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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2017	Feb. 28, 2018	Jun. 30, 2017
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	0001070081
Document Type	10-K
Document Period End Date	Dec. 31, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	Yes
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 682,125,673
Entity Common Stock, Shares Outstanding (in shares)		41,795,687
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 111,792	$ 58,321
Marketable securities	79,454	173,345
Trade receivables, net	40,394	24,929
Inventory	10,754	0
Prepaid expenses and other current assets	6,669	4,691
Total current assets	249,063	261,286
Fixed assets, net	8,376	7,429
Intangible assets, net	132,993	0
Deposits and other assets	1,221	630
Total assets	391,653	269,345
Current liabilities:
Accounts payable and accrued expenses	76,446	48,759
Deferred revenue	3,937	0
Other current liabilities	1,665	865
Total current liabilities	82,048	49,624
Deferred revenue - long-term	7,954	1,587
Long-term debt	144,971	98,216
Other long-term liabilities	243	335
Total liabilities	235,216	149,762
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017. Authorized 125,000,000 shares; issued and outstanding 34,169,410 shares at December 31, 2016	42	34
Additional paid-in capital	966,534	856,142
Accumulated other comprehensive income (loss)	3,969	(1,485)
Accumulated deficit	(814,108)	(735,108)
Total stockholders’ equity	156,437	119,583
Total liabilities and stockholders’ equity	$ 391,653	$ 269,345

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 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)	41,612,395	34,169,410
Common stock, outstanding shares (in shares)	41,612,395	34,169,410

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Revenues:
Net product revenue	$ 174,066	$ 81,447	$ 33,696
Collaboration and grant revenue	20,326	1,258	3,070
Total revenues	194,392	82,705	36,766
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	4,577	0	0
Amortization of acquired intangible asset	15,380	0	0
Research and development	117,456	117,633	121,816
Selling, general and administrative	121,271	97,130	82,080
Total operating expenses	258,684	214,763	203,896
Loss from operations	(64,292)	(132,058)	(167,130)
Interest expense, net	(12,094)	(8,276)	(2,367)
Other expense, net	(1,279)	(1,207)	(465)
Loss before income tax expense	(77,665)	(141,541)	(169,962)
Income tax expense	(1,335)	(569)	(485)
Net loss attributable to common stockholders	$ (79,000)	$ (142,110)	$ (170,447)
Weighted-average shares outstanding:
Basic and diluted (in shares)	39,183,073	34,044,584	33,626,248
Net loss per share—basic and diluted (in dollars per share)	$ (2.02)	$ (4.17)	$ (5.07)

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Statement of Comprehensive Income [Abstract]
Net loss	$ (79,000)	$ (142,110)	$ (170,447)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities, net of tax	225	386	(202)
Foreign currency translation gain (loss)	5,229	(671)	(261)
Comprehensive loss	$ (73,546)	$ (142,395)	$ (170,910)

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common stock	Additional paid-in capital	Accumulated other comprehensive (loss) income	Accumulated deficit
Balance at the beginning of the period at Dec. 31, 2014	$ 298,467	$ 33	$ 721,722	$ (737)	$ (422,551)
Balance (in shares) at Dec. 31, 2014		32,898,392
Increase (Decrease) in Stockholders' Equity
Equity component of the convertible notes issuance, net	55,754		55,754
Exercise of options	8,711	$ 1	8,710
Exercise of options (in shares)		656,248
Restricted stock vesting and issuance	0
Restricted stock vesting and issuance (in shares)		361,919
Share-based compensation expense	33,979		33,979
Net loss	(170,447)				(170,447)
Comprehensive loss	(463)			(463)
Balance at the end of the period at Dec. 31, 2015	226,001	$ 34	820,165	(1,200)	(592,998)
Balance (in shares) at Dec. 31, 2015		33,916,559
Increase (Decrease) in Stockholders' Equity
Exercise of options	968	$ 0	968
Exercise of options (in shares)		89,216
Restricted stock vesting and issuance	0
Restricted stock vesting and issuance (in shares)		163,635
Share-based compensation expense	35,009		35,009
Net loss	(142,110)				(142,110)
Comprehensive loss	(285)			(285)
Balance at the end of the period at Dec. 31, 2016	119,583	$ 34	856,142	(1,485)	(735,108)
Balance (in shares) at Dec. 31, 2016		34,169,410
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to acquisition	75,191	$ 7	75,184
Issuance of common stock related to acquisition (in shares)		6,683,598
Exercise of options	2,182	$ 0	2,182
Exercise of options (in shares)		202,085
Restricted stock vesting and issuance	1	$ 1
Restricted stock vesting and issuance (in shares)		287,531
Issuance of common stock in connection with an employee stock purchase plan	2,467	$ 0	2,467
Issuance of common stock in connection with an employee stock purchase plan (in shares)		269,771
Share-based compensation expense	30,559		30,559
Net loss	(79,000)				(79,000)
Comprehensive loss	5,454			5,454
Balance at the end of the period at Dec. 31, 2017	$ 156,437	$ 42	$ 966,534	$ 3,969	$ (814,108)
Balance (in shares) at Dec. 31, 2017		41,612,395

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Cash flows from operating activities
Net loss	$ (79,000)	$ (142,110)	$ (170,447)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	17,682	3,290	2,876
Change in valuation of warrant liability	0	(47)	(140)
Amortization of premiums on investments	535	1,885	2,480
Amortization of debt issuance costs	433	302	107
Share-based compensation expense	30,559	35,009	33,979
Non-cash interest expense	6,755	6,065	2,146
Disposal of asset	5	0	(37)
Benefit for deferred income taxes	199	(199)	0
Unrealized foreign currency transaction (gains) losses, net	(459)	1,202	0
Changes in operating assets and liabilities:
Inventory, net	(6,454)	0	0
Prepaid expenses and other current assets	(1,784)	1,171	(2,107)
Trade receivables, net	(12,203)	(14,842)	(6,907)
Deposits and other assets	(544)	(278)	131
Accounts payable and accrued expenses	24,011	4,259	16,981
Other long-term liabilities	733	(799)	(92)
Deferred revenue	9,469	1,526	(3,307)
Net cash used in operating activities	(10,063)	(103,566)	(124,337)
Cash flows from investing activities
Purchases of fixed assets	(3,101)	(1,776)	(2,720)
Purchases of marketable securities	(81,368)	(85,377)	(223,762)
Sale & redemption of marketable securities	174,749	191,634	205,671
Acquisition, including transaction costs	(77,163)	0	0
Net cash provided by (used in) investing activities	13,117	104,481	(20,811)
Cash flows from financing activities
Proceeds from exercise of options	2,182	968	8,711
Proceeds from shares issued under employee stock purchase plan	2,468	0	0
Proceeds from issuance of secured term loan	40,000	0	0
Proceeds from issuance of convertible notes	0	0	150,000
Net cash provided by financing activities	44,218	968	154,061
Effect of exchange rate changes on cash	6,199	(1,584)	(639)
Net increase in cash and cash equivalents	53,471	299	8,274
Cash and cash equivalents, beginning of period	58,321	58,022	49,748
Cash and cash equivalents, end of period	111,792	58,321	58,022
Supplemental disclosure of cash information
Cash paid for interest	6,271	4,513	0
Cash paid for income taxes	1,101	943	111
Supplemental disclosures of non-cash information related to investing and financing activities
Change in unrealized gain (loss) on marketable securities	225	386	(202)
MidCap Financial Trust
Cash flows from financing activities
Debt issuance costs	(432)	0	0
Convertible debt
Cash flows from financing activities
Debt issuance costs	$ 0	$ 0	$ (4,650)

The Company	12 Months Ended
The Company	Dec. 31, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) are a science-led global biopharmaceutical company focused on the discovery, development and commercialization of clinically-differentiated medicines that provide benefits to patients with rare disorders. The Company has launched two rare disease products and has a global commercial footprint. The Company’s recent ability to commercialize products is the foundation that drives its continued investment in a robust pipeline of transformative medicines and its mission to provide access to best-in-class treatments for patients who have an unmet medical need. The Company has two products, Translarna™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged 5 years and over in the 31 member states of the European Economic Area, or EEA. Emflaza is approved in the United States for the treatment of DMD in patients five years and older. The Company’s marketing authorization for Translarna 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 June 2017 and is effective, unless extended, through August 5, 2018. In February 2018, the Company submitted a marketing authorization renewal request to the EMA. 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. In June 2014, the Company initiated reimbursed early access programs, or EAP programs, for Translarna for nmDMD patients in selected territories in the EEA and recorded its first sales of Translarna in the third quarter of 2014 pursuant to an EAP program. In December 2014, the Company recorded its first commercial sales in Germany. As of December 31, 2017, Translarna was available in over 25 countries on a commercial basis or pursuant to the EAP program. The Company expects to expand its launch activities across the EEA pursuant to the marketing authorization granted by the EMA throughout 2018 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, (the "FDA"), for which the FDA granted a standard review. In October 2017, the Office of Drug Evaluation I of the FDA issued a complete response letter for the NDA, stating that it was unable to approve the application in its current form. In response, the Companyfiled a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied PTC’s appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company intends to follow the FDA’s recommendation and will collect such dystrophin data using newer technologies via procedures and methods that will be mutually agreeable to the Company and the FDA. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework. 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 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 April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. Emflaza is approved in the United States for the treatment of DMD in 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, (the "Asset Purchase Agreement"), by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The Transaction was accounted for as an asset acquisition. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights 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 comprised of $75.0 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 $65.0 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 over the expected commercial life of the asset, and a single $50.0 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement. As of December 31, 2017, the Company had an accumulated deficit of approximately $814.1 million. The Company has financed its operations to date primarily through the private offering in August 2015 of 3.00% convertible senior notes due 2022 (see Note 7), public offerings of common stock in February 2014 and October 2014, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, convertible debt financings, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates.

Summary of significant accounting policies

12 Months Ended

Dec. 31, 2017

Accounting Policies [Abstract]

Summary of significant accounting policies

Basis of presentation

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

Use of estimates

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

Consolidation

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

Segment and geographic information

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

Cash equivalents

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

Marketable securities

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

Fixed assets

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



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

Concentration of credit risk

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

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

Inventories and cost of product sales

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

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

In January 2017, the European Commission granted a one-year 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 considered recovery of the costs to be probable and began capitalizing production costs in inventory, effective January 1, 2017. Since January 1, 2017, production costs are expensed as cost of product sales when the related products are sold. The costs for a portion of the inventory available for sale were 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 prior to January 1, 2017 are not directly comparable to future cost of products sold and gross margin after January 1, 2017.

In April 2017, the Company completed the Transaction (see Note 3). Emflaza, both in tablet and suspension form, received approval from the FDA in February 2017 as a treatment for DMD in patients five years of age and older in the United States. The Company began the commercialization of Emflaza in the United States shortly after the Transaction was completed. The Company utilizes third parties for the commercial distribution of Emflaza, including a third-party logistics company to warehouse Emflaza as well as a specialty pharmacy to sell and distribute Emflaza to patients. All of the Company's supply and manufacturing needs for Emflaza are fulfilled pursuant to exclusive supply agreements assumed by the Company upon close of the Transaction. Production costs are expensed as cost of product sales when the related products are sold.

Inventory

Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. 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 and Emflaza 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. Inventory used for marketing efforts are charged to selling, general and administrative expense.

The following table summarizes the components of the Company’s inventory for the periods indicated:



	December 31, 2017		December 31, 2016
Raw materials	$	452	$	—
Work in progress	3,912		—
Finished goods	6,390		—
Total inventory	$	10,754	$	—

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. The Company has not recorded any inventory write downs as of the current period. Additionally, though the Company’s product is subject to strict quality control and monitoring 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, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales.

