PTC Therapeutics (PTCT) 10-Q 29 Oct 20 2020 Q3 Quarterly report Financial data

Cover

Cover - shares	9 Months Ended
	Sep. 30, 2020	Oct. 27, 2020
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2020
Document Transition Report	false
Entity File Number	001-35969
Entity Registrant Name	PTC Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3416587
Entity Address, Address Line One	100 Corporate Court
Entity Address, City or Town	South Plainfield,
Entity Address, State or Province	NJ
Entity Address, Postal Zip Code	07080
City Area Code	908
Local Phone Number	222-7000
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Title of 12(b) Security	Common Stock, $0.001 par value per share
Trading Symbol	PTCT
Security Exchange Name	NASDAQ
Entity Common Stock, Shares Outstanding		68,235,739
Entity Central Index Key	0001070081
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q3

Consolidated Balance Sheets (un

Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 433,970	$ 288,028
Marketable securities	707,049	398,535
Trade receivables, net	56,786	55,538
Inventory, net	19,481	19,285
Prepaid expenses and other current assets	26,888	17,898
Total current assets	1,244,174	779,284
Fixed assets, net	28,141	21,549
Intangible assets, net	712,536	710,500
Goodwill	82,341	82,341
Operating lease ROU assets	85,810	13,693
Deposits and other assets	28,057	16,415
Total assets	2,181,059	1,623,782
Current liabilities:
Accounts payable and accrued expenses	218,561	159,276
Current portion of long-term debt	0	20,000
Deferred revenue	5,992	8,242
Operating lease liabilities- current	5,859	5,153
Finance lease liabilities- current	1,251	0
Liability for sale of future royalties - current	22,159	0
Deferred consideration payable	0	40,000
Other current liabilities	0	3,186
Total current liabilities	253,822	235,857
Deferred revenue- long term	0	3,415
Long-term debt	302,971	293,859
Contingent consideration payable	234,100	356,300
Deferred tax liability	130,863	130,862
Operating lease liabilities- noncurrent	81,674	9,018
Finance lease liabilities- noncurrent	22,608	0
Liability for sale of future royalties- noncurrent	642,099	0
Other long-term liabilities	1,968	141
Total liabilities	1,670,105	1,029,452
Stockholders' equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 67,809,560 shares at September 30, 2020. Authorized 125,000,000 shares; issued and outstanding 61,935,870 shares at December 31, 2019.	68	62
Additional paid-in capital	2,101,136	1,795,351
Accumulated other comprehensive income	(35,727)	(10,584)
Accumulated deficit	(1,554,523)	(1,190,499)
Total stockholders' equity	510,954	594,330
Total liabilities and stockholders' equity	$ 2,181,059	$ 1,623,782

Consolidated Balance Sheets (_2

Consolidated Balance Sheets (unaudited) (Parenthetical) - $ / shares	Sep. 30, 2020	Dec. 31, 2019
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)	67,809,560	61,935,870
Common stock, outstanding shares (in shares)	67,809,560	61,935,870

Consolidated Statements of Oper

Consolidated Statements of Operations (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Revenues:
Revenue	$ 118,404	$ 71,416	$ 261,902	$ 210,521
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible assets	4,667	3,006	14,056	8,593
Amortization of acquired intangible assets	9,630	7,025	26,309	19,677
Research and development	92,998	63,076	359,630	175,621
Selling, general and administrative	57,840	49,284	169,708	139,044
Change in the fair value of deferred and contingent consideration	8,400	9,500	16,980	35,960
Settlement of deferred and contingent consideration	0	0	10,613	0
Total operating expenses	173,535	131,891	597,296	378,895
Loss from operations	(55,131)	(60,475)	(335,394)	(168,374)
Interest expense, net	(21,039)	(2,666)	(32,060)	(7,028)
Other income, net	28,766	2,800	26,242	2,509
Loss before income tax expense	(47,404)	(60,341)	(341,212)	(172,893)
Income tax (expense) benefit	(22,288)	344	(22,594)	(1,006)
Net loss attributable to common stockholders	$ (69,692)	$ (59,997)	$ (363,806)	$ (173,899)
Weighted-average shares outstanding:
Basic and diluted (in shares)	67,641,171	56,463,528	65,068,281	57,798,968
Net loss per share-basic and diluted (in dollars per share)
Net loss per share-basic and diluted (in dollars per share)	$ (1.03)	$ (1.06)	$ (5.59)	$ (3.01)
Net product revenue
Revenues:
Revenue	$ 82,708	$ 71,369	$ 226,143	$ 209,899
Collaboration and grant revenue
Revenues:
Revenue	35,000	47	35,063	622
Royalty revenue
Revenues:
Revenue	$ 696	$ 0	$ 696	$ 0

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Statement of Comprehensive Income [Abstract]
Net loss	$ (69,692)	$ (59,997)	$ (363,806)	$ (173,899)
Other comprehensive (loss) income:
Unrealized gain on marketable securities, net of tax	(1,016)	(463)	1,639	435
Foreign currency translation loss, net of tax	(24,695)	(843)	(26,782)	(1,281)
Comprehensive loss	$ (95,403)	$ (61,303)	$ (388,949)	$ (174,745)

Consolidated Statements of Stoc

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Common stock	Additional paid-in capital	Accumulated other comprehensive income (loss)	Accumulated deficit	Total
Balance (in shares) at Dec. 31, 2018	50,606,147
Balance at the beginning of the period at Dec. 31, 2018	$ 51	$ 1,288,137	$ 1,462	$ (938,923)	$ 350,727
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)	10,102,899
Issuance of common stock related to equity offering	$ 10	323,746			323,756
Equity component of the convertible notes issuance, net		119,489			119,489
Issuance of common stock related to rights exchange					0
Exercised (in shares)	645,435
Exercise of options		12,195			12,195
Restricted stock vesting and issuance, net (in shares)	169,792
Issuance of common stock in connection with an employee stock purchase plan (in shares)	54,719
Issuance of common stock in connection with an employee stock purchase plan		1,564			1,564
Share-based compensation expense		30,668			30,668
Net loss				(173,899)	(173,899)
Comprehensive loss			(846)		(846)
Balance (in shares) at Sep. 30, 2019	61,578,992
Balance at the end of the period at Sep. 30, 2019	$ 61	1,775,799	616	(1,112,822)	663,654
Balance (in shares) at Jun. 30, 2019	58,707,185
Balance at the beginning of the period at Jun. 30, 2019	$ 58	1,539,530	1,922	(1,052,825)	488,685
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)	2,539,174
Issuance of common stock related to equity offering	$ 3	99,208			99,211
Equity component of the convertible notes issuance, net		119,489			119,489
Exercised (in shares)	334,433
Exercise of options		7,088			7,088
Restricted stock vesting and issuance, net (in shares)	(1,800)
Share-based compensation expense		10,484			10,484
Net loss				(59,997)	(59,997)
Comprehensive loss			(1,306)		(1,306)
Balance (in shares) at Sep. 30, 2019	61,578,992
Balance at the end of the period at Sep. 30, 2019	$ 61	1,775,799	616	(1,112,822)	663,654
Balance (in shares) at Dec. 31, 2019	61,935,870
Balance at the beginning of the period at Dec. 31, 2019	$ 62	1,795,351	(10,584)	(1,190,499)	594,330
Balance (in shares) at Jun. 30, 2020	67,240,679
Balance at the end of the period at Jun. 30, 2020	$ 67	2,067,274	(10,016)	(1,484,831)	572,494
Balance (in shares) at Dec. 31, 2019	61,935,870
Balance at the beginning of the period at Dec. 31, 2019	$ 62	1,795,351	(10,584)	(1,190,499)	594,330
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)	542,470
Issuance of common stock related to equity offering	$ 1	28,091			28,092
Payments for asset acquisitions, shares (in shares)	845,364
Payments for asset acquisitions, share, value	$ 1	42,868			42,869
Issuance of common stock related to rights exchange (in shares)	2,821,176
Issuance of common stock related to rights exchange	$ 3	150,525			150,528
Exercised (in shares)	1,426,026
Exercise of options	$ 1	32,986			32,987
Restricted stock vesting and issuance, net (in shares)	179,963
Issuance of common stock in connection with an employee stock purchase plan (in shares)	58,691
Issuance of common stock in connection with an employee stock purchase plan		2,406			2,406
Share-based compensation expense		48,909			48,909
Other				(218)	(218)
Net loss				(363,806)	(363,806)
Comprehensive loss			(25,143)		(25,143)
Balance (in shares) at Sep. 30, 2020	67,809,560
Balance at the end of the period at Sep. 30, 2020	$ 68	2,101,136	(35,727)	(1,554,523)	510,954
Balance (in shares) at Jun. 30, 2020	67,240,679
Balance at the beginning of the period at Jun. 30, 2020	$ 67	2,067,274	(10,016)	(1,484,831)	572,494
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)	173,956
Issuance of common stock related to equity offering		9,141			9,141
Exercised (in shares)	391,738
Exercise of options	$ 1	7,942			7,943
Restricted stock vesting and issuance, net (in shares)	3,187
Share-based compensation expense		16,779			16,779
Net loss				(69,692)	(69,692)
Comprehensive loss			(25,711)		(25,711)
Balance (in shares) at Sep. 30, 2020	67,809,560
Balance at the end of the period at Sep. 30, 2020	$ 68	$ 2,101,136	$ (35,727)	$ (1,554,523)	$ 510,954

Consolidated Statements of Cash

Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Cash flows from operating activities
Net loss	$ (363,806)	$ (173,899)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities [Abstract]
Depreciation and amortization	31,088	22,903
Non-cash operating lease expense	4,295	2,446
Non-cash finance lease amortization expense	41,382	0
Non-cash royalty revenue related to sale of future royalties	(299)	0
Non-cash interest expense on liability related to sale of future royalties	14,557	0
Change in valuation of deferred and contingent consideration	16,980	35,960
Settlement of deferred and contingent consideration	10,613	0
Non-cash stock consideration, acquisition	42,869	0
Unrealized gain on equity investment	(852)	(2,529)
Unrealized gain on ClearPoint convertible debt security	(633)	0
Non-cash interest expense	16,678	6,583
Loss on disposal of asset	25	0
Amortization of discounts on investments, net	(559)	(1,374)
Amortization of debt issuance costs	766	434
Share-based compensation expense	48,909	30,668
Unrealized foreign currency transaction (gains) losses, net	(27,077)	205
Changes in operating assets and liabilities:
Inventory, net	390	(1,574)
Prepaid expenses and other current assets	(9,289)	(11,771)
Trade receivables, net	121	5,879
Deposits and other assets	(217)	(1,073)
Accounts payable and accrued expenses	54,390	695
Other liabilities	(4,096)	(3,567)
Deferred revenue	(5,940)	1,581
Net cash used in operating activities	(129,705)	(88,433)
Cash flows from investing activities
Purchases of fixed assets	(11,491)	(9,104)
Purchase of convertible debt security	(10,000)	0
Purchases of marketable securities	(1,006,946)	(239,386)
Sale and redemption of marketable securities	700,627	114,500
Acquisition of product rights and licenses	(25,618)	(20,250)
Purchase of equity investment	0	(4,000)
Net cash provided by (used in) investing activities	(353,428)	(158,240)
Cash flows from financing activities
Proceeds from issuance of convertible notes	0	279,571
Proceeds from exercise of options	32,987	12,195
Termination and exit fees related to payoff of secured term loan	(597)	0
Net proceeds from public offerings	28,092	324,262
Repayment of senior secured term loan	(28,333)	(6,667)
Payments on deferred consideration obligation	(38,100)	0
Proceeds from employee stock purchase plan	2,406	1,564
Payment of finance lease principal	(17,829)	0
Cash consideration received from Royalty Purchase Agreement	650,000	0
Net cash provided by financing activities	628,626	610,925
Effect of exchange rate changes on cash	449	(2,673)
Net decrease in cash and cash equivalents	145,942	361,579
Cash and cash equivalents, and restricted cash beginning of period	295,528	169,498
Cash and cash equivalents, and restricted cash end of period	441,470	531,077
Supplemental disclosure of cash information
Cash paid for interest	9,802	7,042
Cash paid for income taxes	1,562	1,931
Supplemental disclosure of non-cash investing and financing activity
Unrealized gain on marketable securities, net of tax	1,639	435
Right-of-use assets obtained in exchange for operating lease obligations	76,657	16,120
Right-of-use assets obtained in exchange for finance lease obligations	41,382	0
Acquisition of product rights and licenses	13,786	7,432
Issuance of common stock related to rights exchange	150,528	0
Accrued transaction costs related to public offerings	0	506
Accrued transaction costs related to issuance of convertible notes	$ 0	$ 298

The Company

The Company	9 Months Ended
	Sep. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	PTC Therapeutics, Inc. Notes to Consolidated Financial Statements (unaudited) September 30, 2020 In thousands (except per share data unless otherwise noted) 1. The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-driven 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 diversified 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 has marketing authorization in the European Economic Area (the “EEA”) for the treatment of nonsense mutation Duchenne muscular dystrophy (“nmDMD”), in ambulatory patients aged 2 years and older and in Brazil for the treatment of nmDMD in ambulatory patients aged 5 years and older, subject to annual renewal and other conditions. In July 2020, the European Commission approved the removal of the statement “efficacy has not been demonstrated in non-ambulatory patients” from the indication statement for Translarna. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. The Company has a pipeline of gene therapy product candidates for rare monogenic diseases that affect the central nervous system (“CNS”) including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase (“AADC deficiency”), a rare CNS disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. The Company is preparing a biologics license application ("BLA") for PTC-AADC for the treatment of AADC deficiency in the United States and it anticipates submitting a BLA to the United States Food and Drug Administration ("FDA") in the first half of 2021. In January 2020, the Company submitted a marketing authorization application ("MAA") to the European Medicines Agency (“EMA”) for PTC-AADC for the treatment of AADC deficiency in the EEA, and the Company expects an opinion from the Committee for Medical Products for Human Use (“CHMP”) in the first half of 2021. 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 pursuant to the Company’s Collaboration and License Agreement with Akcea Therapeutics, Inc. (“Akcea”). Tegsedi has received marketing authorization in the United States, the European Union (the “EU”) and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis (“hATTR amyloidosis”). Waylivra has received marketing authorization in the EU for the treatment of familial chylomicronemia syndrome (“FCS”). The Company filed for marketing authorization for Waylivra for the treatment of FCS with ANVISA, the Brazilian health regulatory authority, in June 2020 and, subject to potential delays in the review process related to the COVID-19 pandemic, expects a regulatory decision on approval from ANVISA in 2021. The Company also has a spinal muscular atrophy ("SMA") collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc., referred to collectively as Roche, and the Spinal Muscular Atrophy Foundation ("SMA Foundation"). The SMA program has one approved product, Evrysdi™ (risdiplam), which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. Evrysdi also received marketing authorization for the treatment of SMA in Brazil in October 2020 and the EMA accepted the MAA filed by Roche for Evrysdi for the treatment of SMA in August 2020. On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, including certain compounds that the Company has begun to develop as part of its Bio-e platform, (the “Asset Acquisition”) pursuant to an asset purchase agreement by and between the Company and BioElectron, dated October 1, 2019 (the “Asset Acquisition Agreement”). The transaction was accounted for as an asset acquisition. The two most advanced molecules in the Company’s Bio-e platform are vatiquinone and PTC857. The Company initiated a registration-directed Phase 2/3 placebo-controlled trial of vatiquinone in approximately 60 children with mitochondrial disease and associated refractory epilepsy in the third quarter of 2020. The Company expects to initiate a registration-directed Phase 3 trial of vatiquinone in approximately 100 patients with Friedrich ataxia in the fourth quarter of 2020. In the second quarter of 2020, the Company initiated a Phase 1 trial in healthy volunteers to evaluate the safety and pharmacology of PTC857, which the Company believes has the potential to address multiple CNS disorders with glucocerebrosidase Parkinson’s disease as its first planned indication. The Company completed dosing within the single ascending dose study and expects to complete dosing within the multiple ascending dose study from the Phase 1 trial by the end of 2020. In June 2020, the FDA authorized the initiation of a Phase 2/3 clinical trial evaluating PTC299, a dihydroorotate dehydrogenase inhibitor that the Company has also been developing in oncological indications, as a potential treatment for COVID-19. The integrated Phase 2/3 study, which has been initiated and is being conducted in two stages, will evaluate the efficacy and safety of PTC299 in patients hospitalized with SARS-CoV-2 infection. The Company expects Stage 1 of the clinical trial to be completed in the fourth quarter of 2020 and it anticipates reporting top-line results from both stages in the first half of 2021. 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 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 June 2020 and is effective, unless extended, through August 5, 2021. 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. Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application (“NDA”), over protest with 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 the Company’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 final study muscle biopsies for the patients in Study 045 were completed in October 2020 and the Company has begun the process of analyzing the samples according to its protocol. The Company expects to report top-line results from Study 045 in the first quarter of 2021 followed by a potential resubmission of the NDA for Translarna for the treatment of nmDMD thereafter. 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 August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc. (“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 On April 29, 2020, the Company, certain of the former equity holders of Agilis, and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC, entered into a Rights Exchange Agreement (the “Rights Exchange Agreement”). Pursuant to the Rights Exchange Agreement, the Company issued 2,821,176 shares of its common stock (the “Common Stock Consideration”) and paid $36.9 million (the “Cash Consideration”), in the aggregate, to such former equityholders of Agilis (the “Participating Rightholders”) in exchange for the cancellation and forfeiture by the Participating Rightholders of their rights to receive certain milestone-based contingent payments under the Merger Agreement, pursuant to which the Company completed the Merger. Pursuant to the terms of the Rights Exchange Agreement, the Participating Rightholders have canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments that would have been due upon the passing of the second anniversary of the closing of the Merger, regardless of whether the milestones were achieved. The Rights Exchange Agreement has no effect on the Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightholders’ rights to receive $211.6 million, in the aggregate, of the milestone payments described above. As a result, all other rights and obligations under the Merger Agreement remain in effect pursuant to their terms, including the Company’s obligation to pay up to an aggregate maximum amount of $20.0 million upon the achievement of certain development milestones (representing the remaining portion of potential development milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement while excluding the remaining $2.4 million milestone payment that was due and paid in the three month period ended September 30, 2020 upon the passing of the second anniversary of the closing of the Merger), up to an aggregate maximum amount of $361.0 million upon the achievement of certain regulatory milestones (representing the remaining portion of potential regulatory milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement), up to a maximum aggregate amount of $150.0 million upon the achievement of certain net sales milestones and a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% to 6%, pursuant to the terms of the Merger Agreement. Refer to Note 5 for further details regarding the Rights Exchange Agreement. On May 29, 2020, the Company completed its acquisition of Censa Pharmaceuticals, Inc. (“Censa”) pursuant to an Agreement and Plan of Merger, dated as of May 5, 2020 (the "Censa Merger Agreement"), by and among the Company, Hydro Merger Sub, Inc., the Company’s wholly owned, indirect subsidiary, and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representative Services LLC (the "Censa Merger"). The transaction was accounted for as an asset acquisition. In connection with the Censa Merger, the Company acquired PTC923, which is being pursued as a possible treatment for orphan metabolic diseases associated with defects in the tetrahydrobiopterin biochemical pathways, including phenylketonuria ("PKU"). Refer to Note 3 for further details. As of September 30, 2020, the Company had an accumulated deficit of approximately $1,554.5 million. The Company has financed its operations to date primarily through the private offerings in September 2019 of 1.50% convertible senior notes due 2026 and in August 2015 of 3.00% convertible senior notes due 2022 (see Note 11), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offerings" of its common stock, its initial public offering of common stock in June 2013, proceeds from the Royalty Purchase Agreement (see Note 2), private placements of its convertible preferred stock, collaborations, bank debt, the Company’s credit and security agreement (the "Credit Agreement"), with MidCap Financial Trust, or MidCap Financial, as administrative agent and MidCap Financial and other certain institutions as lenders thereto (see Note 11), 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 has 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.

