Months	3,995	15,993
Government obligations
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	3,202	7,190
Total Marketable securities, More Than 12 Months	$ 0	$ 0

Fair value of financial instr35

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2017	Dec. 31, 2016
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2016	$ 865
Change in fair value	464
Payments	(1,064)
March 31, 2017	$ 265	$ 865
Minimum | SARs
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility	67.00%	48.00%
Risk-free interest rate (as a percent)	0.97%	0.44%
Strike price (in dollars per share)	$ 6.76	$ 6.76
Expected life	9 months 4 days	4 days
Maximum | SARs
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility	69.00%	71.00%
Risk-free interest rate (as a percent)	1.50%	1.47%
Strike price (in dollars per share)	$ 30.86	$ 30.86
Expected life	2 years 9 months 4 days	3 years
Common stock | SARs
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 9.84	$ 10.91
Warrants
Changes in the fair value of warrant liability and SARs liability
December 31, 2016	$ 1
Change in fair value	0
Payments	0
March 31, 2017	$ 1	$ 1
Warrants | Minimum
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility	55.00%	62.00%
Risk-free interest rate (as a percent)	0.76%	0.62%
Strike price (in dollars per share)	$ 128	$ 128
Expected life	2 months 16 days	4 months 24 days
Warrants | Maximum
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility	69.00%	67.00%
Risk-free interest rate (as a percent)	1.39%	1.34%
Strike price (in dollars per share)	$ 2,520	$ 2,520
Expected life	2 years 5 months 23 days	2 years 8 months 12 days
Warrants | Common stock
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 9.84	$ 10.91

Other comprehensive income (l36

Other comprehensive income (loss) and accumulated other comprehensive items (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2017USD ($)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Beginning Balance	$ (1,485)
Other comprehensive (loss) income before reclassifications	609
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	609
Ending Balance	(876)
Unrealized Gains/(Losses) On Marketable Securities, net of tax
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Beginning Balance	(203)
Other comprehensive (loss) income before reclassifications	(22)
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	(22)
Ending Balance	(225)
Foreign Currency Translation
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Beginning Balance	(1,282)
Other comprehensive (loss) income before reclassifications	631
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	631
Ending Balance	$ (651)

Accounts payable and accrued 37

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 7,605	$ 13,649
Consulting and contracted research	8,827	11,505
Professional fees	2,298	1,237
Sales allowance and other costs	19,088	13,245
Accounts payable	3,579	6,298
Other	3,756	2,825
Accounts payable and accrued expenses	$ 45,153	$ 48,759

Warrants (Details)

Warrants (Details) - Warrants - Common stock - $ / shares	Mar. 31, 2017	Dec. 31, 2016
2,017
Warrants
Warrant shares (in shares)	6,250	6,250
Exercise price (in dollars per share)	$ 128	$ 128
2,019
Warrants
Warrant shares (in shares)	7,030	7,030
Exercise price (in dollars per share)	$ 128	$ 128
2,019
Warrants
Warrant shares (in shares)	130	130
Exercise price (in dollars per share)	$ 2,520	$ 2,520

Net loss per share - Numerator

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Numerator
Net loss	$ (29,057)	$ (41,233)
Denominator
Denominator for basic and diluted net loss per share (in shares)	34,305,948	33,919,169
Net loss per share:
Basic and diluted (in dollars per share)	$ (0.85)	$ (1.22)

Net loss per share - Antidiluti

Net loss per share - Antidilutive (Details) - shares	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Net loss per share
Total shares excluded from calculation	7,573,884	6,488,359
Stock Options
Net loss per share
Total shares excluded from calculation	7,007,290	6,034,918
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation	566,594	453,441

Stock award plan Stock award pl

Stock award plan Stock award plan- Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Mar. 31, 2017	Mar. 31, 2016
Stock option plan
Share-based compensation expense					$ 9,029	$ 8,915
Unrecognized compensation cost					$ 63,200
Weighted average remaining service period for recognition of unrecognized compensation cost					2 years 3 months 4 days
Common stock
Stock option plan
Number of shares available for issuance (in shares)					236,792
Unvested restricted stock
Stock option plan
Grants in period (in shares)					328,194
Vested (in shares)					(30,161)
Stock option
Stock option plan
Granted (in shares)					1,244,723
Inducement grants for non-statutory stock options (in shares)					54,900
Expected dividend yield (as a percent)					0.00%
Weighted average grant date fair value (in dollars per share)					$ 7.76
SARs
Stock option plan
Granted (in shares)			897,290
Vesting period					4 years
Vested (in shares)					213,197
Share-based compensation expense					$ 200
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 (in shares)	739,937
2013 Stock Incentive Plan | Unvested restricted stock
Stock option plan
Grants in period (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 additional shares authorized (in shares)				2,500,000
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
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | 1998 Employee, Director and Consultant Stock Option Plan | Common stock | Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)				3,040,444
2013 Long Term Incentive Plan | Minimum
Stock option plan
Annual increase in the number of shares (in shares) on the first day of the fiscal year				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)		1,000,000
Share-based compensation expense					$ 200
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit		5.00%
Stock issued during period, ESPP (in shares)					107,499