Deferred rent

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

Accumulated other comprehensive income (loss)

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

Revenue recognition

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

Net Product Sales

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. Prior to the second quarter of 2017, the Company’s net product sales consisted solely of sales of Translarna for the treatment of nmDMD in territories outside of the United States.

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 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. For the years ended December 31, 2017, 2016 and 2015 the Company recognized Translarna sales of $145.2 million, $81.4 million, and $33.7 million, respectively.

In May 2017, the Company began the commercialization of Emflaza in the United States. The Company recorded product revenue related to the sales of Emflaza in the United States in accordance with ASC 605-15, when persuasive evidence of an arrangement exists, delivery has occurred and title of the product and associated risk of loss has passed to the customer, the price is fixed or determinable and collection from the customer has been reasonably assured. Due to the early stage of the product launch, in the second and third quarters of 2017 the Company determined that it was not able to reliably make certain estimates, including returns, necessary to recognize product revenue upon shipment to distributors or specialty pharmacies. As a result, the Company recorded net product revenue during that period for Emflaza using a deferred revenue recognition model (sell-through). Under the deferred revenue model, the Company did not recognize revenue until Emflaza is shipped to an end-user. During the fourth quarter of 2017, the Company determined that it had sufficient volume of historical activity and visibility into the distribution channel to reasonably make all estimates required under ASC 605 to recognize revenue upon shipment to its specialty pharmacy. The change from the sell-through model to recognizing revenue upon shipment to its specialty pharmacy during the fourth quarter of 2017 was immaterial to the financial statements. For the year ended December 31, 2017, the Company recognized Emflaza sales of $28.8 million.

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 the Financial Accounting Standards Board (FASB), guidance on the milestone method of revenue recognition. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from its 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 million as of December 31, 2017 and $0.7 million million as of December 31, 2016.

Research and development costs

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

Nonrefundable advance payments made for goods and services that will be used in future research and development activities are deferred if the contracted party has not yet performed the related activities. The amount deferred is then recognized as expense when the research and development activities are performed. The deferred research and development advance payments were $0.5 million and $0.4 million as of December 31, 2017 and 2016, respectively.

Fair value of financial instruments

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


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

•

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


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

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

Beneficial conversion

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

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

Warrant liability

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

Share-based compensation

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

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

Income taxes

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

Foreign currency

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

Net (loss) income per share

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

Business combinations and asset acquisitions

The Company evaluates acquisitions of assets and other similar transactions to assess whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen (as adopted in the current period under Accounting Standards Update (ASU) No. 2017-01, "Business Combinations (Topic 805): Clarifying the Definition of a Business"; see "Impact of recently adopted accounting standards" and Note 11 for further details) to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. If the screen is not met, further determination is required as to whether or not the Company has acquired inputs and processes that have the ability to create outputs, which would meet the requirements of a business. If determined to be a business combination, the Company accounts for the transaction under the acquisition method of accounting as indicated in ASC 2017-01, “Business Combinations”, which requires the acquiring entity in a business combination to recognize the fair value of all assets acquired, liabilities assumed, and any non-controlling interest in the acquiree and establishes the acquisition date as the fair value measurement point. Accordingly, the Company recognizes assets acquired and liabilities assumed in business combinations, including contingent assets and liabilities, and non-controlling interest in the acquiree based on the fair value estimates as of the date of acquisition. In accordance with ASC 805, the Company recognizes and measures goodwill as of the acquisition date, as the excess of the fair value of the consideration paid over the fair value of the identified net assets acquired.

The consideration for the Company’s business acquisitions includes future payments that are contingent upon the occurrence of a particular event or events. The obligations for such contingent consideration payments are recorded at fair value on the acquisition date. The contingent consideration obligations are then evaluated each reporting period. Changes in the fair value of contingent consideration obligations, other than changes due to payments, are recognized as a (gain) loss on fair value remeasurement of contingent consideration in the condensed consolidated statements of operations.

If determined to be an asset acquisition, the Company accounts for the transaction under ASC 805-50, which requires the acquiring entity in an asset acquisition to recognize assets (net assets) based on the cost to the acquiring entity on a relative fair value basis, which includes transaction costs in addition to consideration given. No gain or loss is recognized as of the date of acquisition unless the fair value of noncash assets given as consideration differs from the assets' carrying amounts on the acquiring entity's books. Consideration transferred that is noncash will be measured based on either the cost (which shall be measured based on the fair value of the consideration given) or the fair value of the assets (net assets) acquired, whichever is more reliably measurable. Goodwill is not recognized in an asset acquisition and any excess consideration transferred over the fair value of the net assets acquired is allocated to the identifiable assets based on relative fair values.

Contingent consideration payments in asset acquisitions are recognized when the contingency is resolved and the consideration is paid or becomes payable (unless the contingent consideration meets the definition of a derivative, in which case the amount becomes part of the basis in the asset acquired). Upon recognition of the contingent consideration payment, the amount is included in the cost of the acquired asset or group of assets.

Finite-lived intangible assets

The Company records the fair value of purchased intangible assets with finite useful lives as of the transaction date of a business combination or asset acquisition. Purchased intangible assets with finite useful lives are amortized to their estimated residual values over their estimated useful lives.

Impairment of long-lived assets

The Company monitors its long-lived assets and finite-lived intangibles for indicators of impairment. If such indicators are present, the Company assesses the recoverability of affected assets by determining whether the carrying value of such assets is less than the sum of the undiscounted future cash flows of the assets. If such assets are found not to be recoverable, the Company measures the amount of such impairment by comparing the carrying value of the assets to the fair value of the assets, with the fair value generally determined based on the present value of the expected future cash flows associated with the assets. Although current and historical negative cash flows are indicators of impairment, management believes the future cash flows to be received from the long-lived assets and the potential success of the Company’s research programs will exceed the assets’ carrying value, and accordingly, the Company believes that no impairment of long-lived assets exists as of December 31, 2017.

Recent accounting pronouncements

In May 2014, the FASB issued 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. 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 has elected to use the modified retrospective approach (retrospective application with the cumulative effect of applying the updated standard recognized at the date of initial application and providing certain additional disclosures) to adopt this guidance when effective. The Company expects the adoption of the new standard to impact its financial reporting disclosures and internal control framework. The Company has developed implementation controls that allow it to properly and timely adopt the new standard upon effective date. The Company 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. Based on the comprehensive change management project plan implemented, the Company has calculated a one-time transition adjustment under the modified retrospective approach that is immaterial to the financial statements.

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

In April 2015, the FASB issued ASU No. 2015-3, “Interest—Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs topic of the Codification”. This standard provides a simplified presentation of debt issuance costs and requires that debt issuance costs related to a recognized debt liability to be presented on the balance sheet as a direct deduction from the carrying amount of that debt liability, consistent with debt discounts. The standard is effective for public companies for annual periods beginning after December 15, 2015. The Company adopted the guidance on January 1, 2016 on a retrospective basis and reclassed $2.5 million from “Deposits and other assets” to “Long-term debt” on the balance sheet as of December 31, 2015. The Company’s unamortized debt issuance cost at December 31, 2017 was $2.1 million which is included within “Long-term debt” on the consolidated balance sheet.

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 May 2017, the FASB issued ASU No. 2017-09, "Stock Compensation (Topic 718): Scope of Modification Accounting". This standard clarifies when changes to the terms or conditions of a share-based payment award must be accounted for as a modification, with entities applying the modification accounting guidance if the value, vesting conditions or classification of the award changes. In addition to all disclosures about modifications that are required under the current guidance, entities will be also required to disclose that compensation expense has not changed if applicable. This standard is effective for public companies who are SEC filers for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2017, with early adoption permitted, including any interim period for which financial statements have not yet been issued or made available for issuance. The guidance will be applied prospectively to awards modified on or after the adoption date. The Company expects to adopt this guidance when effective.

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. As the Company’s deferred tax assets are provided with full valuation allowance as of December 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 records 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 estimating its forfeiture rate.

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 elected to early adopt ASU No. 2017-01 and applied the guidance to the Transaction, which was accounted for as an asset acquisition under the revised guidance.

Emflaza asset acquisition

12 Months Ended

Dec. 31, 2017

Business Combinations [Abstract]

Emflaza asset acquisition

On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to an Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights 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.

The Company concluded that the Transaction included inputs and processes that did not constitute a business under the revised guidance of ASU No. 2017-01, which allows for a screen to evaluate if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. The Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and accounted for the Transaction as an asset acquisition under ASC 805-50.

The purchase price consisted of total upfront consideration comprised of $75.0 million in cash and 6,683,598 shares of the Company's common stock with a fair value of $75.2 million. In addition, the Company incurred approximately $2.2 million of acquisition costs, which are capitalized in an asset acquisition and included in the total consideration transferred.

Marathon is 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 over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone. In accordance with the guidance for an asset acquisition, the Company will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset.

The following tables present the total purchase consideration and the preliminary allocation of the purchase consideration for the Transaction as of April 20, 2017 (the “Acquisition Date”):



Cash consideration	$	75,000
Fair value of PTC common stock issued to Marathon (6,683,598 shares)	75,190
Acquisition costs	2,163
Total preliminary consideration transferred	$	152,353



Purchase price	$	152,353

Total fair value of tangible assets acquired and liabilities assumed:
Inventory	3,980
Emflaza rights	$	148,373

The Emflaza rights intangible asset is being amortized to cost of product sales over its expected useful life of approximately seven years on a straight line basis. Given the inherent uncertainty of the Company's sales projections, the Company amortizes the asset on a straight line basis.

As of December 31, 2017, the Company recognized accumulated amortization of $15.4 million with respect to the Emflaza rights intangible asset. The estimated future amortization of the Emflaza rights intangible asset is expected to be as follows:



	As of December 31, 2017
2018	$	21,713
2019	21,713
2020	21,713
2021	21,713
2022 and thereafter	46,141
Total	$	132,993

Fair value of financial instruments and investments

12 Months Ended

Dec. 31, 2017

Fair Value Disclosures [Abstract]

Fair value of financial instruments and investments

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

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

The following represents the fair value using the hierarchy described in Note 2 for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of December 31, 2017 and 2016:



	December 31, 2017
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	79,454	$	—	$	79,454	$	—
Warrant liability	$	1	—		—		1
Stock appreciation rights liability	$	1,665	—		—		1,665



	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

The Company uses the market approach to measure fair value for its financial assets. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The Company’s marketable securities investments classified as Level 2 primarily utilize broker to value these securities. No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the year ended December 31, 2017.

The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2017 and 2016:



	December 31, 2017
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	13,775	$	52	$	—		$	13,827
Corporate debt securities	65,657		—		(30		)	65,627
Government obligations	—		—		—			—
	$	79,432	$	52	$	(30	)	$	79,454



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

Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. During the year ended December 31, 2017, the Company did not have any realized gains or losses from the sale of marketable securities. The cost of securities sold is based on the specific identification method. The Company evaluates investments with unrealized losses to determine if the losses are other than temporary. At December 31, 2017, the Company held securities with an unrealized loss position that were not considered to be other-than-temporarily impaired as the Company has the ability to hold such investments until recovery of their fair value. In addition, the Company considered the financial condition, credit ratings and near-term prospects of the issuers, and the magnitude of the losses as compared to the cost and the length of time the investments have been in an unrealized loss position when determining if the losses are other than temporary.