Summary of significant accounti

Summary of significant accounting policies	9 Months Ended
	Sep. 30, 2020
Accounting Policies [Abstract]
Summary of significant accounting policies	The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2019 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 2, 2020 (the "2019 Form 10-K"). Additional significant accounting policies adopted during the nine month period ended September 30, 2020 are discussed in further detail below. Basis of presentation The accompanying financial information as of September 30, 2020 and for the three and nine months ended September 30, 2020 and 2019 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2019 and notes thereto included in the 2019 Form 10-K. In the opinion of management, the unaudited financial information as of September 30, 2020 and for the three and nine months ended September 30, 2020 and 2019 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders’ equity, and cash flows. The results of operations for the three and nine month periods ended September 30, 2020 are not necessarily indicative of the results to be expected for the year ended December 31, 2020 or for any other interim period or for any other future year. Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, royalty revenue, certain accruals related to the Company’s research and development expenses, valuation procedures for liability for sale of future royalties, valuation procedures for convertible notes, 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. Restricted cash Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the twelve-month period ended December 31, 2019 in connection with obligations under a facility lease for our leased biologics manufacturing facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Beginning of ​ ​ ​ period- End of period- ​ December 31, September 30, ​ 2019 ​ 2020 Cash and cash equivalents ​ $ 288,028 ​ $ 433,970 Restricted cash included in deposits and other assets ​ 7,500 ​ 7,500 Total Cash, cash equivalents and restricted cash per statement of cash flows ​ $ 295,528 ​ $ 441,470 ​ 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. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three month and nine month periods ended September 30, 2020, no allowance was recorded for credit losses. Inventory and cost of product sales Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products 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. Amounts related to clinical development programs and marketing efforts are immaterial. The following table summarizes the components of the Company’s inventory for the periods indicated: ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 Raw materials ​ $ 946 ​ $ 874 Work in progress ​ 8,600 ​ 9,652 Finished goods ​ 9,935 ​ 8,759 Total inventory ​ $ 19,481 ​ $ 19,285 ​ 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. For the three and nine months ended September 30, 2020, inventory write downs were immaterial. No write downs were recorded for the three and nine month periods ended September 30, 2019. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2020 and 2019, 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. Production costs are expensed as cost of product sales when the related products are sold. Revenue recognition Net product revenue The Company’s net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products 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 the product, 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 the 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 product sales. 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 related to Medicaid and other government pricing programs, 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. 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 three months ended September 30, 2020 and 2019, net product sales outside of the United States were $44.2 million and $48.5 million, respectively, and net product sales in the United States were $38.5 million and $22.9 million, respectively. For the nine months ended September 30, 2020 and 2019, net product sales outside of the United States were $124.0 million and $141.6 million, respectively, and net product sales in the United States were $102.1 million and $68.3 million, respectively. 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. 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 and royalty 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 royalties from product sales at the later of when the related sales occur or when the performance obligation to which the royalty has been allocated has been satisfied. If it is probable that a significant revenue reversal will not occur, the Company will estimate the royalty payments using the most likely amount method. 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 $0.1 million as of September 30, 2020 and $0.3 million as of December 31, 2019. Bad debt expense was immaterial for the three and nine month periods ended September 30, 2020 and 2019. For the three and nine month periods ended September 30, 2020, no allowances were recorded for credit losses. Liability for sale of future royalties On July 17, 2020, the Company, RPI Intermediate Finance Trust (“RPI”), and, for the limited purposes set forth in the agreement, Royalty Pharma PLC, entered into a Royalty Purchase Agreement (the “Royalty Purchase Agreement”). Pursuant to the Royalty Purchase Agreement, the Company sold to RPI 42.933% (the “Assigned Royalty Payment”) of the Company’s right to receive sales-based royalty payments (the “Royalty”) on worldwide net sales of Evrysdi and any other product developed pursuant to the License and Collaboration Agreement (the “License Agreement”), dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation under the SMA program. In consideration for the sale of the Assigned Royalty Payments, RPI paid the Company $650.0 million in cash consideration. The Company has retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the License Agreement, which milestone payments equal $362.5 million in the aggregate as of September 30, 2020. The Royalty Purchase Agreement will terminate 60 days following the earlier of the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the License Agreement and the date on which RPI has received $1.3 billion in respect of the Assigned Royalty Payments. The cash consideration obtained pursuant to the Royalty Purchase Agreement is classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability will be amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The Company will utilize the prospective method to account for subsequent changes in the estimated future payments to be made to RPI. Refer to Note 11 for further details. ​ Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset 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. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company’s outlook and market performance of the Company’s industry and recent and forecasted financial performance. 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 at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassess its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount. Income Taxes O On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2020. 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 of $122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company’s policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful. The $650.0 million cash consideration received from RPI pursuant to the Royalty Purchase Agreement was treated as taxable income in the current year and resulted in a current tax provision of $22.1 million related to state income taxes after considering the state NOL and tax credits. The Company did not generate a federal income tax liability after considering the federal NOL and tax credits. Leases The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating and finance leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating and finance lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments. Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases. Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories. A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates. The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. See Note 4 Leases for additional information. Recently issued accounting standards In August 2020, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2020-06, “Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity.” ASU 2020-06 simplifies the accounting for convertible instruments by removing certain separation models in Subtopic 470- 20, Debt—Debt with Conversion and Other Options, for convertible instruments. Under ASU 2020-06, the embedded conversion features no longer are separated from the host contract for convertible instruments with conversion features that are not required to be accounted for as derivatives under Topic 815, Derivatives and Hedging, or that do not result in substantial premiums accounted for as paid-in capital. Consequently, a convertible debt instrument will be accounted for as a single liability measured at its amortized cost and a convertible preferred stock will be accounted for as a single equity instrument measured at its historical cost, as long as no other features require bifurcation and recognition as derivatives. By removing those separation models, the interest rate of convertible debt instruments typically will be closer to the coupon interest rate when applying the guidance in Topic 835, Interest. The amendments under ASU 2020-06 also include revisions related to the derivatives scope exception for contracts in an entity’s own equity and earnings per share. The amendments under ASU 2020-06 are effective for public business entities that meet the definition of a SEC filer, excluding entities eligible to be smaller reporting companies as defined by the SEC, for fiscal years beginning after December 15, 2021, including interim periods within those fiscal years. For all other entities, the amendments are effective for fiscal years beginning after December 15, 2023, including interim periods within those fiscal years. Early adoption is permitted, but no earlier than fiscal years beginning after December 15, 2020, including interim periods within those fiscal years. The FASB specified that an entity should adopt the guidance as of the beginning of its annual fiscal year. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU 2020-06 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements In December 2019, the FASB issued ASU 2019-12,"Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes”. ASU 2019-12 simplifies the accounting for income taxes by removing certain exceptions to the general principles in Topic 740. The amendments also improve consistent application of and simplify GAAP for other areas of Topic 740 by clarifying and amending the existing guidance. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2020. For all other entities, it is effective for annual periods beginning after December 15, 2021 and interim periods in annual periods beginning after December 15, 2022. Early adoption is permitted, including adoption in any interim period. The Company early adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments - Credit Losses, which expands the scope of the practical expedient that allows entities to exclude the accrued interest component of amortized cost from various disclosures required by ASC 326 to also include certain disclosures required by ASC 320. Entities that elect to apply the practical expedient must disclose the total amount of accrued interest that they exclude from their disclosures of amortized cost. The amendments have the same effective dates as ASU 2016-13 (Topic 326) for entities that have not yet adopted that standard. The Company adopted ASU 2016-13 and ASU 2019-11 effective January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its accounting policy for marketable securities within this footnote as well as its fair value footnote (Note 5) with additional disclosures as required by the standard upon adoption. 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 adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its fair value footnote (Note 5) with additional and modified disclosures as required by the standard upon adoption. In August 2018, the FASB issued ASU 2018-15,"Intangibles - Goodwill and Other - Internal-Use Software (Su

Acquisition Censa Acquisition

Acquisition Censa Acquisition	9 Months Ended
	Sep. 30, 2020
Business Combinations [Abstract]
Acquisition	Censa Acquisition On May 29, 2020, the Company acquired Censa, pursuant to the Censa Merger Agreement. Upon the closing of the Censa Merger, the Company paid to the Censa securityholders (i) cash consideration of $15.0 million, which consisted of an upfront payment of $10.4 million and an additional $4.6 million for the net assets on Censa’s opening balance sheet as of the date of the acquisition, and (ii) 845,364 shares of the Company’s common stock, which were valued at $42.9 million based on the closing stock price on the acquisition date. The number of shares issued was determined using a 30-day VWAP pursuant to the Censa Merger Agreement. The Company determined that substantially all of the fair value is concentrated in PTC923 and accounted for the transaction as an asset acquisition under ASC 805-50. The purchase price consisted of the cash consideration of $15.0 million and $42.9 million in the Company’s common stock, in addition to $0.7 million of acquisition costs. As such, the total consideration transferred was determined to be $58.6 million. The opening balance sheet net assets of $4.6 million, which consisted of cash of $3.8 million and other current assets of $0.8 million, were determined to be non-qualifying assets and recorded at their fair values, respectively. The remaining consideration of $54.0 million was allocated to PTC923. As PTC923 is an IPR&D asset, the Company concluded that it did not have any alternative future use, and accordingly, the fair value amount allocated to the IPR&D was expensed. Of the $54.0 million, $53.3 million is included in research and development expense and $0.7 million is included in selling, general, and administrative expense within the Company’s statement of operations for the nine month period ended September 30, 2020. Subject to the terms and conditions of the Censa Merger Agreement, Censa securityholders may become entitled to receive contingent payments from the Company based on (i) the achievement of certain development and regulatory milestones up to an aggregate maximum amount of $217.5 million for PTC923’s two most advanced programs and receipt of a priority review voucher from the FDA as set forth in the Censa Merger Agreement, (ii) $109.0 million in development and regulatory milestones for each additional indication of PTC923, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $160.0 million, (iv) a percentage of annual net sales during specified terms, ranging from single to low double digits of the applicable net sales threshold amount, and (v) any sublicense fees paid to the Company in consideration of any sublicense of Censa’s intellectual property to commercialize PTC923, on a country-by-country basis, which contingent payment shall equal to a mid-double digit percentage of any such sublicense fees. Pursuant to the Censa Merger Agreement, the Company has the option to pay the initial $30.0 million development milestone, for the completion of enrollment of a Phase 3 clinical trial for PTC923 for PKU, if achieved, in cash or shares of the Company’s common stock. The Company will record the milestone and royalty payments when they become payable. Milestone payments prior to FDA approval of PTC923 for PKU (or other indications) will be expensed accordingly and milestone payments that will only occur after PTC923 for PKU (or other indications) is FDA approved, will be capitalized and amortized over their expected useful lives.

Leases

Leases	9 Months Ended
	Sep. 30, 2020
Leases [Abstract]
Leases	The Company leases office space in South Plainfield, New Jersey for its principal office under three noncancelable operating leases through May 2022 and August 2024, in addition to office space in various countries for international employees primarily through workspace providers. The Company also leases approximately 220,500 square feet of office, manufacturing and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”) pursuant to a Lease Agreement (the “Lease”) with Hopewell Campus Owner LLC (the “Landlord”). The rental term of the Lease commenced on July 1, 2020 and has an initial term of fifteen years (the “Initial Term”), with two consecutive ten year renewal periods, each at the Company’s option. The aggregate rent for the Initial Term will be approximately $111.5 million. The rental rate for the renewal periods will be 95% of the Prevailing Market Rate (as defined in the Lease) and determined at the time of the exercise of the renewal. The Company is also responsible for maintaining certain insurance and the payment of proportional taxes, utilities and common area operating expenses. The Lease contains customary events of default, representations, warranties and covenants. Subject to the terms of the Lease, the Company has a right of first refusal to rent certain other space of the Campus, which would be triggered upon the Landlord’s issuance of a second round proposal or letter of intent to another tenant for such space. The Company also may seek to build a new separate building on the Campus, which may not contain less than 75,000 square feet (the “New Building”). Upon receipt of notice of the Company’s intention to build the New Building, the Landlord may, in its sole discretion, construct and lease the New Building to the Company or enter into a ground lease with the Company permitting the Company to construct the New Building. Rent terms for the New Building would be determined based on the land value, construction and project costs subject to whether the Landlord or Company constructs the New Building. The Company entered into a lease agreement with COE Bridgewater LLC on March 20, 2020 relating to the lease of office and laboratory space located in Bridgewater, New Jersey. This lease replaced the Company’s existing lease on the property beginning on May 1, 2020 and includes additional rental property of approximately 59,000 square feet. The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s leases have remaining operating lease terms ranging from 0.1 14.8 On June 19, 2020, the Company entered into a commercial manufacturing service agreement for a term of 12.5 The components of operating lease expense were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended Three Months Ended Nine Months Ended Nine Months Ended ​ ​ ​ September 30, 2020 ​ September 30, 2019 ​ September 30, 2020 ​ September 30, 2019 ​ Operating Lease Cost ​ ​ ​ ​ ​ ​ ​ ​ Fixed lease cost ​ $ 4,097 ​ $ 1,431 ​ $ 7,896 ​ $ 3,078 ​ Variable lease cost ​ 890 ​ 184 ​ 1,914 ​ 488 ​ Short-term lease cost ​ 175 ​ 94 ​ 340 ​ 235 ​ Total operating lease cost ​ $ 5,162 ​ $ 1,709 ​ $ 10,150 ​ $ 3,801 ​ ​ Total operating lease cost is a component of operating expenses on the consolidated statements of operations. Supplemental balance sheet information related to leases was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease ROU asset ​ $ 85,810 ​ $ 13,693 ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease liabilities- current ​ $ 5,859 ​ $ 5,153 ​ Operating lease liabilities- noncurrent ​ 81,674 ​ 9,018 ​ Total operating lease liability ​ $ 87,533 ​ $ 14,171 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ Finance lease liabilities- current ​ $ 1,251 ​ $ — ​ Finance lease liabilities- noncurrent ​ 22,608 ​ — ​ Total finance lease liability ​ $ 23,859 ​ $ — ​ ​ The Company’s leases in Bridgewater, New Jersey and Hopewell Township, New Jersey are the primary drivers of the increase in total operating lease ROU asset and total operating lease liability from December 31, 2019 to September 30, 2020. Supplemental lease term and discount rate information related to leases was as follows as of September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ ​ ​ ​ ​ ​ ​ Weighted-average remaining lease terms - operating leases (years) 11.66 ​ 3.38 ​ Weighted-average discount rate - operating leases ​ 8.64 % 7.33 % ​ Weighted-average remaining lease terms - finance lease (years) 12.25 ​ — ​ Weighted-average discount rate - finance lease 7.80 % — ​ ​ Supplemental cash flow information related to leases was as follows as of September 30, 2020 and 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended September 30, ​ ​ 2020 2019 ​ Cash paid for amounts included in the measurement of lease liabilities: ​ ​ ​ ​ Operating cash flows from operating leases ​ $ 5,611 ​ $ 2,751 ​ Financing cash flows from finance lease ​ ​ 17,829 ​ ​ — ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use assets obtained in exchange for lease obligations: ​ ​ ​ Operating leases ​ $ 76,657 ​ $ 16,120 ​ Finance lease ​ ​ 41,382 ​ ​ — ​ ​ Future minimum lease payments under non-cancelable leases as of September 30, 2020 were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating Leases Finance Lease ​ 2020 (excludes the nine months ended September 30, 2020) ​ $ 2,842 ​ $ — ​ 2021 ​ 13,472 ​ 3,000 ​ 2022 ​ 13,229 ​ 3,000 ​ 2023 ​ 12,831 ​ 3,000 ​ 2024 and thereafter ​ 104,142 ​ 27,000 ​ Total lease payments ​ 146,516 ​ 36,000 ​ Less: Imputed Interest expense ​ 58,983 ​ 12,141 ​ Total ​ $ 87,533 ​ $ 23,859 ​ ​ In conjunction with the Asset Acquisition, the Company acquired BioElectron’s lease in Mountainview, California. As substantially all of the fair value of the gross assets acquired was related to vatiquinone, the relative fair value allocated to the right of use asset and corresponding lease liability for the Mountainview lease was determined to be immaterial, and accordingly is not included in the tables above. The future minimum lease payments for the Mountainview lease as of September 30, 2020 are $0.4 million, $1.8 million, and $1.4 million for 2020, 2021 and 2022, respectively.

