PTC Therapeutics (PTCT) 10-K 1 Mar 19 2018 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($)	12 Months Ended
	Dec. 31, 2018	Feb. 25, 2019	Jun. 30, 2018
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	1,070,081
Document Type	10-K
Document Period End Date	Dec. 31, 2018
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-Known Seasoned Issuer	Yes
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Public Float			$ 1,521,120,427
Entity Common Stock, Shares Outstanding		58,401,698
Document Fiscal Year Focus	2,018
Document Fiscal Period Focus	FY

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 169,498	$ 111,792	$ 58,321	$ 58,022
Marketable securities	58,088	79,454
Trade receivables, net	67,907	40,394
Inventory	16,117	10,754
Prepaid expenses and other current assets	9,247	6,669
Total current assets	320,857	249,063
Fixed assets, net	12,694	8,376
Intangible assets, net	701,031	132,993
Goodwill	82,341	0
Deposits and other assets	2,299	1,221
Total assets	1,119,222	391,653
Current liabilities:
Accounts payable and accrued expenses	128,199	76,446
Current portion of long-term debt	11,667	0
Deferred revenue	3,716	3,937
Other current liabilities	3,814	1,665
Deferred consideration payable- current	19,400	0
Total current liabilities	166,796	82,048
Deferred revenue - long-term	9,722	7,954
Long-term debt	141,347	144,971
Contingent consideration payable	310,240	0
Deferred consideration payable- long-term	18,300	0
Deferred tax liability	122,032	0
Other long-term liabilities	58	243
Total liabilities	768,495	235,216
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 50,606,147 shares at December 31, 2018. Authorized 125,000,000 shares; issued and outstanding 41,612,395 shares at December 31, 2017.	51	42
Additional paid-in capital	1,288,137	966,534
Accumulated other comprehensive income	1,462	3,969
Accumulated deficit	(938,923)	(814,108)
Total stockholders’ equity	350,727	156,437	$ 119,583	$ 226,001
Total liabilities and stockholders’ equity	$ 1,119,222	$ 391,653

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 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)	50,606,147	41,612,395
Common stock, outstanding shares (in shares)	50,606,147	41,612,395

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset	$ 12,670	$ 4,577	$ 0
Amortization of acquired intangible asset	22,877	15,380	0
Research and development	171,984	117,456	117,633
Selling, general and administrative	153,548	121,271	97,130
Change in the fair value of deferred and contingent consideration	19,340	0	0
Total operating expenses	380,419	258,684	214,763
Loss from operations	(115,685)	(64,292)	(132,058)
Interest expense, net	(12,554)	(12,094)	(8,276)
Other income (expense), net	129	(1,279)	(1,207)
Loss before income tax expense	(128,110)	(77,665)	(141,541)
Income tax benefit (expense)	29	(1,335)	(569)
Net loss attributable to common stockholders	$ (128,081)	$ (79,000)	$ (142,110)
Weighted-average shares outstanding:
Basic and diluted (in shares)	46,576,313	39,183,073	34,044,584
Net loss per share—basic and diluted (in dollars per share)	$ (2.75)	$ (2.02)	$ (4.17)
Net product revenue	$ 264,734	$ 194,392	$ 82,705
Net product revenue
Weighted-average shares outstanding:
Net product revenue	263,005	174,066	81,447
Collaboration and grant revenue
Weighted-average shares outstanding:
Net product revenue	$ 1,729	$ 20,326	$ 1,258

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Statement of Comprehensive Income [Abstract]
Net loss	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (128,081)	$ (79,000)	$ (142,110)
Other comprehensive loss:
Unrealized gain on marketable securities, net of tax									9	225	386
Foreign currency translation (loss) gain									(2,516)	5,229	(671)
Comprehensive loss									$ (130,588)	$ (73,546)	$ (142,395)

Consolidated Statements of Stoc

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common stock	Additional paid-in capital	Accumulated other comprehensive (loss) income	Accumulated deficit
Balance (in shares) at Dec. 31, 2015		33,916,559
Balance at the beginning of the period at Dec. 31, 2015	$ 226,001	$ 34	$ 820,165	$ (1,200)	$ (592,998)
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)		89,216
Exercise of options	968	$ 0	968
Restricted stock vesting and issuance (in shares)		163,635
Restricted stock vesting and issuance	0
Share-based compensation expense	35,009		35,009
Net loss	(142,110)				(142,110)
Comprehensive loss	(285)			(285)
Balance (in shares) at Dec. 31, 2016		34,169,410
Balance at the end of the period at Dec. 31, 2016	119,583	$ 34	856,142	(1,485)	(735,108)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to acquisition (in shares)		6,683,598
Issuance of common stock related to acquisition	75,191	$ 7	75,184
Exercise of options (in shares)		202,085
Exercise of options	2,182	$ 0	2,182
Restricted stock vesting and issuance (in shares)		287,531
Restricted stock vesting and issuance	1	$ 1
Issuance of common stock in connection with an employee stock purchase plan (in shares)		269,771
Issuance of common stock in connection with an employee stock purchase plan	2,467		2,467
Share-based compensation expense	30,559		30,559
Net loss	(79,000)				(79,000)
Comprehensive loss	5,454			5,454
Balance (in shares) at Dec. 31, 2017		41,612,395
Balance at the end of the period at Dec. 31, 2017	$ 156,437	$ 42	966,534	3,969	(814,108)
Common stock, authorized shares (in shares)	125,000,000
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to acquisition	$ 155,860	$ 3	155,857
Issuance of common stock related to equity offering (in shares)		4,600,000
Issuance of common stock related to equity offering	117,916	$ 5	117,911
Exercise of options (in shares)		633,973
Exercise of options	10,868	$ 1	10,867
Restricted stock vesting and issuance (in shares)		119,691
Restricted stock vesting and issuance	0	$ 0
Issuance of common stock in connection with an employee stock purchase plan (in shares)		139,181
Issuance of common stock in connection with an employee stock purchase plan	2,787	$ 0	2,787
Share-based compensation expense	33,252		33,252
Receivable from investor	929		929
Net loss	(128,081)				(128,081)
Comprehensive loss	(2,507)			(2,507)
Balance (in shares) at Dec. 31, 2018		50,606,147
Balance at the end of the period at Dec. 31, 2018	$ 350,727	$ 51	$ 1,288,137	$ 1,462	$ (938,923)
Common stock, authorized shares (in shares)	125,000,000

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Cash flows from operating activities
Net loss	$ (128,081)	$ (79,000)	$ (142,110)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	26,087	17,682	3,290
Change in valuation of warrant liability	0	0	(47)
Change in the fair value of deferred and contingent consideration	19,340	0	0
Amortization of (discounts) premiums on investments, net	(433)	535	1,885
Amortization of debt issuance costs	524	433	302
Share-based compensation expense	33,252	30,559	35,009
Non-cash interest expense	7,518	6,755	6,065
Disposal of asset	2	5	0
Benefit for deferred income taxes	0	199	(199)
Unrealized foreign currency transaction (gains) losses, net	(59)	(459)	1,202
Changes in operating assets and liabilities:
Inventory, net	(5,823)	(6,454)	0
Prepaid expenses and other current assets	(1,609)	(1,784)	1,171
Trade receivables, net	(29,589)	(12,203)	(14,842)
Deposits and other assets	(1,093)	(544)	(278)
Accounts payable and accrued expenses	43,877	24,011	4,259
Other liabilities	1,932	733	(799)
Deferred revenue	6,514	9,469	1,526
Net cash used in operating activities	(27,641)	(10,063)	(103,566)
Cash flows from investing activities
Purchases of fixed assets	(7,097)	(3,101)	(1,776)
Purchases of marketable securities	(68,614)	(81,368)	(85,377)
Sale & redemption of marketable securities	90,423	174,749	191,634
Acquisition of product rights	(8,433)	(77,163)	0
Business acquisition, net of cash acquired	(48,892)	0	0
Net cash (used in) provided by investing activities	(42,613)	13,117	104,481
Cash flows from financing activities
Proceeds from exercise of options	10,868	2,182	968
Proceeds from shares issued under employee stock purchase plan	2,787	2,468	0
Debt issuance costs related to secured term loan	0	(432)	0
Net proceeds from public offering	117,916	0	0
Proceeds from issuance of secured term loan	0	40,000	0
Net cash provided by financing activities	131,571	44,218	968
Effect of exchange rate changes on cash	(3,611)	6,199	(1,584)
Net increase in cash and cash equivalents	57,706	53,471	299
Cash and cash equivalents, beginning of period	111,792	58,321	58,022
Cash and cash equivalents, end of period	169,498	111,792	58,321
Supplemental disclosure of cash information
Cash paid for interest	7,773	6,271	4,513
Cash paid for income taxes	1,583	1,101	943
Supplemental disclosures of non-cash information related to investing and financing activities
Change in unrealized gain on marketable securities, net of tax	9	225	386
Acquisition of product rights and licenses	$ (5,981)	$ 0	$ 0

Acquisitions

Acquisitions	12 Months Ended
	Dec. 31, 2018
Business Combinations [Abstract]
Acquisitions	Acquisitions Agilis Acquisition 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 $ 290.5 million . 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 $ 38.1 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 $533.7 million summarized as follows: Fair Value Cash consideration $ 49,221 Fair value of PTC common stock issued 155,860 Estimated fair value of deferred consideration payable 38,100 Estimated fair value of contingent consideration payable 290,500 Total consideration $ 533,681 The Company recorded the assets acquired and liabilities assumed as of the date of acquisition based on the information available at that time. The Company finalized its accounting for the Merger during the three month period ended December 31, 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, the measurement period adjustments recorded during the period from the acquisition date through December 31, 2018 , and the final allocation of the purchase price as of December 31, 2018 . Preliminary Measurement Period Adjustments Final Allocation as of December 31, 2018 Cash and cash equivalents $ 328 $ — $ 328 Prepaid expenses and other current assets 181 — 181 Fixed assets 153 — 153 Other assets 38 — 38 Intangible assets - IPR&D 480,000 96,500 576,500 Accounts payable and accrued expenses (3,828 ) — (3,828 ) Deferred tax liability (115,200 ) (6,832 ) (122,032 ) Fair value of net assets acquired $ 361,672 $ 89,668 $ 451,340 Goodwill 100,309 (17,968 ) 82,341 Total purchase price $ 461,981 $ 71,700 $ 533,681 The Company incurred approximately $1.7 million in acquisition related expenses as of December 31, 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 was capitalized as of the acquisition date and 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 December 31, 2018 was $ 8.7 million . Pro-Forma Financial Information Associated with the Agilis Acquisition (Unaudited) The following table summarizes certain supplemental pro forma financial information for the twelve-month periods ended December 31, 2018 and 2017 as if the Merger had occurred as of January 1, 2017. The unaudited pro-forma financial information for the twelve-month period ended December 31, 2018 reflects adjustments of $1.7 million related to acquisition fees that are non-recurring in nature. There were no adjustments related to the twelve-month period ended December 31, 2017. Twelve Months Ended December 31, 2018 2017 Revenues $ 264,734 $ 194,392 Net loss attributable to common stockholders $ (138,083 ) $ (93,333 ) Emflaza Acquisition On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to an Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction. The Company concluded that the Transaction included inputs and processes that did not constitute a business under the revised guidance of ASU No. 2017-01, which allows for a screen to evaluate if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. The Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and accounted for the Transaction as an asset acquisition under ASC 805-50. The purchase price consisted of total upfront consideration comprised of $75.0 million in cash and 6,683,598 shares of the Company's common stock with a fair value of $75.2 million . In addition, the Company incurred approximately $2.2 million of acquisition costs, which are capitalized in an asset acquisition and included in the total consideration transferred. Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone. In accordance with the guidance for an asset acquisition, the Company will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset. Refer to Note 18 for further details. The following tables present the total purchase consideration and the preliminary allocation of the purchase consideration for the Transaction as of April 20, 2017 (the “Acquisition Date”): Cash consideration $ 75,000 Fair value of PTC common stock issued to Marathon (6,683,598 shares) 75,190 Acquisition costs 2,163 Total preliminary consideration transferred $ 152,353 Purchase price $ 152,353 Total fair value of tangible assets acquired and liabilities assumed: Inventory 3,980 Emflaza rights $ 148,373 The Emflaza rights intangible asset is being amortized to cost of product sales over its expected useful life of approximately seven years. Given the inherent uncertainty of the Company's sales projections, the Company amortizes the asset on a straight line basis. Refer to Note 18 for further details.

Summary of significant accounti

Summary of significant accounting policies	12 Months Ended
	Dec. 31, 2018
Accounting Policies [Abstract]
Summary of significant accounting policies	Summary of significant accounting policies Basis of presentation The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) and include all adjustments necessary for the fair presentation of the Company’s financial position for the periods presented. Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes, allowance for doubtful accounts, inventory, acquired intangible assets, 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. Consolidation The consolidated financial statements include the accounts of PTC Therapeutics, Inc. and its wholly owned subsidiaries. All inter-company accounts, transactions, and profits have been eliminated in consolidation. Segment and geographic information Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision making group, in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating and reporting segment. Cash equivalents The Company considers all highly liquid investments with a maturity of 90 days or less at the time of purchase to be cash equivalents. Cash equivalents are carried at cost which approximates fair value due to their short-term nature. Marketable securities The Company considers securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. The Company evaluates securities with unrealized losses to determine whether such losses, if any, are other than temporary. Fixed assets Fixed assets are stated at cost. Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows: Leasehold improvements Lesser of useful life or lease term Computer equipment and software 3 years Furniture, fixtures, and lab equipment 7 years Concentration of credit risk The Company’s financial instruments that are exposed to credit risks consist primarily of cash and cash equivalents, available-for-sale marketable securities and accounts receivable. The Company maintains its cash and cash equivalents in bank accounts, which, at times, exceed federally insured limits. The Company has not experienced any credit losses in these accounts and does not believe it is exposed to any significant credit risk on these funds. The Company’s investment policy includes guidelines on the quality of the financial institutions and financial instruments the Company is allowed to invest in, which the Company believes minimizes the exposure to concentration of credit risk. The Company is subject to credit risk from its accounts receivable related to its product sales. The payment terms are predetermined and the Company evaluates the creditworthiness of each customer or distributor on a regular basis. The Company reserves all uninsured amounts billed directly to a patient until the time of cash receipt as collectability is not reasonably assured at the time the product is received. To date, the Company has not incurred any credit losses. Inventories and cost of product sales In January 2017, the European Commission granted a one -year renewal of the Company’s marketing authorization for Translarna for the treatment of nmDMD. Until this renewal, the Company had considered the authorization to be subject to risk and did not capitalize productions costs in inventory as it was not probable that such costs would be recovered. With the renewal, the Company considered recovery of the costs to be probable and began capitalizing production costs in inventory, effective January 1, 2017. Since January 1, 2017, production costs are expensed as cost of product sales when the related products are sold. The costs for a portion of the inventory available for sale were expensed as research and development costs prior to the January 2017 annual renewal of the Translarna marketing authorization and as such the cost of products sold and related gross margins prior to January 1, 2017 are not directly comparable to future cost of products sold and gross margin after January 1, 2017. In April 2017, the Company completed the Transaction (see Note 3). Emflaza, both in tablet and suspension form, received approval from the FDA in February 2017 as a treatment for DMD in patients five years of age and older in the United States. The Company began the commercialization of Emflaza in the United States shortly after the Transaction was completed. The Company utilizes third parties for the commercial distribution of Emflaza, including a third-party logistics company to warehouse Emflaza as well as a specialty pharmacy to sell and distribute Emflaza to patients. All of the Company's supply and manufacturing needs for Emflaza are fulfilled pursuant to exclusive supply agreements assumed by the Company upon close of the Transaction. Production costs are expensed as cost of product sales when the related products are sold. Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Translarna and Emflaza product which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. The following table summarizes the components of the Company’s inventory for the periods indicated: December 31, 2018 December 31, 2017 Raw materials $ 1,431 $ 452 Work in progress 9,324 3,912 Finished goods 5,362 6,390 Total inventory $ 16,117 $ 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 $1.8 million inventory write down for the twelve month period ended December 31, 2018 primarily related to inventory labeling changes. No write down was recorded for the twelve month period ended December 31, 2017. 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 twelve month periods ended December 31, 2018 and December 31, 2017, 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. Deferred rent The Company has an operating lease for office space. Rent expense is recorded on a straight-line basis over the initial lease term. The difference between the actual cash paid and the straight-line rent expense is recorded as deferred rent. Leasehold improvements made related to this lease, subsequent to its inception, are amortized over the remaining lease term. Accumulated other comprehensive income (loss) Accumulated other comprehensive income (loss) consists of unrealized gains or losses on marketable securities and foreign currency translation adjustments. Revenue recognition 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 allowed 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 FASB 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. For the years ended December 31, 2017 and 2016 the Company recognized Translarna sales of $145.2 million and $81.4 million , respectively. For the year ended December 31, 2017 , the Company recognized Emflaza sales of $28.8 million . 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. For the year ended December 31, 2018 , the Company recognized Translarna net sales of $171.0 million and Emflaza net sales of $92.0 million . 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 $ 0.7 million as of December 31, 2018 and $ 0.8 million as of December 31, 2017 . Bad debt expense was immaterial for the years ended December 31, 2018 , 2017 , and 2016 . Research and development costs Research and development expenses include the clinical development costs associated with the Company’s product development programs and research and development costs associated with the Company’s discovery programs. These expenses include internal research and development costs and the costs of research and development conducted on behalf of the Company by third parties, including sponsored university-based research agreements and clinical study vendors. All research and development costs are expensed as incurred. Costs incurred in obtaining technology licenses are charged immediately to research and development expense if the technology licensed has not reached technological feasibility and has no alternative future uses. Nonrefundable advance payments made for goods and services that will be used in future research and development activities are deferred if the contracted party has not yet performed the related activities. The amount deferred is then recognized as expense when the research and development activities are performed. The deferred research and development advance payments were $2.4 million and $0.5 million as of December 31, 2018 and 2017 , respectively. Fair value of financial instruments The Company follows the fair value measurement rules, which provides guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority). • Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date. • Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs). • Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available. Investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments. Warrant liability Warrants to purchase the Company’s common stock with nonstandard antidilution provisions, regardless of the probability or likelihood that may conditionally obligate the issuer to ultimately transfer assets, are classified as liabilities and are recorded at their estimated fair value at each reporting period. Any change in fair value of these warrants is recorded as gain/(loss) on warrant valuation each reporting period in Other expense, net on the Company’s statement of operations. Share-based compensation The Company measures the cost of employee services received in exchange for an award of equity instruments based on the grant date fair value of the award. Restricted stock awards are measured based on the fair market values of the underlying stock on the dates of grant. For service type awards, share-based compensation expense is recognized on a straight-line basis over the period during which the employee is required to provide service in exchange for the entire award. For awards that vest or begin vesting upon achievement of a performance condition, the Company estimates the likelihood of satisfaction of the performance condition and recognizes compensation expense when achievement of the performance condition is deemed probable using an accelerated attribution model. The fair value of options is calculated using the Black-Scholes option pricing model to determine the fair value of stock options on the date of grant based on key assumptions such as expected volatility and expected term. The Company calculates expected volatility based on a historical volatility analysis of peers that were similar with respect to industry, stage of life cycle, size, and financial leverage and will continue to do so until the historical volatility of its common stock is sufficient to measure expected volatility for future option grants. The Company uses the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option. In connection with the adoption of ASU 2016-9, the Company made a policy election to continue its methodology for estimating its forfeiture rate. 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 December 31, 2018 . In December 2017, the SEC staff issued Staff Accounting Bulletin No. 118, Income Tax Accounting Implications of the Tax Cuts and Jobs Act (SAB 118), which allowed the Company to record provisional amounts during a measurement period not to extend beyond one year of the enactment date. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017. In the fourth quarter of 2018, the Company completed its analysis to determine the effect of the Tax Act and recorded no further adjustments. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized. The Company recorded a deferred tax liability in conjunction with the Merger, further discussed in Note 3, of $122.0 million related to the tax basis difference in the In-Process Research and Development, or 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. Foreign currency The functional currencies of the Company’s foreign subsidiaries primarily are the local currencies of the country in which the subsidiary operates. The Company’s asset and liability accounts are translated using the current exchange rate as of the balance sheet date. Stockholders’ equity accounts are translated using historical rates at the balance sheet date. Revenue and expense accounts are translated using a weighted average exchange rate over the period ended on the balance sheet date. Adjustments resulting from the translation of the financial statements of the Company’s foreign subsidiaries into U.S. dollars are accumulated as a separate component of stockholders’ equity within other comprehensive income. Gains or losses resulting from transactions denominated in foreign currencies are included in other income or expense, within the consolidated statements of income. Net (loss) income per share Basic net (loss) income per share is calculated by dividing the net income attributable to common stockholders by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents. Diluted net income per share is calculated by dividing the net income attributable to common stockholders by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method and the if-converted method. During periods in which the Company incurs net losses, both basic and diluted loss per share is calculated by dividing the net loss by the weighted average shares outstanding—potentially dilutive securities are excluded from the calculation because their effect would be anti-dilutive. Dilutive common stock equivalents are comprised of option