The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2017 are as follows:



	December 31, 2017
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(28	)	$	59,108	$	(2	)	$	6,519	$	(30	)	$	65,627



	December 31, 2016
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(85	)	$	45,482	$	(18	)	$	51,243	$	(103	)	$	96,725

Marketable securities on the balance sheet at December 31, 2017 and 2016 mature as follows:



	December 31, 2017
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	13,827	$	—
Corporate debt securities	55,550		10,077
Government obligations	—		—
Total Marketable securities	$	69,377	$	10,077



	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.

Convertible 3.0% senior notes

In August 2015, the Company issued $150.0 million of 3.0% convertible senior notes due August 15, 2022 (the “Convertible Notes”). Interest is payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The Company separately accounted for the liability and equity components of the Convertible Notes by allocating the proceeds between the liability component and equity component, as further discussed in Note 7. The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the Convertible Notes at December 31, 2017 and 2016 was $115.7 million and $85.2 million, respectively.

The carrying amounts reported in the consolidated balance sheets for cash and cash equivalents, accounts receivable, accounts payable and borrowings under the credit and security agreement with MidCap Financial Trust and other financial institutions (as further discussed in Note 7) approximate fair value because of the immediate or short-term maturity of these financial instruments. The carrying amounts for the credit and security agreement approximate fair value based on market activity for other debt instruments with similar characteristics and comparable risk.

Level 3 valuation

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

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

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability and SARs liability for the years ended December 31, 2017 and 2016:



	Level 3 liabilities
	Warrants			SARs
Beginning balance as of December 31, 2015	$	48		$	—
Fair value of issuances	—			140
Change in fair value	(47		)	725
Ending balance as of December 31, 2016	$	1		$	865
Fair value of issuances	—			—
Change in fair value	—			1,864
Payments	$	—		$	(1,064	)
Ending balance as of December 31, 2017	$	1		$	1,665

Fair value of the warrant liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the preferred stock value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of December 31, 2017 include (i) volatility (69%-69%), (ii) risk free interest rate (1.89%-1.89%), (iii) strike price ($128.00-$2,520.00), (iv) fair value of common stock ($16.68) and (v) expected life (1.6-1.7 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 December 31, 2017 include (i) volatility (31%-70%), (ii) risk free interest rate (1.28%-1.89%), (iii) strike price ($6.76-$30.86), (iv) fair value of common stock ($16.68), and (v) expected life (0.0-2.0 years). The significant assumptions used in preparing the option pricing model for valuing the Company’s SARs as of December 31, 2016 include (i) volatility (48%-71%), (ii) risk free interest rate (0.44%-1.47%), (iii) strike price ($6.76-$30.86), (iv) fair value of common stock ($10.91), and (v) expected life (0.0-3.0 years).

- Definition

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

+ References + Details

Fixed assets

12 Months Ended

Dec. 31, 2017

Property, Plant and Equipment [Abstract]

Fixed assets

Fixed assets, net were as follows at December 31, 2017 and 2016



	December 31,
	2017			2016
Leasehold improvements	$	14,078		$	14,038
Computer equipment and software	5,471			4,622
Furniture, fixtures, and lab equipment	20,776			19,343
Assets in process	895			353
	41,220			38,356
Less accumulated depreciation and amortization	(32,844		)	(30,927		)
	$	8,376		$	7,429

Depreciation expense was approximately $2.3 million, $3.3 million, and $2.9 million for the years ended December 31, 2017, 2016 and 2015, respectively.

Accounts payable and accrued expenses

12 Months Ended

Dec. 31, 2017

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2017 and 2016 consist of the following:



	December 31,
	2017		2016
Employee compensation, benefits, and related accruals	$	17,711	$	13,649
Consulting and contracted research	5,137		11,505
Professional fees	2,116		1,237
Sales allowances and other related costs	33,914		13,245
Accounts payable	15,282		6,298
Other	2,286		2,825
	$	76,446	$	48,759

Debt

12 Months Ended

Dec. 31, 2017

Debt Disclosure [Abstract]

Debt

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

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

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

•

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

•

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


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


•	upon the occurrence of specified corporate events.

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

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

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

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

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

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

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

The Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2017			2016
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,121		)	(2,457		)
Less: Debt discount, net (1)	(42,572		)	(49,327		)
Net carrying amount	$	105,307		$	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 $115.7 million as of December 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 December 31, 2017, the remaining contractual life of the Convertible Notes is approximately 4.6 years.

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



	Year ended December 31,
	2017			2016
Contractual interest expense	$	4,500		$	4,497
Amortization of debt issuance costs	337			302
Amortization of debt discount	6,755			6,065
Total	$	11,592		$	10,864
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure

12 Months Ended

Dec. 31, 2017

Stockholders' Equity Note [Abstract]

Capital structure

Common stock

As of December 31, 2017, the Company’s number of authorized shares of common stock was 125,000,000.

Warrants

All of the Company’s outstanding warrants are classified as liabilities as of December 31, 2017 and 2016 because they contain non-standard antidilution provisions.

The following is a summary of the Company’s outstanding warrants as of December 31, 2017:



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

The following is a summary of the Company’s outstanding warrants as of 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

Earnings per share

12 Months Ended

Dec. 31, 2017

Earnings Per Share [Abstract]

Earnings per share

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

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



	Year ended December 31,
	2017				2016				2015
Numerator
Net loss	$	(79,000	)		$	(142,110	)		$	(170,447	)
Denominator
Denominator for basic and diluted net loss per share	39,183,073				34,044,584				33,626,248
Net loss per share:
Basic and diluted	$	(2.02	)	*	$	(4.17	)	*	$	(5.07	)	*

* For the years ended December 31, 2017, 2016, and 2015, the Company experienced a net loss and therefore did not report any dilutive share impact.

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



	As of December 31,
	2017	2016	2015
Stock Options	6,448,642	5,854,316	4,826,477
Unvested restricted stock	393,011	271,651	344,335
Total	6,841,653	6,125,967	5,170,812

Stock award plan

12 Months Ended

Dec. 31, 2017

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

Stock award plan

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

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

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

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of December 31, 2017, awards for 927,478 shares of common stock were available for issuance.

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

Inducement stock option awards

Pursuant to the Nasdaq inducement grant exception, during the year ended December 31, 2017, the Company issued options to purchase an aggregate of 640,550 shares of common stock to certain new hire employees at a weighted-average exercise price of $14.16 per share. An aggregate of 316,176 of options previously granted as inducement awards were forfeited during the year ended December 31, 2017 in connection with employee separations from the Company.

A summary of stock option activity is as follows:



	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2014	3,432,972		$	25.00
Granted	2,201,800		$	50.81
Exercised	(656,248	)	$	13.27
Forfeited	(152,047	)	$	49.58
Outstanding at December 31, 2015	4,826,477		$	37.20
Granted	1,500,645		$	27.90
Exercised	(89,216	)	$	10.85
Forfeited	(383,590	)	$	47.42
Outstanding at December 31, 2016	5,854,316		$	34.71
Granted	1,913,873		$	12.34
Exercised	(202,085	)	$	10.80
Forfeited	(1,117,462	)	$	33.65
Outstanding at December 31, 2017	6,448,642		$	29.00	7.28	$	13,435
Vested or expected to vest at December 31, 2017	2,522,747		$	23.29	8.39	$	6,822
Exercisable at December 31, 2017	3,778,544		$	33.19	6.48	$	6,167

The fair values of grants made in the years ended December 31, 2017, 2016 and 2015 were contemporaneously estimated on the date of grant using the following assumptions:



	2017	2016	2015
Risk-free interest rate	1.84 - 2.45%	1.30 - 2.24%	1.48 - 2.18%
Expected volatility	76 - 81%	67 - 78%	67 - 69%
Expected term	5.04 - 10.00 years	5.05 - 10.00 years	5.50 - 9.12 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the years ended December 31, 2017, 2016 and 2015 was $8.45, $17.31, and $50.81 per share, respectively.

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

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

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

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2016	271,651		$	19.76
Granted	365,194		$	11.67
Vested	(180,861	)	$	14.19
Forfeited	(62,973	)	$	14.18
Unvested at December 31, 2017	393,011		$	15.64

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

In May 2016, a total of 897,290 SARs were granted to non-executive employees (the 2016 SARs). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the period ending December 31, 2017, the Company recorded $1.9 million in compensation expense related to the 2016 SARs.

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (ESPP or the Plan) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Board. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six-month period through payroll withholdings and may purchase, at the end of the six-month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the period ending December 31, 2017, the Company recorded $0.9 million in compensation expense related to the ESPP.

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



	Year ended December 31,
	2017		2016		2015
Research and development	$	15,456	$	16,812	$	16,138
Selling, general and administrative	15,103		18,197		17,841
Total	$	30,559	$	35,009	$	33,979

As of December 31, 2017, there was approximately $38.2 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s Plans. This cost is expected to be recognized as compensation expense over the weighted average remaining service period of approximately 1.91 years.

Other comprehensive income (loss) and accumulated other comprehensive items

12 Months Ended

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

The following table summarizes other comprehensive income (loss) and the changes in accumulated other comprehensive items, by component, for the years ended December 31, 2017, 2016, and 2015, respectively.



	Unrealized Gains/(Losses) On Marketable Securities			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2014	$	(387	)	$	(350	)	$	(737	)
Other comprehensive loss before reclassifications	(202		)	(261		)	(463		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(202		)	(261		)	(463		)
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income (loss) before reclassifications	386			(671		)	(285		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	386			(671		)	(285		)
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)
Other comprehensive income before reclassifications	225			5,229			5,454
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income	225			5,229			5,454
Balance at December 31, 2017	$	22		$	3,947		$	3,969