Fair value of financial instrum

Fair value of financial instruments and marketable securities	9 Months Ended
	Sep. 30, 2020
Fair Value Disclosures [Abstract]
Fair value of financial instruments and marketable securities	The Company follows the fair value measurement rules, which provide These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority). ● Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date. ● Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs). ● Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available. Cash equivalents and marketable securities 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. In May 2019, the Company purchased $4.0 million of shares of ClearPoint Neuro, Inc.’s ("ClearPoint"), formerly known as MRI Interventions, Inc., common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with ClearPoint, a publicly traded medical device company. The Company determined that the equity investment represents a financial instrument and therefore, recorded it at fair value, which is readily determinable. The equity investment is a component of deposits and other assets on the consolidated balance sheet. During the three and nine month periods ended September 30, 2020, the Company recorded unrealized gains of $2.5 million and $0.9 million, respectively, which are components of other income, net within the consolidated statement of operations. The fair value of the equity investment was $7.0 million as of September 30, 2020. The Company classifies its equity investment in ClearPoint as a Level 1 asset within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted. In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that the Company can convert into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three and nine month periods ended September 30, 2020, the Company recorded unrealized gains of $1.4 million and $0.6 million, respectively, which are components of other income, net within the consolidated statement of operations. The fair value of the convertible debt security was $10.6 million as of September 30, 2020. The convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the equity investment and the convertible debt security, no other items included in deposits and other assets on the consolidated balance sheets are fair valued. Fair value of certain marketable securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices. The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ ​ ​ Quoted prices Significant ​ ​ ​ ​ ​ ​ in active other Significant ​ ​ ​ ​ markets for observable unobservable ​ ​ ​ ​ identical assets inputs inputs ​ Total (level 1) (level 2) (level 3) Marketable securities ​ $ 707,049 ​ $ — ​ $ 707,049 ​ $ — Equity investment in ClearPoint ​ $ 7,045 ​ $ 7,045 ​ $ — ​ $ — ClearPoint convertible debt security ​ $ 10,633 ​ $ — ​ $ 10,633 ​ $ — Contingent consideration payable- development and regulatory milestones ​ $ 138,200 ​ $ — ​ $ — ​ $ 138,200 Contingent consideration payable- net sales milestones and royalties ​ $ 95,900 ​ $ — ​ $ — ​ $ 95,900 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ ​ ​ Quoted prices Significant ​ ​ ​ ​ ​ ​ in active other Significant ​ ​ ​ ​ markets for observable unobservable ​ ​ ​ ​ identical assets inputs inputs ​ Total (level 1) (level 2) (level 3) Marketable securities ​ $ 398,535 ​ $ — ​ $ 398,535 ​ $ — Equity investment in ClearPoint ​ $ 6,194 ​ $ 6,194 ​ $ — ​ $ — Stock appreciation rights liability ​ $ 3,186 ​ $ — ​ $ — ​ $ 3,186 Deferred consideration payable ​ $ 40,000 ​ $ — ​ $ 40,000 ​ $ — Contingent consideration payable- development and regulatory milestones ​ $ 290,500 ​ $ — ​ $ — ​ $ 290,500 Contingent consideration payable- net sales milestones and royalties ​ $ 65,800 ​ $ — ​ $ — ​ $ 65,800 ​ No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2020 and December 31, 2019. The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Amortized Gross Unrealized ​ ​ ​ ​ Cost Gains Losses Fair Value Commercial paper ​ $ 260,392 ​ $ 74 ​ $ (16) ​ $ 260,450 Corporate debt securities ​ 316,198 ​ 2,082 ​ (19) ​ 318,261 Asset-backed securities ​ 35,461 ​ 232 ​ (2) ​ 35,691 Government obligations ​ ​ 92,602 ​ ​ 61 ​ ​ (16) ​ ​ 92,647 Total ​ $ 704,653 ​ $ 2,449 ​ $ (53) ​ $ 707,049 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Amortized Gross Unrealized ​ ​ ​ ​ Cost Gains Losses Fair Value Commercial paper ​ $ 157,936 ​ $ 162 ​ $ — ​ $ 158,098 Corporate debt securities ​ 188,778 ​ 576 ​ (20) ​ 189,334 Asset-backed securities ​ ​ 51,062 ​ ​ 49 ​ ​ (8) ​ ​ 51,103 Total ​ $ 397,776 ​ $ 787 ​ $ (28) ​ $ 398,535 ​ For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. For the three month and nine month periods ended September 30, 2020, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three month and nine month periods ended September 30, 2020, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. For the three month and nine month periods ended September 30, 2020, the Company had $0.3 million and $0.5 million, respectively, realized gains from the sale of marketable securities. Realized gains are reported as a component of interest expense, net in the consolidated statement of operations. The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2020 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Securities in an unrealized loss Securities in an unrealized loss ​ ​ ​ ​ ​ ​ position less than 12 months position greater than 12 months ​ Total ​ Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Commercial paper ​ $ (16) ​ ​ 53,580 ​ ​ — ​ ​ — ​ ​ (16) ​ ​ 53,580 Corporate debt securities ​ ​ (19) ​ ​ 62,811 ​ ​ — ​ ​ — ​ ​ (19) ​ ​ 62,811 Asset-backed securities ​ (2) ​ 2,899 ​ — ​ — ​ (2) ​ 2,899 Government obligations ​ ​ (16) ​ ​ 31,955 ​ ​ — ​ ​ — ​ ​ (16) ​ ​ 31,955 Total ​ $ (53) ​ $ 151,245 ​ $ — ​ $ — ​ $ (53) ​ $ 151,245 ​ 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, 2019 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Securities in an unrealized loss Securities in an unrealized loss ​ ​ ​ ​ ​ ​ position less than 12 months position greater than 12 months ​ Total ​ Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Corporate debt securities ​ $ (20) ​ $ 71,779 ​ $ — ​ $ — ​ $ (20) ​ $ 71,779 Asset-backed securities ​ ​ (8) ​ ​ 24,211 ​ ​ — ​ ​ — ​ ​ (8) ​ ​ 24,211 Total ​ $ (28) ​ $ 95,990 ​ $ — ​ $ — ​ $ (28) ​ $ 95,990 ​ Marketable securities on the balance sheet at September 30, 2020 and December 31, 2019 mature as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Less Than More Than ​ 12 Months 12 Months Commercial paper ​ $ 260,451 ​ $ — Corporate debt securities ​ 260,199 ​ 58,062 Asset-backed securities ​ 14,375 ​ 21,316 Government obligations ​ ​ 39,530 ​ ​ 53,116 Total Marketable securities ​ $ 574,555 ​ $ 132,494 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Less Than More Than ​ 12 Months 12 Months Commercial paper ​ $ 158,098 ​ $ — Corporate debt securities ​ 139,596 ​ 49,738 Asset-backed securities ​ ​ 44,724 ​ ​ 6,379 Total Marketable securities ​ $ 342,418 ​ $ 56,117 ​ The Company classifies all of its marketable securities as current as they are all available for sale and are available for current operations. Convertible senior notes In August 2015, the Company issued $150.0 million of 3.00% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.50% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,” together with the “2022 Convertible Notes,” the “Convertible Notes”). 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 11. 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 2022 Convertible Notes at September 30, 2020 and December 31, 2019 was $171.3 million and $171.2 million, respectively. The estimated fair value of the 2026 Convertible Notes at September 30, 2020 and December 31, 2019 was $329.2 million and $335.0 million, respectively. Deferred and contingent consideration payable Pursuant to the Merger Agreement, Agilis equityholders were previously 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 was required to pay $40.0 million of development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The $40.0 million of development milestones were classified as deferred consideration on the Company’s consolidated balance sheets. Pursuant to the terms of the Rights Exchange Agreement, in the three month period ended June 30, 2020, the Company issued 2,821,176 shares of its common stock and paid $36.9 million in the aggregate, to Participating Rightholders, who in exchange have canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments, or the deferred consideration, that would have been due upon the passing of the second anniversary of the closing of the Merger. As a result of the Rights Exchange Agreement, the remaining deferred consideration payable was $2.4 million, which was paid out in the three month period ended September 30, 2020 upon the passing of the second anniversary of the closing of the Merger. Accordingly, as of September 30, 2020, the remaining balance of the deferred consideration payable was $0. As of result of the Rights Exchange Agreement, the Company recognized a gain of $0.7 million on the settlement of the development milestones and a loss of $11.3 million on the settlement of the regulatory milestones. The $0.7 million gain and $11.3 million loss are included in the settlement of deferred and contingent consideration in the Company’s statement of operations for the nine month period ended September 30, 2020. Additionally, as of the date of the Rights Exchange Agreement, the Company recognized a gain on the fair value of the contingent consideration of $1.0 million related to the portion of regulatory milestones that were forfeited, which is included in the change in fair value of the deferred and contingent liability within the Company’s statement of operations for the nine month period ended September 30, 2020. This non-recurring Level 3 fair value measurement was estimated using the same valuation methodology and unobservable inputs for development and regulatory milestones in the Level 3 valuation section below. In conjunction with the Rights Exchange Agreement, the Company also incurred $2.0 million of transaction fees, which were included in other expense in the Company’s statement of operations for the nine month period ended September 30, 2020. Level 3 valuation 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 last payment of the SARs liability was made in the three month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of September 30, 2020 was $0. The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of deferred and contingent consideration on 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. At September 30, 2020, the weighted average discount rate for the development and regulatory milestones was 4.2% and the weighted average probability of success was 42%. 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. At September 30, 2020, the weighted average discount rate for the net sales milestones and royalties was 12.0% and the weighted average probability of success for the net sales milestones was 48%. The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the SARs liability, and the contingent consideration payable for the periods ended September 30, 2020 and September 30, 2019. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Level 3 liabilities ​ ​ ​ ​ ​ Contingent consideration payable- ​ Contingent consideration payable- ​ ​ ​ ​ ​ development and regulatory ​ net sales milestones and royalties ​ SARs milestones ​ Beginning balance as of December 31, 2019 ​ $ 3,186 ​ $ 290,500 ​ $ 65,800 Additions ​ — ​ — ​ — Change in fair value ​ — ​ (13,120) ​ 30,100 Payments ​ ​ (3,186) ​ ​ — ​ ​ — Rights Exchange settlement ​ ​ — ​ ​ (139,180) ​ ​ — Ending balance as of September 30, 2020 ​ $ — ​ $ 138,200 ​ $ 95,900 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Level 3 liabilities ​ ​ ​ ​ ​ Contingent consideration payable- ​ Contingent consideration payable- ​ ​ ​ ​ ​ development and regulatory ​ net sales milestones and royalties ​ SARs milestones ​ Beginning balance as of December 31, 2018 ​ $ 3,814 ​ $ 257,040 ​ $ 53,200 Additions ​ — ​ — ​ — Change in fair value ​ 2,236 ​ 28,260 ​ 6,400 Payments ​ ​ (3,815) ​ ​ — ​ ​ — Ending balance as of September 30, 2019 ​ $ 2,235 ​ $ 285,300 ​ $ 59,600 ​ The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended September 30, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Fair Value Valuation Technique Unobservable Input Range Contingent consideration payable- ​ $138,200 Probability-adjusted discounted cash flow Potential development and regulatory milestones ​ $0 - $381 million Contingent considerable payable- net sales ​ $95,900 Option-pricing model with Monte Carlo simulation Potential net sales milestones ​ $0 - $150 million ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Fair Value Valuation Technique Unobservable Input Range SARs ​ $3,186 ​ Option-pricing model Volatility 28.93% 0.19% $6.76 - $30.86 $48.03 0.01 years Contingent consideration payable- development and regulatory milestones ​ $290,500 ​ Probability-adjusted discounted cash flow ​ Potential development and regulatory milestones ​ $0 - $555 million Contingent considerable payable- net sales milestones and royalties ​ $65,800 Option-pricing model with Monte Carlo simulation Potential net sales milestones ​ $0 - $150 million ​ The contingent consideration payables are classified Level 3 liabilities as their 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 approaches, including but not limited to, assumptions involving probability adjusted sales estimates for the gene therapy platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

Other comprehensive income (los

Other comprehensive income (loss) and accumulated other comprehensive items	9 Months Ended
	Sep. 30, 2020
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Other comprehensive income (loss) and accumulated other comprehensive items	Other comprehensive income (loss) includes changes in equity that are excluded from net income (loss), such as unrealized gains and losses on marketable securities. The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine month periods ended September 30, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrealized ​ ​ Total ​ ​ Gains/(Losses) ​ ​ ​ ​ Accumulated ​ ​ On ​ Foreign ​ Other ​ ​ Marketable ​ Currency ​ Comprehensive ​ ​ Securities, net of tax ​ Translation ​ Items Balance, June 30, 2020 ​ $ 3,410 ​ $ (13,426) ​ $ (10,016) Other comprehensive loss before reclassifications ​ (1,016) ​ (24,695) ​ (25,711) Amounts reclassified from other comprehensive items ​ — ​ — ​ — Other comprehensive loss before reclassifications ​ (1,016) ​ (24,695) ​ (25,711) Balance, September 30, 2020 ​ $ 2,394 ​ $ (38,121) ​ $ (35,727) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrealized ​ ​ Total ​ ​ Gains ​ ​ ​ ​ Accumulated ​ ​ On ​ Foreign ​ Other ​ ​ Marketable ​ Currency ​ Comprehensive ​ ​ Securities, net of tax ​ Translation ​ Items Balance, December 31, 2019 ​ $ 755 ​ $ (11,339) ​ $ (10,584) Other comprehensive income (loss) before reclassifications ​ 1,639 ​ (26,782) ​ (25,143) Amounts reclassified from other comprehensive items ​ — ​ — ​ — Other comprehensive income (loss) ​ 1,639 ​ (26,782) ​ (25,143) Balance, September 30, 2020 ​ $ 2,394 ​ $ (38,121) ​ $ (35,727)

Accounts payable and accrued ex

Accounts payable and accrued expenses	9 Months Ended
	Sep. 30, 2020
Payables and Accruals [Abstract]
Accounts payable and accrued expenses	Accounts payable and accrued expenses at September 30, 2020 and December 31, 2019 consist of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ ​ 2020 2019 ​ Employee compensation, benefits, and related accruals ​ $ 34,485 ​ $ 38,390 ​ Income tax payable ​ ​ 21,475 ​ ​ 499 ​ Consulting and contracted research ​ 17,659 ​ 12,969 ​ Professional fees ​ 4,590 ​ 3,562 ​ Sales allowance and other costs ​ 50,644 ​ 41,155 ​ Sales rebates and royalties ​ 68,628 ​ 42,997 ​ Accounts payable ​ 15,663 ​ 10,324 ​ Other ​ 5,417 ​ 9,380 ​ Total ​ $ 218,561 ​ $ 159,276 ​

Capitalization

Capitalization	9 Months Ended
	Sep. 30, 2020
Stockholders' Equity Note [Abstract]
Capitalization	In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. During the three and nine month periods ending September 30, 2020, the Company issued and sold an aggregate of 173,956 and 542,470 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $54.39 and $53.37 per share, respectively. During the three and nine month periods ending September 30, 2020, the Company received net proceeds of $9.1 million and $28.1 million, respectively, after deducting underwriting discounts and commissions and other offering expenses payable by the Company. The remaining shares of the Company’s common stock available to be issued and sold, under the At the Market Offering, have an aggregate offering price of up to $93.0 million as of September 30, 2020. As a result of the Rights Exchange Agreement, during the nine month period ended September 30, 2020, the Company issued 2,821,176 shares of its common stock to Participating Rightholders. The shares had a fair value of $150.5 million upon issuance. As a result of the Censa Merger, during the nine month period ended September 30, 2020, the Company issued 845,364 shares of the Company’s common stock to Censa security holders, which were valued at $42.9 million based on the closing stock price on the acquisition date. The number of shares issued was determined using a 30-day VWAP pursuant to the Censa Merger Agreement.