The Company

The Company	12 Months Ended
	Dec. 31, 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’s strategy is to bring best-in-class therapies with differentiated clinical benefit to patients affected by rare disorders and to leverage its global commercial infrastructure to maximize value for its patients and other stakeholders. The Company has two products, Translarna ™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged 5 years and over in the 31 member states of the European Economic Area, or EEA, subject to annual renewal and other conditions. 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 late 2019, with an anticipated commercial launch in the United States in 2020. The Company is also preparing a marketing authorization application, or MAA, for PTC-AADC for the treatment of AADC deficiency in the European Union, or EU, for submission to the European Medicines Agency, or EMA, which will follow its BLA submission to the FDA. 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 filed for marketing authorization with ANVISA, the Brazilian regulatory authority, which granted priority review. It expects approval in Brazil by the end 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 two pivotal clinical trials ongoing to evaluate the safety and effectiveness of risdiplam (RG7916, RO7034067), the lead compound in the SMA program. Roche is preparing an NDA and a MAA for risdiplam for the treatment of SMA in the United States and the EU, respectively, which Roche anticipates submitting to the FDA and the EMA in the second half of 2019. In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages 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. 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. Due to enrollment at a slower pace in certain countries than initially expected, in its February 2019 marketing authorization renewal request, the Company asked the EMA to extend the timeframe for submission of the results of Study 041 to the EMA to the end of the third quarter of 2022. 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 December 31, 2018 , Translarna was available in over 40 countries on a commercial basis or pursuant to the EAP program. The Company expects to expand its commercial activities across the EEA pursuant to the marketing authorization granted by the EMA throughout 2019 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, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, which the Company initiated in the fourth quarter of 2018. The Company expects that a potential re-submission of an NDA could occur in 2020. 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. On April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. Emflaza is approved in the United States for the treatment of DMD in patients five years and older. The Transaction was completed pursuant to an asset purchase agreement, dated March 15, 2017, as amended on April 20, 2017, (the "Asset Purchase Agreement"), by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The Transaction was accounted for as an asset acquisition. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction. Upon the closing of the Transaction, the Company paid to Marathon total upfront consideration comprised of $75.0 million in cash, funded through cash on hand, and 6,683,598 shares of the Company’s common stock. The number of shares of common stock issued at closing was determined by dividing $65.0 million by the volume weighted average price per share of the Company’s common stock on the Nasdaq Stock Market for the 15 trading-day period ending on the third trading day immediately preceding the closing. Marathon will be entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset, and a single $50.0 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement. 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 December 31, 2018 , the Company had an accumulated deficit of approximately $938.9 million . The Company has financed its operations to date primarily through the private offering in August 2015 of 3.00% convertible senior notes due 2022 (see Note 7), public offerings of common stock in February 2014, 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 since May 2017, the Company generated revenue from net sales of Emflaza for the treatment of DMD in the United States. The Company expects that 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.

Fair value of financial instrum

Fair value of financial instruments and investments	12 Months Ended
	Dec. 31, 2018
Fair Value Disclosures [Abstract]
Fair value of financial instruments and investments	Fair value of financial instruments and investments Fair value of certain investments is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the year. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices. The Company reviews its investments on a periodic basis for other-than-temporary impairments. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may have a significant adverse effect on the fair value of the investment. The following represents the fair value using the hierarchy described in Note 2 for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of December 31, 2018 and 2017 : December 31, 2018 Total Quoted prices in active markets for identical assets (level 1) Significant other observable inputs (level 2) Significant unobservable inputs (level 3) Marketable securities $ 58,088 $ — $ 58,088 $ — Warrant liability $ — $ — $ — $ — Stock appreciation rights liability $ 3,814 $ — $ — $ 3,814 Deferred consideration payable $ 37,700 $ — $ 37,700 $ — Contingent consideration payable- development and regulatory milestones $ 257,040 $ — $ — $ 257,040 Contingent consideration payable- net sales milestones and royalties $ 53,200 $ — $ — $ 53,200 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 The Company uses the market approach to measure fair value for its financial assets. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The Company’s marketable securities investments classified as Level 2 primarily utilize broker quotes in a nonactive market to value these securities. No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the years ended December 31, 2018 and 2017 . The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2018 and 2017 : December 31, 2018 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 31,657 $ 43 $ (1 ) $ 31,699 Corporate debt securities 26,399 — (10 ) 26,389 Total $ 58,056 $ 43 $ (11 ) $ 58,088 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 Total $ 79,432 $ 52 $ (30 ) $ 79,454 Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. During the year ended December 31, 2018 , the Company did not have any realized gains or losses from the sale of marketable securities. The cost of securities sold is based on the specific identification method. The Company evaluates investments with unrealized losses to determine if the losses are other than temporary. At December 31, 2018 , 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 and intent to hold such investments until recovery of their amortized cost bases, which may be maturity. The Company has determined that it is not more likely than not that the Company will be required to sell the investments before such recovery. In addition, the Company considered the financial condition, credit ratings and near-term prospects of the issuers, and the magnitude of the losses as compared to the cost and the length of time the investments have been in an unrealized loss position when determining if the losses are other than temporary. The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2018 are as follows: December 31, 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 $ (1 ) $ 1,993 $ — $ — $ (1 ) $ 1,993 Corporate debt securities (7 ) 14,230 (3 ) 10,087 $ (10 ) $ 24,317 Total $ (8 ) $ 16,223 $ (3 ) $ 10,087 $ (11 ) $ 26,310 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 December 31, 2018 and 2017 mature as follows: December 31, 2018 Less Than 12 Months More Than 12 Months Commercial paper $ 31,699 $ — Corporate debt securities 26,389 — Total Marketable securities $ 58,088 $ — 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 7. The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the Convertible Notes at December 31, 2018 and 2017 was $146.6 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 7) approximate fair value because of the immediate or short-term maturity of these financial instruments. The carrying amounts for the credit and security agreement approximate fair value based on market activity for other debt instruments with similar characteristics and comparable risk. Deferred consideration payable Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million and 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. 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 payable at December 31, 2018 was estimated to be $37.7 million by applying a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidates. As of December 31, 2018 , $19.4 million of the deferred consideration payable was classified as current on the balance sheet. Level 3 valuation The warrant liability is classified in Other long-term liabilities on the Company’s balance sheet. The warrant liability is marked-to-market each reporting period with the change in fair value recorded as a gain or loss within Other expense, net on the Company’s statement of operations until the warrants are exercised, expire or other facts and circumstances lead the warrant liability to be reclassified as an equity instrument. The fair value of the warrant liability is determined at each reporting period by utilizing the Black-Scholes option pricing model. The stock appreciation rights (SARs) liability is classified in Other liabilities on the Company’s consolidated balance sheets. The SARs liability is marked-to-market each reporting period with the change in fair value recorded as compensation expense on the Company’s consolidated statements of operations until the SARS vest. The fair value of the SARs liability is determined at each reporting period by utilizing the Black-Scholes option pricing model. The 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 fair value of the development and regulatory milestones is estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. The fair value of the net sales milestones and royalties is determined utilizing an option pricing model with Monte Carlo simulation to simulate a range of possible payment scenarios, and the average of the payments in these scenarios is then discounted to calculate present fair value. The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability, SARs liability, and the contingent consideration payable for the years ended December 31, 2018 and 2017 : Level 3 liabilities Warrants SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2016 $ 1 $ 865 $ — $ — Change in fair value — 1,864 — — Payments — (1,064 ) — — Ending balance as of December 31, 2017 $ 1 $ 1,665 $ — $ — Additions — — 263,500 27,000 Change in fair value (1 ) 4,140 (6,460 ) 26,200 Payments — (1,991 ) — — Ending balance as of December 31, 2018 $ — $ 3,814 $ 257,040 $ 53,200 The following significant unobservable inputs were used in the valuation of the warrant liability, SARs liability, and the contingent consideration payable for the years ended December 31, 2018 and 2017 : December 31, 2018 Fair Value Valuation Technique Unobservable Input Range Warrants — Option-pricing model Volatility 59.39% - 60.48% Risk free interest rate 2.6% Strike price $128.00 - $2,520.00 Fair value of common stock $34.32 Expected life 0.59 - 0.72 years SARs $3,814 Option-pricing model Volatility 46.53% - 59.59% Risk free interest rate 2.44% - 2.63% Strike price $6.76 - $30.86 Fair value of common stock $34.32 Expected life 0.01 - 1.01 years Contingent consideration payable- development and regulatory milestones $257,040 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 5.8% - 8.0% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $53,200 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 89% Potential percentage of net sales for royalties 2% - 6% Discount rate 14.0% Projected years of payments 2021 - 2038 December 31, 2017 Fair Value Valuation Technique Unobservable Input Range Warrants $1 Option-pricing model Volatility 69% Risk free interest rate $1.89 Strike price $128.00 - $2,520.00 Fair value of common stock $16.68 Expected life 1.60 - 1.70 years SARs $1,665 Option-pricing model Volatility 31% - 70% Risk free interest rate 1.28% - 1.89% Strike price $6.76 - $30.86 Fair value of common stock $16.68 Expected life 0.00 - 2.00 years 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.

Fixed assets

Fixed assets	12 Months Ended
	Dec. 31, 2018
Property, Plant and Equipment [Abstract]
Fixed assets	Fixed assets Fixed assets, net were as follows at December 31, 2018 and 2017 : December 31, 2018 2017 Leasehold improvements $ 2,384 $ 14,078 Computer equipment and software 4,609 5,471 Furniture, fixtures, and lab equipment 9,965 20,776 Assets in process 3,219 895 20,177 41,220 Less accumulated depreciation and amortization (7,483 ) (32,844 ) Total $ 12,694 $ 8,376 Depreciation expense was approximately $2.6 million , $2.3 million , and $3.3 million for the years ended December 31, 2018 , 2017 , and 2016 , respectively.

Accounts payable and accrued ex

Accounts payable and accrued expenses	12 Months Ended
	Dec. 31, 2018
Payables and Accruals [Abstract]
Accounts payable and accrued expenses	Accounts payable and accrued expenses Accounts payable and accrued expenses at December 31, 2018 and 2017 consist of the following: December 31, 2018 2017 Employee compensation, benefits, and related accruals $ 27,629 $ 17,711 Consulting and contracted research 11,267 5,137 Professional fees 5,574 2,116 Sales allowances and other related costs 29,417 22,257 Royalties and rebates 31,874 11,657 Accounts payable 6,001 15,282 Other 16,437 2,286 Total $ 128,199 $ 76,446

Debt

Debt	12 Months Ended
	Dec. 31, 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 Company’s ability to draw on the remaining $20.0 million under the senior secured term loan facility expired on December 31, 2018. 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 using the effective interest rate method. 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 December 31, 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 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. There have been no redemptions to date. If the Company undergoes a “fundamental change” (as defined in the Indenture governing the Convertible Notes Indenture), subject to certain conditions, holders of the Convertible Notes may require the Company to repurchase for cash all or part of their Convertible Notes at a repurchase price equal to 100% of the principal amount of the Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The Convertible Notes Indenture contains customary events of default with respect to the Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the Convertible Notes when due and payable) occurring and continuing, the Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the Convertible Notes Trustee at the request of such holders (subject to the provisions of the Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately. The Company accounts for the Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the Convertible Notes, the Company separated the Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven -year term of the Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the Convertible Notes is $57.5 million and was recorded in additional paid-in capital. In accounting for the transaction costs related to the issuance of the Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven -year term of the Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the Notes. The Convertible Notes consist of the following: Year ended Liability component 2018 2017 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,746 ) (2,121 ) Less: Debt discount, net (1) (35,054 ) (42,572 ) Net carrying amount $ 113,200 $ 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 $146.6 million as of December 31, 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 December 31, 2018 , the remaining contractual life of the Convertible Notes is approximately 3.6 years . The following table sets forth total interest expense recognized related to the Convertible Notes: Year ended 2018 2017 Contractual interest expense $ 4,500 $ 4,500 Amortization of debt issuance costs 375 337 Amortization of debt discount 7,518 6,755 Total $ 12,393 $ 11,592 Effective interest rate of the liability component 11.0 % 11.0 %

Capital structure

Capital structure	12 Months Ended
	Dec. 31, 2018
Stockholders' Equity Note [Abstract]
Capital structure	Capital structure Common stock 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. As of December 31, 2018 , the Company’s number of authorized shares of common stock was 125,000,000 . Warrants All of the Company’s outstanding warrants are classified as liabilities as of December 31, 2018 and 2017 because they contain non-standard antidilution provisions. The following is a summary of the Company’s outstanding warrants as of December 31, 2018 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019 The following is a summary of the Company’s outstanding warrants as of December 31, 2017 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019

Earnings per share

Earnings per share	12 Months Ended
	Dec. 31, 2018
Earnings Per Share [Abstract]
Earnings per share	Earnings per share Basic earnings per share is computed by dividing net loss available to common stockholders by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss available to common stockholders by the weighted-average number of common shares plus the effect of dilutive potential common shares outstanding during the period. The following table sets forth the computation of basic and diluted earnings per share for common stockholders: Year ended December 31, 2018 2017 2016 Numerator Net loss $ (128,081 ) $ (79,000 ) $ (142,110 ) Denominator Denominator for basic and diluted net loss per share 46,576,313 39,183,073 34,044,584 Net loss per share: Basic and diluted $ (2.75 ) * $ (2.02 ) * $ (4.17 ) * * For the years ended December 31, 2018 , 2017 , and 2016 , the Company experienced a net loss and therefore did not report any dilutive share impact. The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. As of December 31, 2018 2017 2016 Stock Options 8,534,358 6,448,642 5,854,316 Unvested restricted stock 571,479 393,011 271,651 Total 9,105,837 6,841,653 6,125,967

Stock award plan

Stock award plan	12 Months Ended
	Dec. 31, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock award plan	Stock award plan In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases. On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Board approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan. In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan. In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of December 31, 2018 , awards for 729,689 shares of common stock were available for issuance. The Board of Directors has the authority to select the individuals to whom options are granted and determine the terms of each option, including (i) the number of shares of common stock subject to the option; (ii) the date on which the option becomes exercisable; (iii) the option exercise price, which, in the case of incentive stock options, must be at least 100% ( 110% in the case of incentive stock options granted to a stockholder owning in excess of 10% of the Company’s stock) of the fair market value of the common stock as of the date of grant; and (iv) the duration of the option (which, in the case of incentive stock options, may not exceed ten years). Options typically vest over a three - or four -year period. Inducement stock option awards Pursuant to the Nasdaq inducement grant exception, during the year ended December 31, 2018 , the Company issued options to purchase an aggregate of 1,352,800 shares of common stock to certain new hire employees at a weighted-average exercise price of $37.35 per share. Additionally, during the year ended December 31, 2018 , the Company issued restricted stock units to certain new hire employees that upon vesting, will be converted into an aggregate of 7,000 shares of common stock. An aggregate of 202,432 of options previously granted as inducement awards were forfeited during the year ended December 31, 2018 in connection with employee separations from the Company. A summary of stock option activity is as follows: Number of options Weighted- average exercise price Weighted- average remaining contractual term Aggregate intrinsic value (in thousands) Outstanding at December 31, 2015 4,826,477 $ 37.20 Granted 1,500,645 $ 27.90 Exercised (89,216 ) $ 10.85 Forfeited (383,590 ) $ 47.42 Outstanding at December 31, 2016 5,854,316 $ 34.71 Granted 1,913,873 $ 12.34 Exercised (202,085 ) $ 10.80 Forfeited (1,117,462 ) $ 33.65 Outstanding at December 31, 2017 6,448,642 $ 29.00 Granted 3,181,623 $ 26.64 Exercised (633,973 ) $ 18.61 Forfeited (461,934 ) $ 35.36 Outstanding at December 31, 2018 8,534,358 $ 28.58 7.37 $ 88,454 Vested or expected to vest at December 31, 2018 3,881,360 $ 24.81 8.79 $ 44,893 Exercisable at December 31, 2018 4,410,211 $ 32.01 6.02 $ 40,854 The fair values of grants made in the years ended December 31, 2018 , 2017 and 2016 were contemporaneously estimated on the date of grant using the following assumptions: 2018 2017 2016 Risk-free interest rate 2.25% - 3.10% 1.84% - 2.45% 1.30% - 2.24% Expected volatility 64% - 90% 76% - 81% 67% - 78% Expected term 5.03 - 10.00 years 5.04 - 10.00 years 5.05 - 10.00 years The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the years ended December 31, 2018 , 2017 and 2016 was $17.48 , $8.45 , and $17.31 per share, respectively. Restricted Stock Awards —Restricted stock awards are granted subject to certain restrictions, including in some cases service conditions (restricted stock). The grant-date fair value of restricted stock awards, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period. Restricted Stock Units —Restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock units, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period. The following table summarizes information on the Company’s restricted stock awards and units: Restricted Stock Awards and Units Number of Shares Weighted Average Grant Date Fair Value Unvested at December 31, 2017 393,011 $ 15.64 Granted 354,691 $ 19.09 Vested (114,295 ) $ 16.36 Forfeited (61,928 ) $ 17.24 Unvested at December 31, 2018 571,479 $ 17.61 Stock Appreciation Rights —Stock appreciation rights (SARs) entitle the holder to receive, upon exercise, an amount of the Company’s common stock or cash (or a combination thereof) determined by reference to appreciation, from and after the date of grant, in the fair market value of a share of the Company’s common stock over the measurement price based on the exercise date. In May 2016, a total of 897,290 SARs were granted to non-executive employees (the 2016 SARs). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the period ending December 31, 2018 , the Company recorded $4.1 million in compensation expense related to the 2016 SARs. Employee Stock Purchase Plan —In June 2016, the Company established an Employee Stock Purchase Plan (ESPP or the Plan) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Board. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six -month period through payroll withholdings and may purchase, at the end of the six -month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the period ending December 31, 2018 , the Company recorded $1.0 million in compensation expense related to the ESPP. The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows: Year ended December 31, 2018 2017 2016 Research and development $ 16,096 $ 15,456 $ 16,812 Selling, general and administrative 17,156 15,103 18,197 Total $ 33,252 $ 30,559 $ 35,009 As of December 31, 2018 , there was approximately $62.6 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s Plans. This cost is expected to be recognized as compensation expense over the weighted average remaining service period of approximately 2.96 years.