Collaborations and grants	12 Months Ended
Collaborations and grants	Dec. 31, 2017
Collaborations and grants
Collaborations and grants	Collaborations and grants The Company has ongoing collaborations with the Spinal Muscular Atrophy Foundation (SMA Foundation) and F. Hoffman-La Roche Ltd and Hoffman- La Roche Inc. (collectively, Roche) and early stage discovery arrangements with other institutions. The following are the key terms to the Company’s (i) ongoing collaborations and (ii) early stage discovery and development arrangements. Roche and SMA Foundation In November 2011, the Company and the SMA Foundation entered into a licensing and collaboration agreement with Roche for a spinal muscular atrophy program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s spinal muscular atrophy program, which includes three compounds currently in preclinical development, as well as potential back-up compounds. The Company received a nonrefundable upfront cash payment of $30.0 million during the research term, which was terminated effective December 31, 2014, after which Roche provided the Company with funding, based on an agreed- upon full-time equivalent rate, for an agreed-upon number of full- time equivalent employees that the Company contributed to the research program. The Company applied the multiple element revenue recognition guidance in evaluating the accounting treatment of this collaboration agreement. The Company identified two possible significant deliverables in the collaboration agreement, the license and the research activities. The Company evaluated whether these significant deliverables have stand-alone value and determined that the license does not have standalone value without the ongoing research and development services given the unique nature of the technology. As such, both of these elements were combined as a single unit for accounting purposes. As a result, the Company deferred the $30.0 million upfront payment which was recognized over the estimated performance period of two years, which was the contracted research period. For the years ended December 31, 2017, 2016 and 2015, the Company recognized approximately $20.3 million, $0.4 million and $0.6 million respectively, in collaboration revenue. The balance of the remaining deferred upfront payment was fully recognized as of December 31, 2013. Under the agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. The Company considers that each of the potential milestone events under the agreement would be substantive because the applicable criteria of its revenue recognition policy (see Note 2) would be satisfied. In January 2014, the Company announced the initiation of a Phase 1 clinical program in its spinal muscular atrophy collaboration with Roche and the SMA Foundation which triggered a $7.5 million milestone payment from Roche. The Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its spinal muscular atrophy collaboration with Roche and the SMA Foundation (SMAF) which triggered a $10 million payment from Roche. The Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In October 2017, the Company announced that the Sunfish, a two-part clinical trial in pediatric and adult type 2 and type 3 spinal muscular atrophy initiated in the fourth quarter of 2016 with Roche and SMAF, had transitioned into the pivotal second part of its study. The achievement of this milestone triggered a $20.0 million payment to the Company from Roche. The Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2017. Early stage collaboration and discovery agreements From time to time, the Company has arrangements with several organizations pursuant to which the Company uses its discovery technologies to help identify potential drug candidates. The Company does not take ownership of the potential compounds, but rather provides research services to the collaborator using its specialized technology platform. Generally, these arrangements are structured such that the collaborator and the Company work together to jointly select targets from which to apply its discovery technologies. The research period for the Company to apply its technology is generally three to four years. The Company will typically receive a nonrefundable, upfront cash payment and the collaborator agrees to provide funding for research activities performed on its behalf. The Company applies multiple element revenue recognition guidance in evaluating the accounting treatment for these arrangements. Generally, the two significant deliverables in these arrangements are the license and the research activities. The Company evaluates whether the deliverables have standalone value. Since the Company’s discovery technologies are highly specialized, the Company has generally determined that the license does not have standalone value without the ongoing research and development services and generally accounts for these arrangements as a single unit of accounting. There was no deferred revenue related to these arrangements as of December 31, 2017 and 2016. For the year ended December 31, 2015, the Company recognized approximately $1.8 million in collaboration revenue. The Company is eligible to receive additional payments from its early stage discovery research arrangements if the discovery compounds are ultimately developed and commercialized. The aggregate potential payments the Company is eligible for if all products are developed is $143.0 million and up to $252.0 million in sales milestones upon achievement of specified sales events and up to double digit royalties on worldwide annual net sales of the licensed product. The Company considers that each of the potential milestone events under the agreement would be substantive because the applicable criteria of its revenue recognition policy (see Note 2) would be satisfied. Grant revenue The Company receives grant funding from various institutions and governmental bodies. The grants are typically for early discovery research, and typically the grant program lasts from two to five years. The Company records revenue as the research activities are performed. If the granting agency provides for an upfront payment, the amount is deferred and recognized as revenue as the expenditures are incurred. For the year ended December 31, 2017, the Company did not recognize any grant revenue. For the years ending December 31, 2016 and 2015, the Company recognized $0.9 million and $2.2 million respectively, in grant revenue.

Income taxes

12 Months Ended

Dec. 31, 2017

Income Tax Disclosure [Abstract]

Income taxes

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2017, 2016, and 2015:



	2017		2016		2015
Domestic	(54,588	)	(61,446	)	(50,944	)
Foreign	(23,077	)	(80,095	)	(119,018	)
Total	(77,665	)	(141,541	)	(169,962	)

The Income Tax Provision consisted of the following for the years ended December 31, 2017, 2016 and 2015:



	2017			2016			2015
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(6		)	(2		)	(2		)
Foreign	(1,131		)	(766		)	(483		)
Deferred:
U.S. Federal	(198		)	199			—
U.S. State and Local	—			—			—
Foreign	—			—			—
Total tax expense	$	(1,335	)	$	(569	)	$	(485	)

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



	December 31,
	2017		2016		2015
Federal income tax at statutory rate	34.00	%	34.00	%	34.00	%
State income tax (benefit), net of federal benefit	(1.01	)	3.05		(0.43	)
Permanent differences	(8.48	)	(3.70	)	(6.61	)
Research and development	19.53		16.66		19.50
(Increase) decrease to valuation allowance	29.10		(30.72	)	(20.87	)
Change in deferred tax assets	(64.12	)	—		—
Foreign tax rate differential	(10.33	)	(19.84	)	(24.06	)
Benefit (expense) allocated from other comprehensive income	(0.26	)	0.14		—
Other	(0.15	)	0.01		(1.82	)
Effective income tax rate	(1.72	)%	(0.40	)%	(0.29	)%

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2017 and 2016 are as follows:



	2017			2016
Deferred tax assets:
Accrued Expense	$	625		$	849
Amortization	2,116			46
Depreciation	1,749			2,968
Federal tax credits	80,961			74,475
State tax credits	7,148			4,996
Federal net operating losses	61,068			80,061
State net operating losses	11,884			9,672
Capitalized research and development costs	3,332			7,248
Other	18,815			22,125
Total gross deferred tax assets	187,698			202,440
Less valuation allowance	(177,631		)	(183,015		)
Total deferred tax assets, net of valuation allowance	$	10,067		$	19,425
Deferred tax liabilities:
Convertible debt	$	(9,927	)	$	(19,190	)
OCI unrealized gains	$	(140	)	$	(235	)
Total gross deferred tax assets	(10,067		)	(19,425		)
Net deferred tax assets (liabilities)	$	—		$	—

At December 31, 2017 and 2016, the Company recorded a full valuation allowance against its net deferred tax assets of approximately $177.6 million and $183.0 million, respectively. The change in the valuation allowance during the years ended December 31, 2017 and 2016 was approximately $5.4 million and $43.4 million, respectively. A full valuation allowance has been recorded since, in the judgment of management, these assets are not more likely than not to be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during periods in which those temporary differences and carryforwards become deductible or are utilized. As of December 31, 2017, the Company has approximately $290.8 million and $167.1 million of federal and state net operating loss carryforwards, respectively.

As of December 31, 2017, research and development credit carryforwards for federal and state purposes are approximately $13.2 million and $8.7 million, respectively. In addition, the Orphan Drug Credit Carryover available as of December 31, 2017 is approximately $67.8 million. As a result of the adoption of ASU 2016-09, the Company will no longer exclude $50.4 million tax benefits that arose directly from equity compensation in excess of compensation recognized for financial reporting in its U.S. federal and U.S. state net operating loss carryforwards. There was no net impact on the Company’s opening accumulated deficit upon application of this guidance using the modified retrospective transition method as the total cumulative-effect adjustment for previously deferred excess tax benefits was offset by a related change in the valuation allowance. The federal net operating loss carryforwards begin to expire in 2021, while the federal credit carryforwards begin to expire in 2019. State net operating loss carryforwards begin to expire in 2030, and the state credit carryforwards began to expire in 2016. Sections 382 and 383 of the Internal Revenue Code of 1986 subject the future utilization of net operating losses and certain other tax attributes, such as research and development tax credits, to an annual limitation in the event of certain ownership changes, as defined. The Company has undergone an ownership change and has determined that a “change in ownership” as defined by IRC Section 382 of the Internal Revenue Code of 1986, as amended, and the rules and regulations promulgated thereunder, did occur in June of 2013. Accordingly, about $231.5 million of the Company’s NOL carryforwards are limited and the Company can only use $16.7 million for the first five years from the ownership change and $5.7 million per year going forward. Therefore, $169.2 million of the NOL’s will be freed up over the next 20 years and $62.3 million are expected to expire unused which are not included in the deferred tax assets listed above. In summary, there are $290.8 million of NOLs available, out of which $169.2 million are limited by IRC Section 382. At December 31, 2017, there is $196.7 million available for immediate use and an additional $11.2 million will free up in 2018.

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

For all years through December 31, 2017, the Company generated research credits but has not conducted a study to document the qualified activities. This study may result in an adjustment to the Company’s research and development credit carryforwards; however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the deferred tax asset established for the research and development credit carryforwards and the valuation allowance.

U.S. federal income taxes have not been provided on undistributed earnings of the Company’s international subsidiaries as it is the Company’s intention to reinvest any earnings into the respective subsidiaries. It is not practicable to estimate the amount of tax that might be payable if some or all of such earnings were to be repatriated, and the amount of foreign tax credits that would be available to reduce or eliminate the resulting U.S. income tax liability. As of December 31, 2017 and December 31, 2016 there are no undistributed earnings.

On December 22, 2017, the U.S. government enacted the 2017 Tax Cuts and Jobs Act (the 2017 Tax Act), which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017 which resulted in a provisional benefit of $46.1 million. However, this adjustment was offset by a related change in the valuation allowance. The 2017 Tax Act also imposed a tax for a one-time deemed repatriation of post-1986 unremitted foreign E&P through the year ended December 31, 2017. The Company did not record any provisional tax expense related to the deemed repatriation as it does not have any undistributed foreign earnings. The Global Intangible Low-tax Income (GILTI) provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company expects that it will be subject to incremental U.S. tax on GILTI income beginning in 2018. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the year ended December 31, 2017.

ASC 740, Income Taxes requires the effects of changes in tax laws to be recognized in the period in which the legislation is enacted. However, due to the complexity and significance of the 2017 Tax Act’s provisions, the SEC issued SAB 118, which allows companies to record the tax effects of the 2017 Tax Act on a provisional basis based on a reasonable estimate, and then, if necessary, subsequently adjust such amounts during a limited measurement period as more information becomes available. The measurement period ends when a company has obtained, prepared, and analyzed the information necessary to finalize its accounting, but cannot extend beyond one year from enactment. The 2017 Tax Act did not have a material impact on the Company’s financial statements since its deferred temporary differences are fully offset by a valuation allowance and the Company does not have any significant off shore earnings from which to record the mandatory transition tax. However, given the significant complexity of the 2017 Tax Act, anticipated guidance from the U.S. Treasury about implementing the 2017 Tax Act, and the potential for additional guidance from the SEC or the FASB related to the 2017 Tax Act, these estimates may be adjusted during the measurement period. The provisional amounts disclosed in the Company’s footnotes were based on the its present interpretations of the 2017 Tax Act and current available information, including assumptions and expectations about future events, such as its projected financial performance, and are subject to further refinement as additional information becomes available (including the Company’s actual full fiscal 2018 results of operations, as well as potential new or interpretative guidance issued by the FASB or the Internal Revenue Service and other tax agencies) and further analyses are completed. The Company continues to analyze the changes in certain income tax deductions, assess calculations of earnings and profits in certain foreign subsidiaries, including if those earnings which are held in cash or other assets and gather additional data to compute the full impacts on the Company’s deferred and current tax assets and liabilities.

Commitments and contingencies

12 Months Ended

Dec. 31, 2017

Commitments and Contingencies Disclosure [Abstract]

Commitments and contingencies

Operating leases

The Company leases office space in South Plainfield, New Jersey for its principal office under a noncancelable operating lease through February 2019 in addition to office space in various countries for international employees primarily through workspace providers. Rent expense was approximately $2.2 million, $2.2 million, and $1.8 million for the years ended December 31, 2017, 2016, and 2015, respectively. The Company also leases certain office equipment under operating leases. Future minimum lease payments as of December 31, 2017 are as follows:



2018	$	2,110
2019	1,095
2020	845
2021	712
2022	652
Thereafter	1,274
	$	6,688

Other contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited (Wellcome Trust) for the research and development of small molecule compounds in connection with its oncology 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 oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company made the first development milestone payment of $0.8 million to Wellcome Trust under the oncology program funding agreement during the second quarter of 2016. Additional milestone payments up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement.

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

The Company is currently party to the legal proceedings described in Part I, Item 3. Legal Proceedings of this Annual Report on Form 10-K related to securities class action lawsuits.