Net loss per share

Net loss per share	9 Months Ended
	Sep. 30, 2020
Earnings Per Share [Abstract]
Net loss per share	Basic earnings per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss by the weighted-average number of common shares plus the effect of any dilutive potential common shares outstanding during the period. The following tables set forth the computation of basic and diluted net loss per share: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ ​ Nine Months Ended September 30, ​ ​ ​ 2020 2019 ​ 2020 2019 ​ Numerator ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ (69,692) $ (59,997) ​ $ (363,806) $ (173,899) ​ Denominator ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Denominator for basic and diluted net loss per share ​ 67,641,171 56,463,528 ​ 65,068,281 57,798,968 ​ Net loss per share: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted ​ $ (1.03) * $ (1.06) * ​ $ (5.59) * $ (3.01) * ​ * In the three and nine months ended September 30, 2020 and 2019, the Company experienced a net loss and therefore did not report any dilutive share impact. The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. ​ ​ ​ ​ ​ ​ ​ ​ ​ As of September 30, ​ ​ 2020 2019 Stock Options ​ 11,528,241 ​ 10,743,181 ​ Unvested restricted stock awards and units 961,795 650,103 Total 12,490,036 11,393,284

Stock award plan

Stock award plan	9 Months Ended
	Sep. 30, 2020
Share-based Payment Arrangement [Abstract]
Stock award plan	On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Company’s Board of Directors approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan. In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases. In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan. In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. 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, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of September 30, 2020, awards for 935,092 shares of common stock are available for issuance under the 2013 Long Term Incentive Plan. In January 2020, the Company’s Board of Directors approved the 2020 Inducement Stock Incentive Plan. The 2020 Inducement Stock Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards for up to an aggregate of 1,000,000 shares of common stock. Any grants made under the 2020 Inducement Stock Incentive Plan must be made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company’s new hires’ employment compensation. As of September 30, 2020, awards for 291,025 shares of common stock are available for issuance under the 2020 Inducement Stock Incentive Plan. From January 1, 2020 through September 30, 2020, the Company issued a total of 2,671,660 stock options to various employees. Of those, 667,285 were inducement grants for non-statutory stock options, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan. A summary of stock option activity is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ ​ Weighted- ​ average ​ ​ Aggregate ​ ​ ​ ​ average ​ remaining ​ ​ intrinsic ​ ​ Number of ​ exercise ​ contractual ​ ​ value(in ​ ​ options ​ price ​ term ​ ​ thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2019 11,043,939 ​ $ 31.67 ​ ​ Granted 2,671,660 ​ $ 50.76 ​ ​ Exercised (1,426,026) ​ $ 23.14 ​ ​ Forfeited/Cancelled (761,332) ​ $ 42.96 ​ ​ Outstanding at September 30, 2020 11,528,241 ​ $ 36.37 7.32 years ​ $ 138,286 Vested or Expected to vest at September 30, 2020 5,297,899 ​ $ 40.09 8.70 years ​ $ 44,050 Exercisable at September 30, 2020 5,576,283 ​ $ 32.19 5.84 years ​ $ 90,361 ​ The fair value of grants made in the nine months ended September 30, 2020 was contemporaneously estimated on the date of grant using the following assumptions: ​ ​ ​ ​ ​ ​ Nine months ended ​ September 30, 2020 Risk-free interest rate 0.34% - 1.45% Expected volatility 87.50% - 89.31% Expected term 5.75 ​ The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine month period ended September 30, 2020 was $36.76 per share. The expected term of options was estimated based on the Company’s historical exercise data and the expected volatility of options was estimated based on the Company’s historical stock volatility. The risk-free rate of the options was based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option. Restricted Stock Awards and Restricted Stock Units The following table summarizes information on the Company’s restricted stock awards and units: ​ ​ ​ ​ ​ ​ ​ ​ ​ Restricted Stock Awards and Units ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ ​ ​ Grant ​ ​ Number of ​ Date ​ Shares Fair Value January 1, 2020 ​ 642,419 ​ $ 24.50 Granted 625,390 ​ $ 50.76 Vested (232,263) ​ $ 23.86 Forfeited (73,751) ​ $ 36.28 Unvested at September 30, 2020 961,795 ​ $ 41.05 ​ Stock Appreciation Rights In May 2016, a total of 897,290 SARs were granted to non-executive employees (the "2016 SARs"). The 2016 SARs vested annually in equal installments over four years and were settled in cash on each vest date, which required the Company to remeasure the SARs at each reporting period until vesting occurs. For the nine month period ended September 30, 2020, a total of 132,136 SARs vested. The last payment of the SARs liability was made in the three month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of September 30, 2020 was $0. Employee Stock Purchase Plan six month The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ Nine Months Ended September 30, ​ ​ 2020 2019 2020 2019 ​ Research and development ​ $ 9,220 ​ $ 4,988 ​ $ 25,961 ​ $ 15,191 ​ Selling, general and administrative ​ 7,559 ​ 5,496 ​ 22,948 ​ 15,477 ​ Total ​ $ 16,779 ​ $ 10,484 ​ $ 48,909 ​ $ 30,668 ​ ​ As of September 30, 2020, there was approximately $173.2 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the 2009 Equity and Long Term Incentive Plan, the 2013 Long Term Incentive Plan and equity awards made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 2.91 years.

Debt

Debt	9 Months Ended
	Sep. 30, 2020
Debt Disclosure [Abstract]
Debt	11. Debt Liability for sale of future royalties In July 2020, the Company entered into the Royalty Purchase Agreement. As RPI’s interest is explicitly limited, the $650.0 million cash consideration was classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability will be amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The initial annual effective interest rate was determined to be 11.0%. The Company will utilize the prospective method to account for subsequent changes in the estimated future payments to be made to RPI. Issuance costs related to the transaction were determined to be immaterial. ​ The following table shows the activity within the “liability for sale of future royalties- current” and “liability for sale of future royalties- noncurrent” accounts for the three and nine month periods ended September 30, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, Nine Months Ended September 30, Liability for sale of future royalties- (current and noncurrent) ​ 2020 2020 Beginning balance ​ $ — ​ $ — ​ Proceeds from sale of future royalties ​ 650,000 ​ 650,000 ​ Less: Non-cash royalty revenue payable to RPI ​ ​ (299) ​ ​ (299) ​ Plus: Non-cash interest expense recognized ​ ​ 14,557 ​ ​ 14,557 ​ Ending balance ​ $ 664,258 ​ $ 664,258 ​ Effective interest rate for the period ​ 11.0 % 11.0 % ​ Non-cash interest expense is recorded in the statement of operations within “Interest expense, net”. ​ 2017 Credit Facility In May 2017, the Company entered into the Credit Agreement, which provided 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 "Credit Facility"). 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 were amortized over the term of the Credit Facility. Borrowings under the Credit Agreement bore interest at a rate per annum equal to the London Interbank Offered Rate, or LIBOR, (with a LIBOR floor rate of 1.00%) plus 6.15%. The Company was 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 was required to make monthly interest payments and monthly principal payments. The principal payments were made based on straight-line amortization of the principal over the twenty-four month period. The maturity date of the Credit Agreement was May 1, 2021, unless terminated earlier. On July 1, 2020, the Company terminated the Credit Facility. In connection with the termination of the Credit Facility, the Company repaid outstanding principal of $18.3 million, which was classified as the current portion of long term debt on the consolidated balance sheet and accrued interest of $0.1 million, which was classified within accrued liabilities on the consolidated balance sheet, thereunder totaling $18.4 million. The Company paid an additional $0.6 million in termination and exit fees, which are included as a component of other income, net in the Company’s statement of operations for the three and nine month periods ended September 30, 2020. All liens and security interests securing the term loan made pursuant to the Credit Facility were released upon termination. ​ 2026 Convertible Notes In September 2019, the Company issued, at par value, $287.5 million aggregate principal amount of 1.50% convertible senior notes due 2026, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company. The 2026 Convertible Notes are governed by an indenture (the "2026 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2026 Convertible Notes Trustee"). Holders may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances: ● during any calendar quarter commencing on or after December 31, 2019 (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 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 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 March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company’s common stock or any combination thereof at the Company’s election. The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest. The Company is not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 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 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically. If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The 2026 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 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 2026 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 2026 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 2026 Convertible Notes, the Company separated the 2026 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 2026 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 2026 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 2026 Convertible Notes was $123.0 million and was recorded in additional paid-in capital. In accounting for the transaction costs related to the issuance of the 2026 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2026 Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year The 2026 Convertible Notes consist of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability component September 30, 2020 ​ December 31, 2019 ​ Principal ​ $ 287,500 ​ $ 287,500 ​ Less: Debt issuance costs ​ (4,192) ​ (4,567) ​ Less: Debt discount, net(1) ​ (109,563) ​ (119,350) ​ Net carrying amount ​ $ 173,745 ​ $ 163,583 ​ (1) Included in the consolidated balance sheets within convertible senior notes (due 2026) and amortized to interest expense over the remaining life of the 2026 Convertible Notes using the effective interest rate method. As of September 30, 2020, the remaining contractual life of the 2026 Convertible Notes is approximately 6.0 years. The following table sets forth total interest expense recognized related to the 2026 Convertible Notes: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ ​ Nine Months Ended September 30, ​ ​ ​ ​ 2020 ​ 2019 ​ ​ 2020 ​ 2019 ​ ​ ​ Contractual interest expense ​ $ 1,081 ​ $ 130 ​ ​ $ 3,223 ​ $ 130 ​ ​ ​ Amortization of debt issuance costs ​ 127 ​ ​ 15 ​ ​ 374 ​ 15 ​ ​ ​ Amortization of debt discount ​ ​ 3,313 ​ ​ 391 ​ ​ ​ 9,786 ​ ​ 391 ​ ​ ​ Total ​ $ 4,521 ​ $ 536 ​ ​ $ 13,383 ​ $ 536 ​ ​ ​ Effective interest rate of the liability component ​ 10.2 % ​ 10.2 % ​ 10.2 % ​ 10.2 % ​ ​ ​ 2022 Convertible Notes In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.00% convertible senior notes due 2022. The 2022 Convertible Notes bear cash interest at a rate of 3.00% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The 2022 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 2022 Convertible Notes are governed by an indenture (the "2022 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2022 Convertible Notes Trustee"). Holders may convert their 2022 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 2022 Convertible Notes Indenture) per $1,000 principal amount of 2022 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 2022 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 2022 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 2022 Convertible Notes being converted. The conversion rate for the 2022 Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest. The Company was not permitted to redeem the 2022 Convertible Notes prior to August 20, 2018. As of August 20, 2018, the Company may redeem for cash all or any portion of the 2022 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 2022 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2022 Convertible Notes, which means that the Company is not required to redeem or retire the 2022 Convertible Notes periodically. There have been no redemptions to date. If the Company undergoes a “fundamental change” (as defined in the 2022 Convertible Notes Indenture), subject to certain conditions, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The 2022 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2022 Convertible Notes Indenture contains customary events of default with respect to the 2022 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2022 Convertible Notes when due and payable) occurring and continuing, the 2022 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2022 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2022 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2022 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2022 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 2022 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 2022 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 2022 Convertible Notes, the Company separated the 2022 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 2022 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 In accounting for the transaction costs related to the issuance of the 2022 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2022 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 2022 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 2022 Convertible Notes. ​ The 2022 Convertible Notes consist of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability component September 30, 2020 December 31, 2019 ​ Principal ​ $ 150,000 ​ $ 150,000 ​ Less: Debt issuance costs ​ (986) ​ (1,329) ​ Less: Debt discount, net (1) ​ (19,794) ​ (26,686) ​ Net carrying amount ​ $ 129,220 ​ $ 121,985 ​ (1) Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the 2022 Convertible Notes using the effective interest rate method. As of September 30, 2020, the remaining contractual life of the 2022 Convertible Notes is approximately 1.9 years. The following table sets forth total interest expense recognized related to the 2022 Convertible Notes: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, Nine Months Ended September 30, ​ ​ 2020 2019 2020 2019 ​ Contractual interest expense ​ $ 1,131 ​ $ 1,134 ​ $ 3,375 ​ $ 3,375 ​ ​ Amortization of debt issuance costs ​ 118 ​ 106 ​ 343 ​ 308 ​ ​ Amortization of debt discount ​ 2,372 ​ 2,137 ​ 6,892 ​ 6,192 ​ ​ Total ​ $ 3,621 ​ $ 3,377 ​ $ 10,610 ​ $ 9,875 ​ ​ Effective interest rate of the liability component ​ 11.0 % 11.0 % 11.0 % 11.0 % ​ ​

Commitments and contingencies

Commitments and contingencies	9 Months Ended
	Sep. 30, 2020
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company’s oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement. The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single-digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon the Company’s payment to the SMA Foundation of a specified amount. Pursuant to the asset purchase agreement ("Asset Purchase Agreement") between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC) (“Marathon”), Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone. Pursuant to the Merger Agreement with Agilis, Agilis equityholders were previously 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 Company was required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Pursuant to the terms of the Rights Exchange Agreement, the Participating Rightholders canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments that would have been due upon the passing of the second anniversary of the closing of the Merger, regardless of whether the milestones are achieved. The Rights Exchange Agreement has no effect on the Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightholders’ rights to receive $211.6 million, in the aggregate, of the milestone payments described above. As a result, all other rights and obligations under the Merger Agreement remain in effect pursuant to their terms, including the Company’s obligation to pay up to an aggregate maximum amount of $20.0 million upon the achievement of certain development milestones (representing the remaining portion of potential development milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement while excluding the remaining $2.4 million milestone payment that was due and paid in the three month period ended September 30, 2020 upon the passing of the second anniversary of the closing of the Merger), up to an aggregate maximum amount of $361.0 million upon the achievement of certain regulatory milestones (representing the remaining portion of potential regulatory milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement), up to a maximum aggregate amount of $150.0 million upon the achievement of certain net sales milestones and a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% to 6%, pursuant to the terms of the Merger Agreement. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products. Subject to the terms and conditions of the Censa Merger Agreement, Censa securityholders may become entitled to receive contingent payments from the Company based on (i) the achievement of certain development and regulatory milestones up to an aggregate maximum amount of $217.5 million for PTC923’s two most advanced programs and receipt of a priority review voucher from the FDA as set forth in the Censa Merger Agreement, (ii) $109.0 million in development and regulatory milestones for each additional indication of PTC923, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $160.0 million, (iv) a percentage of annual net sales during specified terms, ranging from single to low double digits of the applicable net sales threshold amount, and (v) any sublicense fees paid to the Company in consideration of any sublicense of Censa’s intellectual property to commercialize PTC923, on a country-by-country basis, which contingent payment shall equal to a mid-double digit percentage of any such sublicense fees. Pursuant to the Censa Merger Agreement, the Company has the option to pay the initial $30.0 million development milestone, for the completion of enrollment of a Phase 3 clinical trial for PTC923 for PKU, if achieved, in cash or shares of the Company’s common stock. 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 (the "Akcea Collaboration and License Agreement"). Pursuant to the Akcea Collaboration and License Agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million. In 2019, a $6.0 million milestone was paid upon receipt of regulatory approval of Waylivra from the EMA and a $4.0 million milestone was paid upon regulatory approval of Tegsedi from ANVISA, the Brazilian health regulatory authority, upon receipt of regulatory approval for Waylivra from ANVISA. In addition, Akcea is eligible to receive an additional milestone payment of $4.0 million upon receipt of regulatory approval for Waylivra from ANVISA. 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 its business, the Company is subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in the Company’s clinical trials or otherwise gain access to its product candidates. The Company is not currently aware of any material legal proceedings against it.

Revenue recognition

Revenue recognition	9 Months Ended
	Sep. 30, 2020
Revenue from Contract with Customer [Abstract]
Revenue recognition	Net product sales The Company views its operations and manages its business in one operating segment. During the three months ended September 30, 2020 and 2019, net product sales in the United States were $38.5 million and $22.9 million, respectively, consisting solely of Emflaza, and net product sales not in the United States were $44.2 million and $48.5 million, respectively, consisting of Translarna, Tegsedi, and Waylivra. For the three months ended September 30, 2020 and 2019, the Company had a total of two and two distributors, respectively, that each accounted for over 10% of the Company’s net product sales. During the nine months ended September 30, 2020 and 2019, net product sales in the United States were $102.1 million and $68.3 million, respectively, consisting solely of Emflaza, and net product sales not in the United States were $124.0 million and $141.6 million, respectively, consisting of Translarna, Tegsedi, and Waylivra. For the nine months ended September 30, 2020 and 2019, the Company had a total of two and two distributors, respectively, that each accounted for over 10% of the Company’s net product sales. The Company’s contract liabilities balances as of September 30, 2020 and as of December 31, 2019 were $6.0 million and $11.7 million, respectively. The Company did not have any contract assets as of September 30, 2020 and as of December 31, 2019. During the three and nine month periods ended September 30, 2020, the Company recognized $2.0 million and $6.0 million of revenue, respectively, related to the amounts included in the contract liability balance at the beginning of the period. For the three and nine month periods ended September 30, 2019, the Company recognized $2.3 million and $2.3 million, respectively, relating to the contract liability balance at the beginning of the period. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine month periods ending September 30, 2020 and 2019. Remaining performance obligations Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of September 30, 2020 and December 31, 2019, the aggregate amount of the transaction price allocated to the remaining performance obligations relating to Translarna net product revenue was $6.0 million and $11.7 million, respectively. The Company expects to recognize revenue within the next Collaboration and Royalty revenue In November 2011, the Company and the SMA Foundation entered into the License Agreement with Roche. Under the terms of the License Agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program. 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 specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. The SMA program currently has one approved product, Evrysdi™ (risdiplam), which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. The first commercial sale of Evrysdi in the United States was made in August 2020. This event triggered a $20.0 million milestone payment to the Company from Roche. In August 2020, the EMA accepted the MAA filed by Roche for Evrysdi for the treatment of SMA, which triggered a $15.0 million milestone payment to the Company from Roche. As of September 30, 2020, the remaining potential research and development event milestones that can be received is $37.5 million, and the remaining potential sales milestones that can be received is $325.0 million. For the three months ended September 30, 2020 and 2019, the Company recognized $35.0 million and $0.1 million of revenue, respectively, related to the licensing and collaboration agreement with Roche. For the nine months ended September 30, 2020 and 2019, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $35.1 million and $0.1 million, respectively. ​ In addition to research and development and sales milestones, the Company is eligible to receive double-digit royalties on worldwide annual net sales of a commercial product under the License Agreement. For the three and nine months ended September 30, 2020, the Company has recognized $0.7 million of royalty revenue related to Evrysdi.

Intangible assets and goodwill

Intangible assets and goodwill	9 Months Ended
	Sep. 30, 2020
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible assets and goodwill	Definite-lived intangibles On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to the Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. In accordance with ASU 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, which is being amortized to cost of product sales over its expected useful life of approximately seven years on a straight line basis. Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In accordance with the guidance for an asset acquisition, the Company records the milestone payment when it becomes payable to Marathon and increases the cost basis for the Emflaza rights intangible asset. As of September 30, 2020 and 2019, milestone payments of $13.8 million and $7.4 million, respectively, were recorded and are included on the balance sheet within accounts payable and accrued expenses. These payments are being amortized over the remaining useful life of the Emflaza rights asset on a straight line basis. Pursuant to the Akcea Collaboration and License Agreement, in May 2019 the Company made a $6.0 million milestone payment to Akcea upon regulatory approval of Waylivra from the EMA. The payment was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life of approximately ten years on a straight line basis. Additionally, in December 2019, the Company made a $4.0 million milestone payment to Akcea upon regulatory approval of Tegsedi from ANVISA. The payment was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life of approximately ten years on a straight line basis. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement related to sales of Waylivra. In accordance with the guidance for an asset acquisition, the Company will record royalty payments when they become payable to Akcea and increase the cost basis for the Waylivra intangible asset. For the three months ended September 30, 2020 and 2019, the Company recognized amortization expense of $9.6 million and $7.0 million, respectively, related to the Emflaza rights, Waylivra, and Tegsedi intangible assets. For the nine months ended September 30, 2020 and 2019, the Company recognized amortization expense of $26.3 million and $19.7 million, respectively. The estimated future amortization of the Emflaza rights, Waylivra, and Tegsedi intangible assets is expected to be as follows: ​ ​ ​ ​ ​ ​ As of September 30, 2020 2020 ​ $ 9,627 2021 ​ 38,506 2022 ​ 38,506 2023 ​ 38,506 2024 and thereafter ​ 10,891 Total ​ $ 136,036 ​ The weighted average remaining amortization period of the definite-lived intangibles as of September 30, 2020 is 3.7 years. Indefinite-lived intangibles In connection with the acquisition of the Company’s gene therapy platform from Agilis, 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 gene therapy platform also includes an 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. Additionally, the gene therapy platform includes two other 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. There have been no changes to the balance of the indefinite-lived intangibles since the Merger. Goodwill As a result of the Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. There were no changes to the recorded value of goodwill for the three and nine month periods ended September 30, 2020.

