PTC Therapeutics (PTCT) 10-Q 5 Nov 18 2018 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2018	Nov. 01, 2018
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	1,070,081
Document Type	10-Q
Document Period End Date	Sep. 30, 2018
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		50,454,834
Document Fiscal Year Focus	2,018
Document Fiscal Period Focus	Q3
Entity Emerging Growth Company	false
Entity Small Business	false

Consolidated Balance Sheets (un

Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017	Sep. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 206,913	$ 111,792	$ 141,838	$ 58,321
Marketable securities	42,491	79,454
Trade receivables, net	42,197	40,394
Inventory, net	13,660	10,754
Prepaid expenses and other current assets	8,020	6,669
Total current assets	313,281	249,063
Fixed assets, net	8,805	8,376
Intangible assets, net	604,612	132,993
Goodwill	100,309	0
Deposits and other assets	1,620	1,221
Total assets	1,028,627	391,653
Current liabilities:
Accounts payable and accrued expenses	102,788	76,446
Current portion of long-term debt	6,667	0
Deferred revenue	2,004	3,937
Other current liabilities	3,463	1,665
Total current liabilities	114,922	82,048
Deferred revenue - long-term	11,156	7,954
Long-term debt	144,258	144,971
Contingent consideration payable	218,700	0
Estimated fair value of deferred consideration payable	38,200	0
Deferred tax liability	115,200	0
Other long-term liabilities	101	243
Total liabilities	642,537	235,216
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 50,432,655 shares at September 30, 2018. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017	51	42
Additional paid-in capital	1,275,004	966,534
Accumulated other comprehensive income	1,628	3,969
Accumulated deficit	(890,593)	(814,108)
Total stockholders’ equity	386,090	156,437
Total liabilities and stockholders’ equity	$ 1,028,627	$ 391,653

Consolidated Balance Sheets (_2

Consolidated Balance Sheets (unaudited) (Parenthetical) - $ / shares	Sep. 30, 2018	Dec. 31, 2017
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)	50,432,655	41,612,395
Common stock, outstanding shares (in shares)	50,432,655	41,612,395

Consolidated Statements of Oper

Consolidated Statements of Operations (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Revenues:
Revenue	$ 53,591	$ 41,853	$ 178,396	$ 116,362
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	3,292	1,582	8,909	2,142
Amortization of acquired intangible asset	5,793	9,716	16,815	9,952
Research and development	54,368	30,024	118,337	88,222
Selling, general and administrative	38,368	31,423	104,882	85,788
Total operating expenses	101,821	72,745	248,943	186,104
Loss from operations	(48,230)	(30,892)	(70,547)	(69,742)
Interest expense, net	(3,118)	(3,421)	(9,306)	(8,648)
Other income (expense), net	734	766	1,066	(1,373)
Loss before income tax expense	(50,614)	(33,547)	(78,787)	(79,763)
Income tax expense	(355)	(191)	(964)	(507)
Net loss attributable to common stockholders	$ (50,969)	$ (33,738)	$ (79,751)	$ (80,270)
Weighted-average shares outstanding:
Basic and diluted (in shares)	48,096,521	41,296,740	45,310,690	38,433,749
Net loss per share-basic and diluted (in dollars per share)
Net loss per share—basic and diluted (in dollars per share)	$ (1.06)	$ (0.82)	$ (1.76)	$ (2.09)
Product
Revenues:
Revenue	$ 53,021	$ 41,780	$ 177,172	$ 116,113
Collaboration and grant revenue
Revenues:
Revenue	$ 570	$ 73	$ 1,224	$ 249

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Statement of Comprehensive Income [Abstract]
Net loss	$ (50,969)	$ (33,738)	$ (79,751)	$ (80,270)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	33	31	(50)	0
Foreign currency translation (loss) gain	(260)	983	(2,291)	4,498
Comprehensive loss	$ (51,196)	$ (32,724)	$ (82,092)	$ (75,772)

Consolidated Statements of Cash

Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017
Cash flows from operating activities
Net loss	$ (79,751)	$ (80,270)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	19,316	11,743
Change in valuation of warrant liability	3	3
Non-cash interest expense	5,563	4,999
Loss on disposal of asset	2	5
Amortization of premiums and accretion of discounts on investments, net	(354)	493
Amortization of debt issuance costs	390	308
Share-based compensation expense	24,773	24,082
Unrealized foreign currency transaction gains	(977)	(364)
Changes in operating assets and liabilities:
Inventory	(3,252)	(3,625)
Prepaid expenses and other current assets	(1,301)	(570)
Trade receivables, net	(2,681)	(10,994)
Deposits and other assets	(385)	(485)
Accounts payable and accrued expenses	18,606	11,807
Other liabilities	1,617	807
Deferred revenue	5,933	10,710
Net cash used in operating activities	(12,498)	(31,351)
Cash flows from investing activities
Purchases of fixed assets	(2,489)	(1,058)
Purchases of marketable securities	(28,656)	(19,467)
Sale and redemption of marketable securities	65,923	164,847
Acquisition of product rights	(3,903)	(77,163)
Business acquisition, net of cash acquired	(48,892)	0
Net cash (used in) / provided by investing activities	(18,017)	67,159
Cash flows from financing activities
Proceeds from exercise of options	8,631	1,437
Net proceeds from public offerings	117,915	0
Proceeds from shares issued under employee stock purchase plan	1,299	1,362
Debt issuance costs related to secured term loan	0	(432)
Proceeds from issuance of secured term loan	0	40,000
Net cash provided by financing activities	127,845	42,367
Effect of exchange rate changes on cash	(2,209)	5,342
Net increase in cash and cash equivalents	95,121	83,517
Cash and cash equivalents, beginning of period	111,792	58,321
Cash and cash equivalents, end of period	206,913	141,838
Supplemental disclosure of cash information
Cash paid for interest	6,927	5,496
Cash paid for income taxes	919	616
Supplemental disclosure of non-cash investing and financing activity
Unrealized gain (loss) on marketable securities	(50)	0
Acquisition of product rights and licenses	$ (4,530)	$ 0

The Company

The Company	9 Months Ended
	Sep. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) is 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’s ability to globally 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 five years and older in the 31 member states of the European Economic Area, or EEA. In July 2018, the European Commission approved a label-extension request to the marketing authorization for Translarna in the EEA to include patients from two to up to five years of age. Emflaza is approved in the United States for the treatment of DMD in patients five years and older. The Company has a pipeline of gene therapy product candidates, including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC, deficiency, or AADC deficiency. The Company is preparing a biologics license application, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which it anticipates submitting to the U.S. Food and Drug Administration, or FDA, in 2019. The Company is also preparing a marketing authorisation application, or MAA, for PTC-AADC for the treatment of AADC deficiency in the European Union, or EU, which it anticipates submitting to the European Medicines Agency, or EMA, in 2019, as well. The Company holds the rights for the commercialization of Tegsedi™ (inotersen) and Waylivra™ (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean. Tegsedi has received marketing authorization in the U.S., EU and Canada for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis. The Company plans to file a request for marketing authorization for Tegsedi with ANVISA, the Brazilian Health Regulatory Authority, in the first half of 2019. Waylivra is currently under regulatory review in EU for the treatment of familial chylomicronemia syndrome, or FCS. The Company also has a spinal muscular atrophy (SMA) collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc., which it refers to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. Currently, its collaboration has three clinical trials ongoing to evaluate the safety and effectiveness of risdiplam (RG7916, RO7034067), the lead compound in the SMA program. In addition, the Company has a pipeline of product candidates that are in early clinical and pre-clinical development. The Company's pre-clinical and discovery programs are focused on the development of new treatments for multiple therapeutic areas, including rare diseases and oncology. 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 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 July 2018 and is effective, unless extended, through August 5, 2019. 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 September 30, 2018 , Translarna was available in over 25 countries on a commercial basis or pursuant to an EAP program. The Company expects to expand its commercial 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 Company filed 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 it is currently designing and expects to initiate such a study by the end of 2018. 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 is entitled to receive contingent payments from the Company based on annual net sales of Emflaza, 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. On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc., or Agilis, pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Merger Agreement”), by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and the Company's wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the "Merger"). Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of $49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. Agilis equityholders may become entitled to receive contingent payments from the Company based on the achievement of certain development, regulatory and net sales milestones as well as based upon a percentage of net sales of certain products. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. As of September 30, 2018 , the Company had an accumulated deficit of approximately $890.6 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 10), public offerings of common stock in February 2014, October 2014 and April 2018, 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. Since 2014, the Company has also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and in May 2017, the Company began to recognize revenue generated from net sales of Emflaza for the treatment of DMD in the United States. The Company expects that the cash flows from the sales of its products, together with the Company's cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

Summary of significant accounti

Summary of significant accounting policies	9 Months Ended
	Sep. 30, 2018
Accounting Policies [Abstract]
Summary of significant accounting policies	Summary of significant accounting policies The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2017 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 6, 2018 (the " 2017 Form 10-K"). Additional significant accounting policies adopted during the nine month period ended September 30, 2018 are discussed in further detail below. Basis of presentation The accompanying financial information as of September 30, 2018 and for the three and nine months ended September 30, 2018 and 2017 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States (GAAP) have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2017 and notes thereto included in the 2017 Form 10-K. In the opinion of management, the unaudited financial information as of September 30, 2018 and for the three and nine months ended September 30, 2018 and 2017 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three and nine month periods ended September 30, 2018 are not necessarily indicative of the results to be expected for the year ended December 31, 2018 or for any other interim period or for any other future year. Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes, allowance for doubtful accounts, inventory, acquired intangible assets, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. Inventory and cost of product sales 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: September 30, 2018 December 31, 2017 Raw materials $ 399 $ 452 Work in progress 5,997 3,912 Finished goods 7,264 6,390 Total inventory $ 13,660 $ 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 recorded a $1.6 million inventory write down for the three month period ended September 30, 2018 primarily related to inventory labeling changes. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2018 , these amounts were immaterial. 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. Revenue recognition In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products (Topic 605) and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to 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. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach, a practical expedient permitted under Topic 606, and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million , which was recorded on January 1, 2018 to the opening balance of accumulated deficit, related to the product sales of Emflaza. The ASC 606 transition adjustment recorded for Emflaza resulted in sales being recognized earlier than under Topic 605, as the deferred revenue recognition model (sell-through) is not applicable under Topic 606. The one-time adjustment consisted of $3.9 million in deferred revenue offset by $0.6 million of variable consideration. The information presented for the periods prior to January 1, 2018 has not been adjusted and is reported under Topic 605. Periods prior to January 1, 2018 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 Prior to the second quarter of 2017, the Company’s net product sales consisted of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition—Products. The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and 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. In May 2017, the Company began the commercialization of Emflaza in the U.S. The Company recorded product revenue related to the sales of Emflaza in the U.S. 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, the Company determined that it was not able to reliably make certain estimates, including returns, necessary to recognize product revenue upon shipment to distributors. As a result, the Company recorded net product revenue for Emflaza using a deferred revenue recognition model (sell-through). Under the deferred revenue model, the Company does not recognize revenue until Emflaza is shipped to the specialty pharmacy. 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 ASC 605-28, Revenue Recognition—Milestone Method. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from 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. Periods commencing January 1, 2018 The Company's net product revenue consists of sales of Translarna in territories outside of the U.S. and sales of Emflaza in the U.S., both for the treatment of DMD. Net product revenue The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide Translarna or Emflaza based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of either Translarna or Emflaza, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to either product sales of Translarna or Emflaza. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month. The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. Historically, returns of Translarna and Emflaza are immaterial to the financial statements. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained. In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. Upon adoption of ASC Topic 606 on January 1, 2018, the Company elected the following practical expedients: • Portfolio Approach - the Company applied the Portfolio Approach to contract reviews within its identified revenue streams that have similar characteristics and the Company believes this approach would not differ materially than if applying ASC Topic 606 to each individual contract. • Significant Financing Component - the Company expects the period between when it transfers a promised good to a customer and when the customer pays for the good or service to be one year or less. • Immaterial Performance Obligations - the Company disregards promises deemed to be immaterial in the context of the contract. • Shipping and Handling Activities - the Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense. Collaboration 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. At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations. For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance. For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company's control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. 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 $0.6 million as of September 30, 2018 and $0.8 million as of December 31, 2017 . Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in-process research and development (IPR&D). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D acquired in a business combination. The Company utilizes the "income method”, and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. IPR&D intangible assets that are determined to have had a drop in their fair value are adjusted downward and an impairment is recognized in the statement of operations. These assets are tested at least annually or sooner when a triggering event occurs that could indicate a potential impairment. Goodwill Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. Income Taxes 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. 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 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 period ended September 30, 2018 . 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 does 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 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. The Company recorded a deferred tax liability in conjunction with the Merger, further discussed in Note 3, of $ 115.2 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful. Recently issued accounting standards In February 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update (“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, as well as the impact on internal control over financial reporting. 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 January 2017, the FASB issued ASU 2017-04, "Simplifying the Test for Goodwill Impairment". This standard simplifies the accounting for goodwill impairment by requiring impairment charges to be based on the first step in today's two-step impairment test under ASC 350. Therefore, entities will record an impairment charge based on the excess of a reporting unit's carrying amount over its fair value. The guidance is effective for annual and interim impairment tests performed in periods beginning after December 15, 2019 for public business entities that meet the definition of an SEC filer, December 15, 2020 for public business entities that are not SEC filers, and December 15, 2021 for all other entities. Early adoption is permitted for all entities for annual and interim goodwill impairment testing dates on or after January 1, 2017. The guidance should be applied on a prospective basis. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2017-04 will have on its consolidated financial statements and accompanying notes. In February 2018, the FASB issued ASU 2018-02, "Income Statement — Reporting Comprehensive Income (Topic 220): Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income". This standard permits the reclassification of tax effects stranded in other comprehensive income as a result of tax reform to retained earnings related to the change in federal tax rate in addition to other stranded effects that relate to the Tax Cuts and Job Act ("the Act") but do not directly relate to the change in the federal rate. ASU 2018-02 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-02 will have on its consolidated financial statements and accompanying notes. In June 2018, the FASB issued ASU 2018-07, "Compensation — Stock Compensation (Topic 718), Improvements to Nonemployee Share-Based Payment Accounting". This standard expands the scope of ASC 718 to include share-based payments granted to nonemployees in exchange for goods or services used or consumed in the entity’s own operations and supersedes the guidance in ASC 505-50. The ASU retains the existing cost attribution guidance, which requires entities to recognize compensation cost for nonemployee awards in the same period and in the same manner they would if they paid cash for the goods or services, but it moves the guidance to ASC 718. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-07 will have on its consolidated financial statements and accompanying notes. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820), Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". This standard eliminates certain disclosure requirements for fair value measurements for all entities, requires public entities to disclose certain new information and modifies some disclosure requirements. The new guidance is effective for all entities for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years. An entity is permitted to early adopt either the entire standard or only the provisions that eliminate or modify requirements. Entities can elect to early adopt in interim periods, including periods for which they have not yet issued financial statements or made their financial statements available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes. In August 2018, the FASB issued ASU 2018-15,"Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract". ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements In May 2014, the FASB issued ASU No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to 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. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million , which was recorded on January 1, 2018 to deferred revenue and accumulated deficit, related to the product sales of Emflaza. The information presented for the periods prior to January 1, 2018 has not been restated and is reported under ASC Topic 605. In January 2016, the FASB issued ASU No. 2016-01, “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. The Company adopted ASU 2016-01 during the three months ended March 31, 2018. In March 2018, the FASB issued ASU 2018-04, "Investments - Debt Securities (Topic 320) and Regulated Operations (Topic 980): Amendments to SEC Paragraphs Pursuant to the SEC Staff Accounting Bulletin ("SAB") No. 117 and SEC Release No. 33-9273 (SEC Update)". This standard supersedes SEC paragraphs in ASC 320, Investments- Debt Securities, as a result of the issuance of SAB 117 and also updates the Codification for a 2011 SEC release and is effective when a registrant adopts ASU 2016-01, which in the case of the Company was during the three months ended March 31, 2018. The adoption of these standards did not have a material impact on the Company’s financial position or results of operations for the period ended and as of September 30, 2018 . In August 2016, the FASB issued ASU No. 2016-15, “Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments”.