In March 2016, three purported securities class action lawsuits were commenced in the United States District Court for the District of New Jersey (one each on March 3, 10, and 11), naming as defendants the Company, the Company’s Chief Executive Officer, and the Company’s former Chief Financial Officer. The lawsuits have been consolidated into one action captioned In re PTC Therapeutics, Inc. Securities Litigation, No. 16-1224 (KM) (the “Securities Class Action”). A consolidated amended complaint was filed on January 13, 2017. The complaint alleges violations of Sections 10(b) and 20(a) and Rule 10b-5 of the Securities Exchange Act of 1934 in connection with allegedly false and misleading statements made by the Company about its business, operations, and prospects as it relates to the NDA for Translarna for the treatment of nmDMD that the Company submitted to the FDA in December 2015. The plaintiffs seek, among other things, compensatory damages for purchasers of the Company’s common stock between November 6, 2014 and February 23, 2016, as well as attorneys’ fees and costs. On February 14, 2017, the defendants filed a motion to dismiss the consolidated amended complaint. On August 28, 2017, the motion to dismiss was granted in part and denied in part. On September 25, 2017, defendants filed an answer and affirmative defenses to the consolidated amended complaint. On January 10, 2018, the parties agreed to a settlement in principle of all legal claims, subject to court approval, which will be funded by the Company’s insurance subject to the applicable deductible. The Company has accrued $0.5 million related to the agreement in principle for the securities class action lawsuits, which represents the remainder of the deductible payable to the Company’s insurance. There is no assurance that the settlement will ultimately be approved or that it will become final. If the settlement does not occur and litigation continues, the Company intends to defend the case.

Other than the matter above, the Company has assessed such legal proceedings and does not believe that it is probable that a liability has been incurred or that the amount of any potential liability can be reasonably estimated. As a result, the Company did not record any loss contingencies for any of these matters. While it is not possible to determine the outcome of the matters described in Part I, Item 3. Legal Proceedings of this Annual Report on Form 10-K, the Company believes that the resolution of all such matters will not have a material adverse effect on its consolidated financial position or liquidity, but could possibly be material to its consolidated results of operations in any one accounting period.

Geographic information

12 Months Ended

Dec. 31, 2017

Segments, Geographical Areas [Abstract]

Geographic information

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



	Year Ended December 31, 2017
	United States		Non-US		Total
Total assets	$	278,108	$	113,545	$	391,653
Property and equipment, net	$	6,272	$	2,104	$	8,376
Revenue	$	49,155	$	145,237	$	194,392



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

401(k) plan	12 Months Ended
401(k) plan	Dec. 31, 2017
Retirement Benefits [Abstract]
401(k) plan	401(k) plan The Company maintains a 401(k) plan for its employees. Employee contributions are voluntary. The Company may match employee contributions in amounts to be determined at the Company’s sole discretion. The Company provides an 84% matching contribution for up to the first 6% of each contributing employee’s base salary contributions. The Company made matching contributions to the 401(k) plan and recorded expense of approximately $1.6 million, $1.1 million and $0.7 million for the years ended December 31, 2017, 2016 and 2015, respectively.

Restructuring

12 Months Ended

Dec. 31, 2017

Restructuring and Related Activities [Abstract]

Restructuring

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



	Balance as of January 1, 2017		Expenses, net		Cash Payments			Balance as of December 31, 2017
2016 workforce reduction	$	22	$	—	$	(22	)	$	—

Subsequent events	12 Months Ended
Subsequent events	Dec. 31, 2017
Subsequent Events [Abstract]
Subsequent events	Subsequent events The Company has evaluated all events or transactions that occurred after December 31, 2017. In the judgment of management, there were no material events that impacted the consolidated financial statements or disclosures.

Selected quarterly financial data (Unaudited)

12 Months Ended

Dec. 31, 2017

Quarterly Financial Information Disclosure [Abstract]

Selected quarterly financial data (Unaudited)

The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2017 and 2016 are as follows:



	For the quarters ending
	March 31			June 30			September 30			December 31
2017:
Net product revenue	$	26,442		$	47,891		$	41,780		$	57,953
Collaboration and grant revenue	105			71			73			20,077
Operating expenses	52,902			60,459			72,745			72,578
(Loss) income from operations	(26,355		)	(12,497		)	(30,892		)	5,452
Net (loss) income	(29,057		)	(17,475		)	(33,738		)	1,270
Basic and diluted net (loss) income per common share(1)(2)	$	(0.85	)	$	(0.44	)	$	(0.82	)	$	0.03
2016:
Net product revenue	$	18,878		$	15,437		$	22,013		$	25,119
Collaboration and grant revenue	17			196			973			72
Operating expenses	57,337			52,193			55,050			50,183
Loss from operations	(38,442		)	(36,560		)	(32,064		)	(24,992		)
Net loss	(41,233		)	(38,914		)	(35,167		)	(26,796		)
Basic and diluted net loss per common share(1)	$	(1.22	)	$	(1.14	)	$	(1.03	)	$	(0.78	)


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


(2)	Diluted net income per common share for the quarter ending December 31, 2017 excludes the conversion of the Convertible Notes as the effect of their inclusion is anti-dilutive during the period.

Summary of significant accounting policies (Policies)

12 Months Ended

Dec. 31, 2017

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Consolidation

Segment and geographic information

Cash equivalents

Marketable securities

Fixed assets

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



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

Concentration of credit risk

Inventories and cost of product sales

Inventory

The following table summarizes the components of the Company’s inventory for the periods indicated:



	December 31, 2017		December 31, 2016
Raw materials	$	452	$	—
Work in progress	3,912		—
Finished goods	6,390		—
Total inventory	$	10,754	$	—

Cost of product sales

Deferred rent

Accumulated other comprehensive income (loss)

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

Revenue recognition

Net Product Sales

Collaboration and Grant Revenue

Allowance for doubtful accounts

Research and development costs

Fair value of financial instruments


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

•


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

Beneficial conversion

Warrant liability

Share-based compensation

Income taxes

Foreign currency

Net (loss) income per share

Business combinations and asset acquisitions

Finite-lived intangible assets

Impairment of long-lived assets

Recent accounting pronouncements

Impact of recently adopted accounting pronouncements

Summary of significant accounting policies (Tables)

12 Months Ended

Dec. 31, 2017

Accounting Policies [Abstract]

Schedule of inventory

The following table summarizes the components of the Company’s inventory for the periods indicated:



	December 31, 2017		December 31, 2016
Raw materials	$	452	$	—
Work in progress	3,912		—
Finished goods	6,390		—
Total inventory	$	10,754	$	—

Schedule of estimated useful life of related assets

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



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

Emflaza asset acquisition (Tables)

12 Months Ended

Dec. 31, 2017

Business Combinations [Abstract]

Schedule of purchase price

The following tables present the total purchase consideration and the preliminary allocation of the purchase consideration for the Transaction as of April 20, 2017 (the “Acquisition Date”):



Cash consideration	$	75,000
Fair value of PTC common stock issued to Marathon (6,683,598 shares)	75,190
Acquisition costs	2,163
Total preliminary consideration transferred	$	152,353

Schedule of recognized identified assets acquired and liabilities assumed



Purchase price	$	152,353

Total fair value of tangible assets acquired and liabilities assumed:
Inventory	3,980
Emflaza rights	$	148,373

Schedule of finite-lived intangible assets, future amortization expense



	As of December 31, 2017
2018	$	21,713
2019	21,713
2020	21,713
2021	21,713
2022 and thereafter	46,141
Total	$	132,993

Fair value of financial instruments and investments (Tables)

12 Months Ended

Dec. 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



	December 31, 2017
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	79,454	$	—	$	79,454	$	—
Warrant liability	$	1	—		—		1
Stock appreciation rights liability	$	1,665	—		—		1,665



	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 December 31, 2017 and 2016:



	December 31, 2017
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	13,775	$	52	$	—		$	13,827
Corporate debt securities	65,657		—		(30		)	65,627
Government obligations	—		—		—			—
	$	79,432	$	52	$	(30	)	$	79,454



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

Available-for-sale securities, continuous unrealized loss position, fair value



	December 31, 2017
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(28	)	$	59,108	$	(2	)	$	6,519	$	(30	)	$	65,627



	December 31, 2016
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(85	)	$	45,482	$	(18	)	$	51,243	$	(103	)	$	96,725

Schedule of marketable securities on the balance sheet

Marketable securities on the balance sheet at December 31, 2017 and 2016 mature as follows:



	December 31, 2017
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	13,827	$	—
Corporate debt securities	55,550		10,077
Government obligations	—		—
Total Marketable securities	$	69,377	$	10,077



	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

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability and SARs liability for the years ended December 31, 2017 and 2016:



	Level 3 liabilities
	Warrants			SARs
Beginning balance as of December 31, 2015	$	48		$	—
Fair value of issuances	—			140
Change in fair value	(47		)	725
Ending balance as of December 31, 2016	$	1		$	865
Fair value of issuances	—			—
Change in fair value	—			1,864
Payments	$	—		$	(1,064	)
Ending balance as of December 31, 2017	$	1		$	1,665

Fixed assets (Tables)

12 Months Ended

Dec. 31, 2017

Property, Plant and Equipment [Abstract]

Schedule of fixed assets, net

Fixed assets, net were as follows at December 31, 2017 and 2016



	December 31,
	2017			2016
Leasehold improvements	$	14,078		$	14,038
Computer equipment and software	5,471			4,622
Furniture, fixtures, and lab equipment	20,776			19,343
Assets in process	895			353
	41,220			38,356
Less accumulated depreciation and amortization	(32,844		)	(30,927		)
	$	8,376		$	7,429

Accounts payable and accrued expenses (Tables)

12 Months Ended

Dec. 31, 2017

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2017 and 2016 consist of the following:



	December 31,
	2017		2016
Employee compensation, benefits, and related accruals	$	17,711	$	13,649
Consulting and contracted research	5,137		11,505
Professional fees	2,116		1,237
Sales allowances and other related costs	33,914		13,245
Accounts payable	15,282		6,298
Other	2,286		2,825
	$	76,446	$	48,759

Debt (Tables)

12 Months Ended

Dec. 31, 2017

Debt Disclosure [Abstract]

Summary of convertible notes

The Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2017			2016
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,121		)	(2,457		)
Less: Debt discount, net (1)	(42,572		)	(49,327		)
Net carrying amount	$	105,307		$	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:



	Year ended December 31,
	2017			2016
Contractual interest expense	$	4,500		$	4,497
Amortization of debt issuance costs	337			302
Amortization of debt discount	6,755			6,065
Total	$	11,592		$	10,864
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure (Tables)

12 Months Ended

Dec. 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 December 31, 2017:



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

The following is a summary of the Company’s outstanding warrants as of 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

- Definition

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

+ References + Details

Earnings per share (Tables)

12 Months Ended

Dec. 31, 2017

Earnings Per Share [Abstract]

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

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



	Year ended December 31,
	2017				2016				2015
Numerator
Net loss	$	(79,000	)		$	(142,110	)		$	(170,447	)
Denominator
Denominator for basic and diluted net loss per share	39,183,073				34,044,584				33,626,248
Net loss per share:
Basic and diluted	$	(2.02	)	*	$	(4.17	)	*	$	(5.07	)	*

* For the years ended December 31, 2017, 2016, and 2015, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding



	As of December 31,
	2017	2016	2015
Stock Options	6,448,642	5,854,316	4,826,477
Unvested restricted stock	393,011	271,651	344,335
Total	6,841,653	6,125,967	5,170,812

Stock award plan (Tables)