Stock award plan - Share Base C

Stock award plan - Share Base Compensation (Details) - Stock option $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2017USD ($)$ / sharesshares
Number of options
Outstanding at the beginning of the period (in shares) | shares	5,854,316
Granted (in shares) | shares	1,244,723
Exercised (in shares) | shares	(9,766)
Forfeited/Cancelled (in shares) | shares	(81,983)
Outstanding at the end of the period (in shares) | shares	7,007,290
Vested or Expected to vest at the end of the period (in shares) | shares	3,296,281
Exercisable at the end of the period (in shares) | shares	3,478,720
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share) | $ / shares	$ 34.71
Granted (in dollars per share) | $ / shares	11.32
Exercised (in dollars per share) | $ / shares	10.85
Forfeited/Cancelled (in dollars per share) | $ / shares	35.64
Outstanding at the end of the period (in dollars per share) | $ / shares	30.56
Vested or Expected to vest at the end of the period (in dollars per share) | $ / shares	28.16
Exercisable at the end of the period (in dollars per share) | $ / shares	$ 33.28
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 10 months 13 days
Vested or Expected to vest at the end of the period	8 years 8 months 4 days
Exercisable at the end of the period	7 years 11 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars) | $	$ 179
Vested or Expected to vest at the end of the period (in dollars) | $	144
Exercisable at the end of the period (in dollars) | $	$ 25
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	1.94%
Expected volatility (as a percent)	76.00%
Expected term	5 years 16 days
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	2.45%
Expected volatility (as a percent)	81.00%
Expected term	10 years

Stock award plan - Restricted S

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	3 Months Ended
	Mar. 31, 2017$ / sharesshares
Number of Shares
Balance at the beginning of the period (in shares) | shares	271,651
Granted (in shares) | shares	328,194
Vested (in shares) | shares	30,161
Forfeited (in shares) | shares	(3,090)
Balance at the end of the period (in shares) | shares	566,594
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) | $ / shares	$ 19.76
Granted (in dollars per share) | $ / shares	11.23
Vested (in dollars per share) | $ / shares	30.86
Forfeited (in dollars per share) | $ / shares	13.98
Balance at the end of the period (in dollars per share) | $ / shares	$ 14.26

Stock award plan Stock award 44

Stock award plan Stock award plan - Share-based compensation expense (Details) (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Stock option plan
Share-based compensation expense	$ 9,029	$ 8,915
Research and development
Stock option plan
Share-based compensation expense	4,467	4,328
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 4,562	$ 4,587

Convertible Senior Notes - Narr

Convertible Senior Notes - Narrative (Details) - Convertible debt - 3.00% Convertible senior notes due 2022	1 Months Ended	3 Months Ended
	Aug. 31, 2015USD ($)item$ / shares	Mar. 31, 2017USD ($)	Dec. 31, 2016USD ($)
Long-term debt
Debt principal amount	$ 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	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	98.00%
Conversion ratio	17.7487
Conversion price per share (in dollars per share) | $ / shares	$ 56.34
Convertible instruments principal and unpaid interest payable upon events of default	100.00%
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	25.00%
Term of the convertible notes	7 years
Adjustments to additional paid in capital, equity component of convertible debt	$ 57,500,000
Net deferred tax liability in connection with convertible notes	$ 22,300,000
Fair value of convertible notes		$ 95,900,000
Remaining contractual life of the convertible notes		5 years 4 months 17 days
Redemption on or after August 20, 2018
Long-term debt
Trading days, number | item	19
Consecutive trading days, period	30 days
Stock price trigger	130.00%
Redemption price	100.00%
Sinking fund	$ 0

Convertible Senior Notes (Detai

Convertible Senior Notes (Details) - 3.00% Convertible senior notes due 2022 - Convertible debt - USD ($)	Mar. 31, 2017	Dec. 31, 2016	Aug. 31, 2015
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(2,378,000)	(2,457,000)
Less: Debt discount, net	(47,727,000)	(49,327,000)
Net carrying amount	$ 99,895,000	$ 98,216,000

Convertible Senior Notes - Inte

Convertible Senior Notes - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Long-term debt
Amortization of debt issuance costs	$ 80	$ 72
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	1,110	1,116
Amortization of debt issuance costs	80	72
Amortization of debt discount	1,600	1,446
Total	$ 2,790	$ 2,634
Effective interest rate of the liability component	11.00%	11.00%

Restructuring (Details)

Restructuring (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2017USD ($)
Research and development and selling, general and administrative expenses
Restructuring Cost and Reserve [Line Items]
Work-force reduction charges	$ 2,500
2016 Workforce Reduction
Restructuring Reserve [Roll Forward]
Restructuring Reserve, Beginning Balance	22
Expenses, net	0
Cash payments	(22)
Restructuring Reserve, Ending Balance	$ 0

Commitments and contingencies (

Commitments and contingencies (Details) - Funding agreement - Wellcome trust $ in Millions	Mar. 31, 2017USD ($)
Other Commitments [Abstract]
Development and regulatory milestone payments which the entity may be obligated to pay	$ 0.8
Maximum
Other Commitments [Abstract]
Development and regulatory milestone payments which the entity may be obligated to pay	$ 22.4

Subsequent events (Details)

Subsequent events (Details) - USD ($)	May 05, 2017	Apr. 20, 2017
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC | Subsequent Event
Subsequent Event [Line Items]
Consideration transferred		$ 140,000,000
Payments to acquire businesses		$ 75,000,000
Equity Interest Issued, number of shares (in shares)		6,683,598
Scenario, Forecast | Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Subsequent Event [Line Items]
Development and regulatory milestone payments which the entity may be obligated to pay		$ 50,000,000
MidCap Financial Trust | Term Loan Facility | Subsequent Event
Subsequent Event [Line Items]
Line of credit facility, maximum borrowing capacity	$ 60,000,000
Proceeds from lines of credit	40,000,000
Line of credit facility, additional capacity available, net product revenue threshold	20,000,000
Line of credit facility, net product revenue threshold, additional capacity	120,000,000
Line of credit facility, net product revenue threshold	$ 100,000,000
London Interbank Offered Rate (LIBOR) | MidCap Financial Trust | Term Loan Facility | Subsequent Event
Subsequent Event [Line Items]
Debt instrument, floor interest rate	1.00%
Debt instrument, basis spread on variable rate	6.15%