Business Combination

Business Combination	9 Months Ended
	Sep. 30, 2018
Business Combinations [Abstract]
Business Combination	Business combination On August 23, 2018, the Company completed its acquisition of Agilis pursuant to the Merger Agreement. Agilis was a privately-held biotechnology company advancing an innovative gene therapy platform for rare monogenic diseases that affect the central nervous system. Upon completion of the Merger, the Company acquired Agilis's lead product candidate, PTC-AADC, for the treatment of AADC deficiency, as well as three other gene therapies that were part of the Agilis platform. Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of $49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. The fair value of the stock on the acquisition date was determined to be $155.9 million . Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million , (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million , (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million , and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2 - 6% . The fair value of the contingent consideration payments at the acquisition date was estimated to be $218.7 million and was determined by applying a probability adjusted, discounted cash flow approach based on development timelines from the acquired product candidates and estimated future sales. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments mentioned above no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payments at the closing date was estimated to be $38.2 million . Refer to Footnote 4 for further fair value considerations. The Company evaluated the acquisition of Agilis under ASU No. 2017-01, Business Combinations: Clarifying the Definition of a Business . Because the business contained both inputs and processes necessary to manage products and provide economic benefits directly to its owners and substantially all the value of the acquisition did not relate to a similar group of assets, it was determined that the acquisition represents a business combination. Therefore, the transaction has been accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the total purchase price of the acquisition is allocated to the net tangible and identifiable intangible assets acquired and liabilities assumed based on their fair values as of the date of acquisition. The fair value of consideration totaled approximately $462.0 million summarized as follows: As of August 23, 2018 Cash consideration $ 49,221 Fair value of PTC common stock issued 155,860 Estimated fair value of deferred consideration payable 38,200 Estimated fair value of contingent consideration payable 218,700 Total consideration $ 461,981 The Company recorded the assets acquired and liabilities assumed as of the date of acquisition based on the information available at that time. As the Company finalizes the fair values of the assets acquired and liabilities assumed, purchase price adjustments may be recorded during the measurement period and such adjustments could be material. The Company will reflect measurement period adjustments, if any, in the period in which the adjustments are recognized. No adjustments have been made as of the acquisition date of August 23, 2018 through the period ended September 30, 2018. The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of August 23, 2018, and through the period ended September 30, 2018: Preliminary Cash and cash equivalents $ 328 Prepaid expenses and other current assets 181 Fixed assets 153 Other assets 38 Intangible assets - in process research and development (“IPRD”) 480,000 Accounts payable and accrued expenses (3,828 ) Deferred tax liability (115,200 ) Fair value of net assets acquired $ 361,672 Goodwill 100,309 Total purchase price $ 461,981 The Company incurred approximately $1.5 million in acquisition related expenses as of September 30, 2018 , which were included in selling, general and administrative expenses in the consolidated statement of operations. The results of Agilis’s operations have been included in the consolidated statements of operations beginning on the acquisition date of August 23, 2018. The fair value of the IPR&D will be capitalized as of the acquisition date and subsequently accounted for as indefinite-lived intangible assets until disposition of the assets or completion or abandonment of the associated research and development efforts. Accordingly, during the development period after the completion of the acquisition, these assets will not be amortized into earnings; rather, these assets will be subject to periodic impairment testing. Upon successful completion of the development efforts, the useful lives of the IPR&D assets will be determined and the assets will be considered definite-lived intangible assets and amortized over their expected useful lives. The goodwill recorded is the excess of the purchase price of the net assets acquired net of any deferred tax adjustments. The Company currently has a deferred tax liability for the indefinite lived IPR&D intangible assets, which have no tax basis and, therefore, will not result in a future tax deduction. The goodwill is not deductible for income tax purposes. The net loss of Agilis included in the consolidated statement of operations for the period August 23, 2018 through September 30, 2018 was $1.9 million . Pro-Forma Financial Information Associated with the Agilis Acquisition (Unaudited) The following table summarizes certain supplemental pro forma financial information for the three and nine-month periods ended September 30, 2018 and 2017 as if the Merger had occurred as of January 1, 2017. The unaudited pro-forma financial information for the three month and nine month periods ended September 30, 2018 reflects adjustments of $0.8 million and $1.5 million , respectively, related to acquisition fees that are non-recurring in nature. There were no adjustments related to the three and nine month periods ended September 30, 2017. Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Revenues $ 53,591 $ 41,853 $ 178,396 $ 116,362 Net loss attributable to common stockholders (52,458 ) (41,606 ) (89,976 ) (90,795 ) Bridge Loan In connection with the Merger Agreement, on July 19, 2018, the Company also entered into a Bridge Loan and Security Agreement, or the Bridge Loan Agreement, by and among the Company, Agilis and certain of Agilis’s domestic subsidiaries, as guarantors. Under the Bridge Loan Agreement, the Company made a term loan advance to Agilis on July 23, 2018 in an original principal amount of $10.0 million . In connection with the closing of the Merger, the original principal amount of $10.0 million plus all accrued and unpaid interest thereon was credited against the cash portion of the upfront consideration paid by the Company pursuant to the terms of the Merger Agreement in satisfaction of Agilis’s outstanding payment obligations under the Bridge Loan Agreement, and the Company will have no further obligation to extend any further loan amounts under the Bridge Loan Agreement.

Fair value of financial instrum

Fair value of financial instruments and marketable securities	9 Months Ended
	Sep. 30, 2018
Fair Value Disclosures [Abstract]
Fair value of financial instruments and marketable securities	Fair value of financial instruments and marketable securities The Company follows the fair value measurement rules, which provide guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority). · Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date. · Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs). · Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available. Cash equivalents and investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables, accounts payable and accrued expenses, and debt approximates fair value due to the short-term nature of those instruments. Fair value of certain marketable securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices. The Company reviews its investments on a periodic basis for other-than-temporary impairments. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may have a significant adverse effect on the fair value of the investment. The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2018 and December 31, 2017 : September 30, 2018 Total Quoted prices Significant Significant Marketable securities $ 42,491 $ — $ 42,491 $ — Warrant liability $ 4 $ — $ — $ 4 Stock appreciation rights liability $ 3,463 $ — $ — $ 3,463 Deferred consideration payable $ 38,200 $ — $ 38,200 $ — Contingent consideration payable $ 218,700 $ — $ — $ 218,700 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 Deferred consideration payable $ — $ — $ — $ — Contingent consideration payable $ — $ — $ — $ — No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the periods ended September 30, 2018 and December 31, 2017 . The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2018 and December 31, 2017 : September 30, 2018 Amortized Gross Unrealized Fair Gains Losses Commercial paper $ 18,441 $ — $ (6 ) $ 18,435 Corporate debt securities 24,078 2 (24 ) 24,056 $ 42,519 $ 2 $ (30 ) $ 42,491 December 31, 2017 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 13,775 $ 52 $ — $ 13,827 Corporate debt securities 65,657 — (30 ) 65,627 $ 79,432 $ 52 $ (30 ) $ 79,454 At September 30, 2018 and 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. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. As of September 30, 2018 and December 31, 2017 , the Company did not have any realized gains/losses from the sale of marketable securities. 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 September 30, 2018 are as follows: September 30, 2018 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 Commercial paper $ (6 ) $ 18,435 $ — $ — $ (6 ) $ 18,435 Corporate debt securities (24 ) 18,067 — — (24 ) 18,067 $ (30 ) $ 36,502 $ — $ — $ (30 ) $ 36,502 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 Marketable securities on the balance sheet at September 30, 2018 and December 31, 2017 mature as follows: September 30, 2018 Less Than 12 Months More Than 12 Months Commercial paper $ 18,435 $ — Corporate debt securities 24,056 — Total Marketable securities $ 42,491 $ — December 31, 2017 Less Than 12 Months More Than 12 Months Commercial paper $ 13,827 $ — Corporate debt securities 55,550 10,077 Total Marketable securities $ 69,377 $ 10,077 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 10. 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 September 30, 2018 and December 31, 2017 was $172.9 million and $115.7 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 10) 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. Deferred consideration payable Pursuant to the Merger Agreement with Agilis, the Company is required to pay $40.0 million of development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payments at the acquisition date was estimated to be $38.2 million based on calculating the present value utilizing discount rates for BBB rated bonds maturing in the years of expected payments. Level 3 valuation The warrant liability is classified in Other long-term liabilities on the Company’s consolidated balance sheets. The warrant liability is marked-to-market each reporting period with the change in fair value recorded as a gain or loss within Other expense, net, on the Company’s consolidated statements of operations until the warrants are exercised, expire or other facts and circumstances lead the warrant liability to be reclassified as an equity instrument. The fair value of the warrant liability is determined at each reporting period by utilizing the Black-Scholes option pricing model. The stock appreciation rights (SARs) liability is classified in Other 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 contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss in the consolidated statements of operations. The Company estimates the fair value of its contingent consideration using a probability weighted discounted cash flow valuation approach based on development timelines and the estimated future sales expected from the Agilis platform. The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the warrant liability, the SARs liability, and the contingent consideration payable for the period ended September 30, 2018 : Level 3 liabilities Warrants SARs Contingent consideration payable Beginning balance as of December 31, 2017 $ 1 $ 1,665 $ — Additions — — 218,700 Change in fair value 3 3,789 — Payments — (1,991 ) $ — Ending balance as of September 30, 2018 $ 4 $ 3,463 $ 218,700 Fair value of the warrant liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the stock fair value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of September 30, 2018 include (i) volatility ( 51% - 54% ), (ii) risk free interest rate ( 2.59% - 2.59% ), (iii) strike price ( $128.00 - $2,520.00 ), (iv) fair value of common stock ( $47.00 ), and (v) expected life ( 0.8 — 1.0 years). 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). 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 September 30, 2018 include (i) volatility ( 45% — 54% ), (ii) risk free interest rate ( 2.19% — 2.70% ), (iii) strike price ( $6.76 - $30.86 ), (iv) fair value of common stock ( $47.00 ), and (v) expected life ( 0.3 — 1.3 years). 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). Fair value of the contingent consideration liability is estimated using a probability weighted discounted cash flow approach. Some of the more significant assumptions made in the valuation include (i) the estimated revenue forecasts, (ii) probabilities of success, and (iii) discount periods and rate. The probability of achievement of regulatory and sales milestones ranged from 25% to 89% . The achievement of certain development milestones ranged from zero to an aggregate maximum amount of $20.0 million , the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher ranged from zero up to an aggregate maximum amount of $535.0 million , the achievement of certain net sales milestones ranged from zero up to an aggregate maximum amount of $150.0 million , and a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2 - 6% , in periods which sales occur. The $20.0 million development milestones mentioned above do not include $40.0 million in development milestone payments that the Company is required to pay no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Such $40 million development milestones have been recorded as deferred consideration payable on the consolidated balance sheets at its estimated fair value, which was estimated to be $38.2 million . The contingent consideration is classified as a Level 3 liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approach, including but not limited to, assumptions involving probability adjusted sales estimates for the Agilis platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

Other comprehensive income (los

Other comprehensive income (loss) and accumulated other comprehensive items	9 Months Ended
	Sep. 30, 2018
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Other comprehensive income (loss) and accumulated other comprehensive items	Other comprehensive income (loss) and accumulated other comprehensive items Other comprehensive income (loss) includes changes in equity that are excluded from net income (loss), such as unrealized gains and losses on marketable securities. The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine months ended September 30, 2018 : Unrealized Foreign Total Balance at June 30, 2018 $ (61 ) $ 1,916 $ 1,855 Other comprehensive income (loss) before reclassifications 33 (260 ) (227 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 33 (260 ) (227 ) Balance at September 30, 2018 $ (28 ) $ 1,656 $ 1,628 Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2017 $ 22 $ 3,947 $ 3,969 Other comprehensive loss before reclassifications (50 ) (2,291 ) (2,341 ) Amounts reclassified from other comprehensive items — — — Other comprehensive loss (50 ) (2,291 ) (2,341 ) Balance at September 30, 2018 $ (28 ) $ 1,656 $ 1,628