12 Months Ended

Dec. 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 options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2014	3,432,972		$	25.00
Granted	2,201,800		$	50.81
Exercised	(656,248	)	$	13.27
Forfeited	(152,047	)	$	49.58
Outstanding at December 31, 2015	4,826,477		$	37.20
Granted	1,500,645		$	27.90
Exercised	(89,216	)	$	10.85
Forfeited	(383,590	)	$	47.42
Outstanding at December 31, 2016	5,854,316		$	34.71
Granted	1,913,873		$	12.34
Exercised	(202,085	)	$	10.80
Forfeited	(1,117,462	)	$	33.65
Outstanding at December 31, 2017	6,448,642		$	29.00	7.28	$	13,435
Vested or expected to vest at December 31, 2017	2,522,747		$	23.29	8.39	$	6,822
Exercisable at December 31, 2017	3,778,544		$	33.19	6.48	$	6,167

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

The fair values of grants made in the years ended December 31, 2017, 2016 and 2015 were contemporaneously estimated on the date of grant using the following assumptions:



	2017	2016	2015
Risk-free interest rate	1.84 - 2.45%	1.30 - 2.24%	1.48 - 2.18%
Expected volatility	76 - 81%	67 - 78%	67 - 69%
Expected term	5.04 - 10.00 years	5.05 - 10.00 years	5.50 - 9.12 years

Summary of information on the Company's restricted stock

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2016	271,651		$	19.76
Granted	365,194		$	11.67
Vested	(180,861	)	$	14.19
Forfeited	(62,973	)	$	14.18
Unvested at December 31, 2017	393,011		$	15.64

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



	Year ended December 31,
	2017		2016		2015
Research and development	$	15,456	$	16,812	$	16,138
Selling, general and administrative	15,103		18,197		17,841
Total	$	30,559	$	35,009	$	33,979

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

12 Months Ended

Dec. 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



	Unrealized Gains/(Losses) On Marketable Securities			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2014	$	(387	)	$	(350	)	$	(737	)
Other comprehensive loss before reclassifications	(202		)	(261		)	(463		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(202		)	(261		)	(463		)
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income (loss) before reclassifications	386			(671		)	(285		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	386			(671		)	(285		)
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)
Other comprehensive income before reclassifications	225			5,229			5,454
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income	225			5,229			5,454
Balance at December 31, 2017	$	22		$	3,947		$	3,969

Income taxes (Tables)

12 Months Ended

Dec. 31, 2017

Income Tax Disclosure [Abstract]

Schedule of Income before Income Tax, Domestic and Foreign

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2017, 2016, and 2015:



	2017		2016		2015
Domestic	(54,588	)	(61,446	)	(50,944	)
Foreign	(23,077	)	(80,095	)	(119,018	)
Total	(77,665	)	(141,541	)	(169,962	)

Components of Income Tax Provision

The Income Tax Provision consisted of the following for the years ended December 31, 2017, 2016 and 2015:



	2017			2016			2015
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(6		)	(2		)	(2		)
Foreign	(1,131		)	(766		)	(483		)
Deferred:
U.S. Federal	(198		)	199			—
U.S. State and Local	—			—			—
Foreign	—			—			—
Total tax expense	$	(1,335	)	$	(569	)	$	(485	)

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

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



	December 31,
	2017		2016		2015
Federal income tax at statutory rate	34.00	%	34.00	%	34.00	%
State income tax (benefit), net of federal benefit	(1.01	)	3.05		(0.43	)
Permanent differences	(8.48	)	(3.70	)	(6.61	)
Research and development	19.53		16.66		19.50
(Increase) decrease to valuation allowance	29.10		(30.72	)	(20.87	)
Change in deferred tax assets	(64.12	)	—		—
Foreign tax rate differential	(10.33	)	(19.84	)	(24.06	)
Benefit (expense) allocated from other comprehensive income	(0.26	)	0.14		—
Other	(0.15	)	0.01		(1.82	)
Effective income tax rate	(1.72	)%	(0.40	)%	(0.29	)%

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

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2017 and 2016 are as follows:



	2017			2016
Deferred tax assets:
Accrued Expense	$	625		$	849
Amortization	2,116			46
Depreciation	1,749			2,968
Federal tax credits	80,961			74,475
State tax credits	7,148			4,996
Federal net operating losses	61,068			80,061
State net operating losses	11,884			9,672
Capitalized research and development costs	3,332			7,248
Other	18,815			22,125
Total gross deferred tax assets	187,698			202,440
Less valuation allowance	(177,631		)	(183,015		)
Total deferred tax assets, net of valuation allowance	$	10,067		$	19,425
Deferred tax liabilities:
Convertible debt	$	(9,927	)	$	(19,190	)
OCI unrealized gains	$	(140	)	$	(235	)
Total gross deferred tax assets	(10,067		)	(19,425		)
Net deferred tax assets (liabilities)	$	—		$	—

Commitments and contingencies (Tables)

12 Months Ended

Dec. 31, 2017

Commitments and Contingencies Disclosure [Abstract]

Schedule of future minimum lease payments

The Company also leases certain office equipment under operating leases. Future minimum lease payments as of December 31, 2017 are as follows:



2018	$	2,110
2019	1,095
2020	845
2021	712
2022	652
Thereafter	1,274
	$	6,688

Geographic information (Tables)

12 Months Ended

Dec. 31, 2017

Segments, Geographical Areas [Abstract]

Summary of financial information based on geographical location

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



	Year Ended December 31, 2017
	United States		Non-US		Total
Total assets	$	278,108	$	113,545	$	391,653
Property and equipment, net	$	6,272	$	2,104	$	8,376
Revenue	$	49,155	$	145,237	$	194,392



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

Restructuring (Tables)

12 Months Ended

Dec. 31, 2017

Restructuring and Related Activities [Abstract]

Restructuring



	Balance as of January 1, 2017		Expenses, net		Cash Payments			Balance as of December 31, 2017
2016 workforce reduction	$	22	$	—	$	(22	)	$	—

Selected quarterly financial data (Tables)

12 Months Ended

Dec. 31, 2017

Quarterly Financial Information Disclosure [Abstract]

Summary of quarterly data



	For the quarters ending
	March 31			June 30			September 30			December 31
2017:
Net product revenue	$	26,442		$	47,891		$	41,780		$	57,953
Collaboration and grant revenue	105			71			73			20,077
Operating expenses	52,902			60,459			72,745			72,578
(Loss) income from operations	(26,355		)	(12,497		)	(30,892		)	5,452
Net (loss) income	(29,057		)	(17,475		)	(33,738		)	1,270
Basic and diluted net (loss) income per common share(1)(2)	$	(0.85	)	$	(0.44	)	$	(0.82	)	$	0.03
2016:
Net product revenue	$	18,878		$	15,437		$	22,013		$	25,119
Collaboration and grant revenue	17			196			973			72
Operating expenses	57,337			52,193			55,050			50,183
Loss from operations	(38,442		)	(36,560		)	(32,064		)	(24,992		)
Net loss	(41,233		)	(38,914		)	(35,167		)	(26,796		)
Basic and diluted net loss per common share(1)	$	(1.22	)	$	(1.14	)	$	(1.03	)	$	(0.78	)


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


(2)	Diluted net income per common share for the quarter ending December 31, 2017 excludes the conversion of the Convertible Notes as the effect of their inclusion is anti-dilutive during the period.

The Company (Details) $ in Thousands		1 Months Ended	12 Months Ended
The Company (Details) $ in Thousands	Apr. 20, 2017 USD ($) shares	Aug. 31, 2014	Dec. 31, 2017 USD ($) country	Dec. 31, 2016 USD ($)	Aug. 31, 2015
Minimum age of ambulatory patient		5 years
Accumulated deficit			$ (814,108)	$ (735,108)
3.00% Convertible senior notes due 2022 \| Convertible debt
Interest rate					3.00%
Marathon Pharmaceuticals, LLC \| Arrangement
Cash consideration	$ 75,000
Equity interest issued or issuable, number of shares (in shares) \| shares	6,683,598
Numerator for calculation of number of shares of equity interests issued to acquire entity	$ 65,000
Trading day period	15 days
Development and regulatory milestone payments which the entity may be obligated to pay	$ 50,000
Translarna
Number of countries made availability of Translama on a commercial basis \| country			25

Summary of significant accounting policies - Fixed Assets (Details)	12 Months Ended
	Dec. 31, 2017
Computer equipment and software
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, and lab equipment \| Minimum
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, and lab equipment \| Maximum
Fixed assets
Estimated useful life	7 years

Summary of significant accounting policies - Narrative (Details)	1 Months Ended	12 Months Ended
	Aug. 31, 2014	Dec. 31, 2017 USD ($) segment	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Segment and geographic information
Number of operating segments \| segment		1
Minimum age of ambulatory patient	5 years
Allowance for doubtful accounts		$ 800,000	$ 700,000
Deferred research and development advance payments		500,000	400,000
Impairment of long-lived assets		0
Summary
Income tax expense		$ (1,335,000)	(569,000)	$ (485,000)
Renewal Of Marketing Authorization, Period		1 year
Long-term Debt
Summary
Unamortized debt issuance cost		$ 2,100,000
Accounting Standards Update 2015-03 \| Long-term Debt
Summary
Unamortized debt issuance cost				2,500,000
Accounting Standards Update 2015-03 \| Deposits and Other Assets
Summary
Unamortized debt issuance cost				(2,500,000)
Translarna
Summary
Sales		145,200,000	$ 81,400,000	$ 33,700,000
Emflaza
Summary
Sales		$ 28,800,000

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Raw materials	$ 452	$ 0
Work in progress	3,912	0
Finished goods	6,390	0
Total inventory	$ 10,754	$ 0

Emflaza asset acquisition - Narrative (Details) - USD ($) $ in Thousands		12 Months Ended
	Apr. 20, 2017	Dec. 31, 2017
Finite-Lived Intangible Assets [Line Items]
Issuance of common stock related to acquisition		$ 75,191
Intellectual Property
Finite-Lived Intangible Assets [Line Items]
Accumulated amortization		$ 15,400
Intellectual Property \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 75,000
Issuance of common stock related to acquisition (in shares)		6,683,598
Issuance of common stock related to acquisition	75,190
Acquisition costs	$ 2,163
Useful life	7 years
Non-collaborative Arrangement Transactions [Member] \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 75,000
Development and regulatory milestone payments which the entity may be obligated to pay	$ 50,000

Emflaza asset acquisition - Purchase consideration (Details) - USD ($) $ in Thousands		12 Months Ended
	Apr. 20, 2017	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 77,163	$ 0	$ 0
Issuance of common stock related to acquisition		$ 75,191
Intellectual Property \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 75,000
Issuance of common stock related to acquisition	75,190
Acquisition costs	2,163
Total preliminary consideration transferred	$ 152,353

Emflaza asset acquisition - Allocation of the purchase consideration (Details) - Marathon Pharmaceuticals, LLC $ in Thousands	Apr. 20, 2017 USD ($)
Finite-Lived Intangible Assets [Line Items]
Inventory	$ 3,980
Intellectual Property
Finite-Lived Intangible Assets [Line Items]
Purchase price	152,353
Emflaza rights	$ 148,373

Emflaza asset acquisition - Estimated future amortization (Details) - Intellectual Property - Marathon Pharmaceuticals, LLC $ in Thousands	Dec. 31, 2017 USD ($)
Finite-Lived Intangible Assets [Line Items]
2018	$ 21,713
2019	21,713
2020	21,713
2021	21,713
2022 and thereafter	46,141
Total	$ 132,993

Fair value of financial instruments and investments - Recurring Basis (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 79,454	$ 173,345
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	79,454	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	1,665	865
Recurring basis \| Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	79,454	173,345
Warrant liability	1	1
Stock appreciation rights liability	$ 1,665	$ 865