Other comprehensive income (los

Other comprehensive income (loss) and accumulated other comprehensive items	12 Months Ended
	Dec. 31, 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 loss, such as unrealized gains and losses on marketable securities. The following table summarizes other comprehensive income (loss) and the changes in accumulated other comprehensive items, by component, for the years ended December 31, 2018 , 2017 , and 2016 , respectively. Unrealized (Losses)/Gains On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2015 $ (589 ) $ (611 ) $ (1,200 ) Other comprehensive income (loss) before reclassifications 386 (671 ) (285 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 386 (671 ) (285 ) Balance at December 31, 2016 $ (203 ) $ (1,282 ) $ (1,485 ) Other comprehensive income before reclassifications 225 5,229 5,454 Amounts reclassified from other comprehensive items — — — Other comprehensive income 225 5,229 5,454 Balance at December 31, 2017 $ 22 $ 3,947 $ 3,969 Other comprehensive income (loss) before reclassifications 9 (2,516 ) (2,507 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 9 (2,516 ) (2,507 ) Balance at December 31, 2018 $ 31 $ 1,431 $ 1,462

Revenue recognition

Revenue recognition	12 Months Ended
	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Revenue recognition	Revenue recognition Net product sales During the twelve months ended December 31, 2018 , net product sales in the United States were $92.0 million consisting solely of Emflaza, and net product sales not in the United States were $171.0 million and consisting solely of Translarna. The following table presents changes in the Company’s contract liabilities from December 31, 2017 to December 31, 2018 : Balance as of Additions Deductions ASC 606 Adjustment Balance as of Deferred Revenue $ 11,891 $ 6,417 $ (1,433 ) $ (3,937 ) $ 12,938 The Company did not have any contract assets for the During the twelve months ended December 31, 2018 . During the twelve months ended December 31, 2018 , the Company recognized revenue in the period from: December 31, Amounts included in contract liabilities at the beginning of the period $ — Performance obligations satisfied in previous period — Performance obligations satisfied in current period 263,005 Total product revenue $ 263,005 The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the twelve months ended December 31, 2018 . Remaining performance obligations Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of December 31, 2018 , the aggregate amount of transaction price allocated to remaining performance obligations relating to Translarna net product revenue was $12.9 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 December 31, Adjustments As reported Balances without adoption of Topic 606 Assets Current assets: Cash and cash equivalents $ 169,498 $ — $ 169,498 Marketable securities 58,088 — 58,088 Trade receivables, net 67,907 — 67,907 Inventory 16,117 (84 ) 16,033 Prepaid expenses and other current assets 9,247 — 9,247 Total current assets 320,857 (84 ) 320,773 Fixed assets, net 12,694 — 12,694 Intangible assets, net 701,031 — 701,031 Goodwill 82,341 — 82,341 Deposits and other assets 2,299 — 2,299 Total assets $ 1,119,222 $ (84 ) $ 1,119,138 Liabilities and stockholders’ equity Current liabilities: Accounts payable and accrued expenses $ 128,199 $ (2,120 ) $ 126,079 Current portion of long-term debt 11,667 — 11,667 Deferred revenue 3,716 10,563 14,279 Other current liabilities 3,814 — 3,814 Deferred consideration payable- current 19,400 — 19,400 Total current liabilities 166,796 8,443 175,239 Deferred revenue - long-term 9,722 — 9,722 Long-term debt 141,347 — 141,347 Contingent consideration payable 310,240 — 310,240 Deferred consideration payable - long-term 18,300 — 18,300 Deferred tax liability 122,032 — 122,032 Other long-term liabilities 58 — 58 Total liabilities 768,495 8,443 776,938 Stockholders’ equity: Common stock 51 — 51 Additional paid-in capital 1,288,137 — 1,288,137 Accumulated other comprehensive income 1,462 — 1,462 Accumulated deficit (938,923 ) (8,527 ) (947,450 ) Total stockholders’ equity 350,727 (8,527 ) 342,200 Total liabilities and stockholders’ equity $ 1,119,222 $ (84 ) $ 1,119,138 Consolidated statements of operations Impact of changes in accounting policies Twelve Months Ended As reported for the period ended December 31, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 263,005 $ (5,177 ) $ 257,828 Collaboration and grant revenue 1,729 — 1,729 Total revenues 264,734 (5,177 ) 259,557 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 12,670 (84 ) 12,586 Amortization of acquired intangible asset 22,877 — 22,877 Research and development 171,984 — 171,984 Selling, general and administrative 153,548 — 153,548 Change in the fair value of deferred and contingent consideration 19,340 — 19,340 Total operating expenses 380,419 (84 ) 380,335 Loss from operations (115,685 ) (5,093 ) (120,778 ) Interest expense, net (12,554 ) — (12,554 ) Other income, net 129 — 129 Loss before income tax expense (128,110 ) (5,093 ) (133,203 ) Income tax benefit 29 — 29 Net loss attributable to common stockholders $ (128,081 ) $ (5,093 ) $ (133,174 ) iii. Consolidated statements of comprehensive loss Impact of changes in accounting policies Twelve Months Ended As reported for the period ended December 31, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (128,081 ) $ (5,093 ) $ (133,174 ) Other comprehensive loss: Unrealized gain on marketable securities, net of tax 9 — 9 Foreign currency translation loss (2,516 ) — (2,516 ) Comprehensive loss $ (130,588 ) $ (5,093 ) $ (135,681 ) iv. Consolidated statements of cash flows Impact of changes in accounting policies As reported for the period ended December 31, Adjustments Balances without adoption of Topic 606 Cash flows from operating activities Net loss $ (128,081 ) $ (5,093 ) $ (133,174 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 26,087 — 26,087 Change in valuation of deferred and contingent consideration 19,340 — 19,340 Amortization of premiums on investments (433 ) — (433 ) Amortization of debt issuance costs 524 — 524 Share-based compensation expense 33,252 — 33,252 Non-cash interest expense 7,518 — 7,518 Disposal of asset 2 — 2 Unrealized foreign currency transaction (gains) losses, net (59 ) — (59 ) Changes in operating assets and liabilities: 0 Inventory, net (5,823 ) (84 ) (5,907 ) Prepaid expenses and other current assets (1,609 ) — (1,609 ) Trade receivables, net (29,589 ) — (29,589 ) Deposits and other assets (1,093 ) — (1,093 ) Accounts payable and accrued expenses 43,877 (2,120 ) 41,757 Other long-term liabilities 1,932 — 1,932 Deferred revenue 6,514 7,297 13,811 Net cash used in operating activities (27,641 ) — (27,641 ) Cash flows from investing activities Purchases of fixed assets (7,097 ) — (7,097 ) Purchases of marketable securities (68,614 ) — (68,614 ) Sale & redemption of marketable securities 90,423 — 90,423 Acquisition of product rights (8,433 ) — (8,433 ) Business acquisition, net of cash acquired (48,892 ) — (48,892 ) Net cash used in investing activities (42,613 ) — (42,613 ) Cash flows from financing activities Proceeds from exercise of options 10,868 — 10,868 Proceeds from shares issued under employee stock purchase plan 2,787 — 2,787 Net proceeds from public offerings 117,916 — 117,916 Net cash provided by financing activities 131,571 — 131,571 Effect of exchange rate changes on cash (3,611 ) — (3,611 ) Net increase in cash and cash equivalents 57,706 — 57,706 Cash and cash equivalents, beginning of period 111,792 — 111,792 Cash and cash equivalents, end of period $ 169,498 $ — $ 169,498 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 3 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 2 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 2 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 certain 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 $10.0 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 December 31, 2018 is $87.5 million . The remaining potential sales milestones as of December 31, 2018 is $325.0 million upon achievement of certain sales events. In addition, the Company is eligible to receive up to double digit royalties on worldwide annual net sales of a commercial product. For the twelve months ended December 31, 2018 , 2017 , and 2016 , the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.2 million , $20.3 million , and $0.4 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 3 to 4 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 2 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 twelve months ended December 31, 2018 , 2017 , and 2016 , 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 twelve months ended December 31, 2018 , 2017 , and 2016 , the Company did not recognize any revenue related to early stage collaborations. Grant revenue The Company receives grant funding from various institutions and governmental bodies. The grants are typically for early discovery research, and typically the grant program lasts from two to five years. The Company records revenue as the research activities are performed. If the granting agency provides for an upfront payment, the amount is deferred and recognized as revenue as the expenditures are incurred. For the year ended December 31, 2018 and 2017 , the Company did not recognize any grant revenue. For the year ending December 31, 2016, the Company recognized $0.9 million in grant revenue.

Income taxes

Income taxes	12 Months Ended
	Dec. 31, 2018
Income Tax Disclosure [Abstract]
Income taxes	Income taxes The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2018 , 2017 , and 2016 : 2018 2017 2016 Domestic (68,461 ) (54,588 ) (61,446 ) Foreign (59,649 ) (23,077 ) (80,095 ) Total (128,110 ) (77,665 ) (141,541 ) The Income Tax Provision consisted of the following for the years ended December 31, 2018 , 2017 and 2016 : 2018 2017 2016 Current: U.S. Federal $ — $ — $ — U.S. State and Local (38 ) (6 ) (2 ) Foreign (669 ) (1,131 ) (766 ) Deferred: U.S. Federal — (198 ) 199 U.S. State and Local — — — Foreign 736 — — Total tax benefit (expense) $ 29 $ (1,335 ) $ (569 ) A reconciliation of the U.S. statutory income tax rate to the Company’s effective tax rate is as follows: December 31, 2018 2017 2016 Federal income tax provision at statutory rate 21.00 % 34.00 % 34.00 % State income tax provision, net of federal benefit 0.05 (1.01 ) 3.05 Permanent differences (6.41 ) (8.48 ) (3.70 ) Research and development 6.49 19.53 16.66 Change in valuation allowances 2.20 29.10 (30.72 ) Change in deferred tax assets (14.22 ) (64.12 ) — Foreign tax rate differential (9.10 ) (10.33 ) (19.84 ) Benefit allocated from other comprehensive income — (0.26 ) 0.14 Other 0.01 (0.15 ) 0.01 Effective income tax rate 0.02 % (1.72 )% (0.40 )% Accounting for income taxes under U.S. GAAP requires that individual tax-paying entities of the company offset all deferred tax liabilities and assets within each particular tax jurisdiction and present them as a noncurrent deferred tax liability or asset. Amounts in different tax jurisdictions cannot be offset against each other. The noncurrent deferred income tax asset is recorded within deposits and other assets on the balance sheet. The amount of deferred income taxes are as follows: 2018 2017 Assets: Noncurrent deferred income taxes $ 736 $ — Liabilities: Noncurrent deferred income taxes (122,032 ) — Deferred income taxes - net $ (121,296 ) $ — The significant components of the Company’s deferred tax assets and liabilities at December 31, 2018 and 2017 are as follows: 2018 2017 Deferred tax assets: Accrued expense $ 714 $ 625 Amortization 5,148 2,116 Depreciation 1,601 1,749 Federal tax credits 89,070 80,961 State tax credits 5,473 7,148 Federal net operating losses 62,159 61,068 State net operating losses 165 11,884 Foreign net operating losses 736 — Capitalized research and development costs 2,093 3,332 Share based compensation and other 21,411 18,815 Total gross deferred tax assets 188,570 187,698 Less valuation allowance (180,481 ) (177,631 ) Total deferred tax assets, net of valuation allowance $ 8,089 $ 10,067 Deferred tax liabilities: Convertible debt $ (7,353 ) $ (9,927 ) OCI unrealized (gains)/losses — (140 ) Indefinite lived intangible (122,032 ) — Total gross deferred tax liabilities (129,385 ) (10,067 ) Net deferred tax assets (liabilities) $ (121,296 ) $ — At December 31, 2018 and 2017 , the Company recorded valuation allowance against its net deferred tax assets of approximately $180.5 million and $177.6 million , respectively. The change in the valuation allowance during the years ended December 31, 2018 and 2017 was approximately $2.8 million and $5.4 million , respectively. A valuation allowance has been recorded since, in the judgment of management, these assets are not more likely than not to be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during periods in which those temporary differences and carryforwards become deductible or are utilized. As of December 31, 2018 , the Company incurred approximately $296.0 million , $202.4 million , $5.9 million of federal, state, and foreign net operating loss carryforwards, respectively. As a result of the adoption of ASU 2016-09, the Company no longer excludes tax benefits that arose directly from equity compensation in excess of compensation recognized for financial reporting in its U.S. federal and U.S. state net operating loss carryforwards. During 2018, the Company acquired IPR&D as part of the acquisition of Agilis. This asset is currently considered an indefinite-lived intangible with no related book amortization and tested for impairment, annually. As the IPR&D has no tax basis and is an indefinite-lived intangible, the deferred tax liability created at the time of acquisition is not considered positive evidence of future income and is presented as a deferred tax liability in the balance sheet. As of December 31, 2018 , research and development credit carryforwards for federal and state purposes are approximately $15.2 million and $6.6 million , respectively. In addition, the Orphan Drug Credit Carryover available as of December 31, 2018 is approximately $74.0 million . As a result of U.S. tax reform legislation, federal net operating losses generated in 2018 carryforward indefinitely, however, the Company has federal net operating losses that pre-date U.S. tax reform legislation which begin to expire in 2021 and federal credit carryforwards that begin to expire in 2019. State net operating loss carryforwards begin to expire in 2030, and the state credit carryforwards began to expire in 2016. Sections 382 and 383 of the Internal Revenue Code of 1986 subject the future utilization of net operating losses and certain other tax attributes, such as research and development tax credits, to an annual limitation in the event of certain ownership changes, as defined. The Company has undergone an ownership change and has determined that a “change in ownership” as defined by IRC Section 382 of the Internal Revenue Code of 1986, as amended, and the rules and regulations promulgated thereunder, did occur in June of 2013. Accordingly, about $231.5 million of the Company’s NOL carryforwards are limited and the Company can only use $16.7 million for the first five years from the ownership change and $5.7 million per year going forward. Therefore, $169.2 million of the NOL’s will be freed up over the next 20 years and $62.3 million are expected to expire unused which are not included in the deferred tax assets listed above. In summary, there are $296.0 million of NOLs available, out of which $231.5 million are limited by IRC Section 382. At December 31, 2018 , there is $194.5 million available for immediate use and an additional $5.7 million will free up in 2019. The income tax expense for the years ended December 31, 2018 and 2017 differed from the amounts computed by applying the U.S. federal income tax rate of 21% and 34% respectively, to loss before tax expense as a result of foreign taxes, nondeductible expenses, tax credits generated, true up of net operating loss carryforwards, and increase in the Company’s valuation allowance. The Company applies the elements of FASB ASC 740-10 regarding accounting for uncertainty in income taxes. This clarifies the accounting for uncertainty in income taxes recognized in financial statements and required impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. As of December 31, 2018 the Company did not have any unrecognized tax benefits and has not accrued any interest or penalties through 2018 . The Company does not expect to have any unrecognized tax benefits within the next twelve months. The Company’s policy is to recognize interest and penalties related to tax matters within the income tax provision. Tax years beginning in 2014 are generally subject to examination by taxing authorities, although net operating losses from all years are subject to examinations and adjustments for at least three years following the year in which the attributes are used. The Company concluded the examination from the United States Internal Revenue Service for tax year 2014 noting adjustments to the U.S. federal net operating loss carryforwards and research and development credit carryforwards. No other examinations are in process. For all years through December 31, 2016, the Company generated research credits but has not conducted a study to document the qualified activities. This study may result in an adjustment to the Company’s research and development credit carryforwards; however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the deferred tax asset established for the research and development credit carryforwards and the valuation allowance. As a result of U.S. tax reform legislation, distributions of profits from non-U.S. subsidiaries are not expected to cause a significant incremental U.S. tax impact in the future. However, distributions may be subject to non-U.S. withholding taxes if profits are distributed from certain jurisdictions. U.S. federal income taxes have not been provided on undistributed earnings of our international subsidiaries as it is our intention to reinvest any earnings into the respective subsidiaries. It is not practicable to estimate the amount of tax that might be payable if some or all of such earnings were to be repatriated due to the legal structure and complexity of U.S. and local tax laws. As of December 31, 2018 and December 31, 2017 there are no undistributed earnings. We have completed our accounting for the income tax effects of U.S. tax reform legislation and included measurement period adjustments in 2018. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017 which resulted in a provisional benefit of $46.1 million which was offset by an associated change in the valuation allowance.

Commitments and contingencies

Commitments and contingencies	12 Months Ended
	Dec. 31, 2018
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and contingencies Operating leases The Company leases office space in South Plainfield, New Jersey for its principal office under three noncancelable operating leases through May 2022, August 2024 and October 2024 in addition to office space in various countries for international employees primarily through workspace providers. Rent expense was approximately $2.7 million , $2.2 million , and $2.2 million for the years ended December 31, 2018 , 2017 , and 2016 , respectively. The Company also leases certain office equipment under operating leases. Future minimum lease payments as of December 31, 2018 are as follows: 2019 $ 3,216 2020 2,900 2021 2,409 2022 2,082 2023 and thereafter 3,321 Total $ 13,928 Other contingencies Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited (Wellcome Trust) for the research and development of small molecule compounds in connection with its oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company made the first development milestone payment of $0.8 million to Wellcome Trust under the oncology program funding agreement during the second quarter of 2016. Additional milestone payments up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement. The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single- digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon its payment to the SMA Foundation of a specified amount. 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. From time to time in the ordinary course of our business, we are subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in our clinical trials or otherwise gain access to our product candidates. We are not currently aware of any material legal proceedings against us.

Geographic information

Geographic information	12 Months Ended
	Dec. 31, 2018
Segments, Geographical Areas [Abstract]
Geographic information	Geographic information The Company views its operations and manages its business in one operating segment. The following table presents financial information based on the geographic location of the facilities of the Company as of and for the years ended: Year Ended December 31, 2018 United States Non-US Total Total assets $ 1,013,977 $ 105,245 $ 1,119,222 Property and equipment, net $ 10,497 $ 2,197 $ 12,694 Revenue $ 93,694 $ 171,040 $ 264,734 Year Ended December 31, 2017 United States Non-US Total Total assets $ 278,108 $ 113,545 $ 391,653 Property and equipment, net $ 6,272 $ 2,104 $ 8,376 Revenue $ 49,155 $ 145,237 $ 194,392

401(k) plan

401(k) plan	12 Months Ended
	Dec. 31, 2018
Retirement Benefits [Abstract]
401(k) plan	401(k) plan The Company maintains a 401(k) plan for its employees. Employee contributions are voluntary. The Company may match employee contributions in amounts to be determined at the Company’s sole discretion. The Company provides an 92% matching contribution for up to the first 6% of each contributing employee’s base salary contributions. The Company made matching contributions to the 401(k) plan and recorded expense of approximately $2.2 million , $1.6 million and $1.1 million for the years ended December 31, 2018 , 2017 and 2016 , respectively.

Restructuring

Restructuring	12 Months Ended
	Dec. 31, 2018
Restructuring and Related Activities [Abstract]
Restructuring	Restructuring In March 2016, the Company commenced implementation of a reorganization of its operations intended to improve efficiency and better align the Company’s costs and employment structure with its strategic plans. The Company completed its reorganization in June 2016 and recorded a one-time charge of $2.5 million for the year ended December 31, 2016. The total $2.5 million in one-time charges is related to work-force reduction, recorded in research and development and selling, general and administrative expenses in the accompanying statement of operations. All restructuring payments were made prior to December 31, 2017 and as such, the balance of accrued restructuring expenses was $0 as of December 31, 2017 and December 31, 2018, respectively.