Accounts payable and accrued ex

Accounts payable and accrued expenses	9 Months Ended
	Sep. 30, 2018
Payables and Accruals [Abstract]
Accounts payable and accrued expenses	Accounts payable and accrued expenses Accounts payable and accrued expenses at September 30, 2018 and December 31, 2017 consist of the following: September 30, December 31, Employee compensation, benefits, and related accruals $ 18,003 $ 17,711 Consulting and contracted research 8,111 5,137 Professional fees 3,541 2,116 Sales allowance and other costs 27,027 22,257 Sales rebates and royalties 26,818 11,657 Accounts payable 6,538 15,282 Other 12,750 2,286 $ 102,788 $ 76,446

Capitalization

Capitalization	9 Months Ended
	Sep. 30, 2018
Stockholders' Equity Note [Abstract]
Capitalization	Capitalization In April 2018, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 4,600,000 shares of common stock under the registration statement at a public offering price of $27.04 per share, including 600,000 shares issued upon exercise by the underwriters of their option to purchase additional shares. The Company received net proceeds of approximately $117.9 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company. Warrants All of the Company’s outstanding warrants were classified as liabilities as of September 30, 2018 and December 31, 2017 because they contained non-standard antidilution provisions. The following is a summary of the Company’s outstanding warrants as of September 30, 2018 and December 31, 2017 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019

Net loss per share

Net loss per share	9 Months Ended
	Sep. 30, 2018
Earnings Per Share [Abstract]
Net loss per share	Net loss per share Basic earnings per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss by the weighted-average number of common shares plus the effect of any dilutive potential common shares outstanding during the period. The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Numerator Net loss $ (50,969 ) $ (33,738 ) $ (79,751 ) $ (80,270 ) Denominator Denominator for basic and diluted net loss per share 48,096,521 41,296,740 45,310,690 38,433,749 Net loss per share: Basic and diluted $ (1.06 ) * $ (0.82 ) * $ (1.76 ) * $ (2.09 ) * *In the three and nine months ended September 30, 2018 and 2017 , 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 September 30, 2018 2017 Stock Options 9,545,522 6,612,765 Unvested restricted stock awards and units 580,347 402,853 Total 10,125,869 7,015,618

Stock award plan

Stock award plan	9 Months Ended
	Sep. 30, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock award plan	Stock award plan On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Board approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan. In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases. In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan. In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of September 30, 2018 , awards for 665,194 shares of common stock are available for issuance. From January 1, 2018 through September 30, 2018 , the Company issued a total of 2,914,139 stock options to various employees. Of those, 1,115,650 were inducement grants for non-statutory stock options. The inducement grant awards were made pursuant to the Nasdaq inducement grant exception as a material component of the Company's new hires’ employment compensation and not under the 2013 Long Term Incentive Plan. A summary of stock option activity is as follows: Number of Weighted- Weighted- Aggregate (in Outstanding at December 31, 2017 6,448,642 $ 29.00 Granted 2,914,139 $ 25.84 Exercised 512,145 $ 17.03 Forfeited/Cancelled (329,404 ) $ 34.20 Outstanding at September 30, 2018 9,545,522 $ 28.44 7.45 years $ 172,859 Vested or Expected to vest at September 30, 2018 3,914,413 $ 24.38 8.93 years $ 89,547 Exercisable at September 30, 2018 4,316,071 $ 32.33 5.99 years $ 77,003 The fair value of grants made in the nine months ended September 30, 2018 was contemporaneously estimated on the date of grant using the following assumptions: Nine months ended Risk-free interest rate 2.25%—3.03% Expected volatility 64%—90% Expected term 5.04 – 10.00 years The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine -month period ended September 30, 2018 was $17.04 per share. The Company uses the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. The expected volatility of share options was estimated based on a historical volatility analysis of peers that were similar to the Company with respect to industry, stage of life cycle, size, and financial leverage. The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option. Restricted Stock Awards —Restricted stock awards are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock awards, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period. Restricted Stock Units —Restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock units, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period. The following table summarizes information on the Company’s restricted stock awards and units: Restricted Stock Awards and Units Number of Weighted January 1, 2018 393,011 $ 15.64 Granted 354,691 $ 19.09 Vested (113,795 ) $ 16.36 Forfeited (53,560 ) $ 17.24 Unvested at September 30, 2018 580,347 $ 17.60 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 ended September 30, 2018 , a total of 177,329 SARs vested. For the period ended September 30, 2018 , the Company recorded $3.7 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 ended September 30, 2018 , the Company recorded $0.7 million in compensation expense related to the ESPP. The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Research and development $ 4,431 $ 3,624 $ 12,109 $ 11,986 Selling, general and administrative 4,511 3,544 12,664 12,096 Total $ 8,942 $ 7,168 $ 24,773 $ 24,082 As of September 30, 2018 , there was approximately $67.5 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the 2009 Equity and Long Term Incentive Plan, the 2013 Long Term Incentive Plan and equity awards made pursuant to the Nasdaq inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 3.00 years.

Debt

Debt	9 Months Ended
	Sep. 30, 2018
Debt Disclosure [Abstract]
Debt	Debt 2017 Credit Facility In May 2017, the Company entered into a credit and security agreement (the "Credit Facility") with MidCap Financial Trust, a Delaware statutory trust (“MidCap”), as administrative agent and MidCap and certain other financial institutions as lenders thereunder (the “Credit Agreement”) that provides for a senior secured term loan facility of $60.0 million , of which $40.0 million was drawn by the Company on May 5, 2017. The remaining $20.0 million under the senior secured term loan facility will become available to the Company upon its demonstration (on or prior to December 31, 2018) of net product revenue equaling or exceeding $120.0 million for the trailing 12 month period. The Company capitalized approximately $0.4 million of debt issuance costs, which were netted against the carrying value of the Credit Facility and will be amortized over the term of the Credit Facility. Borrowings under the Credit Agreement bear interest at a rate per annum equal to LIBOR (with a LIBOR floor rate of 1.00% ) plus 6.15% . The Company is obligated to make interest only payments (payable monthly in arrears) through April 30, 2019. Commencing on May 1, 2019 and continuing for the remaining twenty-four months of the facility, the Company will be required to make monthly interest payments and monthly principal payments. The principal payments are to be made based on straight-line amortization of the principal over the twenty-four month period. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier. The Credit Facility is subject to certain financial covenants. As of September 30, 2018 , the Company was in compliance with all required covenants. Convertible Notes In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.0% convertible senior notes due 2022 (the "Convertible Notes"). The Convertible Notes bear cash interest at a rate of 3.0% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The Convertible Notes will mature on August 15, 2022, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $145.4 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company. The Convertible Notes are governed by an indenture (the Convertible Notes Indenture) with U.S Bank National Association as trustee (the Convertible Notes Trustee). Holders may convert their Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding February 15, 2022 only under the following circumstances: · during any calendar quarter commencing on or after September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day; · during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the Convertible Notes Indenture) per $1,000 principal amount of Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day; · during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or · upon the occurrence of specified corporate events. On or after February 15, 2022, until the close of business on the business day immediately preceding the maturity date, holders may convert their Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay cash up to the aggregate principal amount of the Convertible Notes to be converted and deliver shares of its common stock in respect of the remainder, if any, of its conversion obligation in excess of the aggregate principal amount of Convertible Notes being converted. The conversion rate for the Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock. The Company was not permitted to redeem the Convertible Notes prior to August 20, 2018. As of August 20, 2018, the Company may redeem for cash all or any portion of the Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the Convertible Notes, which means that the Company is not required to redeem or retire the Convertible Notes periodically. If the Company undergoes a “fundamental change” (as defined in the Indenture governing the Convertible Notes Indenture), subject to certain conditions, holders of the Convertible Notes may require the Company to repurchase for cash all or part of their Convertible Notes at a repurchase price equal to 100% of the principal amount of the Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The Convertible Notes Indenture contains customary events of default with respect to the Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the Convertible Notes when due and payable) occurring and continuing, the Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the Convertible Notes Trustee at the request of such holders (subject to the provisions of the Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately. The Company accounts for the Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the Convertible Notes, the Company separated the Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven -year term of the Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the Convertible Notes is $57.5 million and was recorded in additional paid-in capital. In accounting for the transaction costs related to the issuance of the Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven -year term of the Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the Notes. The Convertible Notes consist of the following: Liability component September 30, 2018 December 31, 2017 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,844 ) (2,121 ) Less: Debt discount, net(1) (37,009 ) (42,572 ) Net carrying amount $ 111,147 $ 105,307 (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 $172.9 million as of September 30, 2018 . The Company estimates the fair value of its Convertible Notes utilizing market quotations for debt that have quoted prices in active markets. As of September 30, 2018 , the remaining contractual life of the Convertible Notes is approximately 3.9 years. The following table sets forth total interest expense recognized related to the Convertible Notes: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Contractual interest expense $ 1,134 $ 1,134 $ 3,375 $ 3,375 Amortization of debt issuance costs 95 86 277 249 Amortization of debt discount 1,919 1,725 5,563 4,999 Total $ 3,148 $ 2,945 $ 9,215 $ 8,623 Effective interest rate of the liability component 11 % 11 % 11 % 11 %

Commitments and contingencies

Commitments and contingencies	9 Months Ended
	Sep. 30, 2018
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and contingencies Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company's 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’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement. The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single- digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon the Company's payment to the SMA Foundation of a specified amount. Pursuant to the Merger Agreement with Agilis, the Company is required to pay $40.0 million of development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The Company may also be obligated to pay additional development, regulatory approval, and net sales milestones and net sales royalties. Refer to Note 3 for further details. The Company also has a Collaboration and License Agreement with Akcea for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million . An additional $6.0 million is payable within 30 days after receipt of regulatory approval of Waylivra from the FDA or the EMA, whichever occurs earlier. In addition, Akcea is eligible to receive milestone payments, on a Product-by-Product basis, of $4.0 million upon receipt of regulatory approval for a product from ANVISA, the Brazilian Health Regulatory Authority, subject to a maximum aggregate amount of $8.0 million for all such products. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement. 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. Additionally, the Company has royalty payments associated with Translarna and Emflaza product net sales, payable quarterly or annually in accordance with the terms of the related agreements. In the period ended September 30, 2018, two lawsuits the Company was involved in were settled and dismissed (refer to Part II, Item 1. Legal Proceedings for further details on the dismissed lawsuits).