Subsequent events

Subsequent events	9 Months Ended
	Sep. 30, 2020
Subsequent Events [Abstract]
Subsequent events	15. Subsequent events In October 2020, Chugai Pharmaceutical Co., Ltd., a subsidiary of Roche, filed an NDA in Japan for Evrysdi for the treatment of SMA, which triggered a $7.5 million milestone payable to the Company from Roche.

Summary of significant accoun_2

Summary of significant accounting policies (Policies)	9 Months Ended
	Sep. 30, 2020
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The accompanying financial information as of September 30, 2020 and for the three and nine months ended September 30, 2020 and 2019 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2019 and notes thereto included in the 2019 Form 10-K. In the opinion of management, the unaudited financial information as of September 30, 2020 and for the three and nine months ended September 30, 2020 and 2019 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders’ equity, and cash flows. The results of operations for the three and nine month periods ended September 30, 2020 are not necessarily indicative of the results to be expected for the year ended December 31, 2020 or for any other interim period or for any other future year.
Use of estimates	Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, royalty revenue, certain accruals related to the Company’s research and development expenses, valuation procedures for liability for sale of future royalties, valuation procedures for convertible notes, 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.
Restricted Cash	Restricted cash Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the twelve-month period ended December 31, 2019 in connection with obligations under a facility lease for our leased biologics manufacturing facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Beginning of ​ ​ ​ period- End of period- ​ December 31, September 30, ​ 2019 ​ 2020 Cash and cash equivalents ​ $ 288,028 ​ $ 433,970 Restricted cash included in deposits and other assets ​ 7,500 ​ 7,500 Total Cash, cash equivalents and restricted cash per statement of cash flows ​ $ 295,528 ​ $ 441,470 ​
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. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three month and nine month periods ended September 30, 2020, no allowance was recorded for credit losses.
Inventory and cost of product sales	Inventory and cost of product sales Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products 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. Amounts related to clinical development programs and marketing efforts are immaterial. The following table summarizes the components of the Company’s inventory for the periods indicated: ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 Raw materials ​ $ 946 ​ $ 874 Work in progress ​ 8,600 ​ 9,652 Finished goods ​ 9,935 ​ 8,759 Total inventory ​ $ 19,481 ​ $ 19,285 ​ 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. For the three and nine months ended September 30, 2020, inventory write downs were immaterial. No write downs were recorded for the three and nine month periods ended September 30, 2019. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2020 and 2019, 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. Production costs are expensed as cost of product sales when the related products are sold.
Revenue recognition	Revenue recognition Net product revenue The Company’s net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products 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 the product, 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 the 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 product sales. 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 related to Medicaid and other government pricing programs, 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. 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 three months ended September 30, 2020 and 2019, net product sales outside of the United States were $44.2 million and $48.5 million, respectively, and net product sales in the United States were $38.5 million and $22.9 million, respectively. For the nine months ended September 30, 2020 and 2019, net product sales outside of the United States were $124.0 million and $141.6 million, respectively, and net product sales in the United States were $102.1 million and $68.3 million, respectively. 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. 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 and royalty 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 royalties from product sales at the later of when the related sales occur or when the performance obligation to which the royalty has been allocated has been satisfied. If it is probable that a significant revenue reversal will not occur, the Company will estimate the royalty payments using the most likely amount method. 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. The allowance for doubtful accounts was $0.1 million as of September 30, 2020 and $0.3 million as of December 31, 2019. Bad debt expense was immaterial for the three and nine month periods ended September 30, 2020 and 2019. For the three and nine month periods ended September 30, 2020, no allowances were recorded for credit losses.
Liability for sale of future royalties	Liability for sale of future royalties On July 17, 2020, the Company, RPI Intermediate Finance Trust (“RPI”), and, for the limited purposes set forth in the agreement, Royalty Pharma PLC, entered into a Royalty Purchase Agreement (the “Royalty Purchase Agreement”). Pursuant to the Royalty Purchase Agreement, the Company sold to RPI 42.933% (the “Assigned Royalty Payment”) of the Company’s right to receive sales-based royalty payments (the “Royalty”) on worldwide net sales of Evrysdi and any other product developed pursuant to the License and Collaboration Agreement (the “License Agreement”), dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation under the SMA program. In consideration for the sale of the Assigned Royalty Payments, RPI paid the Company $650.0 million in cash consideration. The Company has retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the License Agreement, which milestone payments equal $362.5 million in the aggregate as of September 30, 2020. The Royalty Purchase Agreement will terminate 60 days following the earlier of the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the License Agreement and the date on which RPI has received $1.3 billion in respect of the Assigned Royalty Payments. The cash consideration obtained pursuant to the Royalty Purchase Agreement is classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability will be amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The Company will utilize the prospective method to account for subsequent changes in the estimated future payments to be made to RPI. Refer to Note 11 for further details.
Indefinite-lived intangible assets	Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset 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. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company’s outlook and market performance of the Company’s industry and recent and forecasted financial performance.
Goodwill	Goodwill Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassess its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount.
Income Taxes	Income Taxes O On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2020. 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 of $122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company’s policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful. The $650.0 million cash consideration received from RPI pursuant to the Royalty Purchase Agreement was treated as taxable income in the current year and resulted in a current tax provision of $22.1 million related to state income taxes after considering the state NOL and tax credits. The Company did not generate a federal income tax liability after considering the federal NOL and tax credits.
Leases	Leases The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating and finance leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating and finance lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments. Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases. Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories. A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates. The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. See Note 4 Leases for additional information.
Recently issued accounting standards	Recently issued accounting standards In August 2020, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2020-06, “Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity.” ASU 2020-06 simplifies the accounting for convertible instruments by removing certain separation models in Subtopic 470- 20, Debt—Debt with Conversion and Other Options, for convertible instruments. Under ASU 2020-06, the embedded conversion features no longer are separated from the host contract for convertible instruments with conversion features that are not required to be accounted for as derivatives under Topic 815, Derivatives and Hedging, or that do not result in substantial premiums accounted for as paid-in capital. Consequently, a convertible debt instrument will be accounted for as a single liability measured at its amortized cost and a convertible preferred stock will be accounted for as a single equity instrument measured at its historical cost, as long as no other features require bifurcation and recognition as derivatives. By removing those separation models, the interest rate of convertible debt instruments typically will be closer to the coupon interest rate when applying the guidance in Topic 835, Interest. The amendments under ASU 2020-06 also include revisions related to the derivatives scope exception for contracts in an entity’s own equity and earnings per share. The amendments under ASU 2020-06 are effective for public business entities that meet the definition of a SEC filer, excluding entities eligible to be smaller reporting companies as defined by the SEC, for fiscal years beginning after December 15, 2021, including interim periods within those fiscal years. For all other entities, the amendments are effective for fiscal years beginning after December 15, 2023, including interim periods within those fiscal years. Early adoption is permitted, but no earlier than fiscal years beginning after December 15, 2020, including interim periods within those fiscal years. The FASB specified that an entity should adopt the guidance as of the beginning of its annual fiscal year. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU 2020-06 will have on its consolidated financial statements and accompanying notes. Impact of recently adopted accounting pronouncements In December 2019, the FASB issued ASU 2019-12,"Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes”. ASU 2019-12 simplifies the accounting for income taxes by removing certain exceptions to the general principles in Topic 740. The amendments also improve consistent application of and simplify GAAP for other areas of Topic 740 by clarifying and amending the existing guidance. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2020. For all other entities, it is effective for annual periods beginning after December 15, 2021 and interim periods in annual periods beginning after December 15, 2022. Early adoption is permitted, including adoption in any interim period. The Company early adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments - Credit Losses, which expands the scope of the practical expedient that allows entities to exclude the accrued interest component of amortized cost from various disclosures required by ASC 326 to also include certain disclosures required by ASC 320. Entities that elect to apply the practical expedient must disclose the total amount of accrued interest that they exclude from their disclosures of amortized cost. The amendments have the same effective dates as ASU 2016-13 (Topic 326) for entities that have not yet adopted that standard. The Company adopted ASU 2016-13 and ASU 2019-11 effective January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its accounting policy for marketable securities within this footnote as well as its fair value footnote (Note 5) with additional disclosures as required by the standard upon adoption. 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 adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its fair value footnote (Note 5) with additional and modified disclosures as required by the standard upon adoption. 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 adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the 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 adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

Summary of significant accoun_3

Summary of significant accounting policies (Tables)	9 Months Ended
	Sep. 30, 2020
Accounting Policies [Abstract]
Reconciliation of cash	The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Beginning of ​ ​ ​ period- End of period- ​ December 31, September 30, ​ 2019 ​ 2020 Cash and cash equivalents ​ $ 288,028 ​ $ 433,970 Restricted cash included in deposits and other assets ​ 7,500 ​ 7,500 Total Cash, cash equivalents and restricted cash per statement of cash flows ​ $ 295,528 ​ $ 441,470
Schedule of Inventory	The following table summarizes the components of the Company’s inventory for the periods indicated: ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 Raw materials ​ $ 946 ​ $ 874 Work in progress ​ 8,600 ​ 9,652 Finished goods ​ 9,935 ​ 8,759 Total inventory ​ $ 19,481 ​ $ 19,285

Leases - (Tables)

Leases - (Tables)	9 Months Ended
	Sep. 30, 2020
Leases [Abstract]
Lease costs	The components of operating lease expense were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended Three Months Ended Nine Months Ended Nine Months Ended ​ ​ ​ September 30, 2020 ​ September 30, 2019 ​ September 30, 2020 ​ September 30, 2019 ​ Operating Lease Cost ​ ​ ​ ​ ​ ​ ​ ​ Fixed lease cost ​ $ 4,097 ​ $ 1,431 ​ $ 7,896 ​ $ 3,078 ​ Variable lease cost ​ 890 ​ 184 ​ 1,914 ​ 488 ​ Short-term lease cost ​ 175 ​ 94 ​ 340 ​ 235 ​ Total operating lease cost ​ $ 5,162 ​ $ 1,709 ​ $ 10,150 ​ $ 3,801 ​ ​ Total operating lease cost is a component of operating expenses on the consolidated statements of operations. Supplemental balance sheet information related to leases was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease ROU asset ​ $ 85,810 ​ $ 13,693 ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease liabilities- current ​ $ 5,859 ​ $ 5,153 ​ Operating lease liabilities- noncurrent ​ 81,674 ​ 9,018 ​ Total operating lease liability ​ $ 87,533 ​ $ 14,171 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ Finance lease liabilities- current ​ $ 1,251 ​ $ — ​ Finance lease liabilities- noncurrent ​ 22,608 ​ — ​ Total finance lease liability ​ $ 23,859 ​ $ — ​ ​ The Company’s leases in Bridgewater, New Jersey and Hopewell Township, New Jersey are the primary drivers of the increase in total operating lease ROU asset and total operating lease liability from December 31, 2019 to September 30, 2020. Supplemental lease term and discount rate information related to leases was as follows as of September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 December 31, 2019 ​ ​ ​ ​ ​ ​ ​ Weighted-average remaining lease terms - operating leases (years) 11.66 ​ 3.38 ​ Weighted-average discount rate - operating leases ​ 8.64 % 7.33 % ​ Weighted-average remaining lease terms - finance lease (years) 12.25 ​ — ​ Weighted-average discount rate - finance lease 7.80 % — ​ ​ Supplemental cash flow information related to leases was as follows as of September 30, 2020 and 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended September 30, ​ ​ 2020 2019 ​ Cash paid for amounts included in the measurement of lease liabilities: ​ ​ ​ ​ Operating cash flows from operating leases ​ $ 5,611 ​ $ 2,751 ​ Financing cash flows from finance lease ​ ​ 17,829 ​ ​ — ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use assets obtained in exchange for lease obligations: ​ ​ ​ Operating leases ​ $ 76,657 ​ $ 16,120 ​ Finance lease ​ ​ 41,382 ​ ​ — ​
Lease payments - Operating Leases	Future minimum lease payments under non-cancelable leases as of September 30, 2020 were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating Leases Finance Lease ​ 2020 (excludes the nine months ended September 30, 2020) ​ $ 2,842 ​ $ — ​ 2021 ​ 13,472 ​ 3,000 ​ 2022 ​ 13,229 ​ 3,000 ​ 2023 ​ 12,831 ​ 3,000 ​ 2024 and thereafter ​ 104,142 ​ 27,000 ​ Total lease payments ​ 146,516 ​ 36,000 ​ Less: Imputed Interest expense ​ 58,983 ​ 12,141 ​ Total ​ $ 87,533 ​ $ 23,859 ​
Lease payments - Finance Leases	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating Leases Finance Lease ​ 2020 (excludes the nine months ended September 30, 2020) ​ $ 2,842 ​ $ — ​ 2021 ​ 13,472 ​ 3,000 ​ 2022 ​ 13,229 ​ 3,000 ​ 2023 ​ 12,831 ​ 3,000 ​ 2024 and thereafter ​ 104,142 ​ 27,000 ​ Total lease payments ​ 146,516 ​ 36,000 ​ Less: Imputed Interest expense ​ 58,983 ​ 12,141 ​ Total ​ $ 87,533 ​ $ 23,859 ​

Fair value of financial instr_2

Fair value of financial instruments and marketable securities - (Tables)	9 Months Ended
	Sep. 30, 2020
Fair Value Disclosures [Abstract]
Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis	The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ ​ ​ Quoted prices Significant ​ ​ ​ ​ ​ ​ in active other Significant ​ ​ ​ ​ markets for observable unobservable ​ ​ ​ ​ identical assets inputs inputs ​ Total (level 1) (level 2) (level 3) Marketable securities ​ $ 707,049 ​ $ — ​ $ 707,049 ​ $ — Equity investment in ClearPoint ​ $ 7,045 ​ $ 7,045 ​ $ — ​ $ — ClearPoint convertible debt security ​ $ 10,633 ​ $ — ​ $ 10,633 ​ $ — Contingent consideration payable- development and regulatory milestones ​ $ 138,200 ​ $ — ​ $ — ​ $ 138,200 Contingent consideration payable- net sales milestones and royalties ​ $ 95,900 ​ $ — ​ $ — ​ $ 95,900 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ ​ ​ Quoted prices Significant ​ ​ ​ ​ ​ ​ in active other Significant ​ ​ ​ ​ markets for observable unobservable ​ ​ ​ ​ identical assets inputs inputs ​ Total (level 1) (level 2) (level 3) Marketable securities ​ $ 398,535 ​ $ — ​ $ 398,535 ​ $ — Equity investment in ClearPoint ​ $ 6,194 ​ $ 6,194 ​ $ — ​ $ — Stock appreciation rights liability ​ $ 3,186 ​ $ — ​ $ — ​ $ 3,186 Deferred consideration payable ​ $ 40,000 ​ $ — ​ $ 40,000 ​ $ — Contingent consideration payable- development and regulatory milestones ​ $ 290,500 ​ $ — ​ $ — ​ $ 290,500 Contingent consideration payable- net sales milestones and royalties ​ $ 65,800 ​ $ — ​ $ — ​ $ 65,800
Summary of marketable securities accounted for as available-for-sale securities	The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2020 and December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Amortized Gross Unrealized ​ ​ ​ ​ Cost Gains Losses Fair Value Commercial paper ​ $ 260,392 ​ $ 74 ​ $ (16) ​ $ 260,450 Corporate debt securities ​ 316,198 ​ 2,082 ​ (19) ​ 318,261 Asset-backed securities ​ 35,461 ​ 232 ​ (2) ​ 35,691 Government obligations ​ ​ 92,602 ​ ​ 61 ​ ​ (16) ​ ​ 92,647 Total ​ $ 704,653 ​ $ 2,449 ​ $ (53) ​ $ 707,049 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Amortized Gross Unrealized ​ ​ ​ ​ Cost Gains Losses Fair Value Commercial paper ​ $ 157,936 ​ $ 162 ​ $ — ​ $ 158,098 Corporate debt securities ​ 188,778 ​ 576 ​ (20) ​ 189,334 Asset-backed securities ​ ​ 51,062 ​ ​ 49 ​ ​ (8) ​ ​ 51,103 Total ​ $ 397,776 ​ $ 787 ​ $ (28) ​ $ 398,535
Summary of unrealized losses and fair values of available-for-sale securities in a continuous unrealized loss position	The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2020 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Securities in an unrealized loss Securities in an unrealized loss ​ ​ ​ ​ ​ ​ position less than 12 months position greater than 12 months ​ Total ​ Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Commercial paper ​ $ (16) ​ ​ 53,580 ​ ​ — ​ ​ — ​ ​ (16) ​ ​ 53,580 Corporate debt securities ​ ​ (19) ​ ​ 62,811 ​ ​ — ​ ​ — ​ ​ (19) ​ ​ 62,811 Asset-backed securities ​ (2) ​ 2,899 ​ — ​ — ​ (2) ​ 2,899 Government obligations ​ ​ (16) ​ ​ 31,955 ​ ​ — ​ ​ — ​ ​ (16) ​ ​ 31,955 Total ​ $ (53) ​ $ 151,245 ​ $ — ​ $ — ​ $ (53) ​ $ 151,245 ​ 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, 2019 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Securities in an unrealized loss Securities in an unrealized loss ​ ​ ​ ​ ​ ​ position less than 12 months position greater than 12 months ​ Total ​ Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Corporate debt securities ​ $ (20) ​ $ 71,779 ​ $ — ​ $ — ​ $ (20) ​ $ 71,779 Asset-backed securities ​ ​ (8) ​ ​ 24,211 ​ ​ — ​ ​ — ​ ​ (8) ​ ​ 24,211 Total ​ $ (28) ​ $ 95,990 ​ $ — ​ $ — ​ $ (28) ​ $ 95,990
Schedule of marketable securities on the balance sheet	Marketable securities on the balance sheet at September 30, 2020 and December 31, 2019 mature as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Less Than More Than ​ 12 Months 12 Months Commercial paper ​ $ 260,451 ​ $ — Corporate debt securities ​ 260,199 ​ 58,062 Asset-backed securities ​ 14,375 ​ 21,316 Government obligations ​ ​ 39,530 ​ ​ 53,116 Total Marketable securities ​ $ 574,555 ​ $ 132,494 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Less Than More Than ​ 12 Months 12 Months Commercial paper ​ $ 158,098 ​ $ — Corporate debt securities ​ 139,596 ​ 49,738 Asset-backed securities ​ ​ 44,724 ​ ​ 6,379 Total Marketable securities ​ $ 342,418 ​ $ 56,117
Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability and SARs liability	The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the SARs liability, and the contingent consideration payable for the periods ended September 30, 2020 and September 30, 2019. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Level 3 liabilities ​ ​ ​ ​ ​ Contingent consideration payable- ​ Contingent consideration payable- ​ ​ ​ ​ ​ development and regulatory ​ net sales milestones and royalties ​ SARs milestones ​ Beginning balance as of December 31, 2019 ​ $ 3,186 ​ $ 290,500 ​ $ 65,800 Additions ​ — ​ — ​ — Change in fair value ​ — ​ (13,120) ​ 30,100 Payments ​ ​ (3,186) ​ ​ — ​ ​ — Rights Exchange settlement ​ ​ — ​ ​ (139,180) ​ ​ — Ending balance as of September 30, 2020 ​ $ — ​ $ 138,200 ​ $ 95,900 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Level 3 liabilities ​ ​ ​ ​ ​ Contingent consideration payable- ​ Contingent consideration payable- ​ ​ ​ ​ ​ development and regulatory ​ net sales milestones and royalties ​ SARs milestones ​ Beginning balance as of December 31, 2018 ​ $ 3,814 ​ $ 257,040 ​ $ 53,200 Additions ​ — ​ — ​ — Change in fair value ​ 2,236 ​ 28,260 ​ 6,400 Payments ​ ​ (3,815) ​ ​ — ​ ​ — Ending balance as of September 30, 2019 ​ $ 2,235 ​ $ 285,300 ​ $ 59,600
Fair Value Measurement Inputs and Valuation Techniques	The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended September 30, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Fair Value Valuation Technique Unobservable Input Range Contingent consideration payable- ​ $138,200 Probability-adjusted discounted cash flow Potential development and regulatory milestones ​ $0 - $381 million Contingent considerable payable- net sales ​ $95,900 Option-pricing model with Monte Carlo simulation Potential net sales milestones ​ $0 - $150 million ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Fair Value Valuation Technique Unobservable Input Range SARs ​ $3,186 ​ Option-pricing model Volatility 28.93% 0.19% $6.76 - $30.86 $48.03 0.01 years Contingent consideration payable- development and regulatory milestones ​ $290,500 ​ Probability-adjusted discounted cash flow ​ Potential development and regulatory milestones ​ $0 - $555 million Contingent considerable payable- net sales milestones and royalties ​ $65,800 Option-pricing model with Monte Carlo simulation Potential net sales milestones ​ $0 - $150 million