Fair value of financial instruments and investments - Marketable Securities, Unrealized Gains (Losses) (Details) - USD ($)	Dec. 31, 2017	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy	$ 0
Marketable securities accounted for as available-for-sale securities
Amortized Cost	79,432,000	$ 173,347,000
Gross Unrealized Gains	52,000	101,000
Gross Unrealized Losses	(30,000)	(103,000)
Fair Value	79,454,000	173,345,000
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	13,775,000	12,919,000
Gross Unrealized Gains	52,000	47,000
Gross Unrealized Losses	0	0
Fair Value	13,827,000	12,966,000
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	65,657,000	153,240,000
Gross Unrealized Gains	0	52,000
Gross Unrealized Losses	(30,000)	(103,000)
Fair Value	65,627,000	153,189,000
Government obligations
Marketable securities accounted for as available-for-sale securities
Amortized Cost	0	7,188,000
Gross Unrealized Gains	0	2,000
Gross Unrealized Losses	0	0
Fair Value	$ 0	$ 7,190,000

Fair value of financial instruments and investments - Unrealized Loss Position (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Available-for-sale Securities, Continuous Unrealized Loss Position, Accumulated Loss [Abstract]
Securities in an unrealized loss position less than 12 months, unrealized losses	$ (28)	$ (85)
Securities in an unrealized loss position greater than 12 months, fair value	59,108	45,482
Securities in an unrealized loss position greater than 12 months, unrealized losses	(2)	(18)
Securities in an unrealized loss position greater than 12 months, fair value	6,519	51,243
Total, unrealized losses	(30)	(103)
Total, fair value	$ 65,627	$ 96,725

Fair value of financial instruments and investments - Marketable Securities, Balance Sheet Disclosures (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Marketable securities on the balance sheet
Less Than 12 Months	$ 69,377	$ 157,352
More Than 12 Months	10,077	15,993
Commercial paper
Marketable securities on the balance sheet
Less Than 12 Months	13,827	12,966
More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Less Than 12 Months	55,550	137,196
More Than 12 Months	10,077	15,993
Government obligations
Marketable securities on the balance sheet
Less Than 12 Months	0	7,190
More Than 12 Months	$ 0	$ 0

Fair value of financial instruments and investments - Convertible Senior Notes (Details) - 3.00% Convertible senior notes due 2022 - Convertible debt - USD ($)	Dec. 31, 2017	Dec. 31, 2016	Aug. 31, 2015
Financial assets and liabilities measured at fair value on recurring basis
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Interest rate			3.00%
Debt instrument	$ 115,700,000	$ 85,200,000

Fair value of financial instruments and investments - Fair Value of Liabilities (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Warrants
Changes in the fair value of warrant liability
Beginning balance	$ 1	$ 48
Fair value of issuances	0	0
Change in fair value	0	(47)
Payments	0
Ending balance	$ 1	$ 1
Warrants \| Minimum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility	69.00%	62.00%
Risk-free interest rate	1.89%	0.62%
Strike price (in dollars per share)	$ 128.00	$ 128.00
Expected life	1 year 7 months 2 days	5 months 12 days
Warrants \| Maximum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility	69.00%	67.00%
Risk-free interest rate	1.89%	1.34%
Strike price (in dollars per share)	$ 2,520.00	$ 2,520.00
Expected life	1 year 8 months 19 days	2 years 8 months 19 days
Warrants \| Common stock
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 16.68	$ 10.91
Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	$ 865	$ 0
Fair value of issuances	0	140
Change in fair value	1,864	725
Payments	(1,064)
Ending balance	$ 1,665	$ 865
Stock Appreciation Rights (SARs) \| Minimum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility	31.00%	48.00%
Risk-free interest rate	1.28%	0.44%
Strike price (in dollars per share)	$ 6.76	$ 6.76
Expected life	0 days	0 days
Stock Appreciation Rights (SARs) \| Maximum
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Volatility	70.00%	71.00%
Risk-free interest rate	1.89%	1.47%
Strike price (in dollars per share)	$ 30.86	$ 30.86
Expected life	2 years	3 years
Stock Appreciation Rights (SARs) \| Common stock
Assumption used to estimate the fair value of warrant liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 16.68	$ 10.91

Fixed assets (Details) - USD ($) $ in Thousands	12 Months Ended
Fixed assets (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Fixed assets
Gross fixed assets	$ 41,220	$ 38,356
Less accumulated depreciation and amortization	(32,844)	(30,927)
Net fixed assets	8,376	7,429
Depreciation expense	2,300	3,300	$ 2,900
Leasehold improvements
Fixed assets
Gross fixed assets	14,078	14,038
Computer equipment and software
Fixed assets
Gross fixed assets	5,471	4,622
Furniture, fixtures, and lab equipment
Fixed assets
Gross fixed assets	20,776	19,343
Assets in process
Fixed assets
Gross fixed assets	$ 895	$ 353

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 17,711	$ 13,649
Consulting and contracted research	5,137	11,505
Professional fees	2,116	1,237
Sales allowances and other related costs	33,914	13,245
Accounts payable	15,282	6,298
Other	2,286	2,825
Accounts payable and accrued expenses	$ 76,446	$ 48,759

Debt - 2017 Credit Facility (Details) - MidCap Financial Trust - USD ($)		1 Months Ended
	May 05, 2017	May 31, 2017
Long-term debt
Line of credit facility, maximum borrowing capacity		$ 60,000,000.0
Proceeds from lines of credit	$ 40,000,000
Additional capacity available		20,000,000
Net product revenue threshold, additional capacity		$ 120,000,000
Net product revenue threshold, additional capacity, trailing period		12 months
Debt issuance costs, line of credit arrangements		$ 400,000
Interest payment period		24 months
LIBOR
Long-term debt
Floor interest rate		1.00%
Basis spread on variable rate		6.15%

Debt - 2015 Convertible Notes (Details)	1 Months Ended	12 Months Ended
Debt - 2015 Convertible Notes (Details)	Aug. 31, 2015 USD ($) day $ / shares	Dec. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)
Long-term debt
Additional paid-in capital		$ 966,534,000	$ 856,142,000
3.00% Convertible senior notes due 2022 \| Convertible debt
Long-term debt
Debt instrument	$ 150,000,000	150,000,000	150,000,000
Interest rate	3.00%
Net proceeds from issuance of convertible notes	$ 145,400,000
Trading days, number \| day	20
Consecutive trading days, period \| day	30
Stock price trigger	130.00%
Business days, period	5 days
Consecutive trading-day period	5 days
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	0.0177
Conversion price per share \| $ / shares	$ 56.34
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default	25.00%
Convertible instruments principal and unpaid interest payable upon events of default	100.00%
Term of the convertible notes	7 years
Additional paid-in capital		57,500,000
Net deferred tax liability in connection with convertible notes	$ 22,300,000
Debt instrument		$ 115,700,000	$ 85,200,000
Remaining amortization period		4 years 7 months 13 days
3.00% Convertible senior notes due 2022 \| Convertible debt \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| day	19
Consecutive trading days, period \| day	30
Stock price trigger	130.00%
Redemption price	100.00%

Debt - Schedule of Notes (Details) - Convertible debt - 3.00% Convertible senior notes due 2022 - USD ($)	Dec. 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	(2,121,000)	(2,457,000)
Less: Debt discount, net	(42,572,000)	(49,327,000)
Net carrying amount	$ 105,307,000	$ 98,216,000

Debt - Interest Expense (Details) - USD ($) $ in Thousands	12 Months Ended
Debt - Interest Expense (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Long-term debt
Amortization of debt issuance costs	$ 433	$ 302	$ 107
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	4,500	4,497
Amortization of debt issuance costs	337	302
Amortization of debt discount	6,755	6,065
Total	$ 11,592	$ 10,864
Effective interest rate of the liability component	11.00%	11.00%

Capital structure - Narrative (Details) - shares	Dec. 31, 2017	Dec. 31, 2016
Capital structure
Common stock, authorized shares (in shares)	125,000,000	125,000,000
Common stock
Capital structure
Common stock, authorized shares (in shares)	125,000,000

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

Earnings per share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Numerator
Net loss	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (26,796)	$ (35,167)	$ (38,914)	$ (41,233)	$ (79,000)	$ (142,110)	$ (170,447)
Denominator
Denominator for basic and diluted net loss per share (in shares)									39,183,073	34,044,584	33,626,248
Net loss per share:
Basic and diluted (in dollars per share)	$ 0.03	$ (0.82)	$ (0.44)	$ (0.85)	$ (0.78)	$ (1.03)	$ (1.14)	$ (1.22)	$ (2.02)	$ (4.17)	$ (5.07)
Total shares excluded from calculation (in shares)									6,841,653	6,125,967	5,170,812
Stock Options
Net loss per share:
Total shares excluded from calculation (in shares)									6,448,642	5,854,316	4,826,477
Unvested restricted stock
Net loss per share:
Total shares excluded from calculation (in shares)									393,011	271,651	344,335

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended			12 Months Ended
	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Stock option plan
Additional compensation recognized due to modifications to the options granted							$ 1,900
Share-based compensation expense					$ 30,559	$ 35,009	$ 33,979
Unrecognized compensation cost					$ 38,200
Weighted average remaining service period for recognition of unrecognized compensation cost					1 year 10 months 28 days
Unvested restricted stock
Stock option plan
Options granted (in shares)					365,194
Stock option
Stock option plan
Granted (in shares)					1,913,873	1,500,645	2,201,800
Forfeited (in shares)					1,117,462	383,590	152,047
Expected dividend yield					0.00%	0.00%	0.00%
Weighted average grant date fair value (in dollars per share)					$ 8.45	$ 17.31	$ 50.81
Stock option \| Maximum
Stock option plan
Vesting period					4 years
Stock option \| Minimum
Stock option plan
Vesting period					3 years
Stock Appreciation Rights (SARs)
Stock option plan
Granted (in shares)			897,290
Vesting period			4 years
Share-based compensation expense					$ 1,900
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)					1,000,000
Award requisite service period					6 months
Purchase price of common stock					85.00%
Employee stock purchase plan, voting percentage limit		5.00%
Share-based compensation expense					$ 900
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan \| Unvested restricted stock
Stock option plan
Options granted (in shares)	735,324
2013 Stock Incentive Plan \| Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)				0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan \| Stock option
Stock option plan
Stockholder's specified ownership percentage					10.00%
Expiration period					10 years
2009 Equity and Long Term Incentive Plan \| Stock option \| Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date					100.00%
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date					110.00%
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)				122,296
2013 Long Term Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)					927,478
Number of shares subject to outstanding awards (in shares)				3,040,444
Annual increase in the number of shares on the first day of the fiscal year (in shares)				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Inducement grant plan \| Stock option
Stock option plan
Granted (in shares)					640,550
Granted (in dollars per share)					$ 14.16
Forfeited (in shares)					316,176

Stock award plan - Stock Option Activity (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Number of options
Outstanding at the beginning of the period (in shares)	5,854,316	4,826,477	3,432,972
Granted (in shares)	1,913,873	1,500,645	2,201,800
Exercised (in shares)	(202,085)	(89,216)	(656,248)
Forfeited (in shares)	(1,117,462)	(383,590)	(152,047)
Outstanding at the end of the period (in shares)	6,448,642	5,854,316	4,826,477
Vested or expected to vest at the end of the period (in shares)	2,522,747
Exercisable at the end of the period (in shares)	3,778,544
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 34.71	$ 37.20	$ 25.00
Granted (in dollars per share)	12.34	27.90	50.81
Exercised (in dollars per share)	10.80	10.85	13.27
Forfeited (in dollars per share)	33.65	47.42	49.58
Outstanding at the end of the period (in dollars per share)	29.00	$ 34.71	$ 37.20
Vested or expected to vest at the end of the period (in dollars per share)	23.29
Exercisable at the end of the period (in dollars per share)	$ 33.19
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 3 months 11 days
Vested or expected to vest at the end of the period	8 years 4 months 21 days
Exercisable at the end of the period	6 years 5 months 23 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars)	$ 13,435
Vested or expected to vest at the end of the period (in dollars)	6,822
Exercisable at the end of the period (in dollars)	$ 6,167