Revenue recognition

Revenue recognition	9 Months Ended
	Sep. 30, 2018
Revenue from Contract with Customer [Abstract]
Revenue recognition	Revenue recognition Net product sales The Company views its operations and manages its business in one operating segment. During the three and nine months ended September 30, 2018 , net product sales in the United States were $22.6 million and $62.2 million, respectively, consisting solely of Emflaza, and net product sales not in the United States were $30.4 million and $115.0 million, respectively, consisting solely of Translarna. The following table presents changes in the Company’s contract liabilities from December 31, 2017 to September 30, 2018 : Balance as of Additions Deductions ASC 606 Adjustment Balance as of Deferred Revenue $ 11,891 $ 4,706 $ — $ (3,937 ) $ 12,660 The Company did not have any contract assets for the three and nine months ended September 30, 2018 . During the three and nine months ended September 30, 2018 , the Company recognized revenue in the period from: Three Months Ended September 30, 2018 Nine Months Ended September 30, 2018 Amounts included in contract liabilities at the beginning of the period $ — $ — Performance obligations satisfied in previous period — — Performance obligations satisfied in current period 53,021 177,172 Total product revenue $ 53,021 $ 177,172 The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine months ended September 30, 2018 . Remaining performance obligations Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of September 30, 2018 , the aggregate amount of transaction price allocated to remaining performance obligations relating to Translarna net product revenue was $12.7 million . The Company expects to recognize revenue over the next one to three years as the specific timing for satisfying the performance obligations is contingent upon a number of factors, including customers’ needs and schedules. The impact of adoption using the modified retrospective method on the Company’s consolidated financial statements is as follows: i. Consolidated balance sheets Impact of changes in accounting policies As reported September 30, Adjustments As reported Balances without adoption of Topic 606 Assets Current assets: Cash and cash equivalents $ 206,913 $ — $ 206,913 Marketable securities 42,491 — 42,491 Trade receivables, net 42,197 — 42,197 Inventory 13,660 (84 ) 13,576 Prepaid expenses and other current assets 8,020 — 8,020 Total current assets 313,281 (84 ) 313,197 Fixed assets, net 8,805 — 8,805 Intangible assets, net 604,612 — 604,612 Goodwill 100,309 — 100,309 Deposits and other assets 1,620 — 1,620 Total assets $ 1,028,627 $ (84 ) $ 1,028,543 Liabilities and stockholders’ equity Current liabilities: Accounts payable and accrued expenses $ 102,788 $ (794 ) $ 101,994 Current portion of long-term debt 6,667 — 6,667 Deferred revenue 2,004 5,120 7,124 Other current liabilities 3,463 — 3,463 Total current liabilities 114,922 4,326 119,248 Deferred revenue - long-term 11,156 — 11,156 Long-term debt 144,258 — 144,258 Contingent consideration payable 218,700 — 218,700 Deferred consideration payable 38,200 — 38,200 Deferred tax liability 115,200 — 115,200 Other long-term liabilities 101 — 101 Total liabilities 642,537 4,326 646,863 Stockholders’ equity: Common stock 51 — 51 Additional paid-in capital 1,275,004 — 1,275,004 Accumulated other comprehensive income 1,628 — 1,628 Accumulated deficit (890,593 ) (4,410 ) (895,003 ) Total stockholders’ equity 386,090 (4,410 ) 381,680 Total liabilities and stockholders’ equity $ 1,028,627 $ (84 ) $ 1,028,543 ii. Consolidated statements of operations Impact of changes in accounting policies Three Months Ended As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 53,021 $ (834 ) $ 52,187 Collaboration and grant revenue 570 — 570 Total revenues 53,591 (834 ) 52,757 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 3,292 (17 ) 3,275 Amortization of acquired intangible asset 5,793 — 5,793 Research and development 54,368 — 54,368 Selling, general and administrative 38,368 — 38,368 Total operating expenses 101,821 (17 ) 101,804 Loss from operations (48,230 ) (817 ) (49,047 ) Interest expense, net (3,118 ) — (3,118 ) Other expense, net 734 — 734 Loss before income tax expense (50,614 ) (817 ) (51,431 ) Income tax expense (355 ) — (355 ) Net loss attributable to common stockholders $ (50,969 ) $ (817 ) $ (51,786 ) Impact of changes in accounting policies Year to Date As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 177,172 $ (1,059 ) $ 176,113 Collaboration and grant revenue 1,224 — 1,224 Total revenues 178,396 (1,059 ) 177,337 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 8,909 (84 ) 8,825 Amortization of acquired intangible asset 16,815 — 16,815 Research and development 118,337 — 118,337 Selling, general and administrative 104,882 — 104,882 Total operating expenses 248,943 (84 ) 248,859 Loss from operations (70,547 ) (975 ) (71,522 ) Interest expense, net (9,306 ) — (9,306 ) Other income, net 1,066 — 1,066 Loss before income tax expense (78,787 ) (975 ) (79,762 ) Income tax expense (964 ) — (964 ) Net loss attributable to common stockholders $ (79,751 ) $ (975 ) $ (80,726 ) iii. Consolidated statements of comprehensive loss Impact of changes in accounting policies Three Months Ended As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (50,969 ) $ (817 ) $ (51,786 ) Other comprehensive loss: Unrealized gain on marketable securities, net of tax 33 — 33 Foreign currency translation loss (260 ) — (260 ) Comprehensive loss $ (51,196 ) $ (817 ) $ (52,013 ) Impact of changes in accounting policies Year to Date As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (79,751 ) $ (975 ) $ (80,726 ) Other comprehensive loss: Unrealized loss on marketable securities, net of tax (50 ) — (50 ) Foreign currency translation loss (2,291 ) — (2,291 ) Comprehensive loss $ (82,092 ) $ (975 ) $ (83,067 ) iv. Consolidated statements of cash flows Impact of changes in accounting policies As reported for the period ended September 30, Adjustments Balances without adoption of Topic 606 Cash flows from operating activities Net loss $ (79,751 ) $ (975 ) $ (80,726 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 19,316 — 19,316 Change in valuation of warrant liability 3 — 3 Non-cash interest expense 5,563 — 5,563 Loss on disposal of asset 2 — 2 Amortization of premiums and accretion of discounts on investments, net (354 ) — (354 ) Amortization of debt issuance costs 390 — 390 Share-based compensation expense 24,773 — 24,773 Unrealized foreign currency transaction gain (977 ) — (977 ) Changes in operating assets and liabilities: 0 Inventory, net (3,252 ) (84 ) (3,336 ) Prepaid expenses and other current assets (1,301 ) — (1,301 ) Trade receivables, net (2,681 ) — (2,681 ) Deposits and other assets (385 ) — (385 ) Accounts payable and accrued expenses 18,606 (794 ) 17,812 Other liabilities 1,617 — 1,617 Deferred revenue 5,933 1,853 7,786 Net cash used in operating activities (12,498 ) — (12,498 ) Cash flows from investing activities Purchases of fixed assets (2,489 ) — (2,489 ) Purchases of marketable securities (28,656 ) — (28,656 ) Sale and redemption of marketable securities 65,923 — 65,923 Acquisition of product rights (3,903 ) — (3,903 ) Business acquisition, net of cash acquired (48,892 ) — (48,892 ) Net cash (used in) / provided by investing activities (18,017 ) — (18,017 ) Cash flows from financing activities Proceeds from exercise of options 8,631 — 8,631 Net proceeds from public offerings 117,915 — 117,915 Proceeds from shares issued under employee stock purchase plan 1,299 — 1,299 Net cash provided by financing activities 127,845 — 127,845 Effect of exchange rate changes on cash (2,209 ) — (2,209 ) Net increase in cash and cash equivalents 95,121 — 95,121 Cash and cash equivalents, beginning of period 111,792 — 111,792 Cash and cash equivalents, end of period $ 206,913 $ — $ 206,913 Collaboration revenue 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 identified two material promises in the collaboration agreement, the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises were bundled into one distinct performance obligation. 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. As of adoption of ASC Topic 606 on January 1, 2018, all performance obligations had been satisfied and the balance of the remaining deferred upfront payment was fully recognized. 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. In August 2013, a lead development compound, RG7800, was selected to move into IND-enabling studies, which triggered a milestone payment to the Company from Roche of $10 million . Under ASC Topic 605, 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, 2013. 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. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its spinal muscular atrophy collaboration with Roche and the SMA Foundation which triggered a $10 million payment from Roche. Under ASC Topic 605, 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 SMA Foundation, 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. Under ASC Topic 605, 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. The remaining potential research and development event milestones that can be received as of September 30, 2018 is $87.5 million . For the nine months ended September 30, 2018 and 2017 , the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.2 million and $0.2 million , respectively. 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. Generally, the two material promises in these arrangements are the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises are bundled into one distinct performance obligation. As of adoption of ASC Topic 606 on January 1, 2018, all deferred revenue related to these arrangements had been recognized. For the nine months ended September 30, 2018 and 2017 , the Company did not recognize any revenue related to discovery agreements. 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 will recognize revenue when it is probable the milestones will be achieved (see Note 2). For the nine months ended September 30, 2018 and 2017 , the Company did not recognize any revenue related to early stage collaborations.

Intangible assets and goodwill

Intangible assets and goodwill	9 Months Ended
	Sep. 30, 2018
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible assets and goodwill	Intangible assets and goodwill Definite-lived intangibles On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to the 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. In accordance with ASU No. 2017-01, the Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and as such accounted for the transaction as an asset acquisition under ASC 805-50 and recorded an intangible asset of $148.4 million . 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. 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 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. For the three and nine month periods ended September 30, 2018 , the Company recorded $4.5 million and $8.4 million of milestone payments, respectively, which were added to the cost basis for the Emflaza rights intangible asset and will be amortized prospectively on a straight-line basis over the remaining life of the asset. As of September 30, 2018 , the $4.5 million milestone payment was recorded on the balance sheet within accrued expenses as a contingent payment payable to Marathon. For the three and nine months ended September 30, 2018 , the Company recognized amortization expense of $5.8 million and $16.8 million , respectively, related to the Emflaza rights intangible asset. The estimated future amortization of the Emflaza rights intangible asset is expected to be as follows: As of September 30, 2018 2018(1) $ 5,794 2019 23,172 2020 23,172 2021 23,172 2022 and thereafter 49,302 Total $ 124,612 (1) For the three months ended December 31, 2018 . Indefinite-lived intangibles In connection with the acquisition of Agilis (Note 3), the Company acquired rights to PTC-AADC, for the treatment of AADC deficiency. AADC deficiency is a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. The Agilis platform also includes a gene therapy asset targeting Friedreich ataxia, a rare and life-shortening neurodegenerative disease caused by a single defect in the FXN gene which causes reduced production of the frataxin protein. An investigational new drug ("IND") submission with the FDA for this program is expected in 2019. Additionally, the Agilis platform includes two other gene therapy programs targeting CNS disorders, including Angelman syndrome, a rare, genetic, neurological disorder characterized by severe developmental delays. In accordance with the acquisition method of accounting, the Company allocated the acquisition cost for the Merger to the underlying assets acquired and liabilities assumed, based upon the estimated fair values of those assets and liabilities at the date of acquisition. The Company classified the fair value of the acquired IPR&D as indefinite lived intangible assets until the successful completion or abandonment of the associated research and development efforts. The preliminary value allocated to the indefinite lived intangible assets was $480 million . Goodwill As a result of the Merger on August 23, 2018, the Company recorded $ 100.3 million of goodwill. There were no changes to the recorded value of goodwill for the three and nine month periods ended September 30, 2018 . Collaboration and Licensing Agreement On August 1, 2018, the Company entered into a Collaboration and License Agreement with Akcea for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million . An additional $6.0 million is payable within 30 days after receipt of regulatory approval of Waylivra from the United States Food and Drug Administration or the European Medicines Agency, whichever occurs earlier. The Company evaluated the agreement under the guidance in ASC 730 and concluded that the acquired rights to commercialize the products had no alternative future use as of the date of the Merger. Accordingly, the $12.0 million was charged to research and development expense in the consolidated statements of operations for the three and nine month periods ended September 30, 2018 . The Company plans to a file a request for marketing authorizations for Tegsedi with ANVISA in the first half of 2019. Waylivra is currently under regulatory review in the EU.

Subsequent events

Subsequent events	9 Months Ended
	Sep. 30, 2018
Subsequent Events [Abstract]
Subsequent events	Subsequent events The Company has evaluated all subsequent events and transactions through the filing date. There were no material events that impacted the unaudited consolidated financial statements or disclosures.

Summary of significant accoun_2

Summary of significant accounting policies (Policies)	9 Months Ended
	Sep. 30, 2018
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The accompanying financial information as of September 30, 2018 and for the three and nine months ended September 30, 2018 and 2017 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States (GAAP) have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2017 and notes thereto included in the 2017 Form 10-K. In the opinion of management, the unaudited financial information as of September 30, 2018 and for the three and nine months ended September 30, 2018 and 2017 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three and nine month periods ended September 30, 2018 are not necessarily indicative of the results to be expected for the year ended December 31, 2018 or for any other interim period or for any other future year.
Use of estimates	Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes, allowance for doubtful accounts, inventory, acquired intangible assets, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.
Inventory and cost of product sales	Inventory and cost of product sales 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: September 30, 2018 December 31, 2017 Raw materials $ 399 $ 452 Work in progress 5,997 3,912 Finished goods 7,264 6,390 Total inventory $ 13,660 $ 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 recorded a $1.6 million inventory write down for the three month period ended September 30, 2018 primarily related to inventory labeling changes. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2018 , these amounts were immaterial. 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.
Revenue recognition	Revenue recognition In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products (Topic 605) and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to 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. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach, a practical expedient permitted under Topic 606, and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million , which was recorded on January 1, 2018 to the opening balance of accumulated deficit, related to the product sales of Emflaza. The ASC 606 transition adjustment recorded for Emflaza resulted in sales being recognized earlier than under Topic 605, as the deferred revenue recognition model (sell-through) is not applicable under Topic 606. The one-time adjustment consisted of $3.9 million in deferred revenue offset by $0.6 million of variable consideration. The information presented for the periods prior to January 1, 2018 has not been adjusted and is reported under Topic 605. Periods prior to January 1, 2018 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 Prior to the second quarter of 2017, the Company’s net product sales consisted of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition—Products. The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and 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. In May 2017, the Company began the commercialization of Emflaza in the U.S. The Company recorded product revenue related to the sales of Emflaza in the U.S. 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, the Company determined that it was not able to reliably make certain estimates, including returns, necessary to recognize product revenue upon shipment to distributors. As a result, the Company recorded net product revenue for Emflaza using a deferred revenue recognition model (sell-through). Under the deferred revenue model, the Company does not recognize revenue until Emflaza is shipped to the specialty pharmacy. 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 ASC 605-28, Revenue Recognition—Milestone Method. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from 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. Periods commencing January 1, 2018 The Company's net product revenue consists of sales of Translarna in territories outside of the U.S. and sales of Emflaza in the U.S., both for the treatment of DMD. Net product revenue The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide Translarna or Emflaza based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of either Translarna or Emflaza, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to either product sales of Translarna or Emflaza. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month. The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. Historically, returns of Translarna and Emflaza are immaterial to the financial statements. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained. In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. Upon adoption of ASC Topic 606 on January 1, 2018, the Company elected the following practical expedients: • Portfolio Approach - the Company applied the Portfolio Approach to contract reviews within its identified revenue streams that have similar characteristics and the Company believes this approach would not differ materially than if applying ASC Topic 606 to each individual contract. • Significant Financing Component - the Company expects the period between when it transfers a promised good to a customer and when the customer pays for the good or service to be one year or less. • Immaterial Performance Obligations - the Company disregards promises deemed to be immaterial in the context of the contract. • Shipping and Handling Activities - the Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense. Collaboration 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. At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations. For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance. For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company's control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.
Allowance for doubtful accounts	Allowance for doubtful accounts The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends.
Indefinite-lived intangible assets	Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in-process research and development (IPR&D). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D acquired in a business combination. The Company utilizes the "income method”, and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. IPR&D intangible assets that are determined to have had a drop in their fair value are adjusted downward and an impairment is recognized in the statement of operations. These assets are tested at least annually or sooner when a triggering event occurs that could indicate a potential impairment.
Goodwill	Goodwill Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired.
Income Taxes	Income Taxes 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. 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 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 period ended September 30, 2018 . 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 does 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 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. The Company recorded a deferred tax liability in conjunction with the Merger, further discussed in Note 3, of $ 115.2 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful.
Recently issued accounting standards	Recently issued accounting standards In February 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update (“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, as well as the impact on internal control over financial reporting. 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 January 2017, the FASB issued ASU 2017-04, "Simplifying the Test for Goodwill Impairment". This standard simplifies the accounting for goodwill impairment by requiring impairment charges to be based on the first step in today's two-step impairment test under ASC 350. Therefore, entities will record an impairment charge based on the excess of a reporting unit's carrying amount over its fair value. The guidance is effective for annual and interim impairment tests performed in periods beginning after December 15, 2019 for public business entities that meet the definition of an SEC filer, December 15, 2020 for public business entities that are not SEC filers, and December 15, 2021 for all other entities. Early adoption is permitted for all entities for annual and interim goodwill impairment testing dates on or after January 1, 2017. The guidance should be applied on a prospective basis. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2017-04 will have on its consolidated financial statements and accompanying notes. In February 2018, the FASB issued ASU 2018-02, "Income Statement — Reporting Comprehensive Income (Topic 220): Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income". This standard permits the reclassification of tax effects stranded in other comprehensive income as a result of tax reform to retained earnings related to the change in federal tax rate in addition to other stranded effects that relate to the Tax Cuts and Job Act ("the Act") but do not directly relate to the change in the federal rate. ASU 2018-02 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-02 will have on its consolidated financial statements and accompanying notes. In June 2018, the FASB issued ASU 2018-07, "Compensation — Stock Compensation (Topic 718), Improvements to Nonemployee Share-Based Payment Accounting". This standard expands the scope of ASC 718 to include share-based payments granted to nonemployees in exchange for goods or services used or consumed in the entity’s own operations and supersedes the guidance in ASC 505-50. The ASU retains the existing cost attribution guidance, which requires entities to recognize compensation cost for nonemployee awards in the same period and in the same manner they would if they paid cash for the goods or services, but it moves the guidance to ASC 718. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-07 will have on its consolidated financial statements and accompanying notes. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820), Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". This standard eliminates certain disclosure requirements for fair value measurements for all entities, requires public entities to disclose certain new information and modifies some disclosure requirements. The new guidance is effective for all entities for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years. An entity is permitted to early adopt either the entire standard or only the provisions that eliminate or modify requirements. Entities can elect to early adopt in interim periods, including periods for which they have not yet issued financial statements or made their financial statements available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes. In August 2018, the FASB issued ASU 2018-15,"Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract". ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements In May 2014, the FASB issued ASU No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to 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. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million , which was recorded on January 1, 2018 to deferred revenue and accumulated deficit, related to the product sales of Emflaza. The information presented for the periods prior to January 1, 2018 has not been restated and is reported under ASC Topic 605. In January 2016, the FASB issued ASU No. 2016-01, “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. The Company adopted ASU 2016-01 during the three months ended March 31, 2018. In March 2018, the FASB issued ASU 2018-04, "Investments - Debt Securities (Topic 320) and Regulated Operations (Topic 980): Amendments to SEC Paragraphs Pursuant to the SEC Staff Accounting Bulletin ("SAB") No. 117 and SEC Release No. 33-9273 (SEC Update)". This standard supersedes SEC paragraphs in ASC 320, Investments- Debt Securities, as a result of the issuance of SAB 117 and also updates the Codification for a 2011 SEC release and is effective when a registrant adopts ASU 2016-01, which in the case of the Company was during the three months ended March 31, 2018. The adoption of these standards did not have a material impact on the Company’s financial position or results of operations for the period ended and as of September 30, 2018 . 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 Company adopted ASU 2016-15 during the three months ended March 31, 2018. The adoption of this standard did not have a material impact on the Company’s financial position or results of operations for the period ended and as of September 30, 2018 . 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. The Company adopted ASU 2016-18 during the three months ended March 31, 2018. The adoption of this standard did not have a material impact on the Company’s financial position or results of operations for the period ended and as of September 30, 2018 . 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. The Company adopted ASU 2017-09 during the three months ended March 31, 2018. The adoption of this standard did not have a material impact on the Company’s financial position or results of operations for the period ended and as of September 30, 2018 .