Other comprehensive income (l_2

Other comprehensive income (loss) and accumulated other comprehensive items - (Tables)	9 Months Ended
	Sep. 30, 2020
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items	The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine month periods ended September 30, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrealized ​ ​ Total ​ ​ Gains/(Losses) ​ ​ ​ ​ Accumulated ​ ​ On ​ Foreign ​ Other ​ ​ Marketable ​ Currency ​ Comprehensive ​ ​ Securities, net of tax ​ Translation ​ Items Balance, June 30, 2020 ​ $ 3,410 ​ $ (13,426) ​ $ (10,016) Other comprehensive loss before reclassifications ​ (1,016) ​ (24,695) ​ (25,711) Amounts reclassified from other comprehensive items ​ — ​ — ​ — Other comprehensive loss before reclassifications ​ (1,016) ​ (24,695) ​ (25,711) Balance, September 30, 2020 ​ $ 2,394 ​ $ (38,121) ​ $ (35,727) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrealized ​ ​ Total ​ ​ Gains ​ ​ ​ ​ Accumulated ​ ​ On ​ Foreign ​ Other ​ ​ Marketable ​ Currency ​ Comprehensive ​ ​ Securities, net of tax ​ Translation ​ Items Balance, December 31, 2019 ​ $ 755 ​ $ (11,339) ​ $ (10,584) Other comprehensive income (loss) before reclassifications ​ 1,639 ​ (26,782) ​ (25,143) Amounts reclassified from other comprehensive items ​ — ​ — ​ — Other comprehensive income (loss) ​ 1,639 ​ (26,782) ​ (25,143) Balance, September 30, 2020 ​ $ 2,394 ​ $ (38,121) ​ $ (35,727)

Accounts payable and accrued _2

Accounts payable and accrued expenses - (Tables)	9 Months Ended
	Sep. 30, 2020
Payables and Accruals [Abstract]
Schedule of components of accounts payable and accrued expenses	Accounts payable and accrued expenses at September 30, 2020 and December 31, 2019 consist of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ ​ 2020 2019 ​ Employee compensation, benefits, and related accruals ​ $ 34,485 ​ $ 38,390 ​ Income tax payable ​ ​ 21,475 ​ ​ 499 ​ Consulting and contracted research ​ 17,659 ​ 12,969 ​ Professional fees ​ 4,590 ​ 3,562 ​ Sales allowance and other costs ​ 50,644 ​ 41,155 ​ Sales rebates and royalties ​ 68,628 ​ 42,997 ​ Accounts payable ​ 15,663 ​ 10,324 ​ Other ​ 5,417 ​ 9,380 ​ Total ​ $ 218,561 ​ $ 159,276 ​

Net loss per share - (Tables)

Net loss per share - (Tables)	9 Months Ended
	Sep. 30, 2020
Earnings Per Share [Abstract]
Schedule of computation of basic and diluted net loss available to common stockholders	The following tables set forth the computation of basic and diluted net loss per share: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ ​ Nine Months Ended September 30, ​ ​ ​ 2020 2019 ​ 2020 2019 ​ Numerator ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ (69,692) $ (59,997) ​ $ (363,806) $ (173,899) ​ Denominator ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Denominator for basic and diluted net loss per share ​ 67,641,171 56,463,528 ​ 65,068,281 57,798,968 ​ Net loss per share: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted ​ $ (1.03) * $ (1.06) * ​ $ (5.59) * $ (3.01) * ​ * In the three and nine months ended September 30, 2020 and 2019, the Company experienced a net loss and therefore did not report any dilutive share impact.
Schedule of historical dilutive common share equivalents outstanding	The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. ​ ​ ​ ​ ​ ​ ​ ​ ​ As of September 30, ​ ​ 2020 2019 Stock Options ​ 11,528,241 ​ 10,743,181 ​ Unvested restricted stock awards and units 961,795 650,103 Total 12,490,036 11,393,284

Stock award plan - (Tables)

Stock award plan - (Tables)	9 Months Ended
	Sep. 30, 2020
Share-based Payment Arrangement [Abstract]
Summary of stock option activity	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ ​ Weighted- ​ average ​ ​ Aggregate ​ ​ ​ ​ average ​ remaining ​ ​ intrinsic ​ ​ Number of ​ exercise ​ contractual ​ ​ value(in ​ ​ options ​ price ​ term ​ ​ thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2019 11,043,939 ​ $ 31.67 ​ ​ Granted 2,671,660 ​ $ 50.76 ​ ​ Exercised (1,426,026) ​ $ 23.14 ​ ​ Forfeited/Cancelled (761,332) ​ $ 42.96 ​ ​ Outstanding at September 30, 2020 11,528,241 ​ $ 36.37 7.32 years ​ $ 138,286 Vested or Expected to vest at September 30, 2020 5,297,899 ​ $ 40.09 8.70 years ​ $ 44,050 Exercisable at September 30, 2020 5,576,283 ​ $ 32.19 5.84 years ​ $ 90,361 ​
Schedule of assumptions used to estimate fair values of grants made on the date of grant	​ ​ ​ ​ ​ ​ Nine months ended ​ September 30, 2020 Risk-free interest rate 0.34% - 1.45% Expected volatility 87.50% - 89.31% Expected term 5.75
Summary of information on the Company's restricted stock	​ ​ ​ ​ ​ ​ ​ ​ ​ Restricted Stock Awards and Units ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ ​ ​ Grant ​ ​ Number of ​ Date ​ Shares Fair Value January 1, 2020 ​ 642,419 ​ $ 24.50 Granted 625,390 ​ $ 50.76 Vested (232,263) ​ $ 23.86 Forfeited (73,751) ​ $ 36.28 Unvested at September 30, 2020 961,795 ​ $ 41.05
Schedule of share-based compensation expense recorded in the statement of operations	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ Nine Months Ended September 30, ​ ​ 2020 2019 2020 2019 ​ Research and development ​ $ 9,220 ​ $ 4,988 ​ $ 25,961 ​ $ 15,191 ​ Selling, general and administrative ​ 7,559 ​ 5,496 ​ 22,948 ​ 15,477 ​ Total ​ $ 16,779 ​ $ 10,484 ​ $ 48,909 ​ $ 30,668 ​ ​

Debt - (Tables)

Debt - (Tables)	9 Months Ended
	Sep. 30, 2020
Debt Instrument, Redemption [Line Items]
Summary of liability for sale of future royalties	The following table shows the activity within the “liability for sale of future royalties- current” and “liability for sale of future royalties- noncurrent” accounts for the three and nine month periods ended September 30, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, Nine Months Ended September 30, Liability for sale of future royalties- (current and noncurrent) ​ 2020 2020 Beginning balance ​ $ — ​ $ — ​ Proceeds from sale of future royalties ​ 650,000 ​ 650,000 ​ Less: Non-cash royalty revenue payable to RPI ​ ​ (299) ​ ​ (299) ​ Plus: Non-cash interest expense recognized ​ ​ 14,557 ​ ​ 14,557 ​ Ending balance ​ $ 664,258 ​ $ 664,258 ​ Effective interest rate for the period ​ 11.0 % 11.0 %
1.50% Convertible senior notes due 2026
Debt Instrument, Redemption [Line Items]
Summary of convertible notes	​ ​ ​ ​ ​ ​ ​ ​ ​ Liability component September 30, 2020 ​ December 31, 2019 ​ Principal ​ $ 287,500 ​ $ 287,500 ​ Less: Debt issuance costs ​ (4,192) ​ (4,567) ​ Less: Debt discount, net(1) ​ (109,563) ​ (119,350) ​ Net carrying amount ​ $ 173,745 ​ $ 163,583 ​
Summary of interest expense recognized related to the Convertible Notes	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ ​ Nine Months Ended September 30, ​ ​ ​ ​ 2020 ​ 2019 ​ ​ 2020 ​ 2019 ​ ​ ​ Contractual interest expense ​ $ 1,081 ​ $ 130 ​ ​ $ 3,223 ​ $ 130 ​ ​ ​ Amortization of debt issuance costs ​ 127 ​ ​ 15 ​ ​ 374 ​ 15 ​ ​ ​ Amortization of debt discount ​ ​ 3,313 ​ ​ 391 ​ ​ ​ 9,786 ​ ​ 391 ​ ​ ​ Total ​ $ 4,521 ​ $ 536 ​ ​ $ 13,383 ​ $ 536 ​ ​ ​ Effective interest rate of the liability component ​ 10.2 % ​ 10.2 % ​ 10.2 % ​ 10.2 % ​ ​
3.00% Convertible senior notes due 2022
Debt Instrument, Redemption [Line Items]
Summary of convertible notes	​ ​ ​ ​ ​ ​ ​ ​ ​ Liability component September 30, 2020 December 31, 2019 ​ Principal ​ $ 150,000 ​ $ 150,000 ​ Less: Debt issuance costs ​ (986) ​ (1,329) ​ Less: Debt discount, net (1) ​ (19,794) ​ (26,686) ​ Net carrying amount ​ $ 129,220 ​ $ 121,985 ​
Summary of interest expense recognized related to the Convertible Notes	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, Nine Months Ended September 30, ​ ​ 2020 2019 2020 2019 ​ Contractual interest expense ​ $ 1,131 ​ $ 1,134 ​ $ 3,375 ​ $ 3,375 ​ ​ Amortization of debt issuance costs ​ 118 ​ 106 ​ 343 ​ 308 ​ ​ Amortization of debt discount ​ 2,372 ​ 2,137 ​ 6,892 ​ 6,192 ​ ​ Total ​ $ 3,621 ​ $ 3,377 ​ $ 10,610 ​ $ 9,875 ​ ​ Effective interest rate of the liability component ​ 11.0 % 11.0 % 11.0 % 11.0 % ​

Intangible assets and goodwill

Intangible assets and goodwill - (Tables)	9 Months Ended
	Sep. 30, 2020
Goodwill and Intangible Assets Disclosure [Abstract]
Future amortization expense	​ ​ ​ ​ ​ ​ As of September 30, 2020 2020 ​ $ 9,627 2021 ​ 38,506 2022 ​ 38,506 2023 ​ 38,506 2024 and thereafter ​ 10,891 Total ​ $ 136,036

The Company (Details)

The Company (Details) - USD ($) $ in Thousands	Jun. 29, 2020	Apr. 29, 2020	Aug. 23, 2018	Sep. 30, 2020	Sep. 30, 2020	Dec. 31, 2019	Apr. 20, 2017	Aug. 31, 2015
Long-term debt
Retained earnings (accumulated deficit)				$ (1,554,523)	$ (1,554,523)	$ (1,190,499)
Rights Exchange Agreement
Long-term debt
Shares to issue under Rights Exchange Agreement		2,821,176		2,821,176	2,821,176
Cash consideration payment under Rights Exchange Agreement		$ 36,900
Convertible debt | 1.50% Convertible senior notes due 2026
Long-term debt
Interest rate ( as a percent )				1.50%	1.50%	1.50%
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Interest rate ( as a percent )								3.00%
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Long-term debt
Development milestone payments which the entity is obligated to pay							$ 50,000
Agilis
Long-term debt
Cash consideration			$ 49,200
Equity Interest Issued, number of shares (in shares)			3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity			$ 150,000
Trading day period			10 days
Development milestone payments which the entity is obligated to pay		40,000		$ 40,000	$ 40,000
Development milestone payment obligations, net of cancellation and forfeiture					$ 20,000
Milestone obligation payments made				$ 2,400
Net sales amount		150,000
Agilis | Minimum
Long-term debt
Development milestone payments which the entity is obligated to pay	$ 37,600	$ 37,600
Product sales		2.00%		2.00%	2.00%
Agilis | Maximum
Long-term debt
Development milestone payments which the entity is obligated to pay	40,000			$ 60,000	$ 60,000
Priority review voucher amount					535,000
Net sales amount				$ 150,000	$ 150,000
Product sales		6.00%		6.00%	6.00%
Agilis | Rights Exchange Agreement
Long-term debt
Contingent liability, cancellation and forfeiture	$ 211,600	$ 211,600
Priority review voucher amount		174,000
Development milestone payment obligations, net of cancellation and forfeiture		20,000
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture		$ 361,000
Agilis | Rights Exchange Agreement | Maximum
Long-term debt
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture					$ 361,000
Agilis | Non-collaborative Arrangement Transactions
Long-term debt
Development milestone payments which the entity is obligated to pay				$ 40,000	$ 40,000

Summary of significant accoun_4

Summary of significant accounting policies - Narrative (Details) - USD ($) $ in Thousands	Jul. 17, 2020	Dec. 22, 2017	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2019
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Allowance for credit loss			$ 0		$ 0
Inventory write-down				$ 0		$ 0
Letters of Credit			7,500		$ 7,500
Term for letter of credit (in years)					5 years
Operating lease ROU assets			85,810		$ 85,810		$ 13,693
Allowance for doubtful accounts receivable			100		100		300
Federal income tax statutory rate		21.00%
Deferred tax liability							$ 122,000
Cash consideration received from Royalty Purchase Agreement	$ 650,000				650,000	$ 0
State income tax provision			22,100		22,100
Accounts receivable, allowance for credit loss,			0		0
Fifth Anniversary
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Letters of Credit			$ 3,800		$ 3,800
Royalty Purchase Agreement | Assigned Royalty Payments
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Cash consideration received from Royalty Purchase Agreement	$ 650,000

Summary of significant accoun_5

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019	Sep. 30, 2019	Dec. 31, 2018
Accounting Policies [Abstract]
Cash and cash equivalents	$ 433,970	$ 288,028
Restricted cash included in deposits and other assets	7,500	7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 441,470	$ 295,528	$ 531,077	$ 169,498

Summary of significant accoun_6

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Accounting Policies [Abstract]
Raw materials	$ 946	$ 874
Work in progress	8,600	9,652
Finished goods	9,935	8,759
Total inventory	$ 19,481	$ 19,285

Summary of significant accoun_7

Summary of significant accounting policies - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands	Jul. 17, 2020	Sep. 30, 2020	Sep. 30, 2019
Assigned royalty payments
Cash consideration received from Royalty Purchase Agreement	$ 650,000	$ 650,000	$ 0
Assigned royalty payment, retained percentage	57.067%
Revenue recognition, milestone, potential achievements	$ 362,500
Royalty Purchase Agreement | Assigned Royalty Payments
Assigned royalty payments
Assigned royalty payment, percentage	42.933%
Cash consideration received from Royalty Purchase Agreement	$ 650,000
Royalty purchase agreement, termination period	60 days
Royalty purchase agreement, payment maximum	$ 1,300,000