Intangible assets and goodwill

Intangible assets and goodwill	12 Months Ended
	Dec. 31, 2018
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets Disclosure	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 7 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 twelve month period ended December 31, 2018 , the Company recorded $ 14.4 million of milestone payments due to net sales of Emflaza, 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 December 31, 2018 , a milestone payable to Marathon of $6.0 million was recorded on the balance sheet within accrued expenses. For the twelve month periods ended December 31, 2018 and 2017 , the Company recognized amortization expense of $22.9 million and $15.4 million , respectively, related to the Emflaza rights intangible asset, resulting in accumulated amortization of $38.3 million as of December 31, 2018 .The estimated future amortization of the Emflaza rights intangible asset is expected to be as follows: As of December 31, 2018 2019 $ 24,283 2020 24,276 2021 24,277 2022 24,277 2023 and thereafter 27,418 Total $ 124,531 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 late 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 value allocated to the indefinite lived intangible assets was $576.5 million . Goodwill As a result of the Merger on August 23, 2018, the Company recorded $ 82.3 million of goodwill, which included a measurement period adjustment of $18.0 million recorded during the three month period ended December 31, 2018 . This adjustment was related to the finalization of the fair values assigned to the intangible assets and corresponding deferred tax liability, the contingent consideration, and the deferred consideration. Refer to Note 3 for further details. 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 twelve month period ended December 31, 2018 . The Company recently filed a request for marketing authorizations for Tegsedi with ANVISA. Waylivra is currently under regulatory review in the EU.

Subsequent events

Subsequent events	12 Months Ended
	Dec. 31, 2018
Subsequent Events [Abstract]
Subsequent events	Subsequent events In January 2019, 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 7,563,725 shares of common stock under the registration statement at a public offering price of $30.20 per share, including 843,725 shares issued upon exercise by the underwriter of its option to purchase additional shares in February 2019. The Company received net proceeds of approximately $224.1 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

Selected quarterly financial da

Selected quarterly financial data (Unaudited)	12 Months Ended
	Dec. 31, 2018
Quarterly Financial Information Disclosure [Abstract]
Selected quarterly financial data (Unaudited)	Selected quarterly financial data (Unaudited) The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2018 and 2017 are as follows: For the quarters ending March 31 June 30 September 30 December 31 2018: Net product revenue $ 55,981 $ 68,170 $ 53,021 $ 85,833 Collaboration and grant revenue 81 573 570 505 Operating expenses 72,805 74,317 101,821 131,476 Loss from operations (16,743 ) (5,574 ) (48,230 ) (45,138 ) Net loss (19,263 ) (9,520 ) (50,969 ) (48,330 ) Basic and diluted net loss per common share(1) $ (0.46 ) $ (0.21 ) $ (1.06 ) $ (0.96 ) 2017: Net product revenue $ 26,442 $ 47,891 $ 41,780 $ 57,953 Collaboration and grant revenue 105 71 73 20,077 Operating expenses 52,902 60,459 72,745 72,578 (Loss) income from operations (26,355 ) (12,497 ) (30,892 ) 5,452 Net (loss) income (29,057 ) (17,475 ) (33,738 ) 1,270 Basic and diluted net (loss) income per common share(1)(2) $ (0.85 ) $ (0.44 ) $ (0.82 ) $ 0.03 (1) The amounts were computed independently for each quarter and the sum of the quarters may not total the annual amounts. (2) Diluted net income per common share for the quarter ending December 31, 2017 excludes the conversion of the Convertible Notes as the effect of their inclusion is anti-dilutive during the period.

Summary of significant accoun_2

Summary of significant accounting policies (Policies)	12 Months Ended
	Dec. 31, 2018
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) and include all adjustments necessary for the fair presentation of the Company’s financial position for the periods presented.
Use of estimates	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.
Consolidation	Consolidation The consolidated financial statements include the accounts of PTC Therapeutics, Inc. and its wholly owned subsidiaries. All inter-company accounts, transactions, and profits have been eliminated in consolidation.
Segment and geographic information	Segment and geographic information Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision making group, in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating and reporting segment.
Cash equivalents	Cash equivalents The Company considers all highly liquid investments with a maturity of 90 days or less at the time of purchase to be cash equivalents. Cash equivalents are carried at cost which approximates fair value due to their short-term nature.
Marketable securities	Marketable securities The Company considers securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. The Company evaluates securities with unrealized losses to determine whether such losses, if any, are other than temporary.
Fixed assets	Fixed assets Fixed assets are stated at cost. Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows: Leasehold improvements Lesser of useful life or lease term Computer equipment and software 3 years Furniture, fixtures, and lab equipment 7 years
Concentration of credit risk	Concentration of credit risk The Company’s financial instruments that are exposed to credit risks consist primarily of cash and cash equivalents, available-for-sale marketable securities and accounts receivable. The Company maintains its cash and cash equivalents in bank accounts, which, at times, exceed federally insured limits. The Company has not experienced any credit losses in these accounts and does not believe it is exposed to any significant credit risk on these funds. The Company’s investment policy includes guidelines on the quality of the financial institutions and financial instruments the Company is allowed to invest in, which the Company believes minimizes the exposure to concentration of credit risk. The Company is subject to credit risk from its accounts receivable related to its product sales. The payment terms are predetermined and the Company evaluates the creditworthiness of each customer or distributor on a regular basis. The Company reserves all uninsured amounts billed directly to a patient until the time of cash receipt as collectability is not reasonably assured at the time the product is received. To date, the Company has not incurred any credit losses.
Inventories and cost of product sales	Inventories and cost of product sales In January 2017, the European Commission granted a one -year renewal of the Company’s marketing authorization for Translarna for the treatment of nmDMD. Until this renewal, the Company had considered the authorization to be subject to risk and did not capitalize productions costs in inventory as it was not probable that such costs would be recovered. With the renewal, the Company considered recovery of the costs to be probable and began capitalizing production costs in inventory, effective January 1, 2017. Since January 1, 2017, production costs are expensed as cost of product sales when the related products are sold. The costs for a portion of the inventory available for sale were expensed as research and development costs prior to the January 2017 annual renewal of the Translarna marketing authorization and as such the cost of products sold and related gross margins prior to January 1, 2017 are not directly comparable to future cost of products sold and gross margin after January 1, 2017. In April 2017, the Company completed the Transaction (see Note 3). Emflaza, both in tablet and suspension form, received approval from the FDA in February 2017 as a treatment for DMD in patients five years of age and older in the United States. The Company began the commercialization of Emflaza in the United States shortly after the Transaction was completed. The Company utilizes third parties for the commercial distribution of Emflaza, including a third-party logistics company to warehouse Emflaza as well as a specialty pharmacy to sell and distribute Emflaza to patients. All of the Company's supply and manufacturing needs for Emflaza are fulfilled pursuant to exclusive supply agreements assumed by the Company upon close of the Transaction. Production costs are expensed as cost of product sales when the related products are sold. Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Translarna and Emflaza product which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. The following table summarizes the components of the Company’s inventory for the periods indicated: December 31, 2018 December 31, 2017 Raw materials $ 1,431 $ 452 Work in progress 9,324 3,912 Finished goods 5,362 6,390 Total inventory $ 16,117 $ 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 $1.8 million inventory write down for the twelve month period ended December 31, 2018 primarily related to inventory labeling changes. No write down was recorded for the twelve month period ended December 31, 2017. 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 twelve month periods ended December 31, 2018 and December 31, 2017, 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.
Deferred rent	Deferred rent The Company has an operating lease for office space. Rent expense is recorded on a straight-line basis over the initial lease term. The difference between the actual cash paid and the straight-line rent expense is recorded as deferred rent. Leasehold improvements made related to this lease, subsequent to its inception, are amortized over the remaining lease term.
Accumulated other comprehensive income (loss)	Accumulated other comprehensive income (loss) Accumulated other comprehensive income (loss) consists of unrealized gains or losses on marketable securities and foreign currency translation adjustments.
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 allowed 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 FASB 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. For the years ended December 31, 2017 and 2016 the Company recognized Translarna sales of $145.2 million and $81.4 million , respectively. For the year ended December 31, 2017 , the Company recognized Emflaza sales of $28.8 million . 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. For the year ended December 31, 2018 , the Company recognized Translarna net sales of $171.0 million and Emflaza net sales of $92.0 million . 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.
Research and development costs	Research and development costs Research and development expenses include the clinical development costs associated with the Company’s product development programs and research and development costs associated with the Company’s discovery programs. These expenses include internal research and development costs and the costs of research and development conducted on behalf of the Company by third parties, including sponsored university-based research agreements and clinical study vendors. All research and development costs are expensed as incurred. Costs incurred in obtaining technology licenses are charged immediately to research and development expense if the technology licensed has not reached technological feasibility and has no alternative future uses. Nonrefundable advance payments made for goods and services that will be used in future research and development activities are deferred if the contracted party has not yet performed the related activities. The amount deferred is then recognized as expense when the research and development activities are performed.
Fair value of financial instruments	Fair value of financial instruments The Company follows the fair value measurement rules, which provides guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority). • Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date. • Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs). • Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available. Investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments.
Warrant liability	Warrant liability Warrants to purchase the Company’s common stock with nonstandard antidilution provisions, regardless of the probability or likelihood that may conditionally obligate the issuer to ultimately transfer assets, are classified as liabilities and are recorded at their estimated fair value at each reporting period. Any change in fair value of these warrants is recorded as gain/(loss) on warrant valuation each reporting period in Other expense, net on the Company’s statement of operations.
Share-based compensation	Share-based compensation The Company measures the cost of employee services received in exchange for an award of equity instruments based on the grant date fair value of the award. Restricted stock awards are measured based on the fair market values of the underlying stock on the dates of grant. For service type awards, share-based compensation expense is recognized on a straight-line basis over the period during which the employee is required to provide service in exchange for the entire award. For awards that vest or begin vesting upon achievement of a performance condition, the Company estimates the likelihood of satisfaction of the performance condition and recognizes compensation expense when achievement of the performance condition is deemed probable using an accelerated attribution model. The fair value of options is calculated using the Black-Scholes option pricing model to determine the fair value of stock options on the date of grant based on key assumptions such as expected volatility and expected term. The Company calculates expected volatility based on a historical volatility analysis of peers that were similar with respect to industry, stage of life cycle, size, and financial leverage and will continue to do so until the historical volatility of its common stock is sufficient to measure expected volatility for future option grants. The Company uses the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.
Income taxes	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 December 31, 2018 . In December 2017, the SEC staff issued Staff Accounting Bulletin No. 118, Income Tax Accounting Implications of the Tax Cuts and Jobs Act (SAB 118), which allowed the Company to record provisional amounts during a measurement period not to extend beyond one year of the enactment date. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017. In the fourth quarter of 2018, the Company completed its analysis to determine the effect of the Tax Act and recorded no further adjustments. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized. The Company recorded a deferred tax liability in conjunction with the Merger, further discussed in Note 3, of $122.0 million related to the tax basis difference in the In-Process Research and Development, or 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.
Foreign currency	Foreign currency The functional currencies of the Company’s foreign subsidiaries primarily are the local currencies of the country in which the subsidiary operates. The Company’s asset and liability accounts are translated using the current exchange rate as of the balance sheet date. Stockholders’ equity accounts are translated using historical rates at the balance sheet date. Revenue and expense accounts are translated using a weighted average exchange rate over the period ended on the balance sheet date. Adjustments resulting from the translation of the financial statements of the Company’s foreign subsidiaries into U.S. dollars are accumulated as a separate component of stockholders’ equity within other comprehensive income. Gains or losses resulting from transactions denominated in foreign currencies are included in other income or expense, within the consolidated statements of income.
Net (loss) income per share	Net (loss) income per share Basic net (loss) income per share is calculated by dividing the net income attributable to common stockholders by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents. Diluted net income per share is calculated by dividing the net income attributable to common stockholders by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method and the if-converted method. During periods in which the Company incurs net losses, both basic and diluted loss per share is calculated by dividing the net loss by the weighted average shares outstanding—potentially dilutive securities are excluded from the calculation because their effect would be anti-dilutive. Dilutive common stock equivalents are comprised of options and unvested restricted stock outstanding under the Company’s stock option plans.
Business combinations and asset acquisitions	Business combinations and asset acquisitions The Company evaluates acquisitions of assets and other similar transactions to assess whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. If the screen is not met, further determination is required as to whether or not the Company has acquired inputs and processes that have the ability to create outputs, which would meet the requirements of a business. If determined to be a business combination, the Company accounts for the transaction under the acquisition method of accounting as indicated in ASC 2017-01, “Business Combinations”, which requires the acquiring entity in a business combination to recognize the fair value of all assets acquired, liabilities assumed, and any non-controlling interest in the acquiree and establishes the acquisition date as the fair value measurement point. Accordingly, the Company recognizes assets acquired and liabilities assumed in business combinations, including contingent assets and liabilities, and non-controlling interest in the acquiree based on the fair value estimates as of the date of acquisition. In accordance with ASC 805, the Company recognizes and measures goodwill as of the acquisition date, as the excess of the fair value of the consideration paid over the fair value of the identified net assets acquired. The consideration for the Company’s business acquisitions may include future payments that are contingent upon the occurrence of a particular event or events. The obligations for such contingent consideration payments are recorded at fair value on the acquisition date. The contingent consideration obligations are then evaluated each reporting period. Changes in the fair value of contingent consideration obligations, other than changes due to payments, are recognized as a (gain) loss on fair value remeasurement of contingent consideration in the consolidated statements of operations. If determined to be an asset acquisition, the Company accounts for the transaction under ASC 805-50, which requires the acquiring entity in an asset acquisition to recognize assets (net assets) based on the cost to the acquiring entity on a relative fair value basis, which includes transaction costs in addition to consideration given. No gain or loss is recognized as of the date of acquisition unless the fair value of noncash assets given as consideration differs from the assets' carrying amounts on the acquiring entity's books. Consideration transferred that is noncash will be measured based on either the cost (which shall be measured based on the fair value of the consideration given) or the fair value of the assets (net assets) acquired, whichever is more reliably measurable. Goodwill is not recognized in an asset acquisition and any excess consideration transferred over the fair value of the net assets acquired is allocated to the identifiable assets based on relative fair values. Contingent consideration payments in asset acquisitions are recognized when the contingency is resolved and the consideration is paid or becomes payable (unless the contingent consideration meets the definition of a derivative, in which case the amount becomes part of the basis in the asset acquired). Upon recognition of the contingent consideration payment, the amount is included in the cost of the acquired asset or group of assets.
Finite-lived intangible assets	Finite-lived intangible assets The Company records the fair value of purchased intangible assets with finite useful lives as of the transaction date of a business combination or asset acquisition. Purchased intangible assets with finite useful lives are amortized to their estimated residual values over their estimated useful lives.
Impairment of long-lived assets	Impairment of long-lived assets The Company monitors its long-lived assets and finite-lived intangibles for indicators of impairment. If such indicators are present, the Company assesses the recoverability of affected assets by determining whether the carrying value of such assets is less than the sum of the undiscounted future cash flows of the assets. If such assets are found not to be recoverable, the Company measures the amount of such impairment by comparing the carrying value of the assets to the fair value of the assets, with the fair value generally determined based on the present value of the expected future cash flows associated with the assets. The Company believes that no impairment of long-lived assets exists as of December 31, 2018 .
Goodwill and Intangible Assets	Indefinite-lived intangible assets consist of 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. The Company performed its annual test for its IPR&D assets and concluded that no impairment exists as of December 31, 2018 . 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. The Company performed its annual test for goodwill as of October 1, 2018 and concluded that no impairment exists as of December 31, 2018 .
Recent accounting pronouncements	Recent accounting pronouncements In February 2016, the FASB issued 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 will adopt this guidance on January 1, 2019, as well as the package of practical expedients permitted under the transition guidance within the new standard. The Company believes that the adoption of ASU No. 2016-2 will not have a material impact on its consolidated results of operations, and expects to record approximately $10 - $15 million of lease assets and lease liabilities to the balance sheet. 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 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 will adopt this guidance on January 1, 2019. The Company believes that the adoption of ASU No. 2018-02 will not have a material impact 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 will adopt this guidance on January 1, 2019. The Company 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. In November 2018, the FASB issued ASU 2018-18,"Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606”. ASU 2018-18 provides guidance on whether certain transactions between collaborative arrangement participants should be accounted for with revenue under Topic 606. 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. 2018-18 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 November 2015, the FASB issued ASU No. 2015-17, “Income Taxes (Topic 740): Balance Sheet Classification of Deferred Taxes”. This standard requires all deferred tax assets and liabilities to be classified as non-current on the balance sheet instead of separating deferred taxes into current and non-current amounts. In addition, valuation allowance allocations between current and non-current deferred tax assets are no longer required because those allowances also will be classified as non-current. This standard is effective for public companies for annual periods beginning after December 15, 2016. The Company adopted the guidance on January 1, 2017 on a prospective basis. As the Company’s deferred tax assets are provided with full valuation allowance and the deferred tax liability is non-current as of December 31, 2018 , adoption of this standard did not have a significant impact on the Company's financial statements. 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 the guidance on January 1, 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 on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In March 2016, the FASB issued ASU No. 2016-9, “Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting”. This standard requires the recognition of all income tax effects of awards in the income statement when the awards vest or are settled, with Additional Paid in Capital (APIC) pools to be eliminated. In addition, the standard will increase the amount an employer can withhold to cover income taxes on awards and still qualify for the exception to liability classification for shares used to satisfy the employer’s statutory income tax withholding obligation as well as allowing companies to elect whether to account for forfeitures of share-based payments by recognizing forfeitures of awards as they occur or estimating the number of awards expected to be forfeited and adjusting the estimate when it is likely to change, as is currently required. This standard is effective for public companies for fiscal years beginning after December 15, 2016 and interim periods within those years. The Company adopted the guidance on January 1, 2017 and on a prospective basis, the Company records all excess tax benefits and deficiencies as income tax expense or benefit. Due to the Company's history of operating losses, the adoption did not result in changes to the Company's Net loss or Retained earnings. In connection with the adoption of ASU 2016-9, the Company made a policy election to continue its methodology for estimating its forfeiture rate. In 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 the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In November 2016, the FASB issued ASU 2016-16, “Intra-Entity Transfers of Assets Other Than Inventory”. ASU 2016-16 requires companies to account for the income tax effects of intercompany transfers of assets other than inventory (e.g., intangible assets) when the transfer occurs. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. 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 the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In January 2017, the FASB issued ASU No. 2017-01, "Business Combinations (Topic 805): Clarifying the Definition of a Business". This standard changed the definition of a business to help entities determine whether a set of transferred assets and activities is a business. This standard is effective for public companies for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, with early adoption permitted. The Company elected to early adopt ASU No. 2017-01 and applied the guidance to the Transaction, which was accounted for as an asset acquisition under the revised guidance. 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 early adopted this guidance in the fourth quarter ended December 31, 2018 . The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. 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 the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

Acquisitions (Tables)