Summary of significant accoun_3

Summary of significant accounting policies (Tables)	9 Months Ended
	Sep. 30, 2018
Accounting Policies [Abstract]
Schedule of Inventory	The following table summarizes the components of the Company’s inventory for the periods indicated: September 30, 2018 December 31, 2017 Raw materials $ 399 $ 452 Work in progress 5,997 3,912 Finished goods 7,264 6,390 Total inventory $ 13,660 $ 10,754

Business Combination (Tables)

Business Combination (Tables)	9 Months Ended
	Sep. 30, 2018
Business Combinations [Abstract]
Schedule of business acquisitions	The fair value of consideration totaled approximately $462.0 million summarized as follows: As of August 23, 2018 Cash consideration $ 49,221 Fair value of PTC common stock issued 155,860 Estimated fair value of deferred consideration payable 38,200 Estimated fair value of contingent consideration payable 218,700 Total consideration $ 461,981
Assets acquired and liabilities assumed	The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of August 23, 2018, and through the period ended September 30, 2018: Preliminary Cash and cash equivalents $ 328 Prepaid expenses and other current assets 181 Fixed assets 153 Other assets 38 Intangible assets - in process research and development (“IPRD”) 480,000 Accounts payable and accrued expenses (3,828 ) Deferred tax liability (115,200 ) Fair value of net assets acquired $ 361,672 Goodwill 100,309 Total purchase price $ 461,981
Pro forma information	Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Revenues $ 53,591 $ 41,853 $ 178,396 $ 116,362 Net loss attributable to common stockholders (52,458 ) (41,606 ) (89,976 ) (90,795 )

Fair value of financial instr_2

Fair value of financial instruments and marketable securities (Tables)	9 Months Ended
	Sep. 30, 2018
Fair Value Disclosures [Abstract]
Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis	The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2018 and December 31, 2017 : September 30, 2018 Total Quoted prices Significant Significant Marketable securities $ 42,491 $ — $ 42,491 $ — Warrant liability $ 4 $ — $ — $ 4 Stock appreciation rights liability $ 3,463 $ — $ — $ 3,463 Deferred consideration payable $ 38,200 $ — $ 38,200 $ — Contingent consideration payable $ 218,700 $ — $ — $ 218,700 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 Deferred consideration payable $ — $ — $ — $ — Contingent consideration payable $ — $ — $ — $ —
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 September 30, 2018 and December 31, 2017 : September 30, 2018 Amortized Gross Unrealized Fair Gains Losses Commercial paper $ 18,441 $ — $ (6 ) $ 18,435 Corporate debt securities 24,078 2 (24 ) 24,056 $ 42,519 $ 2 $ (30 ) $ 42,491 December 31, 2017 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 13,775 $ 52 $ — $ 13,827 Corporate debt securities 65,657 — (30 ) 65,627 $ 79,432 $ 52 $ (30 ) $ 79,454
Summary of unrealized losses and fair values of available-for-sale securities in a continuous unrealized loss position	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 September 30, 2018 are as follows: September 30, 2018 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 Commercial paper $ (6 ) $ 18,435 $ — $ — $ (6 ) $ 18,435 Corporate debt securities (24 ) 18,067 — — (24 ) 18,067 $ (30 ) $ 36,502 $ — $ — $ (30 ) $ 36,502 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
Schedule of marketable securities on the balance sheet	Marketable securities on the balance sheet at September 30, 2018 and December 31, 2017 mature as follows: September 30, 2018 Less Than 12 Months More Than 12 Months Commercial paper $ 18,435 $ — Corporate debt securities 24,056 — Total Marketable securities $ 42,491 $ — December 31, 2017 Less Than 12 Months More Than 12 Months Commercial paper $ 13,827 $ — Corporate debt securities 55,550 10,077 Total Marketable securities $ 69,377 $ 10,077
Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability and SARs liability	The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the warrant liability, the SARs liability, and the contingent consideration payable for the period ended September 30, 2018 : Level 3 liabilities Warrants SARs Contingent consideration payable Beginning balance as of December 31, 2017 $ 1 $ 1,665 $ — Additions — — 218,700 Change in fair value 3 3,789 — Payments — (1,991 ) $ — Ending balance as of September 30, 2018 $ 4 $ 3,463 $ 218,700

Other comprehensive income (l_2

Other comprehensive income (loss) and accumulated other comprehensive items (Tables)	9 Months Ended
	Sep. 30, 2018
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items	The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine months ended September 30, 2018 : Unrealized Foreign Total Balance at June 30, 2018 $ (61 ) $ 1,916 $ 1,855 Other comprehensive income (loss) before reclassifications 33 (260 ) (227 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 33 (260 ) (227 ) Balance at September 30, 2018 $ (28 ) $ 1,656 $ 1,628 Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2017 $ 22 $ 3,947 $ 3,969 Other comprehensive loss before reclassifications (50 ) (2,291 ) (2,341 ) Amounts reclassified from other comprehensive items — — — Other comprehensive loss (50 ) (2,291 ) (2,341 ) Balance at September 30, 2018 $ (28 ) $ 1,656 $ 1,628

Accounts payable and accrued _2

Accounts payable and accrued expenses (Tables)	9 Months Ended
	Sep. 30, 2018
Payables and Accruals [Abstract]
Schedule of components of accounts payable and accrued expenses	Accounts payable and accrued expenses at September 30, 2018 and December 31, 2017 consist of the following: September 30, December 31, Employee compensation, benefits, and related accruals $ 18,003 $ 17,711 Consulting and contracted research 8,111 5,137 Professional fees 3,541 2,116 Sales allowance and other costs 27,027 22,257 Sales rebates and royalties 26,818 11,657 Accounts payable 6,538 15,282 Other 12,750 2,286 $ 102,788 $ 76,446

Capitalization (Tables)

Capitalization (Tables)	9 Months Ended
	Sep. 30, 2018
Stockholders' Equity Note [Abstract]
Summary of the Company's outstanding warrants	The following is a summary of the Company’s outstanding warrants as of September 30, 2018 and December 31, 2017 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019

Net loss per share (Tables)

Net loss per share (Tables)	9 Months Ended
	Sep. 30, 2018
Earnings Per Share [Abstract]
Schedule of computation of basic and diluted net loss available to common stockholders	The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Numerator Net loss $ (50,969 ) $ (33,738 ) $ (79,751 ) $ (80,270 ) Denominator Denominator for basic and diluted net loss per share 48,096,521 41,296,740 45,310,690 38,433,749 Net loss per share: Basic and diluted $ (1.06 ) * $ (0.82 ) * $ (1.76 ) * $ (2.09 ) * *In the three and nine months ended September 30, 2018 and 2017 , the Company experienced a net loss and therefore did not report any dilutive share impact.
Schedule of historical dilutive common share equivalents outstanding	The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. As of September 30, 2018 2017 Stock Options 9,545,522 6,612,765 Unvested restricted stock awards and units 580,347 402,853 Total 10,125,869 7,015,618

Stock award plan (Tables)

Stock award plan (Tables)	9 Months Ended
	Sep. 30, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Summary of stock option activity	A summary of stock option activity is as follows: Number of Weighted- Weighted- Aggregate (in Outstanding at December 31, 2017 6,448,642 $ 29.00 Granted 2,914,139 $ 25.84 Exercised 512,145 $ 17.03 Forfeited/Cancelled (329,404 ) $ 34.20 Outstanding at September 30, 2018 9,545,522 $ 28.44 7.45 years $ 172,859 Vested or Expected to vest at September 30, 2018 3,914,413 $ 24.38 8.93 years $ 89,547 Exercisable at September 30, 2018 4,316,071 $ 32.33 5.99 years $ 77,003
Schedule of assumptions used to estimate fair values of grants made on the date of grant	The fair value of grants made in the nine months ended September 30, 2018 was contemporaneously estimated on the date of grant using the following assumptions: Nine months ended Risk-free interest rate 2.25%—3.03% Expected volatility 64%—90% Expected term 5.04 – 10.00 years
Summary of information on the Company's restricted stock	The following table summarizes information on the Company’s restricted stock awards and units: Restricted Stock Awards and Units Number of Weighted January 1, 2018 393,011 $ 15.64 Granted 354,691 $ 19.09 Vested (113,795 ) $ 16.36 Forfeited (53,560 ) $ 17.24 Unvested at September 30, 2018 580,347 $ 17.60
Schedule of share-based compensation expense recorded in the statement of operations	The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Research and development $ 4,431 $ 3,624 $ 12,109 $ 11,986 Selling, general and administrative 4,511 3,544 12,664 12,096 Total $ 8,942 $ 7,168 $ 24,773 $ 24,082

Debt (Tables)

Debt (Tables)	9 Months Ended
	Sep. 30, 2018
Debt Disclosure [Abstract]
Summary of convertible notes	The Convertible Notes consist of the following: Liability component September 30, 2018 December 31, 2017 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,844 ) (2,121 ) Less: Debt discount, net(1) (37,009 ) (42,572 ) Net carrying amount $ 111,147 $ 105,307 (1) Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the Convertible Notes using the effective interest rate method.
Summary of interest expense recognized related to the Convertible Notes	The following table sets forth total interest expense recognized related to the Convertible Notes: Three Months Ended September 30, Nine Months Ended September 30, 2018 2017 2018 2017 Contractual interest expense $ 1,134 $ 1,134 $ 3,375 $ 3,375 Amortization of debt issuance costs 95 86 277 249 Amortization of debt discount 1,919 1,725 5,563 4,999 Total $ 3,148 $ 2,945 $ 9,215 $ 8,623 Effective interest rate of the liability component 11 % 11 % 11 % 11 %

Revenue recognition (Tables)