Stock award plan - Assumptions Used (Details) - Stock option	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Minimum
Valuation assumptions
Risk-free interest rate	1.84%	1.30%	1.48%
Expected volatility	76.00%	67.00%	67.00%
Expected term	5 years 15 days	5 years 17 days	5 years 6 months
Maximum
Valuation assumptions
Risk-free interest rate	2.45%	2.24%	2.18%
Expected volatility	81.00%	78.00%	69.00%
Expected term	10 years	10 years	9 years 1 month 13 days

Stock award plan - Restricted Stock Activity (Details) - Unvested restricted stock	12 Months Ended
	Dec. 31, 2017 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	271,651
Granted (in shares) \| shares	365,194
Vested (in shares) \| shares	(180,861)
Forfeited (in shares) \| shares	(62,973)
Balance at the end of the period (in shares) \| shares	393,011
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	11.67
Vested (in dollars per share) \| $ / shares	14.19
Forfeited (in dollars per share) \| $ / shares	14.18
Balance at the end of the period (in dollars per share) \| $ / shares	$ 15.64

Stock award plan - Share-based Compensation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 30,559	$ 35,009	$ 33,979
Research and development
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	15,456	16,812	16,138
Selling, general and administrative
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 15,103	$ 18,197	$ 17,841

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	$ 119,583	$ 226,001	$ 298,467
Other comprehensive income before reclassifications	5,454	(285)	(463)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income	5,454	(285)	(463)
Balance at the end of the period	156,437	119,583	226,001
Unrealized Gains/(Losses) On Marketable Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(203)	(589)	(387)
Other comprehensive income before reclassifications	225	386	(202)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income	225	386	(202)
Balance at the end of the period	22	(203)	(589)
Foreign Currency Translation
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(1,282)	(611)	(350)
Other comprehensive income before reclassifications	5,229	(671)	(261)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income	5,229	(671)	(261)
Balance at the end of the period	3,947	(1,282)	(611)
Accumulated other comprehensive (loss) income
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	(1,485)	(1,200)	(737)
Balance at the end of the period	$ 3,969	$ (1,485)	$ (1,200)

Collaborations and grants (Details)		1 Months Ended				12 Months Ended
Collaborations and grants (Details)	Jan. 02, 2011 deliverable	Oct. 31, 2017 USD ($)	Nov. 30, 2014 USD ($)	Jan. 31, 2014 USD ($)	Nov. 30, 2011 USD ($) compound	Dec. 31, 2017 USD ($) deliverable	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborations and grants
Grant revenue						$ 0	$ 900,000	$ 2,200,000
Minimum
Collaborations and grants
Term of grant program						2 years
Maximum
Collaborations and grants
Term of grant program						5 years
Collaboration agreement \| Development event milestones
Collaborations and grants
Collaboration revenue recognized		$ 20,000,000	$ 10,000,000	$ 7,500,000
Collaboration agreement \| Roche and SMA Foundation
Collaborations and grants
Number of compounds in preclinical development \| compound					3
Deferred revenue					$ 30,000,000
Number of significant deliverables \| deliverable						2
Research period for applying technology					2 years
Collaboration revenue recognized						$ 20,300,000	400,000	$ 600,000
Collaboration agreement \| Roche and SMA Foundation \| Development event milestones
Collaborations and grants
Additional consideration receivable upon achievement of specified events						135,000,000
Collaboration agreement \| Roche and SMA Foundation \| Sales milestones
Collaborations and grants
Additional consideration receivable upon achievement of specified events						325,000,000
Early stage collaboration and discovery agreements
Collaborations and grants
Deferred revenue						$ 0	0
Number of significant deliverables \| deliverable	2
Collaboration revenue recognized							$ 1,800,000
Early stage collaboration and discovery agreements \| Minimum
Collaborations and grants
Research period for applying technology						3 years
Early stage collaboration and discovery agreements \| Maximum
Collaborations and grants
Research period for applying technology						4 years
Early stage collaboration and discovery agreements \| Development event milestones
Collaborations and grants
Additional consideration receivable upon achievement of specified events						$ 143,000,000
Early stage collaboration and discovery agreements \| Sales milestones \| Maximum
Collaborations and grants
Additional consideration receivable upon achievement of specified events						$ 252,000,000

Income taxes - Loss from operations before tax (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Tax Disclosure [Abstract]
Domestic	$ (54,588)	$ (61,446)	$ (50,944)
Foreign	(23,077)	(80,095)	(119,018)
Total	$ (77,665)	$ (141,541)	$ (169,962)

Income taxes - Provision for Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Current:
U.S. Federal	$ 0	$ 0	$ 0
U.S. State and Local	(6)	(2)	(2)
Foreign	(1,131)	(766)	(483)
Deferred:
U.S. Federal	(198)	199	0
U.S. State and Local	0	0	0
Foreign	0	0	0
Total tax expense	$ (1,335)	$ (569)	$ (485)

Income taxes - Tax Rate Reconciliation (Details)	12 Months Ended
Income taxes - Tax Rate Reconciliation (Details)	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Reconciliation of the U.S. statutory income tax rate to the entity's effective tax rate
Federal income tax at statutory rate	34.00%	34.00%	34.00%
State income tax (benefit), net of federal benefit	(1.01%)	3.05%	(0.43%)
Permanent differences	(8.48%)	(3.70%)	(6.61%)
Research and development	19.53%	16.66%	19.50%
(Increase) decrease to valuation allowance	29.10%	(30.72%)	(20.87%)
Change in deferred tax assets	(64.12%)	0.00%	0.00%
Foreign tax rate differential	(10.33%)	(19.84%)	(24.06%)
Benefit (expense) allocated from other comprehensive income	(0.26%)	0.14%	0.00%
Other	(0.15%)	0.01%	(1.82%)
Effective income tax rate	(1.72%)	(0.40%)	(0.29%)

Income taxes - Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Deferred tax assets:
Accrued Expense	$ 625	$ 849
Amortization	2,116	46
Depreciation	1,749	2,968
Federal tax credits	80,961	74,475
State tax credits	7,148	4,996
Federal net operating losses	61,068	80,061
State net operating losses	11,884	9,672
Capitalized research and development costs	3,332	7,248
Other	18,815	22,125
Total gross deferred tax assets	187,698	202,440
Less valuation allowance	(177,631)	(183,015)
Total deferred tax assets, net of valuation allowance	10,067	19,425
Deferred tax liabilities:
Convertible debt	(9,927)	(19,190)
OCI unrealized gains	(140)	(235)
Total gross deferred tax assets	(10,067)	(19,425)
Net deferred tax assets (liabilities)	$ 0	$ 0

Income taxes - Narrative (Details) - USD ($) $ in Thousands	12 Months Ended
Income taxes - Narrative (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Operating loss carryforwards
Valuation allowance	$ 177,631	$ 183,015
Valuation allowance, deferred tax asset, increase (decrease)	5,400	$ 43,400
Orphan drug credit carryover	67,800
Limited NOL carryforwards	231,500
Operating loss carryforwards, not subject to expiration	169,200
Operating loss carryforwards, subject to expiration	62,300
Operating loss carryforwards for immediate use	196,700
Operating loss carryforwards in next twelve months	$ 11,200
Federal income tax at statutory rate	34.00%	34.00%	34.00%
Uncertain tax position	$ 0
Change In tax rate, deferred tax asset, provisional income tax expense	46,100
First five years from ownership change
Operating loss carryforwards
Net operating loss carryforwards	16,700
After five years
Operating loss carryforwards
Net operating loss carryforwards	5,700
Federal
Operating loss carryforwards
Net operating loss carryforwards	290,800
Research and development credit carryforwards	13,200
State
Operating loss carryforwards
Net operating loss carryforwards	167,100
Research and development credit carryforwards	8,700
Accounting Standards Update 2016-09
Operating loss carryforwards
Share-based compensation cost	$ 50,400

Commitments and contingencies - Narrative (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015	Jan. 10, 2018	Jun. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Operating leases, rent expense	$ 2.2	$ 2.2	$ 1.8
Funding agreement \| Wellcome trust limited
Other contingencies
Development and regulatory milestone payments which the entity may be obligated to pay	$ 22.4				$ 0.8
Subsequent Event
Other contingencies
Litigation settlement				$ 0.5

Commitments and contingencies - Operating Leases, Future Lease Payments (Details) $ in Thousands	Dec. 31, 2017 USD ($)
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2018	$ 2,110
2019	1,095
2020	845
2021	712
2022	652
Thereafter	1,274
Total future minimum lease payments	$ 6,688

Geographic information (Details) $ in Thousands	12 Months Ended
Geographic information (Details) $ in Thousands	Dec. 31, 2017 USD ($) segment	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Segments, Geographical Areas [Abstract]
Number of operating segments \| segment	1
Segment Reporting Information [Line Items]
Total assets	$ 391,653	$ 269,345
Property and equipment, net	8,376	7,429
Revenue	194,392	82,705	$ 36,766
United States
Segment Reporting Information [Line Items]
Total assets	278,108	223,098
Property and equipment, net	6,272	6,439
Revenue	49,155	1,206
Non-US
Segment Reporting Information [Line Items]
Total assets	113,545	46,247
Property and equipment, net	2,104	990
Revenue	$ 145,237	$ 81,499

401(k) plan (Details) - USD ($) $ in Millions	12 Months Ended
401(k) plan (Details) - USD ($) $ in Millions	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Retirement Benefits [Abstract]
Matching contribution up to the first 6% of employee's base salary	84.00%
Percentage of employee's base salary, matched by employer	6.00%
Expense recorded	$ 1.6	$ 1.1	$ 0.7

Restructuring - Narrative (Details) $ in Millions	Dec. 31, 2016 USD ($)
Restructuring and Related Activities [Abstract]
Restructuring charge	$ 2.5

Restructuring - 2016 workforce reduction (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2017 USD ($)
Restructuring Reserve [Roll Forward]
January 1, 2017	$ 22
Expenses, net	0
Cash Payments	(22)
December 31, 2017	$ 0

Selected quarterly financial data (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Quarterly Financial Information Disclosure [Abstract]
Net product revenue	$ 57,953	$ 41,780	$ 47,891	$ 26,442	$ 25,119	$ 22,013	$ 15,437	$ 18,878	$ 174,066	$ 81,447	$ 33,696
Collaboration and grant revenue	20,077	73	71	105	72	973	196	17	20,326	1,258	3,070
Operating expenses	72,578	72,745	60,459	52,902	50,183	55,050	52,193	57,337	258,684	214,763	203,896
Loss from operations	5,452	(30,892)	(12,497)	(26,355)	(24,992)	(32,064)	(36,560)	(38,442)	(64,292)	(132,058)	(167,130)
Net loss attributable to common stockholders	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (26,796)	$ (35,167)	$ (38,914)	$ (41,233)	$ (79,000)	$ (142,110)	$ (170,447)
Net loss per share—basic and diluted (in dollars per share)	$ 0.03	$ (0.82)	$ (0.44)	$ (0.85)	$ (0.78)	$ (1.03)	$ (1.14)	$ (1.22)	$ (2.02)	$ (4.17)	$ (5.07)