Acquisitions (Tables)	12 Months Ended
	Dec. 31, 2018
Business Combinations [Abstract]
Schedule of Business Acquisitions	The fair value of consideration totaled approximately $533.7 million summarized as follows: Fair Value Cash consideration $ 49,221 Fair value of PTC common stock issued 155,860 Estimated fair value of deferred consideration payable 38,100 Estimated fair value of contingent consideration payable 290,500 Total consideration $ 533,681
Preliminary Allocation and Purchase Consideration	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, the measurement period adjustments recorded during the period from the acquisition date through December 31, 2018 , and the final allocation of the purchase price as of December 31, 2018 . Preliminary Measurement Period Adjustments Final Allocation as of December 31, 2018 Cash and cash equivalents $ 328 $ — $ 328 Prepaid expenses and other current assets 181 — 181 Fixed assets 153 — 153 Other assets 38 — 38 Intangible assets - IPR&D 480,000 96,500 576,500 Accounts payable and accrued expenses (3,828 ) — (3,828 ) Deferred tax liability (115,200 ) (6,832 ) (122,032 ) Fair value of net assets acquired $ 361,672 $ 89,668 $ 451,340 Goodwill 100,309 (17,968 ) 82,341 Total purchase price $ 461,981 $ 71,700 $ 533,681 Purchase price $ 152,353 Total fair value of tangible assets acquired and liabilities assumed: Inventory 3,980 Emflaza rights $ 148,373
Business Acquisition, Pro Forma Information	The following table summarizes certain supplemental pro forma financial information for the twelve-month periods ended December 31, 2018 and 2017 as if the Merger had occurred as of January 1, 2017. The unaudited pro-forma financial information for the twelve-month period ended December 31, 2018 reflects adjustments of $1.7 million related to acquisition fees that are non-recurring in nature. There were no adjustments related to the twelve-month period ended December 31, 2017. Twelve Months Ended December 31, 2018 2017 Revenues $ 264,734 $ 194,392 Net loss attributable to common stockholders $ (138,083 ) $ (93,333 )
Schedule of Purchase Price	The following tables present the total purchase consideration and the preliminary allocation of the purchase consideration for the Transaction as of April 20, 2017 (the “Acquisition Date”): Cash consideration $ 75,000 Fair value of PTC common stock issued to Marathon (6,683,598 shares) 75,190 Acquisition costs 2,163 Total preliminary consideration transferred $ 152,353

Summary of significant accoun_3

Summary of significant accounting policies (Tables)	12 Months Ended
	Dec. 31, 2018
Accounting Policies [Abstract]
Schedule of estimated useful life of related assets	Depreciation is computed starting when the asset is placed into service on a straight-line basis over the estimated useful life of the related asset as follows: Leasehold improvements Lesser of useful life or lease term Computer equipment and software 3 years Furniture, fixtures, and lab equipment 7 years
Schedule of inventory	The following table summarizes the components of the Company’s inventory for the periods indicated: December 31, 2018 December 31, 2017 Raw materials $ 1,431 $ 452 Work in progress 9,324 3,912 Finished goods 5,362 6,390 Total inventory $ 16,117 $ 10,754

Fair value of financial instr_2

Fair value of financial instruments and investments (Tables)	12 Months Ended
	Dec. 31, 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 in Note 2 for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of December 31, 2018 and 2017 : December 31, 2018 Total Quoted prices in active markets for identical assets (level 1) Significant other observable inputs (level 2) Significant unobservable inputs (level 3) Marketable securities $ 58,088 $ — $ 58,088 $ — Warrant liability $ — $ — $ — $ — Stock appreciation rights liability $ 3,814 $ — $ — $ 3,814 Deferred consideration payable $ 37,700 $ — $ 37,700 $ — Contingent consideration payable- development and regulatory milestones $ 257,040 $ — $ — $ 257,040 Contingent consideration payable- net sales milestones and royalties $ 53,200 $ — $ — $ 53,200 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
Summary of marketable securities accounted for as available-for-sale securities	The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2018 and 2017 : December 31, 2018 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 31,657 $ 43 $ (1 ) $ 31,699 Corporate debt securities 26,399 — (10 ) 26,389 Total $ 58,056 $ 43 $ (11 ) $ 58,088 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 Total $ 79,432 $ 52 $ (30 ) $ 79,454
Available-for-sale securities, continuous unrealized loss position, fair value	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, 2018 are as follows: December 31, 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 $ (1 ) $ 1,993 $ — $ — $ (1 ) $ 1,993 Corporate debt securities (7 ) 14,230 (3 ) 10,087 $ (10 ) $ 24,317 Total $ (8 ) $ 16,223 $ (3 ) $ 10,087 $ (11 ) $ 26,310 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 December 31, 2018 and 2017 mature as follows: December 31, 2018 Less Than 12 Months More Than 12 Months Commercial paper $ 31,699 $ — Corporate debt securities 26,389 — Total Marketable securities $ 58,088 $ — 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
Fair value of the Company's Level 3 valuation for warrant liability	The following significant unobservable inputs were used in the valuation of the warrant liability, SARs liability, and the contingent consideration payable for the years ended December 31, 2018 and 2017 : December 31, 2018 Fair Value Valuation Technique Unobservable Input Range Warrants — Option-pricing model Volatility 59.39% - 60.48% Risk free interest rate 2.6% Strike price $128.00 - $2,520.00 Fair value of common stock $34.32 Expected life 0.59 - 0.72 years SARs $3,814 Option-pricing model Volatility 46.53% - 59.59% Risk free interest rate 2.44% - 2.63% Strike price $6.76 - $30.86 Fair value of common stock $34.32 Expected life 0.01 - 1.01 years Contingent consideration payable- development and regulatory milestones $257,040 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 5.8% - 8.0% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $53,200 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 89% Potential percentage of net sales for royalties 2% - 6% Discount rate 14.0% Projected years of payments 2021 - 2038 December 31, 2017 Fair Value Valuation Technique Unobservable Input Range Warrants $1 Option-pricing model Volatility 69% Risk free interest rate $1.89 Strike price $128.00 - $2,520.00 Fair value of common stock $16.68 Expected life 1.60 - 1.70 years SARs $1,665 Option-pricing model Volatility 31% - 70% Risk free interest rate 1.28% - 1.89% Strike price $6.76 - $30.86 Fair value of common stock $16.68 Expected life 0.00 - 2.00 years The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the warrant liability, SARs liability, and the contingent consideration payable for the years ended December 31, 2018 and 2017 : Level 3 liabilities Warrants SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2016 $ 1 $ 865 $ — $ — Change in fair value — 1,864 — — Payments — (1,064 ) — — Ending balance as of December 31, 2017 $ 1 $ 1,665 $ — $ — Additions — — 263,500 27,000 Change in fair value (1 ) 4,140 (6,460 ) 26,200 Payments — (1,991 ) — — Ending balance as of December 31, 2018 $ — $ 3,814 $ 257,040 $ 53,200

Fixed assets (Tables)

Fixed assets (Tables)	12 Months Ended
	Dec. 31, 2018
Property, Plant and Equipment [Abstract]
Schedule of fixed assets, net	Fixed assets, net were as follows at December 31, 2018 and 2017 : December 31, 2018 2017 Leasehold improvements $ 2,384 $ 14,078 Computer equipment and software 4,609 5,471 Furniture, fixtures, and lab equipment 9,965 20,776 Assets in process 3,219 895 20,177 41,220 Less accumulated depreciation and amortization (7,483 ) (32,844 ) Total $ 12,694 $ 8,376

Accounts payable and accrued _2

Accounts payable and accrued expenses (Tables)	12 Months Ended
	Dec. 31, 2018
Payables and Accruals [Abstract]
Schedule of components of accounts payable and accrued expenses	Accounts payable and accrued expenses at December 31, 2018 and 2017 consist of the following: December 31, 2018 2017 Employee compensation, benefits, and related accruals $ 27,629 $ 17,711 Consulting and contracted research 11,267 5,137 Professional fees 5,574 2,116 Sales allowances and other related costs 29,417 22,257 Royalties and rebates 31,874 11,657 Accounts payable 6,001 15,282 Other 16,437 2,286 Total $ 128,199 $ 76,446

Debt (Tables)

Debt (Tables)	12 Months Ended
	Dec. 31, 2018
Debt Disclosure [Abstract]
Summary of convertible notes	The Convertible Notes consist of the following: Year ended Liability component 2018 2017 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,746 ) (2,121 ) Less: Debt discount, net (1) (35,054 ) (42,572 ) Net carrying amount $ 113,200 $ 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: Year ended 2018 2017 Contractual interest expense $ 4,500 $ 4,500 Amortization of debt issuance costs 375 337 Amortization of debt discount 7,518 6,755 Total $ 12,393 $ 11,592 Effective interest rate of the liability component 11.0 % 11.0 %

Capital structure (Tables)

Capital structure (Tables)	12 Months Ended
	Dec. 31, 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 December 31, 2018 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019 The following is a summary of the Company’s outstanding warrants as of December 31, 2017 : Warrant shares Exercise price Expiration Common stock 7,030 $ 128.00 2019 Common stock 130 $ 2,520.00 2019

Earnings per share (Tables)

Earnings per share (Tables)	12 Months Ended
	Dec. 31, 2018
Earnings Per Share [Abstract]
Schedule of computation of basic and diluted net loss per share for common stockholders	The following table sets forth the computation of basic and diluted earnings per share for common stockholders: Year ended December 31, 2018 2017 2016 Numerator Net loss $ (128,081 ) $ (79,000 ) $ (142,110 ) Denominator Denominator for basic and diluted net loss per share 46,576,313 39,183,073 34,044,584 Net loss per share: Basic and diluted $ (2.75 ) * $ (2.02 ) * $ (4.17 ) * * For the years ended December 31, 2018 , 2017 , and 2016 , the Company experienced a net loss and therefore did not report any dilutive share impact.
Schedule of historical dilutive common share equivalents outstanding	The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. As of December 31, 2018 2017 2016 Stock Options 8,534,358 6,448,642 5,854,316 Unvested restricted stock 571,479 393,011 271,651 Total 9,105,837 6,841,653 6,125,967

Stock award plan (Tables)

Stock award plan (Tables)	12 Months Ended
	Dec. 31, 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 options Weighted- average exercise price Weighted- average remaining contractual term Aggregate intrinsic value (in thousands) Outstanding at December 31, 2015 4,826,477 $ 37.20 Granted 1,500,645 $ 27.90 Exercised (89,216 ) $ 10.85 Forfeited (383,590 ) $ 47.42 Outstanding at December 31, 2016 5,854,316 $ 34.71 Granted 1,913,873 $ 12.34 Exercised (202,085 ) $ 10.80 Forfeited (1,117,462 ) $ 33.65 Outstanding at December 31, 2017 6,448,642 $ 29.00 Granted 3,181,623 $ 26.64 Exercised (633,973 ) $ 18.61 Forfeited (461,934 ) $ 35.36 Outstanding at December 31, 2018 8,534,358 $ 28.58 7.37 $ 88,454 Vested or expected to vest at December 31, 2018 3,881,360 $ 24.81 8.79 $ 44,893 Exercisable at December 31, 2018 4,410,211 $ 32.01 6.02 $ 40,854
Schedule of assumptions used to estimate fair values of grants made on the date of grant	The fair values of grants made in the years ended December 31, 2018 , 2017 and 2016 were contemporaneously estimated on the date of grant using the following assumptions: 2018 2017 2016 Risk-free interest rate 2.25% - 3.10% 1.84% - 2.45% 1.30% - 2.24% Expected volatility 64% - 90% 76% - 81% 67% - 78% Expected term 5.03 - 10.00 years 5.04 - 10.00 years 5.05 - 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 Shares Weighted Average Grant Date Fair Value Unvested at December 31, 2017 393,011 $ 15.64 Granted 354,691 $ 19.09 Vested (114,295 ) $ 16.36 Forfeited (61,928 ) $ 17.24 Unvested at December 31, 2018 571,479 $ 17.61
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: Year ended December 31, 2018 2017 2016 Research and development $ 16,096 $ 15,456 $ 16,812 Selling, general and administrative 17,156 15,103 18,197 Total $ 33,252 $ 30,559 $ 35,009

Other comprehensive income (l_2

Other comprehensive income (loss) and accumulated other comprehensive items (Tables)	12 Months Ended
	Dec. 31, 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 table summarizes other comprehensive income (loss) and the changes in accumulated other comprehensive items, by component, for the years ended December 31, 2018 , 2017 , and 2016 , respectively. Unrealized (Losses)/Gains On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2015 $ (589 ) $ (611 ) $ (1,200 ) Other comprehensive income (loss) before reclassifications 386 (671 ) (285 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 386 (671 ) (285 ) Balance at December 31, 2016 $ (203 ) $ (1,282 ) $ (1,485 ) Other comprehensive income before reclassifications 225 5,229 5,454 Amounts reclassified from other comprehensive items — — — Other comprehensive income 225 5,229 5,454 Balance at December 31, 2017 $ 22 $ 3,947 $ 3,969 Other comprehensive income (loss) before reclassifications 9 (2,516 ) (2,507 ) Amounts reclassified from other comprehensive items — — — Other comprehensive income (loss) 9 (2,516 ) (2,507 ) Balance at December 31, 2018 $ 31 $ 1,431 $ 1,462

Revenue recognition (Tables)

Revenue recognition (Tables)	12 Months Ended
	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Contract liabilities, rollforward and revenue recognition	The following table presents changes in the Company’s contract liabilities from December 31, 2017 to December 31, 2018 : Balance as of Additions Deductions ASC 606 Adjustment Balance as of Deferred Revenue $ 11,891 $ 6,417 $ (1,433 ) $ (3,937 ) $ 12,938 The Company did not have any contract assets for the During the twelve months ended December 31, 2018 . During the twelve months ended December 31, 2018 , the Company recognized revenue in the period from: December 31, Amounts included in contract liabilities at the beginning of the period $ — Performance obligations satisfied in previous period — Performance obligations satisfied in current period 263,005 Total product revenue $ 263,005
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 December 31, Adjustments As reported Balances without adoption of Topic 606 Assets Current assets: Cash and cash equivalents $ 169,498 $ — $ 169,498 Marketable securities 58,088 — 58,088 Trade receivables, net 67,907 — 67,907 Inventory 16,117 (84 ) 16,033 Prepaid expenses and other current assets 9,247 — 9,247 Total current assets 320,857 (84 ) 320,773 Fixed assets, net 12,694 — 12,694 Intangible assets, net 701,031 — 701,031 Goodwill 82,341 — 82,341 Deposits and other assets 2,299 — 2,299 Total assets $ 1,119,222 $ (84 ) $ 1,119,138 Liabilities and stockholders’ equity Current liabilities: Accounts payable and accrued expenses $ 128,199 $ (2,120 ) $ 126,079 Current portion of long-term debt 11,667 — 11,667 Deferred revenue 3,716 10,563 14,279 Other current liabilities 3,814 — 3,814 Deferred consideration payable- current 19,400 — 19,400 Total current liabilities 166,796 8,443 175,239 Deferred revenue - long-term 9,722 — 9,722 Long-term debt 141,347 — 141,347 Contingent consideration payable 310,240 — 310,240 Deferred consideration payable - long-term 18,300 — 18,300 Deferred tax liability 122,032 — 122,032 Other long-term liabilities 58 — 58 Total liabilities 768,495 8,443 776,938 Stockholders’ equity: Common stock 51 — 51 Additional paid-in capital 1,288,137 — 1,288,137 Accumulated other comprehensive income 1,462 — 1,462 Accumulated deficit (938,923 ) (8,527 ) (947,450 ) Total stockholders’ equity 350,727 (8,527 ) 342,200 Total liabilities and stockholders’ equity $ 1,119,222 $ (84 ) $ 1,119,138 Consolidated statements of operations Impact of changes in accounting policies Twelve Months Ended As reported for the period ended December 31, Adjustments As reported Balances without adoption of Topic 606 Revenues: Net product revenue $ 263,005 $ (5,177 ) $ 257,828 Collaboration and grant revenue 1,729 — 1,729 Total revenues 264,734 (5,177 ) 259,557 Operating expenses: Cost of product sales, excluding amortization of acquired intangible asset 12,670 (84 ) 12,586 Amortization of acquired intangible asset 22,877 — 22,877 Research and development 171,984 — 171,984 Selling, general and administrative 153,548 — 153,548 Change in the fair value of deferred and contingent consideration 19,340 — 19,340 Total operating expenses 380,419 (84 ) 380,335 Loss from operations (115,685 ) (5,093 ) (120,778 ) Interest expense, net (12,554 ) — (12,554 ) Other income, net 129 — 129 Loss before income tax expense (128,110 ) (5,093 ) (133,203 ) Income tax benefit 29 — 29 Net loss attributable to common stockholders $ (128,081 ) $ (5,093 ) $ (133,174 ) iii. Consolidated statements of comprehensive loss Impact of changes in accounting policies Twelve Months Ended As reported for the period ended December 31, Adjustments As reported Balances without adoption of Topic 606 Net loss $ (128,081 ) $ (5,093 ) $ (133,174 ) Other comprehensive loss: Unrealized gain on marketable securities, net of tax 9 — 9 Foreign currency translation loss (2,516 ) — (2,516 ) Comprehensive loss $ (130,588 ) $ (5,093 ) $ (135,681 ) iv. Consolidated statements of cash flows Impact of changes in accounting policies As reported for the period ended December 31, Adjustments Balances without adoption of Topic 606 Cash flows from operating activities Net loss $ (128,081 ) $ (5,093 ) $ (133,174 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 26,087 — 26,087 Change in valuation of deferred and contingent consideration 19,340 — 19,340 Amortization of premiums on investments (433 ) — (433 ) Amortization of debt issuance costs 524 — 524 Share-based compensation expense 33,252 — 33,252 Non-cash interest expense 7,518 — 7,518 Disposal of asset 2 — 2 Unrealized foreign currency transaction (gains) losses, net (59 ) — (59 ) Changes in operating assets and liabilities: 0 Inventory, net (5,823 ) (84 ) (5,907 ) Prepaid expenses and other current assets (1,609 ) — (1,609 ) Trade receivables, net (29,589 ) — (29,589 ) Deposits and other assets (1,093 ) — (1,093 ) Accounts payable and accrued expenses 43,877 (2,120 ) 41,757 Other long-term liabilities 1,932 — 1,932 Deferred revenue 6,514 7,297 13,811 Net cash used in operating activities (27,641 ) — (27,641 ) Cash flows from investing activities Purchases of fixed assets (7,097 ) — (7,097 ) Purchases of marketable securities (68,614 ) — (68,614 ) Sale & redemption of marketable securities 90,423 — 90,423 Acquisition of product rights (8,433 ) — (8,433 ) Business acquisition, net of cash acquired (48,892 ) — (48,892 ) Net cash used in investing activities (42,613 ) — (42,613 ) Cash flows from financing activities Proceeds from exercise of options 10,868 — 10,868 Proceeds from shares issued under employee stock purchase plan 2,787 — 2,787 Net proceeds from public offerings 117,916 — 117,916 Net cash provided by financing activities 131,571 — 131,571 Effect of exchange rate changes on cash (3,611 ) — (3,611 ) Net increase in cash and cash equivalents 57,706 — 57,706 Cash and cash equivalents, beginning of period 111,792 — 111,792 Cash and cash equivalents, end of period $ 169,498 $ — $ 169,498

Income taxes (Tables)