Revenue recognition (Tables)	9 Months Ended
	Sep. 30, 2018
Revenue from Contract with Customer [Abstract]
Contract liabilities, rollforward and revenue recognition	During the three and nine months ended September 30, 2018 , the Company recognized revenue in the period from: Three Months Ended September 30, 2018 Nine Months Ended September 30, 2018 Amounts included in contract liabilities at the beginning of the period $ — $ — Performance obligations satisfied in previous period — — Performance obligations satisfied in current period 53,021 177,172 Total product revenue $ 53,021 $ 177,172 The following table presents changes in the Company’s contract liabilities from December 31, 2017 to September 30, 2018 : Balance as of Additions Deductions ASC 606 Adjustment Balance as of Deferred Revenue $ 11,891 $ 4,706 $ — $ (3,937 ) $ 12,660
Schedule of New Accounting Pronouncements and Changes in Accounting Principles	The impact of adoption using the modified retrospective method on the Company’s consolidated financial statements is as follows: i. Consolidated balance sheets Impact of changes in accounting policies As reported September 30, Adjustments As reported Balances without adoption of Topic 606 Assets Current assets: Cash and cash equivalents $ 206,913 $ — $ 206,913 Marketable securities 42,491 — 42,491 Trade receivables, net 42,197 — 42,197 Inventory 13,660 (84 ) 13,576 Prepaid expenses and other current assets 8,020 — 8,020 Total current assets 313,281 (84 ) 313,197 Fixed assets, net 8,805 — 8,805 Intangible assets, net 604,612 — 604,612 Goodwill 100,309 — 100,309 Deposits and other assets 1,620 — 1,620 Total assets $ 1,028,627 $ (84 ) $ 1,028,543 Liabilities and stockholders’ equity Current liabilities: Accounts payable and accrued expenses $ 102,788 $ (794 ) $ 101,994 Current portion of long-term debt 6,667 — 6,667 Deferred revenue 2,004 5,120 7,124 Other current liabilities 3,463 — 3,463 Total current liabilities 114,922 4,326 119,248 Deferred revenue - long-term 11,156 — 11,156 Long-term debt 144,258 — 144,258 Contingent consideration payable 218,700 — 218,700 Deferred consideration payable 38,200 — 38,200 Deferred tax liability 115,200 — 115,200 Other long-term liabilities 101 — 101 Total liabilities 642,537 4,326 646,863 Stockholders’ equity: Common stock 51 — 51 Additional paid-in capital 1,275,004 — 1,275,004 Accumulated other comprehensive income 1,628 — 1,628 Accumulated deficit (890,593 ) (4,410 ) (895,003 ) Total stockholders’ equity 386,090 (4,410 ) 381,680 Total liabilities and stockholders’ equity $ 1,028,627 $ (84 ) $ 1,028,543 ii. Consolidated statements of operations Impact of changes in accounting policies Three Months Ended As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 53,021 $ (834 ) $ 52,187 Collaboration and grant revenue 570 — 570 Total revenues 53,591 (834 ) 52,757 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 3,292 (17 ) 3,275 Amortization of acquired intangible asset 5,793 — 5,793 Research and development 54,368 — 54,368 Selling, general and administrative 38,368 — 38,368 Total operating expenses 101,821 (17 ) 101,804 Loss from operations (48,230 ) (817 ) (49,047 ) Interest expense, net (3,118 ) — (3,118 ) Other expense, net 734 — 734 Loss before income tax expense (50,614 ) (817 ) (51,431 ) Income tax expense (355 ) — (355 ) Net loss attributable to common stockholders $ (50,969 ) $ (817 ) $ (51,786 ) Impact of changes in accounting policies Year to Date As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 177,172 $ (1,059 ) $ 176,113 Collaboration and grant revenue 1,224 — 1,224 Total revenues 178,396 (1,059 ) 177,337 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 8,909 (84 ) 8,825 Amortization of acquired intangible asset 16,815 — 16,815 Research and development 118,337 — 118,337 Selling, general and administrative 104,882 — 104,882 Total operating expenses 248,943 (84 ) 248,859 Loss from operations (70,547 ) (975 ) (71,522 ) Interest expense, net (9,306 ) — (9,306 ) Other income, net 1,066 — 1,066 Loss before income tax expense (78,787 ) (975 ) (79,762 ) Income tax expense (964 ) — (964 ) Net loss attributable to common stockholders $ (79,751 ) $ (975 ) $ (80,726 ) iii. Consolidated statements of comprehensive loss Impact of changes in accounting policies Three Months Ended As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (50,969 ) $ (817 ) $ (51,786 ) Other comprehensive loss: Unrealized gain on marketable securities, net of tax 33 — 33 Foreign currency translation loss (260 ) — (260 ) Comprehensive loss $ (51,196 ) $ (817 ) $ (52,013 ) Impact of changes in accounting policies Year to Date As reported for the period ended September 30, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (79,751 ) $ (975 ) $ (80,726 ) Other comprehensive loss: Unrealized loss on marketable securities, net of tax (50 ) — (50 ) Foreign currency translation loss (2,291 ) — (2,291 ) Comprehensive loss $ (82,092 ) $ (975 ) $ (83,067 ) iv. Consolidated statements of cash flows Impact of changes in accounting policies As reported for the period ended September 30, Adjustments Balances without adoption of Topic 606 Cash flows from operating activities Net loss $ (79,751 ) $ (975 ) $ (80,726 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 19,316 — 19,316 Change in valuation of warrant liability 3 — 3 Non-cash interest expense 5,563 — 5,563 Loss on disposal of asset 2 — 2 Amortization of premiums and accretion of discounts on investments, net (354 ) — (354 ) Amortization of debt issuance costs 390 — 390 Share-based compensation expense 24,773 — 24,773 Unrealized foreign currency transaction gain (977 ) — (977 ) Changes in operating assets and liabilities: 0 Inventory, net (3,252 ) (84 ) (3,336 ) Prepaid expenses and other current assets (1,301 ) — (1,301 ) Trade receivables, net (2,681 ) — (2,681 ) Deposits and other assets (385 ) — (385 ) Accounts payable and accrued expenses 18,606 (794 ) 17,812 Other liabilities 1,617 — 1,617 Deferred revenue 5,933 1,853 7,786 Net cash used in operating activities (12,498 ) — (12,498 ) Cash flows from investing activities Purchases of fixed assets (2,489 ) — (2,489 ) Purchases of marketable securities (28,656 ) — (28,656 ) Sale and redemption of marketable securities 65,923 — 65,923 Acquisition of product rights (3,903 ) — (3,903 ) Business acquisition, net of cash acquired (48,892 ) — (48,892 ) Net cash (used in) / provided by investing activities (18,017 ) — (18,017 ) Cash flows from financing activities Proceeds from exercise of options 8,631 — 8,631 Net proceeds from public offerings 117,915 — 117,915 Proceeds from shares issued under employee stock purchase plan 1,299 — 1,299 Net cash provided by financing activities 127,845 — 127,845 Effect of exchange rate changes on cash (2,209 ) — (2,209 ) Net increase in cash and cash equivalents 95,121 — 95,121 Cash and cash equivalents, beginning of period 111,792 — 111,792 Cash and cash equivalents, end of period $ 206,913 $ — $ 206,913

Intangible assets and goodwill

Intangible assets and goodwill (Tables)	9 Months Ended
	Sep. 30, 2018
Goodwill and Intangible Assets Disclosure [Abstract]
Future amortization expense	The estimated future amortization of the Emflaza rights intangible asset is expected to be as follows: As of September 30, 2018 2018(1) $ 5,794 2019 23,172 2020 23,172 2021 23,172 2022 and thereafter 49,302 Total $ 124,612 (1) For the three months ended December 31, 2018 .

The Company (Details)

The Company (Details) $ in Thousands	Aug. 23, 2018USD ($)shares	Apr. 20, 2017USD ($)shares	Aug. 31, 2014member_state	Sep. 30, 2018USD ($)productcountry	Dec. 31, 2017USD ($)	Aug. 31, 2015
Long-term debt
Number of products | product				2
Number of member states of the European Economic Area | member_state			31
Development milestone payments which the entity is obligated to pay				$ 4,500
Retained earnings (accumulated deficit)				$ (890,593)	$ (814,108)
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Interest rate						3.00%
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Long-term debt
Cash consideration		$ 75,000
Equity Interest Issued, 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 milestone payments which the entity is obligated to pay		$ 50,000
Translarna
Long-term debt
Number of countries | country				25
Agilis
Long-term debt
Cash consideration	$ 49,221
Equity Interest Issued, number of shares (in shares) | shares	3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity	$ 150,000
Trading day period	10 days
Development milestone payments which the entity is obligated to pay	$ 40,000			$ 40,000
Agilis | Non-collaborative Arrangement Transactions
Long-term debt
Development milestone payments which the entity is obligated to pay	$ 40,000			$ 40,000

Summary of significant accoun_4

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Accounting Policies [Abstract]
Raw materials	$ 399	$ 452
Work in progress	5,997	3,912
Finished goods	7,264	6,390
Total inventory	$ 13,660	$ 10,754

Summary of significant accoun_5

Summary of significant accounting policies - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018	Jan. 01, 2018	Dec. 31, 2017
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Inventory write-down	$ 1,600
Allowance for doubtful accounts receivable	600	$ 600		$ 800
Deferred tax liability	115,200	115,200		0
Retained earnings (accumulated deficit)	$ (890,593)	(890,593)		$ (814,108)
ASC 606 Adjustment		(3,937)
Adjustments
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Retained earnings (accumulated deficit)			$ 3,300
Variable consideration		$ 600

Business Combination - Narrativ

Business Combination - Narrative (Details) - USD ($) $ in Thousands	Aug. 23, 2018	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Jul. 23, 2018	Dec. 31, 2017
Business Acquisition [Line Items]
Development milestone payments which the entity is obligated to pay		$ 4,500		$ 4,500
Contingent consideration payable		218,700		218,700			$ 0
Estimated fair value of deferred consideration payable		38,200		38,200			$ 0
Agilis
Business Acquisition [Line Items]
Cash consideration	$ 49,221
Equity Interest Issued, number of shares (in shares)	3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity	$ 150,000
Trading day period	10 days
Fair value of PTC common stock issued	$ 155,860
Development milestone payments which the entity is obligated to pay	40,000	40,000		40,000
Contingent consideration payable	218,700	218,700		218,700
Estimated fair value of deferred consideration payable	38,200
Total preliminary consideration transferred	$ 461,981
Acquisition related costs		1,500
Earnings (loss) of acquiree since acquisition date, actual		1,900
Due from related parties						$ 10,000
Net loss attributable to common stockholders		(52,458)	$ (41,606)	(89,976)	$ (90,795)
Maximum | Agilis
Business Acquisition [Line Items]
Development milestone payments which the entity is obligated to pay		60,000		60,000
Milestone, potential achievements, priority review voucher amount				535,000
Milestone, potential achievements, net sales amount		$ 150,000		$ 150,000
Milestone, potential achievements, product sales		6.00%		6.00%
Minimum | Agilis
Business Acquisition [Line Items]
Milestone, potential achievements, product sales		2.00%		2.00%
Acquisition-related Costs | Agilis
Business Acquisition [Line Items]
Net loss attributable to common stockholders		$ 800		$ 1,500

Business Combination - Consider

Business Combination - Consideration Transfered (Details) - USD ($) $ in Thousands	Aug. 23, 2018	Sep. 30, 2018	Dec. 31, 2017
Business Acquisition [Line Items]
Estimated fair value of deferred consideration payable		$ 38,200	$ 0
Contingent consideration payable		218,700	$ 0
Agilis
Business Acquisition [Line Items]
Cash consideration	$ 49,221
Fair value of PTC common stock issued	155,860
Estimated fair value of deferred consideration payable	38,200
Contingent consideration payable	218,700	$ 218,700
Total preliminary consideration transferred	$ 461,981

Business Combination - Assets a

Business Combination - Assets and Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Business Acquisition [Line Items]
Goodwill	$ 100,309	$ 0
Agilis
Business Acquisition [Line Items]
Cash and cash equivalents	328
Prepaid expenses and other current assets	181
Fixed assets	153
Other assets	38
Intangible assets - in process research and development (“IPRD”)	480,000
Accounts payable and accrued expenses	(3,828)
Deferred tax liability	(115,200)
Fair value of net assets acquired	361,672
Goodwill	100,309
Purchase price	$ 461,981

Business Combination - Pro-form

Business Combination - Pro-forma financial information (Details) - Agilis - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Business Acquisition [Line Items]
Revenues	$ 53,591	$ 41,853	$ 178,396	$ 116,362
Net loss attributable to common stockholders	$ (52,458)	$ (41,606)	$ (89,976)	$ (90,795)

Fair value of financial instr_3

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 42,491	$ 79,454
Deferred consideration payable	38,200	0
Contingent consideration payable	218,700	0
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	42,491	79,454
Warrant Liability	4	1
Stock appreciation rights liability	3,463	1,665
Deferred consideration payable	38,200	0
Contingent consideration payable	218,700	0
Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	0
Warrant Liability	0	0
Stock appreciation rights liability	0	0
Deferred consideration payable	0	0
Contingent consideration payable	0	0
Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	42,491	79,454
Warrant Liability	0	0
Stock appreciation rights liability	0	0
Deferred consideration payable	38,200	0
Contingent consideration payable	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	4	1
Stock appreciation rights liability	3,463	1,665
Deferred consideration payable	0	0
Contingent consideration payable	$ 218,700	$ 0

Fair value of financial instr_4

Fair value of financial instruments and marketable securities - Narrative (Details)	9 Months Ended	12 Months Ended
	Sep. 30, 2018USD ($)$ / shares	Dec. 31, 2017USD ($)$ / shares	Aug. 23, 2018USD ($)	Apr. 08, 2018$ / shares	Aug. 31, 2015USD ($)
Financial assets and liabilities measured at fair value on recurring basis
Transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy	$ 0	$ 0
Realized gain (loss)	0	0
Fair value of shares (in dollars per share) | $ / shares				$ 27.04
Development milestone payments which the entity is obligated to pay	4,500,000
Estimated fair value of deferred consideration payable	$ 38,200,000	$ 0
Warrants
Financial assets and liabilities measured at fair value on recurring basis
Fair value of shares (in dollars per share) | $ / shares	$ 47	$ 16.68
Minimum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares		128
Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	25.00%
Maximum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares		2,520
Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	89.00%
SARs
Financial assets and liabilities measured at fair value on recurring basis
Fair value of shares (in dollars per share) | $ / shares	$ 47	$ 16.68
3.00% Convertible senior notes due 2022 | Convertible debt
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%
Fair value of convertible notes	$ 172,900,000	$ 115,700,000
Measurement Input, Price Volatility | Minimum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.51	0.69
Measurement Input, Price Volatility | Maximum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.54	0.69
Measurement Input, Price Volatility | SARs | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.45	0.31
Measurement Input, Price Volatility | SARs | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.54	0.70
Measurement Input, Risk Free Interest Rate | Minimum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.0259	0.0189
Measurement Input, Risk Free Interest Rate | Maximum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.0259	0.0189
Measurement Input, Risk Free Interest Rate | SARs | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.0219	0.0128
Measurement Input, Risk Free Interest Rate | SARs | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Derivative liability, measurement input	0.0270	0.0189
Measurement Input, Strike Price | Minimum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares	128
Measurement Input, Strike Price | Maximum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares	2,520
Measurement Input, Strike Price | SARs | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares	6.76	6.76
Measurement Input, Strike Price | SARs | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Warrants, exercise price (in dollars per share) | $ / shares	30.86	30.86
Measurement Input, Expected Term | Minimum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, term	10 months 2 days	1 year 7 months 6 days
Measurement Input, Expected Term | Maximum | Warrants
Financial assets and liabilities measured at fair value on recurring basis
Warrants, term	11 months 23 days	1 year 8 months 12 days
Measurement Input, Expected Term | SARs | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Warrants, term	3 months 4 days	0 days
Measurement Input, Expected Term | SARs | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Warrants, term	1 year 3 months 4 days	2 years
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay	$ 40,000,000		$ 40,000,000
Estimated fair value of deferred consideration payable			38,200,000
Agilis | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Development milestone, potential achievements	$ 20,000,000
Agilis | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	2.00%
Agilis | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	2.00%
Development milestone, potential achievements	$ 0
Milestone, potential achievements, priority review voucher amount	0
Milestone, potential achievements, net sales amount	$ 0
Agilis | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	6.00%
Development milestone payments which the entity is obligated to pay	$ 60,000,000
Milestone, potential achievements, priority review voucher amount	535,000,000
Milestone, potential achievements, net sales amount	$ 150,000,000
Agilis | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Milestone, potential achievements, product sales	6.00%
Development milestone, potential achievements	$ 20,000,000
Milestone, potential achievements, priority review voucher amount	535,000,000
Milestone, potential achievements, net sales amount	150,000,000
Non-collaborative Arrangement Transactions | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay	40,000,000		$ 40,000,000
Non-collaborative Arrangement Transactions | Agilis | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay	$ 40,000,000