Acquisitions - Narrative (Detai

Acquisitions - Narrative (Details) - USD ($) $ in Thousands	May 29, 2020	Sep. 30, 2020
Finite-Lived Intangible Assets [Line Items]
Payments for asset acquisitions, share, value		$ 42,869
Censa
Finite-Lived Intangible Assets [Line Items]
Payments for asset acquisitions	$ 15,000
Payments for asset acquisitions, upfront payment	10,400
Payments for asset acquisitions, net assets	$ 4,600
Payments for asset acquisitions, shares (in shares)	845,364	845,364
Payments for asset acquisitions, share, value	$ 42,900	$ 42,900
Consideration for asset acquisitions	$ 15,000
Equity Interest Issued, number of shares (in shares)	42,900,000
Asset acquisition, transaction costs	$ 700
Asset acquisition, consideration transferred	58,600
Asset acquisition, cash	3,800
Asset acquisition, other assets	800
Asset acquisition, in-process research and development	54,000
Asset acquisition, research and development expense	53,300
Asset acquisition, selling, general And administrative expense	700
Asset acquisition, milestone, amount	217,500
Asset acquisition, development and regulatory milestones	109,000
Asset acquisition, net sales milestone	160,000
Asset acquisition, initial milestone	$ 30,000

Acquisitions - Preliminary Allo

Acquisitions - Preliminary Allocation of purchase price (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Business Combinations [Abstract]
Goodwill	$ 82,341	$ 82,341

Leases - Narrative (Details)

Leases - Narrative (Details) $ in Thousands	Jun. 19, 2020	Sep. 30, 2020USD ($)ft²leaseitem	Sep. 30, 2019USD ($)	Sep. 30, 2020USD ($)ft²leaseitem	Sep. 30, 2019USD ($)	May 01, 2020ft²	Dec. 31, 2019ft²
Lessee, Lease, Description [Line Items]
Number of operating leases | lease		3		3
Operating lease, expense		$ 5,200	$ 1,700	$ 10,200	$ 3,800
Finance lease expense		$ 500		$ 500
Renewal Term ( in years )		10 years		10 years
Aggregate rent, Initial term		$ 146,516		$ 146,516
2020 (excludes the nine months ended September 30, 2020)		2,842		2,842
2021		13,472		13,472
2022		13,229		13,229
Fixed lease cost		4,097	1,431	7,896	3,078
Research and development		$ 92,998	$ 63,076	$ 359,630	$ 175,621
MassBio
Lessee, Lease, Description [Line Items]
Written notice required for early lease termination	24 months
Lessee, Finance Lease, Term of Contract		12 years 6 months		12 years 6 months
Research and development		$ 41,400		$ 41,400
Minimum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )		3 months 18 days		3 months 18 days
Maximum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )		6 years 10 months 24 days		6 years 10 months 24 days
New Building
Lessee, Lease, Description [Line Items]
Area of real estate property | ft²		75,000		75,000
Renewal Term ( in years )		10 years		10 years
Hopewell Campus
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )		15 years		15 years
Area of real estate property | ft²							220,500
Number of terms | item		2		2
Aggregate rent, Initial term		$ 111,500		$ 111,500
Percent of market rate		95.00%		95.00%
Mountainview
Lessee, Lease, Description [Line Items]
2020 (excludes the nine months ended September 30, 2020)		$ 400		$ 400
2021		1,800		1,800
2022		$ 1,400		$ 1,400
Bridgewater
Lessee, Lease, Description [Line Items]
Area of real estate property | ft²						59,000

Leases - Lease costs (Details)

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Leases [Abstract]
Fixed lease cost	$ 4,097	$ 1,431	$ 7,896	$ 3,078
Variable lease cost	890	184	1,914	488
Short-term lease cost	175	94	340	235
Total operating lease cost	$ 5,162	$ 1,709	$ 10,150	$ 3,801

Leases - Balance sheet (Details

Leases - Balance sheet (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Leases [Abstract]
Operating lease ROU assets	$ 85,810	$ 13,693
Operating lease liabilities- current	5,859	5,153
Operating lease liabilities- noncurrent	81,674	9,018
Total operating lease liability	87,533	14,171
Finance lease liabilities- current	1,251	0
Finance lease liabilities- noncurrent	22,608	0
Finance Lease, Liability	$ 23,859	$ 0

Leases - Supplemental lease ter

Leases - Supplemental lease terms (Details)	Sep. 30, 2020	Dec. 31, 2019
Leases [Abstract]
Weighted-average remaining lease terms - operating leases (years)	5 years 10 months 13 days	3 years 4 months 17 days
Weighted-average discount rate - operating leases	8.64%	7.33%
Weighted-average remaining lease terms - finance lease (years)	12 years 6 months
Weighted-average discount rate - finance lease	7.80%

Leases - Lease payments (Detail

Leases - Lease payments (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Leases [Abstract]
2020 (excludes the nine months ended September 30, 2020)	$ 2,842
2021	13,472
2022	13,229
2023	12,831
2024 and thereafter	104,142
Total lease payments	146,516
Less: Imputed Interest expense	58,983
Total	87,533	$ 14,171
2021	3,000
2022	3,000
2023	3,000
2024 and thereafter	27,000
Total lease payments	36,000
Less: Imputed Interest expense	12,141
Total	$ 23,859	$ 0

Leases - Cash flow (Details)

Leases - Cash flow (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Leases [Abstract]
Operating cash flows from operating leases	$ 5,611	$ 2,751
Financing cash flows from finance lease	17,829	0
Right-of-use assets obtained in exchange for operating lease obligations	76,657	16,120
Right-of-use assets obtained in exchange for finance lease obligations	$ 41,382	$ 0

Fair value of financial instr_3

Fair value of financial instruments and marketable securities - Narrative (Details) - USD ($)	1 Months Ended	3 Months Ended		6 Months Ended	9 Months Ended
	Jan. 31, 2020	Sep. 30, 2020	Sep. 30, 2019	Jun. 30, 2020	Sep. 30, 2020	Sep. 30, 2019	Jun. 29, 2020	Apr. 29, 2020	Dec. 31, 2019	May 31, 2019	Aug. 31, 2015
Financial assets and liabilities measured at fair value on recurring basis
Write downs of available for sale debt securities		$ 0			$ 0
Realized gain (loss) from sale of marketable securities		300,000			500,000
Increase in allowance for credit losses		0			0
Deferred consideration payable		0			0				$ 40,000,000
Unrealized gain (loss) on equity investment					852,000	$ 2,529,000
Investment In MRI		$ 7,000,000			7,000,000
Purchase of convertible debt investment	$ 10,000,000				$ 10,000,000	0
Conversion price per share (in dollars per share)		$ 6			$ 6
Debt instrument, convertible, period					5 years
Marketable securities		$ 707,049,000			$ 707,049,000				398,535,000
Transfers of assets measured between Level 1, Level 2, and Level 3		0			0				0
Non-cash stock consideration, acquisition					42,869,000	0
Operating Expenses		173,535,000	$ 131,891,000		597,296,000	378,895,000
Business Combination, Contingent Consideration Arrangements, Change in Amount of Contingent Consideration, Asset		(8,400,000)	$ (9,500,000)		(16,980,000)	$ (35,960,000)
Debt Securities, Available-for-sale, Unrealized Gain		1,400,000			$ 600,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Issuance of common stock related to rights exchange (in shares)					2,821,176
SARs
Financial assets and liabilities measured at fair value on recurring basis
Liability value		0			$ 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		$ 150,000,000
Interest rate ( as a percent )											3.00%
Fair value of convertible notes		171,300,000			171,300,000				171,200,000
Conversion price per share (in dollars per share)											$ 56.34
1.50% Convertible senior notes due 2026 | Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal		$ 287,500,000			$ 287,500,000				$ 287,500,000
Interest rate ( as a percent )		1.50%			1.50%				1.50%
Fair value of convertible notes		$ 329,200,000			$ 329,200,000				$ 335,000,000
Conversion price per share (in dollars per share)		$ 52.52			$ 52.52
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay		$ 40,000,000			$ 40,000,000			$ 40,000,000
Net sales amount								$ 150,000,000
Deferred consideration payable		0			0
Non-cash stock consideration, acquisition		36,900,000
Milestone Payment Obligations							$ 174,000,000
Gain Of Settlement, Development Milestones		700,000
Loss Of Settlement, Regulatory Milestones		11,300,000
Business Combination, Contingent Consideration Arrangements, Change in Amount of Contingent Consideration, Asset		1,000,000
Contingent Consideration, Transaction Fees		$ 2,000,000			$ 2,000,000
Agilis | Common stock
Financial assets and liabilities measured at fair value on recurring basis
Issuance of common stock related to rights exchange (in shares)				2,821,176
Agilis | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Product sales		2.00%			2.00%			2.00%
Development milestone payments which the entity is obligated to pay							37,600,000	$ 37,600,000
Agilis | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Product sales		6.00%			6.00%			6.00%
Development milestone payments which the entity is obligated to pay		$ 60,000,000			$ 60,000,000		$ 40,000,000
Priority review voucher amount					535,000,000
Net sales amount		150,000,000			150,000,000
Non-collaborative Arrangement Transactions | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay		40,000,000			40,000,000
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Estimated fair value of deferred consideration payable		2,400,000			2,400,000				40,000,000
Liability value		95,900,000			95,900,000				65,800,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Shares owned										$ 4,000,000
Fair value of shares (in dollars per share)										$ 3.10
Unrealized gain (loss) on equity investment		2,500,000			900,000
Deferred consideration payable | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		$ 10,633,000			$ 10,633,000
Development and Regulatory Milestone | Probability of Success | Weighted Average | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		42			42
Development and Regulatory Milestone | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Liability value		$ 138,200,000			$ 138,200,000				$ 290,500,000
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.031			0.031				0.022
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.053			0.053				0.047
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Weighted Average | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		4.2			4.2
Development and Regulatory Milestone | Agilis | Probability of Success | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.25			0.25				0.25
Development and Regulatory Milestone | Agilis | Probability of Success | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.94			0.94				0.94
Liability, Net Sales Milestones and Royalties | Probability of Success | Weighted Average | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		48			48
Liability, Net Sales Milestones and Royalties | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Liability value		$ 95,900,000			$ 95,900,000				$ 65,800,000
Liability, Net Sales Milestones and Royalties | Agilis | Measurement Input, Discount Rate | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.120			0.120				0.145
Liability, Net Sales Milestones and Royalties | Agilis | Probability of Success | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.25			0.25				0.25
Liability, Net Sales Milestones and Royalties | Agilis | Probability of Success | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement		0.94			0.94				0.89

Fair value of financial instr_4

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 707,049	$ 398,535
Contingent consideration payable	234,100	356,300
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Equity investment in ClearPoint	7,045	6,194
Stock appreciation rights liability		3,186
Deferred consideration payable	2,400	40,000
Contingent consideration payable	138,200	290,500
Contingent consideration payable- net sales milestones and royalties	95,900	65,800
Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Equity investment in ClearPoint	7,045	6,194
Stock appreciation rights liability		0
Deferred consideration payable		0
Contingent consideration payable	0	0
Contingent consideration payable- net sales milestones and royalties	0	0
Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Equity investment in ClearPoint	0	0
Stock appreciation rights liability		0
Deferred consideration payable		40,000
Contingent consideration payable	0	0
Contingent consideration payable- net sales milestones and royalties	0	0
Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Equity investment in ClearPoint	0	0
Stock appreciation rights liability		3,186
Deferred consideration payable		0
Contingent consideration payable	138,200	290,500
Contingent consideration payable- net sales milestones and royalties	95,900	65,800
Marketable securities | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	707,049	398,535
Marketable securities | Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	0
Marketable securities | Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	707,049	398,535
Marketable securities | Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	$ 0
Deferred consideration payable | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	10,633
Deferred consideration payable | Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0
Deferred consideration payable | Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	10,633
Deferred consideration payable | Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 0

Fair value of financial instr_5

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2020	Dec. 31, 2019
Debt Securities, Available-for-sale [Line Items]
Write downs of available for sale debt securities	$ 0	$ 0
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	53	53	$ 28
Amortized Cost	704,653	704,653	397,776
Gross Unrealized, Gain	2,449	2,449	787
Gross Unrealized, Loss	(53)	(53)	(28)
Fair Value	707,049	707,049	398,535
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	53	53	28
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	16	16
Amortized Cost	260,392	260,392	157,936
Gross Unrealized, Gain	74	74	162
Gross Unrealized, Loss	(16)	(16)	0
Fair Value	260,450	260,450	158,098
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	16	16
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	19	19	20
Amortized Cost	316,198	316,198	188,778
Gross Unrealized, Gain	2,082	2,082	576
Gross Unrealized, Loss	(19)	(19)	(20)
Fair Value	318,261	318,261	189,334
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	19	19	20
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	2	2	8
Amortized Cost	35,461	35,461	51,062
Gross Unrealized, Gain	232	232	49
Gross Unrealized, Loss	(2)	(2)	(8)
Fair Value	35,691	35,691	51,103
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	2	2	$ 8
Government obligations
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	16	16
Amortized Cost	92,602	92,602
Gross Unrealized, Gain	61	61
Gross Unrealized, Loss	(16)	(16)
Fair Value	92,647	92,647
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	$ 16	$ 16

Fair value of financial instr_6

Fair value of financial instruments and marketable securities - Fair Value Measurement Inputs and Valuation Techniques (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Significant unobservable inputs (level 3)
Level 3 roll forward
Additions		$ 0
SARs
Level 3 roll forward
Ending Balance	$ 0
SARs | Significant unobservable inputs (level 3)
Level 3 roll forward
Beginning Balance	3,186	3,814
Additions	0
Change in fair value	0	2,236
Payments	(3,186)	(3,815)
Ending Balance	0	2,235
Commitments | Significant unobservable inputs (level 3)
Level 3 roll forward
Beginning Balance	290,500	257,040
Additions	0	0
Change in fair value	(13,120)	28,260
Payments	0	0
Ending Balance	138,200	285,300
Liability, Net Sales Milestones and Royalties | Agilis
Level 3 roll forward
Beginning Balance	65,800
Ending Balance	95,900
Liability, Net Sales Milestones and Royalties | Agilis | Significant unobservable inputs (level 3)
Level 3 roll forward
Beginning Balance	65,800	53,200
Additions	0	0
Change in fair value	30,100	6,400
Payments	0	0
Ending Balance	$ 95,900	$ 59,600

Fair value of financial instr_7

Fair value of financial instruments and marketable securities - Unrealized Loss Positions (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2020	Dec. 31, 2019
Unrealized losses
Securities in an unrealized loss position less than 12 months	$ (53)	$ (53)	$ (28)
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	(53)	(53)	(28)
Fair Value
Securities in an unrealized loss position less than 12 months	151,245	151,245	95,990
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	151,245	151,245	95,990
Write downs of available for sale debt securities	0	0
Commercial paper
Unrealized losses
Securities in an unrealized loss position less than 12 months	(16)	(16)
Securities in an unrealized loss position greater than 12 months	0	0
Total	(16)	(16)
Fair Value
Securities in an unrealized loss position less than 12 months	53,580	53,580
Securities in an unrealized loss position greater than 12 months	0	0
Total	53,580	53,580
Corporate debt securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(19)	(19)	(20)
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	(19)	(19)	(20)
Fair Value
Securities in an unrealized loss position less than 12 months	62,811	62,811	71,779
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	62,811	62,811	71,779
Asset-backed securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(2)	(2)	(8)
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	(2)	(2)	(8)
Fair Value
Securities in an unrealized loss position less than 12 months	2,899	2,899	24,211
Securities in an unrealized loss position greater than 12 months	0	0	0
Total	2,899	2,899	$ 24,211
Government obligations
Unrealized losses
Securities in an unrealized loss position less than 12 months	(16)	(16)
Securities in an unrealized loss position greater than 12 months	0	0
Total	(16)	(16)
Fair Value
Securities in an unrealized loss position less than 12 months	31,955	31,955
Securities in an unrealized loss position greater than 12 months	0	0
Total	$ 31,955	$ 31,955

Fair value of financial instr_8

Fair value of financial instruments and marketable securities - Marketable securities (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 574,555	$ 342,418
Total Marketable securities, More Than 12 Months	132,494	56,117
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	260,451	158,098
Total Marketable securities, More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	260,199	139,596
Total Marketable securities, More Than 12 Months	58,062	49,738
Asset-backed securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	14,375	44,724
Total Marketable securities, More Than 12 Months	21,316	$ 6,379
Government obligations
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	39,530
Total Marketable securities, More Than 12 Months	$ 53,116