Income taxes (Tables)	12 Months Ended
	Dec. 31, 2018
Income Tax Disclosure [Abstract]
Schedule of Income before Income Tax, Domestic and Foreign	The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2018 , 2017 , and 2016 : 2018 2017 2016 Domestic (68,461 ) (54,588 ) (61,446 ) Foreign (59,649 ) (23,077 ) (80,095 ) Total (128,110 ) (77,665 ) (141,541 )
Components of Income Tax Provision	The Income Tax Provision consisted of the following for the years ended December 31, 2018 , 2017 and 2016 : 2018 2017 2016 Current: U.S. Federal $ — $ — $ — U.S. State and Local (38 ) (6 ) (2 ) Foreign (669 ) (1,131 ) (766 ) Deferred: U.S. Federal — (198 ) 199 U.S. State and Local — — — Foreign 736 — — Total tax benefit (expense) $ 29 $ (1,335 ) $ (569 )
Schedule of reconciliation of the U.S. statutory income tax rate to the Company's effective tax rate	A reconciliation of the U.S. statutory income tax rate to the Company’s effective tax rate is as follows: December 31, 2018 2017 2016 Federal income tax provision at statutory rate 21.00 % 34.00 % 34.00 % State income tax provision, net of federal benefit 0.05 (1.01 ) 3.05 Permanent differences (6.41 ) (8.48 ) (3.70 ) Research and development 6.49 19.53 16.66 Change in valuation allowances 2.20 29.10 (30.72 ) Change in deferred tax assets (14.22 ) (64.12 ) — Foreign tax rate differential (9.10 ) (10.33 ) (19.84 ) Benefit allocated from other comprehensive income — (0.26 ) 0.14 Other 0.01 (0.15 ) 0.01 Effective income tax rate 0.02 % (1.72 )% (0.40 )%
Schedule of significant components of the Company's deferred tax assets and liabilities	The significant components of the Company’s deferred tax assets and liabilities at December 31, 2018 and 2017 are as follows: 2018 2017 Deferred tax assets: Accrued expense $ 714 $ 625 Amortization 5,148 2,116 Depreciation 1,601 1,749 Federal tax credits 89,070 80,961 State tax credits 5,473 7,148 Federal net operating losses 62,159 61,068 State net operating losses 165 11,884 Foreign net operating losses 736 — Capitalized research and development costs 2,093 3,332 Share based compensation and other 21,411 18,815 Total gross deferred tax assets 188,570 187,698 Less valuation allowance (180,481 ) (177,631 ) Total deferred tax assets, net of valuation allowance $ 8,089 $ 10,067 Deferred tax liabilities: Convertible debt $ (7,353 ) $ (9,927 ) OCI unrealized (gains)/losses — (140 ) Indefinite lived intangible (122,032 ) — Total gross deferred tax liabilities (129,385 ) (10,067 ) Net deferred tax assets (liabilities) $ (121,296 ) $ —

Commitments and contingencies (

Commitments and contingencies (Tables)	12 Months Ended
	Dec. 31, 2018
Commitments and Contingencies Disclosure [Abstract]
Schedule of future minimum lease payments	The Company also leases certain office equipment under operating leases. Future minimum lease payments as of December 31, 2018 are as follows: 2019 $ 3,216 2020 2,900 2021 2,409 2022 2,082 2023 and thereafter 3,321 Total $ 13,928

Geographic information (Tables)

Geographic information (Tables)	12 Months Ended
	Dec. 31, 2018
Segments, Geographical Areas [Abstract]
Summary of financial information based on geographical location	The following table presents financial information based on the geographic location of the facilities of the Company as of and for the years ended: Year Ended December 31, 2018 United States Non-US Total Total assets $ 1,013,977 $ 105,245 $ 1,119,222 Property and equipment, net $ 10,497 $ 2,197 $ 12,694 Revenue $ 93,694 $ 171,040 $ 264,734 Year Ended December 31, 2017 United States Non-US Total Total assets $ 278,108 $ 113,545 $ 391,653 Property and equipment, net $ 6,272 $ 2,104 $ 8,376 Revenue $ 49,155 $ 145,237 $ 194,392

Intangible assets and goodwill

Intangible assets and goodwill (Tables)	12 Months Ended
	Dec. 31, 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 December 31, 2018 2019 $ 24,283 2020 24,276 2021 24,277 2022 24,277 2023 and thereafter 27,418 Total $ 124,531

Selected quarterly financial _2

Selected quarterly financial data (Tables)	12 Months Ended
	Dec. 31, 2018
Quarterly Financial Information Disclosure [Abstract]
Summary of quarterly data	The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2018 and 2017 are as follows: For the quarters ending March 31 June 30 September 30 December 31 2018: Net product revenue $ 55,981 $ 68,170 $ 53,021 $ 85,833 Collaboration and grant revenue 81 573 570 505 Operating expenses 72,805 74,317 101,821 131,476 Loss from operations (16,743 ) (5,574 ) (48,230 ) (45,138 ) Net loss (19,263 ) (9,520 ) (50,969 ) (48,330 ) Basic and diluted net loss per common share(1) $ (0.46 ) $ (0.21 ) $ (1.06 ) $ (0.96 ) 2017: Net product revenue $ 26,442 $ 47,891 $ 41,780 $ 57,953 Collaboration and grant revenue 105 71 73 20,077 Operating expenses 52,902 60,459 72,745 72,578 (Loss) income from operations (26,355 ) (12,497 ) (30,892 ) 5,452 Net (loss) income (29,057 ) (17,475 ) (33,738 ) 1,270 Basic and diluted net (loss) income per common share(1)(2) $ (0.85 ) $ (0.44 ) $ (0.82 ) $ 0.03 (1) The amounts were computed independently for each quarter and the sum of the quarters may not total the annual amounts. (2) Diluted net income per common share for the quarter ending December 31, 2017 excludes the conversion of the Convertible Notes as the effect of their inclusion is anti-dilutive during the period.

The Company (Details)

The Company (Details) $ in Thousands	Aug. 23, 2018USD ($)shares	Apr. 20, 2017USD ($)shares	Aug. 31, 2014	Dec. 31, 2018USD ($)country	Dec. 31, 2017USD ($)	Aug. 31, 2015
Minimum age of ambulatory patient			5 years
Accumulated deficit				$ (938,923)	$ (814,108)
3.00% Convertible senior notes due 2022 | Convertible debt
Interest rate						3.00%
Marathon Pharmaceuticals, LLC | Non-collaborative Arrangement Transactions
Cash consideration		$ 75,000
Equity interest issued or issuable, number of shares (in shares) | shares		6,683,598
Numerator for calculation of number of shares of equity interests issued to acquire entity		$ 65,000
Trading day period		15 days
Development milestone payment obligations		$ 50,000
Translarna
Number of countries (over) | country				40
Agilis
Cash consideration	$ 49,221
Equity interest issued or issuable, 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 payment obligations	$ 40,000			$ 40,000
Agilis | Non-collaborative Arrangement Transactions
Development milestone payment obligations	$ 40,000			$ 40,000

Acquisitions - Narrative (Detai

Acquisitions - Narrative (Details) - USD ($)	Aug. 23, 2018	Apr. 20, 2017	Dec. 31, 2018	Dec. 31, 2018	Dec. 31, 2017
Finite-Lived Intangible Assets [Line Items]
Contingent consideration payable			$ 310,240,000	$ 310,240,000	$ 0
Issuance of common stock related to acquisition				$ 155,860,000	75,191,000
Useful life				7 years
Intellectual Property | Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 75,000,000
Issuance of common stock related to acquisition (in shares)		6,683,598		6,683,598
Issuance of common stock related to acquisition		$ 75,200,000
Acquisition costs		$ 2,200,000
Useful life		7 years
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 75,000,000
Equity interest issued or issuable, number of shares (in shares)		6,683,598
Numerator for calculation of number of shares of equity interests issued to acquire entity		$ 65,000,000
Trading day period		15 days
Development milestone payment obligations		$ 50,000,000
Agilis
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 49,221,000
Equity interest issued or issuable, number of shares (in shares)	3,500,907
Fair value of PTC common stock issued	$ 155,860,000
Estimated fair value of contingent consideration payable	290,500,000
Deferred consideration payable	38,100,000
Business combination, consideration	533,681,000
Acquisition Related Costs				$ 1,700,000
Net loss attributable to common stockholders				$ (138,083,000)	$ (93,333,000)
Issuance of common stock related to acquisition (in shares)				3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity	$ 150,000,000
Trading day period	10 days
Earnings (loss) of acquire since acquisition date			(8,700,000)
Development milestone payment obligations	$ 40,000,000		40,000,000	$ 40,000,000
Agilis | Non-collaborative Arrangement Transactions
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations	$ 40,000,000		40,000,000	40,000,000
Acquisition-related Costs | Agilis
Finite-Lived Intangible Assets [Line Items]
Net loss attributable to common stockholders				1,700,000
Maximum | Agilis
Finite-Lived Intangible Assets [Line Items]
Priority review voucher amount				535,000,000
Net sales milestones			$ 150,000,000	$ 150,000,000
Percentage of annual net sales			600.00%	600.00%
Development milestone payment obligations			$ 60,000,000	$ 60,000,000
Minimum | Agilis
Finite-Lived Intangible Assets [Line Items]
Percentage of annual net sales			200.00%	200.00%

Acquisitions - Preliminary Allo

Acquisitions - Preliminary Allocation of purchase price (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2018	Aug. 23, 2018	Dec. 31, 2017
Finite-Lived Intangible Assets [Line Items]
Indefinite-lived Intangible Assets Acquired		$ 576,500
Goodwill	$ 82,341	82,341		$ 0
Goodwill Adjustment	18,000
Agilis
Finite-Lived Intangible Assets [Line Items]
Cash and cash equivalents	328	328	$ 328
Prepaid expenses and other current assets	181	181	181
Fixed assets	153	153	153
Other assets	38	38	38
Intangible assets - IPR&D			480,000
Intangible assets - in process research and development (“IPRD”) Adjustment	96,500
Accounts payable and accrued expenses	(3,828)	(3,828)	(3,828)
Deferred tax liability	(122,032)	(122,032)	(115,200)
Deferred tax liability adjustment	(6,832)
Fair value of net assets acquired	451,340	451,340	361,672
Fair value of net assets acquired adjustment	89,668
Goodwill			100,309
Goodwill Adjustment	(17,968)
Total purchase price	533,681	$ 533,681	$ 461,981
Total purchase price adjustment	$ 71,700

Summary of significant accoun_4

Summary of significant accounting policies - Fixed Assets (Details)	12 Months Ended
	Dec. 31, 2018
Computer equipment and software
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, and lab equipment
Fixed assets
Estimated useful life	7 years

Acquisitions -Schedule of Busin

Acquisitions -Schedule of Business Acquisitions (Details) - Agilis $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Significant unobservable inputs (level 3)
Changes in the fair value of warrant liability
Ending balance	$ 53,200
Liability, Development and Regulatory Milestone
Changes in the fair value of warrant liability
Ending balance	257,040
Liability, Development and Regulatory Milestone | Significant unobservable inputs (level 3)
Changes in the fair value of warrant liability
Change in fair value	6,460
Additions	263,500
Payments	0
Ending balance	257,040
Liability, Net Sales Milestones and Royalties
Changes in the fair value of warrant liability
Ending balance	53,200
Liability, Net Sales Milestones and Royalties | Significant unobservable inputs (level 3)
Changes in the fair value of warrant liability
Beginning balance	0
Change in fair value	(26,200)
Additions	27,000
Payments	0
Ending balance	$ 53,200

Summary of significant accoun_5

Summary of significant accounting policies - Narrative (Details)	1 Months Ended	3 Months Ended								12 Months Ended
	Aug. 31, 2014	Dec. 31, 2018USD ($)	Sep. 30, 2018USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Dec. 31, 2017USD ($)	Sep. 30, 2017USD ($)	Jun. 30, 2017USD ($)	Mar. 31, 2017USD ($)	Dec. 31, 2018USD ($)segment	Dec. 31, 2017USD ($)	Dec. 31, 2016USD ($)	Aug. 23, 2018USD ($)	Jan. 01, 2018USD ($)
Segment and geographic information
Number of operating segments | segment										1
Number of Reporting Units | segment										1
Minimum age of ambulatory patient	5 years
Allowance for doubtful accounts		$ 700,000				$ 800,000				$ 700,000	$ 800,000
Deferred research and development advance payments		2,400,000				500,000				2,400,000	$ 500,000
Impairment of long-lived assets										$ 0
Summary
Federal income tax provision at statutory rate										21.00%	34.00%	34.00%
Income tax benefit (expense)										$ 29,000	$ (1,335,000)	$ (569,000)
Renewal Of Marketing Authorization, Period										1 year
Net product revenue		85,833,000	$ 53,021,000	$ 68,170,000	$ 55,981,000	57,953,000	$ 41,780,000	$ 47,891,000	$ 26,442,000	$ 264,734,000	194,392,000	82,705,000
Accumulated deficit		(938,923,000)				$ (814,108,000)				(938,923,000)	(814,108,000)
Contract with Customer, Liability, Cumulative Catch-up Adjustment to Revenue, Change in Measure of Progress										3,937,000
Translarna
Summary
Net product revenue										171,000,000	145,200,000	$ 81,400,000
Emflaza
Summary
Net product revenue										92,000,000	$ 28,800,000
Agilis
Summary
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Deferred Tax Liabilities		$ 122,032,000								122,032,000			$ 115,200,000
Difference between Revenue Guidance in Effect before and after Topic 606
Summary
Cumulative Effect Of New Accounting Principle In Period Of Adoption, Variable Consideration										600,000
Accumulated deficit														$ 3,300,000
Minimum
Summary
Cumulative Effect Of New Accounting Principle In Period Of Adoption, Variable Consideration										10
Maximum
Summary
Cumulative Effect Of New Accounting Principle In Period Of Adoption, Variable Consideration										$ 15

Acquisitions -Business Acquisi

Acquisitions -Business Acquisition, Pro Forma Information (Details) - Agilis - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Business Acquisition [Line Items]
Revenues	$ 264,734	$ 194,392
Net loss attributable to common stockholders	$ (138,083)	$ (93,333)

Summary of significant accoun_6

Summary of significant accounting policies - Inventory (Details) - USD ($)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Accounting Policies [Abstract]
Inventory Write-down	$ 1,800,000
Raw materials	1,431,000	$ 452,000
Work in progress	9,324,000	3,912,000
Finished goods	5,362,000	6,390,000
Total inventory	$ 16,117,000	$ 10,754,000

Acquisitions - Schedule of purc

Acquisitions - Schedule of purchase price (Details) - USD ($) $ in Thousands	Apr. 20, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 8,433	$ 77,163	$ 0
Fair value of PTC common stock issued to Marathon (6,683,598 shares)		$ 155,860	$ 75,191
Intellectual Property | Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 75,000
Fair value of PTC common stock issued to Marathon (6,683,598 shares)	75,200
Acquisition costs	2,200
Total preliminary consideration transferred	$ 152,353

Acquisitions - Total Purchase C

Acquisitions - Total Purchase Consideration (Details) - Marathon Pharmaceuticals, LLC $ in Thousands	Apr. 20, 2017USD ($)
Business Acquisition [Line Items]
Inventory	$ 4,000
Intellectual Property
Business Acquisition [Line Items]
Purchase price	$ 152,353

Fair value of financial instr_3

Fair value of financial instruments and investments - Narrative (Details)	12 Months Ended
	Dec. 31, 2018USD ($)$ / shares	Aug. 23, 2018USD ($)	Dec. 31, 2017USD ($)$ / shares	Aug. 31, 2015USD ($)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 58,088,000		$ 79,454,000
Deferred consideration payable- long-term	18,300,000		0
Contingent consideration payable	310,240,000		0
Deferred consideration payable- current	19,400,000		0
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%
Debt instrument	146,600,000		115,700,000
Warrants
Financial assets and liabilities measured at fair value on recurring basis
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 0		$ 1,000
Warrants | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	128		128
Warrants | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	2,520		2,520
Warrants | Volatility | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.59		0.69
Warrants | Volatility | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.60		0.69
Warrants | Risk free interest rate | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.03		0.02
Warrants | Risk free interest rate | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.03		0.02
Warrants | Expected life | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.59		1.59
Warrants | Expected life | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.72		1.70
Stock Appreciation Rights (SARs)
Financial assets and liabilities measured at fair value on recurring basis
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 3,814,000		$ 1,665,000
Stock Appreciation Rights (SARs) | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	6.76		6.76
Stock Appreciation Rights (SARs) | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	30.86		30.86
Stock Appreciation Rights (SARs) | Volatility | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.47		0.31
Stock Appreciation Rights (SARs) | Volatility | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.60		0.70
Stock Appreciation Rights (SARs) | Risk free interest rate | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.02		0.01
Stock Appreciation Rights (SARs) | Risk free interest rate | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.03		0.02
Stock Appreciation Rights (SARs) | Expected life | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	0.01		0
Stock Appreciation Rights (SARs) | Expected life | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input	1.01		2
Common stock | Warrants | Fair value of common stock
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	34.32		16.68
Common stock | Stock Appreciation Rights (SARs) | Fair value of common stock
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input | $ / shares	34.32		16.68
Fair Value, Measurements, Recurring | Fair Value, Inputs, Level 2
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 58,088,000		$ 79,454,000
Deferred consideration payable	37,700,000
Warrant liability	0		0
Stock appreciation rights liability	0		0
Contingent consideration payable	0
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	0
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	$ 40,000,000	$ 40,000,000
Deferred consideration payable		38,100,000
Agilis | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Percentage of annual net sales	200.00%
Agilis | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	$ 60,000,000
Priority review voucher amount	535,000,000
Net sales milestones	$ 150,000,000
Percentage of annual net sales	600.00%
Non-collaborative Arrangement Transactions | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	$ 40,000,000	$ 40,000,000
Total | Fair Value, Measurements, Recurring
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	58,088,000		79,454,000
Deferred consideration payable	37,700,000
Warrant liability	0		1,000
Stock appreciation rights liability	3,814,000		$ 1,665,000
Contingent consideration payable	257,040,000
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 53,200,000

Fair value of financial instr_4

Fair value of financial instruments and investments - Schedule of financial assets and liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Aug. 23, 2018	Dec. 31, 2017
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	$ 58,088		$ 79,454
Contingent consideration payable	310,240		0
Fair Value, Measurements, Recurring | Total
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	58,088		79,454
Warrant liability	0		1
Stock appreciation rights liability	3,814		1,665
Deferred consideration payable	37,700
Contingent consideration payable	257,040
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	53,200
Fair Value, Measurements, Recurring | Quoted prices in active markets for identical assets (level 1)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0		0
Warrant liability	0		0
Stock appreciation rights liability	0		0
Deferred consideration payable	0
Contingent consideration payable	0
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	0
Fair Value, Measurements, Recurring | Significant other observable inputs (level 2)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	58,088		79,454
Warrant liability	0		0
Stock appreciation rights liability	0		0
Deferred consideration payable	37,700
Contingent consideration payable	0
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	0
Fair Value, Measurements, Recurring | Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0		0
Warrant liability	0		1
Stock appreciation rights liability	3,814		$ 1,665
Deferred consideration payable	0
Contingent consideration payable	257,040
Agilis
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Deferred consideration payable		$ 38,100
Agilis | Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 53,200

Fair value of financial instr_5

Fair value of financial instruments and investments - Marketable Securities, Unrealized Gains (Losses) (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Marketable securities accounted for as available-for-sale securities
Amortized Cost	$ 58,056	$ 79,432
Gross Unrealized Gains	43	52
Gross Unrealized Losses	(11)	(30)
Fair Value	58,088	79,454
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	31,657	13,775
Gross Unrealized Gains	43	52
Gross Unrealized Losses	(1)	0
Fair Value	31,699	13,827
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	26,399	65,657
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(10)	(30)
Fair Value	$ 26,389	$ 65,627