Fair value of financial instr_5

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 42,519	$ 79,432
Gross Unrealized, Gain	2	52
Gross Unrealized, Loss	(30)	(30)
Fair Value	42,491	79,454
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	18,441	13,775
Gross Unrealized, Gain	0	52
Gross Unrealized, Loss	(6)	0
Fair Value	18,435	13,827
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	24,078	65,657
Gross Unrealized, Gain	2	0
Gross Unrealized, Loss	(24)	(30)
Fair Value	$ 24,056	$ 65,627

Fair value of financial instr_6

Fair value of financial instruments and marketable securities - Unrealized Loss Positions (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Unrealized losses
Securities in an unrealized loss position less than 12 months	$ (30)
Securities in an unrealized loss position greater than 12 months	0
Total	(30)
Fair Value
Securities in an unrealized loss position less than 12 months	36,502
Securities in an unrealized loss position greater than 12 months	0
Total	36,502
Commercial paper
Unrealized losses
Securities in an unrealized loss position less than 12 months	(6)
Securities in an unrealized loss position greater than 12 months	0
Total	(6)
Fair Value
Securities in an unrealized loss position less than 12 months	18,435
Securities in an unrealized loss position greater than 12 months	0
Total	18,435
Corporate debt securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(24)	$ (28)
Securities in an unrealized loss position greater than 12 months	0	(2)
Total	(24)	(30)
Fair Value
Securities in an unrealized loss position less than 12 months	18,067	59,108
Securities in an unrealized loss position greater than 12 months	0	6,519
Total	$ 18,067	$ 65,627

Fair value of financial instr_7

Fair value of financial instruments and marketable securities - Marketable securities (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 42,491	$ 69,377
Total Marketable securities, More Than 12 Months	0	10,077
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	18,435	13,827
Total Marketable securities, More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	24,056	55,550
Total Marketable securities, More Than 12 Months	$ 0	$ 10,077

Fair value of financial instr_8

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2018USD ($)
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2017	$ 1,665
Change in fair value	3,789
Payments	(1,991)
September 30, 2018	3,463
Warrants
Changes in the fair value of warrant liability and SARs liability
December 31, 2017	1
Change in fair value	3
Payments	0
September 30, 2018	4
Commitments
Changes in the fair value of warrant liability and SARs liability
December 31, 2017	0
Additions	218,700
Payments	0
September 30, 2018	$ 218,700

Other comprehensive income (l_3

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance		$ 156,437
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	$ (227)	(2,341)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive loss	(227)	(2,341)
Ending balance	386,090	386,090
Unrealized Gains/(Losses) On Marketable Securities, net of tax
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	(61)	22
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	33	(50)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive loss	33	(50)
Ending balance	(28)	(28)
Foreign Currency Translation
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	1,916	3,947
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(260)	(2,291)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive loss	(260)	(2,291)
Ending balance	1,656	1,656
AOCI Attributable to Parent
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	1,855	3,969
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Ending balance	$ 1,628	$ 1,628

Accounts payable and accrued _3

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 18,003	$ 17,711
Consulting and contracted research	8,111	5,137
Professional fees	3,541	2,116
Sales allowance and other costs	27,027	22,257
Sales rebates and royalties	26,818	11,657
Accounts payable	6,538	15,282
Other	12,750	2,286
Accounts payable and accrued expenses	$ 102,788	$ 76,446

Capitalization - Narrative (Det

Capitalization - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	Apr. 08, 2018	Sep. 30, 2018	Sep. 30, 2017
Warrants
Stock issued (in shares)	4,600,000
Share price (in dollars per share)	$ 27.04
Net proceeds from public offerings	$ 117,900	$ 117,915	$ 0
Over-Allotment Option
Warrants
Stock issued (in shares)	600,000

Capitalization - Warrants (Deta

Capitalization - Warrants (Details) - Common stock - 2019 - Warrants	Sep. 30, 2018$ / sharesshares
Warrants
Warrant shares (in shares) | shares	7,030
Exercise price (in dollars per share) | $ / shares	$ 128
Warrant shares (in shares) | shares	130
Exercise price (in dollars per share) | $ / shares	$ 2,520

Net loss per share - Numerator

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Numerator
Net loss	$ (50,969)	$ (33,738)	$ (79,751)	$ (80,270)
Denominator
Denominator for basic and diluted net loss per share (in shares)	48,096,521	41,296,740	45,310,690	38,433,749
Net loss per share:
Basic and diluted (in dollars per share)	$ (1.06)	$ (0.82)	$ (1.76)	$ (2.09)

Net loss per share - Antidiluti

Net loss per share - Antidilutive (Details) - shares	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017
Net loss per share
Total shares excluded from calculation (in shares)	10,125,869	7,015,618
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	9,545,522	6,612,765
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	580,347	402,853

Stock award plan - Narrative (D

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Stock option plan
Share-based compensation expense					$ 8,942	$ 7,168	$ 24,773	$ 24,082
Unrecognized compensation cost					$ 67,500		$ 67,500
Weighted average remaining service period for recognition of unrecognized compensation cost							3 years
Common stock
Stock option plan
Number of shares available for issuance (in shares)					665,194		665,194
Unvested restricted stock
Stock option plan
Grants in period (in shares)							354,691
Stock option
Stock option plan
Granted (in shares)							2,914,139
Inducement grants for non-statutory stock options (in shares)							1,115,650
Expected dividend yield (as a percent)							0.00%
Weighted average grant date fair value (in dollars per share)							$ 17.04
SARs
Stock option plan
Granted (in shares)			897,290
Vesting period							4 years
Vested (in shares)							177,329
Share-based compensation expense							$ 3,700
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan | Unvested restricted stock
Stock option plan
Grants in period (in shares)	735,324
2013 Stock Incentive Plan | Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)					0		0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares available for issuance (in shares)				122,296
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | 1998 Employee, Director and Consultant Stock Option Plan | Common stock | Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)				3,040,444
2013 Long Term Incentive Plan | Minimum
Stock option plan
Annual increase in the number of shares (in shares) on the first day of the fiscal year				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)		1,000,000
Share-based compensation expense							$ 700
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit		5.00%

Stock award plan - Share Base C

Stock award plan - Share Base Compensation (Details) - Stock option $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2018USD ($)$ / sharesshares
Number of options
Outstanding at the beginning of the period (in shares) | shares	6,448,642
Granted (in shares) | shares	2,914,139
Exercised (in shares) | shares	512,145
Forfeited/Cancelled (in shares) | shares	(329,404)
Outstanding at the end of the period (in shares) | shares	9,545,522
Vested or Expected to vest at the end of the period (in shares) | shares	3,914,413
Exercisable at the end of the period (in shares) | shares	4,316,071
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share) | $ / shares	$ 29
Granted (in dollars per share) | $ / shares	25.84
Exercised (in dollars per share) | $ / shares	17.03
Forfeited/Cancelled (in dollars per share) | $ / shares	34.20
Outstanding at the end of the period (in dollars per share) | $ / shares	28.44
Vested or Expected to vest at the end of the period (in dollars per share) | $ / shares	24.38
Exercisable at the end of the period (in dollars per share) | $ / shares	$ 32.33
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 5 months 12 days
Vested or Expected to vest at the end of the period	8 years 11 months 5 days
Exercisable at the end of the period	5 years 11 months 27 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars) | $	$ 172,859
Vested or Expected to vest at the end of the period (in dollars) | $	89,547
Exercisable at the end of the period (in dollars) | $	$ 77,003
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	2.25%
Expected volatility (as a percent)	64.00%
Expected term	5 years 16 days
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	3.03%
Expected volatility (as a percent)	90.00%
Expected term	10 years

Stock award plan - Restricted S

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	9 Months Ended
	Sep. 30, 2018$ / sharesshares
Number of Shares
Balance at the beginning of the period (in shares) | shares	393,011
Granted (in shares) | shares	354,691
Vested (in shares) | shares	(113,795)
Forfeited (in shares) | shares	(53,560)
Balance at the end of the period (in shares) | shares	580,347
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) | $ / shares	$ 15.64
Granted (in dollars per share) | $ / shares	19.09
Vested (in dollars per share) | $ / shares	16.36
Forfeited (in dollars per share) | $ / shares	17.24
Balance at the end of the period (in dollars per share) | $ / shares	$ 17.60

Stock award plan - Share-based

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Stock option plan
Share-based compensation expense	$ 8,942	$ 7,168	$ 24,773	$ 24,082
Research and development
Stock option plan
Share-based compensation expense	4,431	3,624	12,109	11,986
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 4,511	$ 3,544	$ 12,664	$ 12,096

Debt - Narrative (Details)

Debt - Narrative (Details)	May 05, 2017USD ($)	May 31, 2017USD ($)	Aug. 31, 2015USD ($)day$ / shares	Sep. 30, 2018USD ($)	Dec. 31, 2017USD ($)
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Debt principal amount			$ 150,000,000	$ 150,000,000	$ 150,000,000
Interest rate			3.00%
Net proceeds from issuance of convertible notes			$ 145,400,000
Trading days, number | day			20
Consecutive trading days, period | day			30
Stock price trigger			130.00%
Business days, period			5 days
Consecutive trading-day period			5 days
Common stock per principal amount			$ 1,000
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day			98.00%
Conversion ratio			17.7487
Conversion price per share (in dollars per share) | $ / shares			$ 56.34
Convertible instruments principal and unpaid interest payable upon events of default			100.00%
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default			25.00%
Term of the convertible notes			7 years
Adjustments to additional paid in capital, equity component of convertible debt			$ 57,500,000
Net deferred tax liability in connection with convertible notes			$ 22,300,000
Fair value of convertible notes				$ 172,900,000	$ 115,700,000
Remaining contractual life of the convertible notes				3 years 10 months 17 days
Convertible debt | 3.00% Convertible senior notes due 2022 | 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%
Sinking fund			$ 0
MidCap Financial Trust
Long-term debt
Line of credit facility, maximum borrowing capacity		$ 60,000,000
Proceeds from lines of credit	$ 40,000,000
Line of credit facility, additional capacity available, net product revenue threshold		20,000,000
Line of credit facility, net product revenue threshold, additional capacity		$ 120,000,000
Line of credit facility, net product revenue threshold, additional capacity, trailing period		12 months
Debt issuance costs		$ 400,000
Debt instrument, floor interest rate		1.00%
Debt instrument, basis spread on variable rate		6.15%
Debt instrument, interest payment period		24 months

Debt - Convertible Notes (Detai

Debt - Convertible Notes (Details) - 3.00% Convertible senior notes due 2022 - Convertible debt - USD ($)	Sep. 30, 2018	Dec. 31, 2017	Aug. 31, 2015
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(1,844,000)	(2,121,000)
Less: Debt discount, net	(37,009,000)	(42,572,000)
Net carrying amount	$ 111,147,000	$ 105,307,000

Debt - Interest Expense (Detail

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Long-term debt
Amortization of debt issuance costs			$ 390	$ 308
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 1,134	$ 1,134	3,375	3,375
Amortization of debt issuance costs	95	86	277	249
Amortization of debt discount	1,919	1,725	5,563	4,999
Total	$ 3,148	$ 2,945	$ 9,215	$ 8,623
Effective interest rate of the liability component	11.00%	11.00%	11.00%	11.00%

Commitments and contingencies (

Commitments and contingencies (Details) $ in Millions	9 Months Ended
	Sep. 30, 2018USD ($)claim	Aug. 23, 2018USD ($)	Jun. 30, 2016USD ($)
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 4.5
Claims settled and dismissed | claim	2
Akcea
Other Commitments [Abstract]
Upfront licensing fee	$ 12
Development and regulatory milestone payment obligations, period	30 days
Milestone, potential achievements, regulatory approval	$ 4
Akcea | Maximum
Other Commitments [Abstract]
Milestone, potential achievements, regulatory approval	8
Funding agreement | Wellcome trust
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay			$ 0.8
Funding agreement | Wellcome trust | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	22.4
Non-collaborative Arrangement Transactions | Akcea
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	6
Agilis
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	40	$ 40
Agilis | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	60
Agilis | Non-collaborative Arrangement Transactions
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 40	$ 40

Revenue recognition - Narrative

Revenue recognition - Narrative (Details)	Sep. 30, 2018USD ($)	Oct. 31, 2017USD ($)	Nov. 30, 2014USD ($)	Jan. 31, 2014USD ($)	Aug. 31, 2013USD ($)	Nov. 30, 2011USD ($)compound	Sep. 30, 2018USD ($)	Sep. 30, 2018USD ($)deliverablesegment	Sep. 30, 2017USD ($)	Dec. 31, 2017deliverable
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of operating segments | segment								1
Net product revenue							$ 53,021,000	$ 177,172,000
Upfront cash payment								4,706,000
Performance obligations satisfied in current period							53,021,000	177,172,000
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Upfront cash payment						$ 30,000,000
Performance obligations satisfied in current period		$ 20,000,000	$ 10,000,000	$ 7,500,000	$ 10,000,000
Revenues								200,000	$ 200,000
Licensing And Collaboration Agreement | Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements	$ 87,500,000							135,000,000
Licensing And Collaboration Agreement | Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements								325,000,000
Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenues								0	0
Early Stage Collaborations
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenues								0	$ 0
Early Stage Collaborations | Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements								143,000,000
Early Stage Collaborations | Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements								252,000,000
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue							22,600,000	62,200,000
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue							$ 30,400,000	$ 115,000,000
Collaborative Arrangement | Roche And Sma Foundation
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of compounds in preclinical development | compound						3
Number of significant deliverables | deliverable										2
Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of significant deliverables | deliverable								2
Minimum | Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements research period for applying discovery technology								3 years
Maximum | Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements research period for applying discovery technology								4 years