Fair value of financial instr_6

Fair value of financial instruments and investments - Available-for-sale securities (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	$ (8)
Fair Value	16,223
Unrealized losses	(3)
Fair Value	10,087
Unrealized losses	(11)
Fair Value	26,310
Commercial Paper
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	(1)
Fair Value	1,993
Unrealized losses	0
Fair Value	0
Unrealized losses	(1)
Fair Value	1,993
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	(7)	$ (28)
Fair Value	14,230	59,108
Unrealized losses	(3)	(2)
Fair Value	10,087	6,519
Unrealized losses	(10)	(30)
Fair Value	$ 24,317	$ 65,627

Fair value of financial instr_7

Fair value of financial instruments and investments - Marketable Securities, Balance Sheet Disclosures (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Marketable securities on the balance sheet
Less Than 12 Months	$ 58,088	$ 69,377
More Than 12 Months	0	10,077
Commercial paper
Marketable securities on the balance sheet
Less Than 12 Months	31,699	13,827
More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Less Than 12 Months	26,389	55,550
More Than 12 Months	$ 0	$ 10,077

Fair value of financial instr_8

Fair value of financial instruments and investments - Summary of changes in the fair value of the Company's Level 3 valuation (Details) - USD ($)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Warrants
Changes in the fair value of warrant liability
Beginning balance	$ 1,000
Ending balance	0	$ 1,000
Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	1,665,000
Ending balance	3,814,000	1,665,000
Significant unobservable inputs (level 3) | Warrants
Changes in the fair value of warrant liability
Beginning balance	1,000	1,000
Change in fair value	(1,000)	0
Payments	0	0
Additions	0
Ending balance	0	1,000
Significant unobservable inputs (level 3) | Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	1,665,000	865,000
Change in fair value	4,140,000	1,864,000
Payments	(1,991,000)	(1,064,000)
Additions	0
Ending balance	3,814,000	$ 1,665,000
Significant unobservable inputs (level 3) | Agilis
Changes in the fair value of warrant liability
Ending balance	$ 53,200,000

Fair value of financial instr_9

Fair value of financial instruments and investments - Fair Value Liabilities Measured (Details)	Dec. 31, 2018USD ($)$ / shares	Dec. 31, 2017USD ($)$ / shares	Dec. 31, 2016USD ($)
Warrants
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 0	$ 1,000
Stock Appreciation Rights (SARs)
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 3,814,000	$ 1,665,000
Minimum | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	128	128
Minimum | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	6.76	6.76
Minimum | Volatility | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.59	0.69
Minimum | Volatility | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	0.47	0.31
Minimum | Risk free interest rate | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.03	0.02
Minimum | Risk free interest rate | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	0.02	0.01
Minimum | Expected life | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.59	1.59
Minimum | Expected life | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	0.01	0
Maximum | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	2,520	2,520
Maximum | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	30.86	30.86
Maximum | Volatility | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.60	0.69
Maximum | Volatility | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	0.60	0.70
Maximum | Risk free interest rate | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.03	0.02
Maximum | Risk free interest rate | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	0.03	0.02
Maximum | Expected life | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input	0.72	1.70
Maximum | Expected life | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input	1.01	2
Common stock | Fair value of common stock | Warrants
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	34.32	16.68
Common stock | Fair value of common stock | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares	34.32	16.68
Significant unobservable inputs (level 3) | Warrants
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 0	$ 1,000	$ 1,000
Significant unobservable inputs (level 3) | Stock Appreciation Rights (SARs)
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	3,814,000	1,665,000	$ 865,000
Significant unobservable inputs (level 3) | Agilis
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 53,200,000
Liability, Net Sales Milestones and Royalties | Minimum | Probabilities of success | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.25
Liability, Net Sales Milestones and Royalties | Maximum | Probabilities of success | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.89
Liability, Net Sales Milestones and Royalties | Agilis
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 53,200,000
Liability, Net Sales Milestones and Royalties | Agilis | Minimum | Potential net sales milestones | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0
Liability, Net Sales Milestones and Royalties | Agilis | Minimum | Potential percentage of net sales for royalties | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.02
Liability, Net Sales Milestones and Royalties | Agilis | Maximum | Potential net sales milestones | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	150,000,000
Liability, Net Sales Milestones and Royalties | Agilis | Maximum | Potential percentage of net sales for royalties | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.06
Liability, Net Sales Milestones and Royalties | Significant unobservable inputs (level 3) | Agilis
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 53,200,000	$ 0
Liability, Development and Regulatory Milestone | Minimum | Probabilities of success | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.25
Liability, Development and Regulatory Milestone | Maximum | Probabilities of success | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.89
Liability, Development and Regulatory Milestone | Agilis
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 257,040,000
Liability, Development and Regulatory Milestone | Agilis | Minimum | Potential development and regulatory milestones | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0
Liability, Development and Regulatory Milestone | Agilis | Minimum | Discount rates | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.058
Liability, Development and Regulatory Milestone | Agilis | Maximum | Potential development and regulatory milestones | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	555,000,000
Liability, Development and Regulatory Milestone | Agilis | Maximum | Discount rates | Commitments [Member]
Fair value of warrant liability
Alternative Investment, Measurement Input	0.080
Liability, Development and Regulatory Milestone | Significant unobservable inputs (level 3) | Agilis
Fair value of warrant liability
Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability Value	$ 257,040,000

Fixed assets (Details)

Fixed assets (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Fixed assets
Gross fixed assets	$ 20,177	$ 41,220
Less accumulated depreciation and amortization	(7,483)	(32,844)
Net fixed assets	12,694	8,376
Depreciation	2,600	2,300	$ 3,300
Leasehold improvements
Fixed assets
Gross fixed assets	2,384	14,078
Computer equipment and software
Fixed assets
Gross fixed assets	4,609	5,471
Furniture, fixtures, and lab equipment
Fixed assets
Gross fixed assets	9,965	20,776
Assets in process
Fixed assets
Gross fixed assets	$ 3,219	$ 895

Accounts payable and accrued _3

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 27,629	$ 17,711
Consulting and contracted research	11,267	5,137
Professional fees	5,574	2,116
Sales allowances and other related costs	29,417	22,257
Royalties and rebates	31,874	11,657
Accounts payable	6,001	15,282
Other	16,437	2,286
Accounts payable and accrued expenses	$ 128,199	$ 76,446

Debt - 2017 Credit Facility (De

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

Debt - 2015 Convertible Notes (

Debt - 2015 Convertible Notes (Details)	1 Months Ended	12 Months Ended
	Aug. 31, 2015USD ($)day$ / shares	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)
Long-term debt
Additional paid-in capital		$ 1,288,137,000	$ 966,534,000
3.00% Convertible senior notes due 2022 | Convertible debt
Long-term debt
Debt instrument	$ 150,000,000	150,000,000	150,000,000
Interest rate	3.00%
Net proceeds from issuance of convertible notes	$ 145,400,000
Trading days, number | day	20
Consecutive trading days, period | day	30
Stock price trigger	130.00%
Business days, period	5 days
Consecutive trading-day period	5 days
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day	98.00%
Conversion ratio	0.0177
Conversion price per share | $ / shares	$ 56.34
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default	25.00%
Convertible instruments principal and unpaid interest payable upon events of default	100.00%
Term of the convertible notes	7 years
Additional paid-in capital		57,500,000
Net deferred tax liability in connection with convertible notes	$ 22,300,000
Debt instrument		$ 146,600,000	$ 115,700,000
Remaining amortization period		3 years 7 months 13 days
3.00% Convertible senior notes due 2022 | Convertible debt | Redemption on or after August 20, 2018
Long-term debt
Trading days, number | day	19
Consecutive trading days, period | day	30
Stock price trigger	130.00%
Redemption price	100.00%

Debt - Summary of convertible n

Debt - Summary of convertible notes (Details) - Convertible debt - 3.00% Convertible senior notes due 2022 - USD ($)	Dec. 31, 2018	Dec. 31, 2017	Aug. 31, 2015
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(1,746,000)	(2,121,000)
Less: Debt discount, net	(35,054,000)	(42,572,000)
Net carrying amount	$ 113,200,000	$ 105,307,000

Debt - Summary of Interest Expe

Debt - Summary of Interest Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Long-term debt
Amortization of debt issuance costs	$ 524	$ 433	$ 302
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	4,500	4,500
Amortization of debt issuance costs	375	337
Amortization of debt discount	7,518	6,755
Total	$ 12,393	$ 11,592
Effective interest rate of the liability component	11.00%	11.00%

Capital structure - Narrative (

Capital structure - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Apr. 30, 2018	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Capital structure
Issuance of common stock related to equity offering (in shares)	4,600,000
Net proceeds from public offering	$ 0	$ 117,916	$ 0	$ 0
Share Price	$ 27.04
Common stock, authorized shares (in shares)		125,000,000	125,000,000
Common stock
Capital structure
Common stock, authorized shares (in shares)		125,000,000
Over-Allotment Option
Capital structure
Issuance of common stock related to equity offering (in shares)	600,000

Capital structure - Summary of

Capital structure - Summary of Warrants (Details) - Common stock - $ / shares	Dec. 31, 2018	Dec. 31, 2017
2,018
Warrants
Warrant shares (in shares)		7,030
Exercise price (in dollars per share)		$ 128
2019, period one
Warrants
Warrant shares (in shares)	7,030
Exercise price (in dollars per share)	$ 128
2019, period two
Warrants
Warrant shares (in shares)	130	130
Exercise price (in dollars per share)	$ 2,520	$ 2,520

Earnings per share (Details)

Earnings per share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Net loss per share:
Basic and diluted (in dollars per share)	$ (0.96)	$ (1.06)	$ (0.21)	$ (0.46)	$ 0.03	$ (0.82)	$ (0.44)	$ (0.85)	$ (2.75)	$ (2.02)	$ (4.17)
Numerator
Net loss	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (128,081)	$ (79,000)	$ (142,110)
Denominator
Denominator for basic and diluted net loss per share (in shares)									46,576,313	39,183,073	34,044,584
Total shares excluded from calculation (in shares)									9,105,837	6,841,653	6,125,967
Stock Options
Denominator
Total shares excluded from calculation (in shares)									8,534,358	6,448,642	5,854,316
Unvested restricted stock
Denominator
Total shares excluded from calculation (in shares)									571,479	393,011	271,651

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	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Stock option plan
Share-based compensation expense					$ 33,252	$ 30,559	$ 35,009
Unrecognized compensation cost					$ 62,600
Weighted average remaining service period for recognition of unrecognized compensation cost					2 years 11 months 16 days
Unvested restricted stock
Stock option plan
Options granted (in shares)					354,691
Stock option
Stock option plan
Granted (in shares)					3,181,623	1,913,873	1,500,645
Forfeited (in shares)					461,934	1,117,462	383,590
Expected dividend yield					0.00%	0.00%	0.00%
Weighted average grant date fair value (in dollars per share)					$ 17.48	$ 8.45	$ 17.31
Stock option | Minimum
Stock option plan
Vesting period					3 years
Stock option | Maximum
Stock option plan
Vesting period					4 years
Stock Appreciation Rights (SARs)
Stock option plan
Granted (in shares)			897,290
Vesting period			4 years
Share-based compensation expense					$ 4,100
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)					1,000,000
Award requisite service period					6 months
Purchase price of common stock					85.00%
Employee stock purchase plan, voting percentage limit		5.00%
Share-based compensation expense					$ 1,000
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan | Unvested restricted stock
Stock option plan
Options granted (in shares)	735,324
2013 Stock Incentive Plan | Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)				0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan | Stock option
Stock option plan
Stockholder's specified ownership percentage					10.00%
Expiration period					10 years
2009 Equity and Long Term Incentive Plan | Stock option | Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date					100.00%
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date					110.00%
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares available for issuance (in shares)				122,296
2013 Long Term Incentive Plan | Common stock
Stock option plan
Number of shares available for issuance (in shares)					729,689
Number of shares subject to outstanding awards (in shares)				3,040,444
Annual increase in the number of shares on the first day of the fiscal year (in shares)				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Inducement grant plan | Unvested restricted stock
Stock option plan
Granted (in shares)					7,000
Inducement grant plan | Stock option
Stock option plan
Options granted (in shares)					1,352,800
Granted (in dollars per share)					$ 37.35
Forfeited (in shares)					202,432

Stock award plan - Stock Option

Stock award plan - Stock Option Activity (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Number of options
Outstanding at the beginning of the period (in shares)	6,448,642	5,854,316	4,826,477
Granted (in shares)	3,181,623	1,913,873	1,500,645
Exercised (in shares)	(633,973)	(202,085)	(89,216)
Forfeited (in shares)	(461,934)	(1,117,462)	(383,590)
Outstanding at the end of the period (in shares)	8,534,358	6,448,642	5,854,316
Vested or expected to vest at the end of the period (in shares)	3,881,360
Exercisable at the end of the period (in shares)	4,410,211
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 29	$ 34.71	$ 37.20
Granted (in dollars per share)	26.64	12.34	27.90
Exercised (in dollars per share)	18.61	10.80	10.85
Forfeited (in dollars per share)	35.36	33.65	47.42
Outstanding at the end of the period (in dollars per share)	28.58	$ 29	$ 34.71
Vested or expected to vest at the end of the period (in dollars per share)	24.81
Exercisable at the end of the period (in dollars per share)	$ 32.01
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 4 months 13 days
Vested or expected to vest at the end of the period	8 years 9 months 14 days
Exercisable at the end of the period	6 years 8 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars)	$ 88,454
Vested or expected to vest at the end of the period (in dollars)	44,893
Exercisable at the end of the period (in dollars)	$ 40,854

Stock award plan - Assumptions

Stock award plan - Assumptions Used (Details) - Stock option	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Minimum
Valuation assumptions
Risk-free interest rate	2.25%	1.84%	1.30%
Expected volatility	64.00%	76.00%	67.00%
Expected term	5 years 10 days	5 years 14 days	5 years 18 days
Maximum
Valuation assumptions
Risk-free interest rate	3.10%	2.45%	2.24%
Expected volatility	90.00%	81.00%	78.00%
Expected term	10 years	10 years	10 years

Stock award plan - Restricted S

Stock award plan - Restricted Stock Activity (Details) - Unvested restricted stock	12 Months Ended
	Dec. 31, 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	(114,295)
Forfeited (in shares) | shares	(61,928)
Balance at the end of the period (in shares) | shares	571,479
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	$ 17.61

Stock award plan - Share-based

Stock award plan - Share-based Compensation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 33,252	$ 30,559	$ 35,009
Research and development
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	16,096	15,456	16,812
Selling, general and administrative
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 17,156	$ 15,103	$ 18,197

Other comprehensive income (l_3

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	$ 156,437	$ 119,583	$ 226,001
Other comprehensive income (loss) before reclassifications	(2,507)	5,454	(285)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(2,507)	5,454	(285)
Balance at the end of the period	350,727	156,437	119,583
Unrealized (Losses)/Gains On Marketable Securities, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	22	(203)	(589)
Other comprehensive income (loss) before reclassifications	9	225	386
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	9	225	386
Balance at the end of the period	31	22	(203)
Foreign Currency Translation
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	3,947	(1,282)	(611)
Other comprehensive income (loss) before reclassifications	(2,516)	5,229	(671)
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(2,516)	5,229	(671)
Balance at the end of the period	1,431	3,947	(1,282)
Total Accumulated Other Comprehensive Items
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	3,969	(1,485)	(1,200)
Balance at the end of the period	$ 1,462	$ 3,969	$ (1,485)

Revenue recognition - Narrative

Revenue recognition - Narrative (Details) - Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-10-01 - Licensing And Collaboration Agreement $ in Millions	Nov. 30, 2011USD ($)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue, Remaining Performance Obligation, Amount	$ 30
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Period	2 years

Revenue recognition - Contract

Revenue recognition - Contract Liabilities, Rollforward (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Movement in Deferred Revenue [Roll Forward]
Beginning balance	$ 11,891
Additions	6,417
Deductions	(1,433)
ASC 606 Adjustment	(3,937)
Ending balance	$ 12,938

Revenue recognition - Recognize

Revenue recognition - Recognized revenue in the period (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Revenue from Contract with Customer [Abstract]
Amounts included in contract liabilities at the beginning of the period									$ 0
Performance obligations satisfied in previous period									0
Revenue from Contract with Customer, Including Assessed Tax	$ 85,833	$ 53,021	$ 68,170	$ 55,981	$ 57,953	$ 41,780	$ 47,891	$ 26,442	264,734	$ 194,392	$ 82,705
Total product revenue									$ 263,005

Revenue recognition - Balance S

Revenue recognition - Balance Sheet Impacts (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Jan. 01, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 169,498		$ 111,792	$ 58,321	$ 58,022
Marketable securities	58,088		79,454
Trade receivables, net	67,907		40,394
Inventory, net	16,117		10,754
Prepaid expenses and other current assets	9,247		6,669
Total current assets	320,857		249,063
Fixed assets, net	12,694		8,376
Intangible assets, net	701,031		132,993
Goodwill	82,341		0
Deposits and other assets	2,299		1,221
Total assets	1,119,222		391,653
Current liabilities:
Accounts payable and accrued expenses	128,199		76,446
Current portion of long-term debt	11,667		0
Deferred revenue	3,716		3,937
Other current liabilities	3,814		1,665
Total current liabilities	166,796		82,048
Deferred revenue - long-term	9,722		7,954
Long-term debt	141,347		144,971
Contingent consideration payable	310,240		0
Deferred tax liability	122,032		0
Other long-term liabilities	58		243
Total liabilities	768,495		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	1,288,137		966,534
Accumulated other comprehensive income	1,462		3,969
Accumulated deficit	(938,923)		(814,108)
Total stockholders’ equity	350,727		156,437	$ 119,583	$ 226,001
Total liabilities and stockholders’ equity	1,119,222		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	(2,120)
Current portion of long-term debt	0
Deferred revenue	10,563
Other current liabilities	0
Deferred consideration payable- current	0
Total current liabilities	8,443
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	8,443
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	(8,527)
Total stockholders’ equity	(8,527)
Total liabilities and stockholders’ equity	(84)
Balances without adoption of Topic 606
Current assets:
Cash and cash equivalents	169,498		$ 111,792
Marketable securities	58,088
Trade receivables, net	67,907
Inventory, net	16,033
Prepaid expenses and other current assets	9,247
Total current assets	320,773
Fixed assets, net	12,694
Intangible assets, net	701,031
Goodwill	82,341
Deposits and other assets	2,299
Total assets	1,119,138
Current liabilities:
Accounts payable and accrued expenses	126,079
Current portion of long-term debt	11,667
Deferred revenue	14,279
Other current liabilities	3,814
Deferred consideration payable- current	19,400
Total current liabilities	175,239
Deferred revenue - long-term	9,722
Long-term debt	141,347
Contingent consideration payable	310,240
Estimated fair value of deferred consideration payable	18,300
Deferred tax liability	122,032
Other long-term liabilities	58
Total liabilities	776,938
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	1,288,137
Accumulated other comprehensive income	1,462
Accumulated deficit	(947,450)
Total stockholders’ equity	342,200
Total liabilities and stockholders’ equity	$ 1,119,138

Revenue recognition - Income St

Revenue recognition - Income Statement Impacts (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Revenues:
Net product revenue	$ 85,833	$ 53,021	$ 68,170	$ 55,981	$ 57,953	$ 41,780	$ 47,891	$ 26,442	$ 264,734	$ 194,392	$ 82,705
Operating expenses:
Amortization of acquired intangible asset									22,877	15,380	0
Research and development									171,984	117,456	117,633
Selling, general and administrative									153,548	121,271	97,130
Change in the fair value of deferred and contingent consideration									19,340	0	0
Total operating expenses	131,476	101,821	74,317	72,805	72,578	72,745	60,459	52,902	380,419	258,684	214,763
Loss from operations	(45,138)	(48,230)	(5,574)	(16,743)	5,452	(30,892)	(12,497)	(26,355)	(115,685)	(64,292)	(132,058)
Interest expense, net									(12,554)	(12,094)	(8,276)
Other income (expense), net									129	(1,279)	(1,207)
Loss before income tax expense									(128,110)	(77,665)	(141,541)
Income tax benefit (expense)									29	(1,335)	(569)
Net loss attributable to common stockholders	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	(128,081)	(79,000)	(142,110)
Adjustments | ASU 2014-09
Revenues:
Net product revenue									(5,177)
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset									(84)
Amortization of acquired intangible asset									0
Research and development									0
Selling, general and administrative									0
Change in the fair value of deferred and contingent consideration									0
Total operating expenses									(84)
Loss from operations									(5,093)
Interest expense, net									0
Other income (expense), net									0
Loss before income tax expense									(5,093)
Income tax benefit (expense)									0
Net loss attributable to common stockholders									(5,093)
Balances without adoption of Topic 606
Revenues:
Net product revenue									259,557
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible asset									12,586
Amortization of acquired intangible asset									22,877
Research and development									171,984
Selling, general and administrative									153,548
Change in the fair value of deferred and contingent consideration									19,340
Total operating expenses									380,335
Loss from operations									(120,778)
Interest expense, net									(12,554)
Other income (expense), net									129
Loss before income tax expense									(133,203)
Income tax benefit (expense)									29
Net loss attributable to common stockholders									(133,174)
Net product revenue
Revenues:
Net product revenue									263,005	174,066	81,447
Net product revenue | Adjustments | ASU 2014-09
Revenues:
Net product revenue									(5,177)
Net product revenue | Balances without adoption of Topic 606
Revenues:
Net product revenue									257,828
Collaboration and grant revenue
Revenues:
Net product revenue									1,729	$ 20,326	$ 1,258
Collaboration and grant revenue | Adjustments | ASU 2014-09
Revenues:
Net product revenue									0
Collaboration and grant revenue | Balances without adoption of Topic 606
Revenues:
Net product revenue									$ 1,729

Revenue recognition - Comprehen

Revenue recognition - Comprehensive Income Impacts (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (128,081)	$ (79,000)	$ (142,110)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities									9	225	386
Foreign currency translation (loss) gain									(2,516)	5,229	(671)
Comprehensive loss									(130,588)	$ (73,546)	$ (142,395)
Adjustments | ASU 2014-09
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss									(5,093)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities									0
Foreign currency translation (loss) gain									0
Comprehensive loss									(5,093)
Balances without adoption of Topic 606
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net loss									(133,174)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities									9
Foreign currency translation (loss) gain									(2,516)
Comprehensive loss									$ (135,681)

Revenue recognition - Cash Flow

Revenue recognition - Cash Flow Impacts (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	Apr. 30, 2018	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Cash flows from operating activities
Net loss		$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (128,081)	$ (79,000)	$ (142,110)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization										26,087	17,682	3,290
Change in the fair value of deferred and contingent consideration										19,340	0	0
Amortization of premiums and accretion of discounts on investments, net										(433)	535	1,885
Non-cash interest expense										7,518	6,755	6,065
Loss on disposal of asset										2	5	0
Amortization of debt issuance costs										524	433	302
Share-based compensation expense										33,252	30,559	35,009
Unrealized foreign currency transaction gains										(59)	(459)	1,202
Changes in operating assets and liabilities:
Inventory										(5,823)	(6,454)	0
Prepaid expenses and other current assets										(1,609)	(1,784)	1,171
Trade receivables, net										(29,589)	(12,203)	(14,842)
Deposits and other assets										(1,093)	(544)	(278)
Accounts payable and accrued expenses										43,877	24,011	4,259
Deferred revenue										6,514	9,469	1,526
Net cash used in operating activities										(27,641)	(10,063)	(103,566)
Cash flows from investing activities
Purchases of fixed assets										(7,097)	(3,101)	(1,776)
Purchases of marketable securities										(68,614)	(81,368)	(85,377)
Sale & redemption of marketable securities										90,423	174,749	191,634
Acquisition of product rights										(8,433)	(77,163)	0
Business acquisition, net of cash acquired										(48,892)	0	0
Net cash (used in) provided by investing activities										(42,613)	13,117	104,481
Cash flows from financing activities
Proceeds from exercise of options										10,868	2,182	968
Net proceeds from public offerings	$ 0									117,916	0	0
Proceeds from shares issued under employee stock purchase plan										2,787	2,468	0
Net cash provided by financing activities										131,571	44,218	968
Effect of exchange rate changes on cash										(3,611)	6,199	(1,584)
Net increase in cash and cash equivalents										57,706	53,471	299
Cash and cash equivalents, beginning of period					111,792				$ 58,321	111,792	58,321	58,022
Cash and cash equivalents, end of period		169,498				111,792				169,498	111,792	$ 58,321
Adjustments | ASU 2014-09
Cash flows from operating activities
Net loss										(5,093)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization										0
Change in the fair value of deferred and contingent consideration										0
Amortization of premiums and accretion of discounts on investments, net										0
Non-cash interest expense										0
Loss on disposal of asset										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										(2,120)
Other liabilities										0
Deferred revenue										7,297
Net cash used in operating activities										0
Cash flows from investing activities
Purchases of fixed assets										0
Purchases of marketable securities										0
Sale & 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					0
Cash and cash equivalents, end of period		0				0				0	0
Balances without adoption of Topic 606
Cash flows from operating activities
Net loss										(133,174)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization										26,087
Change in the fair value of deferred and contingent consideration										19,340
Amortization of premiums and accretion of discounts on investments, net										(433)
Non-cash interest expense										7,518
Loss on disposal of asset										2
Amortization of debt issuance costs										524
Share-based compensation expense										33,252
Unrealized foreign currency transaction gains										(59)
Changes in operating assets and liabilities:
Inventory										(5,907)
Prepaid expenses and other current assets										(1,609)
Trade receivables, net										(29,589)
Deposits and other assets										(1,093)
Accounts payable and accrued expenses										41,757
Other liabilities										1,932
Deferred revenue										13,811
Net cash used in operating activities										(27,641)
Cash flows from investing activities
Purchases of fixed assets										(7,097)
Purchases of marketable securities										(68,614)
Sale & redemption of marketable securities										90,423
Acquisition of product rights										(8,433)
Business acquisition, net of cash acquired										(48,892)
Net cash (used in) provided by investing activities										(42,613)
Cash flows from financing activities
Proceeds from exercise of options										10,868
Net proceeds from public offerings										117,916
Proceeds from shares issued under employee stock purchase plan										2,787
Net cash provided by financing activities										131,571
Effect of exchange rate changes on cash										(3,611)
Net increase in cash and cash equivalents										57,706
Cash and cash equivalents, beginning of period					$ 111,792					111,792
Cash and cash equivalents, end of period		$ 169,498				$ 111,792				$ 169,498	$ 111,792

Revenue recognition Recenue rec

Revenue recognition Recenue recognition - Roche and SMA Foundation (Details)

Dec. 31, 2018USD ($)

Oct. 31, 2017USD ($)

Nov. 30, 2014USD ($)

Jan. 31, 2014USD ($)

Aug. 31, 2013USD ($)

Nov. 30, 2011USD ($)compound

Dec. 31, 2018USD ($)

Sep. 30, 2018USD ($)

Jun. 30, 2018USD ($)

Mar. 31, 2018USD ($)

Dec. 31, 2017USD ($)

Sep. 30, 2017USD ($)

Jun. 30, 2017USD ($)

Mar. 31, 2017USD ($)

Dec. 31, 2018USD ($)deliverable

Dec. 31, 2017USD ($)deliverable

Dec. 31, 2016USD ($)

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Net Product Sales

$ 263,005,000

Additions

6,417,000

Revenue

264,734,000

$ 194,392,000

Net product revenue

$ 85,833,000

$ 53,021,000

$ 68,170,000

$ 55,981,000

$ 57,953,000

$ 41,780,000

$ 47,891,000

$ 26,442,000

264,734,000

194,392,000

$ 82,705,000

Licensing And Collaboration Agreement

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Performance obligations satisfied in current period

$ 20,000,000

$ 10,000,000

$ 7,500,000

$ 10,000,000

Additions

$ 30,000,000

Revenue

200,000

$ 20,300,000

400,000

Grant [Member]

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Net product revenue

$ 0

$ 900,000

Collaborative Arrangement [Member] | Roche And Sma Foundation [Member]

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Collaborative Arrangements Number of Compounds in Preclinical Development | compound

3

Collaborative Arrangements Number of Significant Deliverables | deliverable

2

Collaboration And Discovery Agreements [Member]

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Collaborative Arrangements Number of Significant Deliverables | deliverable

2

Research And Development Event Milestones | Licensing And Collaboration Agreement

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Revenue Recognition, Milestone, Potential Achievements

$ 87,500,000

$ 135,000,000

Research And Development Event Milestones | Early Stage Collaborations

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Revenue Recognition, Milestone, Potential Achievements

143,000,000

Potential net sales milestones | Licensing And Collaboration Agreement

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Revenue Recognition, Milestone, Potential Achievements

$ 325,000,000

325,000,000

Potential net sales milestones | Early Stage Collaborations

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Revenue Recognition, Milestone, Potential Achievements

$ 252,000,000

Minimum

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Term of Grant Program

2 years

Minimum | Collaboration And Discovery Agreements [Member]

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Collaborative Arrangements Research Period for Applying Discovery Technology

3 years

Maximum

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Term of Grant Program

5 years

Maximum | Collaboration And Discovery Agreements [Member]

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Collaborative Arrangements Research Period for Applying Discovery Technology

4 years

United States

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Net Product Sales

$ 92,000,000

Revenue

93,694,000

$ 49,155,000

Non-US

Revenue, Initial Application Period Cumulative Effect Transition [Line Items]

Net Product Sales

171,000,000

Revenue

$ 171,040,000

$ 145,237,000

Income taxes - Narrative (Detai

Income taxes - Narrative (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Operating loss carryforwards
Valuation allowance	$ 180,481	$ 177,631
Valuation allowance, deferred tax asset, increase (decrease)	2,800	$ 5,400
Deferred Tax Assets, Operating Loss Carryforwards, Limited by IRC Section 382	231,500
Orphan drug credit carryover	74,000
Limited NOL carryforwards	231,500
Operating loss carryforwards, not subject to expiration	169,200
Operating loss carryforwards, subject to expiration	62,300
Operating loss carryforwards for immediate use	194,500
Operating loss carryforwards in next twelve months	$ 5,700
Federal income tax provision at statutory rate	21.00%	34.00%	34.00%
Uncertain tax position	$ 0
Change In tax rate, deferred tax asset, provisional income tax expense	46,100
First five years from ownership change
Operating loss carryforwards
Net operating loss carryforwards	16,700
After five years
Operating loss carryforwards
Net operating loss carryforwards	5,700
Federal
Operating loss carryforwards
Net operating loss carryforwards	296,000
Research and development credit carryforwards	15,200
State
Operating loss carryforwards
Net operating loss carryforwards	202,400
Research and development credit carryforwards	6,600
Foreign Tax Authority
Operating loss carryforwards
Net operating loss carryforwards	$ 5,900

Income taxes - Loss from operat

Income taxes - Loss from operations before tax (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Domestic	$ (68,461)	$ (54,588)	$ (61,446)
Foreign	(59,649)	(23,077)	(80,095)
Total	$ (128,110)	$ (77,665)	$ (141,541)

Income taxes - Provision for Ta

Income taxes - Provision for Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Current:
U.S. Federal	$ 0	$ 0	$ 0
U.S. State and Local	(38)	(6)	(2)
Foreign	(669)	(1,131)	(766)
Deferred:
U.S. Federal	0	(198)	199
U.S. State and Local	0	0	0
Foreign	736	0	0
Total tax benefit (expense)	$ 29	$ (1,335)	$ (569)

Income taxes - Tax Rate Reconci

Income taxes - Tax Rate Reconciliation (Details)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Reconciliation of the U.S. statutory income tax rate to the entity's effective tax rate
Federal income tax provision at statutory rate	21.00%	34.00%	34.00%
State income tax provision, net of federal benefit	0.05%	(1.01%)	3.05%
Permanent differences	(6.41%)	(8.48%)	(3.70%)
Research and development	6.49%	19.53%	16.66%
Change in valuation allowances	2.20%	29.10%	(30.72%)
Change in deferred tax assets	(14.22%)	(64.12%)	0.00%
Foreign tax rate differential	(9.10%)	(10.33%)	(19.84%)
Benefit allocated from other comprehensive income	0.00%	(0.26%)	0.14%
Other	0.01%	(0.15%)	0.01%
Effective income tax rate	0.02%	(1.72%)	(0.40%)

Income taxes - Deferred Tax Ass

Income taxes - Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Deferred tax assets:
Accrued expense	$ 714	$ 625
Amortization	5,148	2,116
Depreciation	1,601	1,749
Federal tax credits	89,070	80,961
State tax credits	5,473	7,148
Federal net operating losses	62,159	61,068
State net operating losses	165	11,884
Foreign net operating losses	736	0
Capitalized research and development costs	2,093	3,332
Share based compensation and other	21,411	18,815
Total gross deferred tax assets	188,570	187,698
Less valuation allowance	(180,481)	(177,631)
Deferred Tax Assets, Net of Valuation Allowance	8,089	10,067
Deferred tax liabilities:
Convertible debt	(7,353)	(9,927)
OCI unrealized (gains)/losses	0	(140)
Indefinite lived intangible	(122,032)	0
Total gross deferred tax liabilities	129,385	10,067
Deferred Tax Liabilities, Net	(121,296)	$ 0
Early Stage Collaborations | Research And Development Event Milestones
Deferred tax liabilities:
Revenue Recognition, Milestone, Potential Achievements	$ 143,000

Commitments and contingencies -

Commitments and contingencies - Narrative (Details)	12 Months Ended
	Dec. 31, 2018USD ($)operating_lease	Dec. 31, 2017USD ($)	Dec. 31, 2016USD ($)	Aug. 23, 2018USD ($)	Jun. 30, 2016USD ($)
Other contingencies
Number of Operating Leases | operating_lease	3
Operating Lease, Expense	$ 2,700,000	$ 2,200,000	$ 2,200,000
Akcea
Other contingencies
Development And Regulatory Milestone Payment Obligations, Period	30 days
Upfront licensing fee	$ 12,000,000
Milestone, Potential Achievements, Regulatory Approval	4,000,000
Funding agreement | Wellcome trust limited
Other contingencies
Development milestone payment obligations	22,400,000				$ 800,000
Non-collaborative Arrangement Transactions | Akcea
Other contingencies
Development milestone payment obligations	6,000,000
Agilis
Other contingencies
Development milestone payment obligations	40,000,000			$ 40,000,000
Agilis | Non-collaborative Arrangement Transactions
Other contingencies
Development milestone payment obligations	40,000,000			$ 40,000,000
Maximum | Akcea
Other contingencies
Milestone, Potential Achievements, Regulatory Approval	8,000,000
Maximum | Agilis
Other contingencies
Development milestone payment obligations	$ 60,000,000

Commitments and contingencies_2

Commitments and contingencies - Lease, Operating Leases, Future Lease Payments (Details) $ in Thousands	Dec. 31, 2018USD ($)
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2,019	$ 3,216
2,020	2,900
2,021	2,409
2,022	2,082
2023 and thereafter	3,321
Total future minimum lease payments	$ 13,928

Geographic information (Details

Geographic information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)segment	Dec. 31, 2017USD ($)
Segments, Geographical Areas [Abstract]
Number of operating segments | segment	1
Segment Reporting Information [Line Items]
Total assets	$ 1,119,222	$ 391,653
Property and equipment, net	12,694	8,376
Revenue	264,734	194,392
United States
Segment Reporting Information [Line Items]
Total assets	1,013,977	278,108
Property and equipment, net	10,497	6,272
Revenue	93,694	49,155
Non-US
Segment Reporting Information [Line Items]
Total assets	105,245	113,545
Property and equipment, net	2,197	2,104
Revenue	$ 171,040	$ 145,237

401(k) plan (Details)

401(k) plan (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Retirement Benefits [Abstract]
Matching contribution (as a percent of total salary)	92.00%
Percentage of employee's base salary, matched by employer	6.00%
Expense recorded	$ 2.2	$ 1.6	$ 1.1

Restructuring - Narrative (Deta

Restructuring - Narrative (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Restructuring and Related Activities [Abstract]
Accrued Restructuring Expenses	$ 0	$ 0
Restructuring charge			$ 2,500

Intangible assets and goodwil_2

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life		7 years
Amortization of acquired intangible asset		$ 22,877	$ 15,380	$ 0
Total allocation of IPR&D assets		576,500
Goodwill	$ 82,341	82,341	0
Goodwill Adjustment	18,000
Akcea
Finite-Lived Intangible Assets [Line Items]
Upfront licensing fee		$ 12,000
Development And Regulatory Milestone Payment Obligations, Period		30 days
Non-collaborative Arrangement Transactions | Akcea
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations	6,000	$ 6,000
Emflaza
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations	14,400	14,400
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Finite-Lived Intangibles					$ 148,400
Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations	6,000	6,000
Intellectual Property
Finite-Lived Intangible Assets [Line Items]
Amortization of acquired intangible asset		22,900	$ 15,400
Finite-Lived Intangible Assets, Accumulated Amortization	$ 38,300	$ 38,300

Intangible assets and goodwil_3

Intangible assets and goodwill - Future Amortization (Details) - USD ($) $ in Thousands	Dec. 31, 2018	Sep. 30, 2018
Finite-Lived Intangible Assets [Line Items]
Total		$ 124,531
Marathon Pharmaceuticals, LLC | Intellectual Property
Finite-Lived Intangible Assets [Line Items]
2,019	$ 24,283
2,020	24,276
2,021	24,277
2,022	24,277
2023 and thereafter	$ 27,418

Subsequent events - Narrative (

Subsequent events - Narrative (Details) - Subsequent Event - USD ($) $ / shares in Units, $ in Millions	Jan. 31, 2019	Feb. 28, 2019
Subsequent Event [Line Items]
Common stock, issued and sold (in shares)	7,563,725
Sale price (in USD per share)	$ 30.20
Exercise of Underwriter (in shares)		843,725
Net proceeds from sale of stock	$ 224.1

Selected quarterly financial _3

Selected quarterly financial data (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Net product revenue	$ 85,833	$ 53,021	$ 68,170	$ 55,981	$ 57,953	$ 41,780	$ 47,891	$ 26,442	$ 264,734	$ 194,392	$ 82,705
Collaboration and grant revenue	505	570	573	81	20,077	73	71	105
Operating expenses	131,476	101,821	74,317	72,805	72,578	72,745	60,459	52,902	380,419	258,684	214,763
Loss from operations	(45,138)	(48,230)	(5,574)	(16,743)	5,452	(30,892)	(12,497)	(26,355)	(115,685)	(64,292)	(132,058)
Net loss attributable to common stockholders	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ 1,270	$ (33,738)	$ (17,475)	$ (29,057)	$ (128,081)	$ (79,000)	$ (142,110)
Net loss per share—basic and diluted (in dollars per share)	$ (0.96)	$ (1.06)	$ (0.21)	$ (0.46)	$ 0.03	$ (0.82)	$ (0.44)	$ (0.85)	$ (2.75)	$ (2.02)	$ (4.17)

Uncategorized Items - ptct-2018

Label	Element	Value
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000
Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000