Revenue recognition - Contract

Revenue recognition - Contract Liabilities, Rollforward (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2018USD ($)
Movement in Deferred Revenue [Roll Forward]
Beginning balance	$ 11,891
Additions	4,706
Deductions	0
ASC 606 Adjustment	(3,937)
Ending balance	$ 12,660

Revenue recognition - Recognize

Revenue recognition - Recognized revenue in the period (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018
Revenue from Contract with Customer [Abstract]
Amounts included in contract liabilities at the beginning of the period	$ 0	$ 0
Performance obligations satisfied in previous period	0	0
Performance obligations satisfied in current period	53,021	177,172
Total product revenue	$ 53,021	$ 177,172

Revenue recognition - Balance S

Revenue recognition - Balance Sheet Impacts (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Jan. 01, 2018	Dec. 31, 2017	Sep. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 206,913		$ 111,792	$ 141,838	$ 58,321
Marketable securities	42,491		79,454
Trade receivables, net	42,197		40,394
Inventory, net	13,660		10,754
Prepaid expenses and other current assets	8,020		6,669
Total current assets	313,281		249,063
Fixed assets, net	8,805		8,376
Intangible assets, net	604,612		132,993
Goodwill	100,309		0
Deposits and other assets	1,620		1,221
Total assets	1,028,627		391,653
Current liabilities:
Accounts payable and accrued expenses	102,788		76,446
Current portion of long-term debt	6,667		0
Deferred revenue	2,004		3,937
Other current liabilities	3,463		1,665
Total current liabilities	114,922		82,048
Deferred revenue - long-term	11,156		7,954
Long-term debt	144,258		144,971
Contingent consideration payable	218,700		0
Estimated fair value of deferred consideration payable	38,200		0
Deferred tax liability	115,200		0
Other long-term liabilities	101		243
Total liabilities	642,537		235,216
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 41,809,398 shares at March 31, 2018. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017	51		42
Additional paid-in capital	1,275,004		966,534
Accumulated other comprehensive income	1,628		3,969
Accumulated deficit	(890,593)		(814,108)
Total stockholders’ equity	386,090		156,437
Total liabilities and stockholders’ equity	1,028,627		391,653
Adjustments
Stockholders’ equity:
Accumulated deficit		$ 3,300
Adjustments | ASU 2014-09
Current assets:
Cash and cash equivalents	0		0
Marketable securities	0
Trade receivables, net	0
Inventory, net	(84)
Prepaid expenses and other current assets	0
Total current assets	(84)
Fixed assets, net	0
Intangible assets, net	0
Goodwill	0
Deposits and other assets	0
Total assets	(84)
Current liabilities:
Accounts payable and accrued expenses	(794)
Current portion of long-term debt	0
Deferred revenue	5,120
Other current liabilities	0
Total current liabilities	4,326
Deferred revenue - long-term	0
Long-term debt	0
Contingent consideration payable	0
Estimated fair value of deferred consideration payable	0
Deferred tax liability	0
Other long-term liabilities	0
Total liabilities	4,326
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 41,809,398 shares at March 31, 2018. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017	0
Additional paid-in capital	0
Accumulated other comprehensive income	0
Accumulated deficit	(4,410)
Total stockholders’ equity	(4,410)
Total liabilities and stockholders’ equity	(84)
Balances without adoption of Topic 606
Current assets:
Cash and cash equivalents	206,913		$ 111,792
Marketable securities	42,491
Trade receivables, net	42,197
Inventory, net	13,576
Prepaid expenses and other current assets	8,020
Total current assets	313,197
Fixed assets, net	8,805
Intangible assets, net	604,612
Goodwill	100,309
Deposits and other assets	1,620
Total assets	1,028,543
Current liabilities:
Accounts payable and accrued expenses	101,994
Current portion of long-term debt	6,667
Deferred revenue	7,124
Other current liabilities	3,463
Total current liabilities	119,248
Deferred revenue - long-term	11,156
Long-term debt	144,258
Contingent consideration payable	218,700
Estimated fair value of deferred consideration payable	38,200
Deferred tax liability	115,200
Other long-term liabilities	101
Total liabilities	646,863
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 41,809,398 shares at March 31, 2018. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017	51
Additional paid-in capital	1,275,004
Accumulated other comprehensive income	1,628
Accumulated deficit	(895,003)
Total stockholders’ equity	381,680
Total liabilities and stockholders’ equity	$ 1,028,543

Revenue recognition - Income St

Revenue recognition - Income Statement Impacts (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Revenues:
Revenue	$ 53,591	$ 41,853	$ 178,396	$ 116,362
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	3,292	1,582	8,909	2,142
Amortization of acquired intangible asset	5,793	9,716	16,815	9,952
Research and development	54,368	30,024	118,337	88,222
Selling, general and administrative	38,368	31,423	104,882	85,788
Total operating expenses	101,821	72,745	248,943	186,104
Loss from operations	(48,230)	(30,892)	(70,547)	(69,742)
Interest expense, net	(3,118)	(3,421)	(9,306)	(8,648)
Other income (expense), net	734	766	1,066	(1,373)
Loss before income tax expense	(50,614)	(33,547)	(78,787)	(79,763)
Income tax expense	(355)	(191)	(964)	(507)
Net loss attributable to common stockholders	(50,969)	(33,738)	(79,751)	(80,270)
Adjustments | ASU 2014-09
Revenues:
Revenue	(834)		(1,059)
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	(17)		(84)
Amortization of acquired intangible asset	0		0
Research and development	0		0
Selling, general and administrative	0		0
Total operating expenses	(17)		(84)
Loss from operations	(817)		(975)
Interest expense, net	0		0
Other income (expense), net	0		0
Loss before income tax expense	(817)		(975)
Income tax expense	0		0
Net loss attributable to common stockholders	(817)		(975)
Balances without adoption of Topic 606
Revenues:
Revenue	52,757		177,337
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	3,275		8,825
Amortization of acquired intangible asset	5,793		16,815
Research and development	54,368		118,337
Selling, general and administrative	38,368		104,882
Total operating expenses	101,804		248,859
Loss from operations	(49,047)		(71,522)
Interest expense, net	(3,118)		(9,306)
Other income (expense), net	734		1,066
Loss before income tax expense	(51,431)		(79,762)
Income tax expense	(355)		(964)
Net loss attributable to common stockholders	(51,786)		(80,726)
Product
Revenues:
Revenue	53,021	41,780	177,172	116,113
Product | Adjustments | ASU 2014-09
Revenues:
Revenue	(834)		(1,059)
Product | Balances without adoption of Topic 606
Revenues:
Revenue	52,187		176,113
Collaboration and grant revenue
Revenues:
Revenue	570	$ 73	1,224	$ 249
Collaboration and grant revenue | Adjustments | ASU 2014-09
Revenues:
Revenue	0		0
Collaboration and grant revenue | Balances without adoption of Topic 606
Revenues:
Revenue	$ 570		$ 1,224

Revenue recognition - Comprehen

Revenue recognition - Comprehensive Income Impacts (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss	$ (50,969)	$ (33,738)	$ (79,751)	$ (80,270)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	33	31	(50)	0
Foreign currency translation (loss) gain	(260)	983	(2,291)	4,498
Comprehensive loss	(51,196)	$ (32,724)	(82,092)	$ (75,772)
Adjustments | ASU 2014-09
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss	(817)		(975)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	0		0
Foreign currency translation (loss) gain	0		0
Comprehensive loss	(817)		(975)
Balances without adoption of Topic 606
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss	(51,786)		(80,726)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	33		(50)
Foreign currency translation (loss) gain	(260)		(2,291)
Comprehensive loss	$ (52,013)		$ (83,067)

Revenue recognition - Cash Flow

Revenue recognition - Cash Flow Impacts (Details) - USD ($) $ in Thousands	Apr. 08, 2018	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Cash flows from operating activities
Net loss		$ (50,969)	$ (33,738)	$ (79,751)	$ (80,270)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization				19,316	11,743
Change in valuation of warrant liability				3	3
Non-cash interest expense				5,563	4,999
Loss on disposal of asset				2	5
Amortization of premiums and accretion of discounts on investments, net				(354)	493
Amortization of debt issuance costs				390	308
Share-based compensation expense				24,773	24,082
Unrealized foreign currency transaction gains				(977)	(364)
Changes in operating assets and liabilities:
Inventory				(3,252)	(3,625)
Prepaid expenses and other current assets				(1,301)	(570)
Trade receivables, net				(2,681)	(10,994)
Deposits and other assets				(385)	(485)
Accounts payable and accrued expenses				18,606	11,807
Other liabilities				1,617	807
Deferred revenue				5,933	10,710
Net cash used in operating activities				(12,498)	(31,351)
Cash flows from investing activities
Purchases of fixed assets				(2,489)	(1,058)
Purchases of marketable securities				(28,656)	(19,467)
Sale and redemption of marketable securities				65,923	164,847
Acquisition of product rights				(3,903)	(77,163)
Business acquisition, net of cash acquired				(48,892)	0
Net cash (used in) / provided by investing activities				(18,017)	67,159
Cash flows from financing activities
Proceeds from exercise of options				8,631	1,437
Net proceeds from public offerings	$ 117,900			117,915	0
Proceeds from shares issued under employee stock purchase plan				1,299	1,362
Net cash provided by financing activities				127,845	42,367
Effect of exchange rate changes on cash				(2,209)	5,342
Net increase in cash and cash equivalents				95,121	83,517
Cash and cash equivalents, beginning of period				111,792	58,321
Cash and cash equivalents, end of period		206,913	$ 141,838	206,913	$ 141,838
Adjustments | ASU 2014-09
Cash flows from operating activities
Net loss		(817)		(975)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization				0
Change in valuation of warrant liability				0
Non-cash interest expense				0
Loss on disposal of asset				0
Amortization of premiums and accretion of discounts on investments, net				0
Amortization of debt issuance costs				0
Share-based compensation expense				0
Unrealized foreign currency transaction gains				0
Changes in operating assets and liabilities:
Inventory				(84)
Prepaid expenses and other current assets				0
Trade receivables, net				0
Deposits and other assets				0
Accounts payable and accrued expenses				(794)
Other liabilities				0
Deferred revenue				1,853
Net cash used in operating activities				0
Cash flows from investing activities
Purchases of fixed assets				0
Purchases of marketable securities				0
Sale and redemption of marketable securities				0
Acquisition of product rights				0
Business acquisition, net of cash acquired				0
Net cash (used in) / provided by investing activities				0
Cash flows from financing activities
Proceeds from exercise of options				0
Net proceeds from public offerings				0
Proceeds from shares issued under employee stock purchase plan				0
Net cash provided by financing activities				0
Effect of exchange rate changes on cash				0
Net increase in cash and cash equivalents				0
Cash and cash equivalents, beginning of period				0
Cash and cash equivalents, end of period		0		0
Balances without adoption of Topic 606
Cash flows from operating activities
Net loss		(51,786)		(80,726)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization				19,316
Change in valuation of warrant liability				3
Non-cash interest expense				5,563
Loss on disposal of asset				2
Amortization of premiums and accretion of discounts on investments, net				(354)
Amortization of debt issuance costs				390
Share-based compensation expense				24,773
Unrealized foreign currency transaction gains				(977)
Changes in operating assets and liabilities:
Inventory				(3,336)
Prepaid expenses and other current assets				(1,301)
Trade receivables, net				(2,681)
Deposits and other assets				(385)
Accounts payable and accrued expenses				17,812
Other liabilities				1,617
Deferred revenue				7,786
Net cash used in operating activities				(12,498)
Cash flows from investing activities
Purchases of fixed assets				(2,489)
Purchases of marketable securities				(28,656)
Sale and redemption of marketable securities				65,923
Acquisition of product rights				(3,903)
Business acquisition, net of cash acquired				(48,892)
Net cash (used in) / provided by investing activities				(18,017)
Cash flows from financing activities
Proceeds from exercise of options				8,631
Net proceeds from public offerings				117,915
Proceeds from shares issued under employee stock purchase plan				1,299
Net cash provided by financing activities				127,845
Effect of exchange rate changes on cash				(2,209)
Net increase in cash and cash equivalents				95,121
Cash and cash equivalents, beginning of period				111,792
Cash and cash equivalents, end of period		$ 206,913		$ 206,913

Revenue recognition - Performan

Revenue recognition - Performance Obligations (Details) - Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-10-01 - USD ($) $ in Millions	Sep. 30, 2018	Nov. 30, 2011
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable	$ 12.7
Minimum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, performance obligation, period	1 year
Maximum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, performance obligation, period	3 years
Licensing And Collaboration Agreement
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable		$ 30
Revenue, performance obligation, period		2 years

Intangible assets and goodwil_2

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life			7 years
Payment for contingent consideration liability, operating activities	$ 4,500		$ 8,400
Development milestone payments which the entity is obligated to pay	4,500		4,500
Amortization of acquired intangible asset	5,793	$ 9,716	16,815	$ 9,952
Total allocation of IPR&D assets			480,000
Goodwill	100,309		100,309		$ 0
Research and development	54,368	$ 30,024	118,337	$ 88,222
Akcea
Finite-Lived Intangible Assets [Line Items]
Upfront licensing fee	12,000		$ 12,000
Development and regulatory milestone payment obligations, period			30 days
Research and development	12,000
Non-collaborative Arrangement Transactions | Akcea
Finite-Lived Intangible Assets [Line Items]
Development milestone payments which the entity is obligated to pay	$ 6,000		$ 6,000
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Finite-Lived Intangibles						$ 148,400

Intangible assets and goodwil_3

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Sep. 30, 2018USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2,018	$ 5,794
2,019	23,172
2,020	23,172
2,021	23,172
2022 and thereafter	49,302
Total	$ 124,612