Fair value of financial instr_9

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) $ in Thousands	9 Months Ended		12 Months Ended
	Sep. 30, 2020USD ($)	Sep. 30, 2019USD ($)	Dec. 31, 2019USD ($)$ / shares
Changes in the fair value of warrant liability and SARs liability
Weighted-average discount rate - finance lease	7.80%
SARs
Changes in the fair value of warrant liability and SARs liability
Ending Balance	$ 0
SARs
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	3,186
Ending Balance			$ 3,186
Measurement Input, Option Volatility | SARs
Fair value of warrant liability
Rights Exchange settlement			0.2893
Measurement Input, Risk Free Interest Rate | SARs
Fair value of warrant liability
Rights Exchange settlement			0.0019
Measurement Input, Expected Term | SARs
Fair value of warrant liability
Expected term (in years)			3 days
Minimum | SARs
Fair value of warrant liability
Rights Exchange settlement | $ / shares			6.76
Maximum | SARs
Fair value of warrant liability
Rights Exchange settlement | $ / shares			30.86
Common stock | Measurement Input, Share Price | SARs
Fair value of warrant liability
Rights Exchange settlement | $ / shares			48.03
Agilis | Liability, Net Sales Milestones and Royalties
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	65,800
Ending Balance	$ 95,900		$ 65,800
Agilis | Liability, Net Sales Milestones and Royalties | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.120		0.145
Agilis | Liability, Net Sales Milestones and Royalties | Minimum | Probability of Success | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.25		0.25
Agilis | Liability, Net Sales Milestones and Royalties | Minimum | Percentage of Sales for Royalties | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.02		0.02
Agilis | Liability, Net Sales Milestones and Royalties | Minimum | Potential Net Sales Milestones [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 0		$ 0
Agilis | Liability, Net Sales Milestones and Royalties | Maximum | Probability of Success | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.94		0.89
Agilis | Liability, Net Sales Milestones and Royalties | Maximum | Percentage of Sales for Royalties | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.06		0.06
Agilis | Liability, Net Sales Milestones and Royalties | Maximum | Potential Net Sales Milestones [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 150,000		$ 150,000
Agilis | Development and Regulatory Milestone
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	290,500
Ending Balance	$ 138,200		$ 290,500
Agilis | Development and Regulatory Milestone | Minimum | Probability of Success | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.25		0.25
Agilis | Development and Regulatory Milestone | Minimum | Development and Regulatory Milestone | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 0		$ 0
Agilis | Development and Regulatory Milestone | Minimum | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.031		0.022
Agilis | Development and Regulatory Milestone | Maximum | Probability of Success | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.94		0.94
Agilis | Development and Regulatory Milestone | Maximum | Development and Regulatory Milestone | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 381,000		$ 555,000
Agilis | Development and Regulatory Milestone | Maximum | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Rights Exchange settlement	0.053		0.047
Significant unobservable inputs (level 3)
Changes in the fair value of warrant liability and SARs liability
Additions		$ 0
Significant unobservable inputs (level 3) | SARs
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	$ 3,186	3,814	$ 3,814
Additions	0
Change in fair value	0	2,236
Payments	(3,186)	(3,815)
Rights Exchange settlement	0
Ending Balance	0	2,235	3,186
Significant unobservable inputs (level 3) | Commitments
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	290,500	257,040	257,040
Additions	0	0
Change in fair value	(13,120)	28,260
Payments	0	0
Rights Exchange settlement	(139,180)
Ending Balance	138,200	285,300	290,500
Significant unobservable inputs (level 3) | Agilis | Liability, Net Sales Milestones and Royalties
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	65,800	53,200	53,200
Additions	0	0
Change in fair value	30,100	6,400
Payments	0	0
Rights Exchange settlement	0
Ending Balance	$ 95,900	$ 59,600	$ 65,800

Other comprehensive income (l_3

Other comprehensive income (loss) and accumulated other comprehensive items - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2020
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	$ 572,494	$ 594,330
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Balance at the end of the period	510,954	510,954
Unrealized Gains/(Losses) On Marketable Securities, net of tax
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	3,410	755
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(1,016)	1,639
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(1,016)	1,639
Balance at the end of the period	2,394	2,394
Foreign Currency Translation
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	(13,426)	(11,339)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(24,695)	(26,782)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(24,695)	(26,782)
Balance at the end of the period	(38,121)	(38,121)
Accumulated other comprehensive income (loss)
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	(10,016)	(10,584)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(25,711)	(25,143)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(25,711)	(25,143)
Balance at the end of the period	$ (35,727)	$ (35,727)

Accounts payable and accrued _3

Accounts payable and accrued expenses - Narrative (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 34,485	$ 38,390
Income tax payable	21,475	499
Consulting and contracted research	17,659	12,969
Professional fees	4,590	3,562
Sales allowance and other costs	50,644	41,155
Sales rebates and royalties	68,628	42,997
Accounts payable	15,663	10,324
Other	5,417	9,380
Accounts payable and accrued expenses	$ 218,561	$ 159,276

Capitalization - Narrative (Det

Capitalization - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	May 29, 2020	Aug. 31, 2019	Sep. 30, 2020	Sep. 30, 2020	Apr. 29, 2020
Warrants
Consideration received on transaction			$ 9,100	$ 28,100
Number of shares issued in transaction (in shares)			173,956	542,470
Payments for asset acquisitions, share, value				$ 42,869
Rights Exchange Agreement
Warrants
Shares to issue under Rights Exchange Agreement			2,821,176	2,821,176	2,821,176
Payments for asset acquisitions, share, value				$ 150,500
Censa
Warrants
Payments for asset acquisitions, shares (in shares)	845,364			845,364
Payments for asset acquisitions, share, value	$ 42,900			$ 42,900
Maximum
Warrants
Consideration received on transaction		$ 125,000
Value of remaining shares available to be issued and sold in transaction			$ 93,000	$ 93,000
Weighted Average
Warrants
Sale of stock, weighted average price per share (in USD per share)			$ 54.39	$ 53.37

Net loss per share - Numerator

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Numerator
Net loss	$ (69,692)	$ (59,997)	$ (363,806)	$ (173,899)
Denominator
Denominator for basic and diluted net loss per share (in shares)	67,641,171	56,463,528	65,068,281	57,798,968
Net loss per share:
Basic and diluted (in dollars per share)	$ (1.03)	$ (1.06)	$ (5.59)	$ (3.01)

Net loss per share - Antidiluti

Net loss per share - Antidilutive (Details) - shares	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Net loss per share
Total shares excluded from calculation (in shares)	12,490,036	11,393,284
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	11,528,241	10,743,181
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	961,795	650,103

Stock award plan - Narrative (D

Stock award plan - Narrative (Details) - USD ($)	Mar. 05, 2013	Jan. 31, 2020	Jun. 30, 2016	May 31, 2016	May 31, 2013	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2016
Stock option plan
Share-based compensation expense						$ 16,779,000	$ 10,484,000	$ 48,909,000	$ 30,668,000
Unrecognized compensation cost						$ 173,200,000		$ 173,200,000
Weighted average remaining service period for recognition of unrecognized compensation cost								2 years 10 months 28 days
Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						935,092		935,092
Unvested restricted stock
Stock option plan
Grants in period (in shares)								625,390
Stock option
Stock option plan
Granted (in shares)								2,671,660
Inducement grants for non-statutory stock options (in shares)								667,285
Expected dividend yield (as a percent)								0.00%
Weighted average grant date fair value (in dollars per share)								$ 36.76
Expected term (in years)								5 years 9 months
Stock option | Maximum
Stock option plan
Risk-free interest rate (as a percent)								1.45%
Expected volatility (as a percent)								89.31%
Stock option | Minimum
Stock option plan
Risk-free interest rate (as a percent)								0.34%
Expected volatility (as a percent)								87.50%
SARs
Stock option plan
Granted (in shares)				897,290
Vesting period										4 years
Vested (in shares)								132,136
Stock appreciation rights liability						$ 0		$ 0
2013 Stock Incentive Plan
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant	0
2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan | Unvested restricted stock
Stock option plan
Grants in period (in shares)	735,324
2013 Stock Incentive Plan | Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						0		0
Number of additional shares authorized (in shares)					2,500,000
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant					122,296
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | 1998 Employee, Director and Consultant Stock Option Plan | Common stock | Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)					3,040,444
2013 Long Term Incentive Plan | Minimum
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number					2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year					4.00%
2020 inducement stock incentive plan [Member] | Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						291,025		291,025
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number		1,000,000
Employee Stock [Member]
Stock option plan
Number of shares authorized (in shares)			1,000,000
Share-based compensation expense						$ 600,000		$ 1,300,000
Award requisite service period			6 months
Purchase price of common stock, percent			85.00%
Employee stock purchase plan, voting percentage limit			5.00%

Stock award plan - Share Base C

Stock award plan - Share Base Compensation (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2020
Number of options
Outstanding at the beginning of the period (in shares)	11,043,939
Granted (in shares)	2,671,660
Exercised (in shares)	(1,426,026)
Forfeited/Cancelled (in shares)	(761,332)
Outstanding at the end of the period (in shares)	11,528,241
Vested or Expected to vest at the end of the period (in shares)	5,297,899
Exercisable at the end of the period (in shares)	5,576,283
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 31.67
Granted (in dollars per share)	50.76
Exercised (in dollars per share)	23.14
Forfeited/Cancelled (in dollars per share)	42.96
Outstanding at the end of the period (in dollars per share)	36.37
Vested or Expected to vest at the end of the period (in dollars per share)	40.09
Exercisable at the end of the period (in dollars per share)	$ 32.19
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 3 months 25 days
Vested or Expected to vest at the end of the period	8 years 8 months 12 days
Exercisable at the end of the period	5 years 10 months 2 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars)	$ 138,286
Vested or Expected to vest at the end of the period (in dollars)	44,050
Exercisable at the end of the period (in dollars)	$ 90,361
Valuation assumptions
Expected term (in years)	5 years 9 months
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	0.34%
Expected volatility (as a percent)	87.50%
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	1.45%
Expected volatility (as a percent)	89.31%

Stock award plan - Restricted S

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	9 Months Ended
	Sep. 30, 2020$ / sharesshares
Number of Shares
Balance at the beginning of the period (in shares) | shares	642,419
Granted (in shares) | shares	625,390
Vested (in shares) | shares	(232,263)
Forfeited (in shares) | shares	(73,751)
Balance at the end of the period (in shares) | shares	961,795
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) | $ / shares	$ 24.50
Granted (in dollars per share) | $ / shares	50.76
Vested (in dollars per share) | $ / shares	23.86
Forfeited (in dollars per share) | $ / shares	36.28
Balance at the end of the period (in dollars per share) | $ / shares	$ 41.05

Stock award plan - Share-based

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jan. 31, 2020	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Stock option plan
Share-based compensation expense		$ 16,779	$ 10,484	$ 48,909	$ 30,668
Research and development
Stock option plan
Share-based compensation expense		9,220	4,988	25,961	15,191
Selling, general and administrative
Stock option plan
Share-based compensation expense		$ 7,559	$ 5,496	$ 22,948	$ 15,477
Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant		935,092		935,092
Common stock | 2020 inducement stock incentive plan [Member]
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number	1,000,000
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant		291,025		291,025

Debt - Liability for Sale of Fu

Debt - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands	Jul. 17, 2020	Sep. 30, 2020	Sep. 30, 2020	Sep. 30, 2019
Debt Disclosure [Abstract]
Proceeds from sale of future royalties	$ 650,000		$ 650,000	$ 0
Proceeds from the sale of future royalties		$ 650,000	650,000
Less: Non-cash royalty revenue payable to RPI		(299)	(299)
Plus: non-cash interest expense recognized		14,557	14,557
Ending balance		$ 664,258	$ 664,258
Effective interest rate of the liability component	11.00%	11.00%	11.00%

Debt - Narrative (Details)

Debt - Narrative (Details)	Jul. 01, 2020USD ($)	May 05, 2017USD ($)	Sep. 30, 2019USD ($)D	May 31, 2017USD ($)	Aug. 31, 2015USD ($)$ / shares	Sep. 30, 2019USD ($)	Sep. 30, 2020USD ($)$ / shares	Sep. 30, 2019USD ($)	Dec. 31, 2019USD ($)
Long-term debt
Long-term debt							$ 302,971,000		$ 293,859,000
Current portion of long-term debt							0		20,000,000
Debt instrument additional amount available for repurchase							$ 37,500,000
Conversion price per share (in dollars per share) | $ / shares							$ 6
Adjustments to additional paid in capital, equity component of convertible debt						$ 119,489,000		$ 119,489,000
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Net carrying amount							$ 129,220,000		121,985,000
Debt principal amount					$ 150,000,000		$ 150,000,000		150,000,000
Interest rate ( as a percent )					3.00%
Net proceeds from issuance of convertible notes					$ 145,400,000
Trading days, number | D			20
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					17.7487
Conversion price per share (in dollars per share) | $ / shares					$ 56.34
Convertible instruments principal and unpaid interest payable upon events of default			100.00%
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default			25.00%
Term of the convertible notes			7 years		7 years
Adjustments to additional paid in capital, equity component of convertible debt					$ 57,500,000
Net deferred tax liability in connection with convertible notes					$ 22,300,000
Fair value of convertible notes							$ 171,300,000		171,200,000
Remaining contractual life of the convertible notes							1 year 10 months 24 days
Convertible debt | 3.00% Convertible senior notes due 2022 | Redemption on or after August 20, 2018
Long-term debt
Trading days, number | D			19
Consecutive trading days, period | D			30
Stock price trigger			130.00%
Redemption price			100.00%
Sinking fund							$ 0
Convertible debt | 1.50% Convertible senior notes due 2026
Long-term debt
Net carrying amount							173,745,000		163,583,000
Debt principal amount							$ 287,500,000		$ 287,500,000
Interest rate ( as a percent )							1.50%		1.50%
Net proceeds from issuance of convertible notes							$ 279,300,000
Conversion ratio			19.0404
Conversion price per share (in dollars per share) | $ / shares							$ 52.52
Term of the convertible notes							6 years
Adjustments to additional paid in capital, equity component of convertible debt			$ 123,000,000
Net deferred tax liability in connection with convertible notes							$ 25,300,000
Fair value of convertible notes							$ 329,200,000		$ 335,000,000
MidCap Financial Trust
Long-term debt
Line of credit facility, maximum borrowing capacity				$ 60,000,000
Proceeds from lines of credit		$ 40,000,000
Line of credit facility, additional capacity available, net product revenue threshold				20,000,000
Debt issuance costs				$ 400,000
Debt instrument, floor interest rate				1.00%
Debt instrument, basis spread on variable rate				6.15%
Debt instrument, interest payment period				24 months
Repayments of line of credit	$ 18,300,000
Payment of accrued interest	100,000
Aggregate repayment of line of credit and accrued interest	18,400,000
Termination and exit fees	$ 600,000

Debt - Convertible Notes (Detai

Debt - Convertible Notes (Details) - Convertible debt - USD ($)	Sep. 30, 2020	Dec. 31, 2019	Aug. 31, 2015
3.00% Convertible senior notes due 2022
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(986,000)	(1,329,000)
Less: Debt discount, net	(19,794,000)	(26,686,000)
Net carrying amount	129,220,000	121,985,000
1.50% Convertible senior notes due 2026
Long-term debt
Principal	287,500,000	287,500,000
Less: Debt issuance costs	(4,192,000)	(4,567,000)
Less: Debt discount, net	(109,563,000)	(119,350,000)
Net carrying amount	$ 173,745,000	$ 163,583,000

Debt - Interest Expense (Detail

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Jul. 17, 2020
Long-term debt
Amortization of debt issuance costs			$ 766	$ 434
Effective interest rate of the liability component	11.00%		11.00%		11.00%
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 1,131	$ 1,134	$ 3,375	3,375
Amortization of debt issuance costs	118	106	343	308
Amortization of debt discount	2,372	2,137	6,892	6,192
Total	$ 3,621	$ 3,377	$ 10,610	$ 9,875
Effective interest rate of the liability component	11.00%	11.00%	11.00%	11.00%
Convertible debt | 1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 1,081	$ 130	$ 3,223	$ 130
Amortization of debt issuance costs	127	15	374	15
Amortization of debt discount	3,313	391	9,786	391
Total	$ 4,521	$ 536	$ 13,383	$ 536
Effective interest rate of the liability component	10.20%	10.20%	10.20%	10.20%

Commitments and contingencies -

Commitments and contingencies - Narrative (Details) - USD ($) $ in Millions	Jun. 29, 2020	Apr. 29, 2020	Dec. 31, 2019	May 31, 2019	Sep. 30, 2020	Sep. 30, 2020	Dec. 31, 2019	May 29, 2020	Apr. 20, 2017	Jun. 30, 2016
Akcea
Other Commitments [Abstract]
Upfront licensing fee						$ 12
Akcea | Maximum
Other Commitments [Abstract]
Milestone payments							$ 4
Censa
Other Commitments [Abstract]
Asset acquisition, milestone, amount								$ 217.5
Asset acquisition, development and regulatory milestones								109
Asset acquisition, net sales milestone								160
Asset acquisition, initial milestone								30
Censa | Maximum
Other Commitments [Abstract]
Asset acquisition, milestone, amount								$ 217.5
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay									$ 50
Non-collaborative Arrangement Transactions | Akcea
Other Commitments [Abstract]
Milestone payments			$ 4	$ 6		4	$ 6
Agilis
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay		$ 40			$ 40	40
Net sales amount		150
Milestone obligation payments made					2.4
Development milestone payment obligations, net of cancellation and forfeiture						20
Development milestone obligation payments made					2.4
Agilis | Rights Exchange Agreement
Other Commitments [Abstract]
Priority review voucher amount		174
Contingent Liability cancellation and forfeiture, Milestone, Potential Achievements, Priority Review Voucher Amount						174
Development milestone payment obligations, cancellation and forfeiture						37.6
Development milestone payment obligations, net of cancellation and forfeiture		20
Contingent liability, cancellation and forfeiture	$ 211.6	211.6
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture		$ 361
Agilis | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	40				60	60
Priority review voucher amount						535
Net sales amount					$ 150	$ 150
Product sales		6.00%			6.00%	6.00%
Agilis | Maximum | Rights Exchange Agreement
Other Commitments [Abstract]
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture						$ 361
Agilis | Minimum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 37.6	$ 37.6
Product sales		2.00%			2.00%	2.00%
Agilis | Non-collaborative Arrangement Transactions
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay					$ 40	$ 40
BioElectron | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay					200	200
Net product revenue | Wellcome trust
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay										$ 0.8
Net product revenue | Wellcome trust | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay					$ 22.4	$ 22.4

Revenue recognition - Narrative

Revenue recognition - Narrative (Details) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Aug. 31, 2020USD ($)	Sep. 30, 2020USD ($)Distributor	Sep. 30, 2019USD ($)Distributor	Sep. 30, 2020USD ($)Distributorsegment	Sep. 30, 2019USD ($)Distributor	Jul. 17, 2020USD ($)	Nov. 30, 2011USD ($)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of operating segments | segment				1
Percentage of net product sales		10.00%	10.00%	10.00%	10.00%
Number of distributors | Distributor		2	2	2	2
Revenue recognition, milestone, potential achievements						$ 362,500
Revenue		$ 118,404	$ 71,416	$ 261,902	$ 210,521
Performance obligations satisfied in period		2,000	2,300	6,000	2,300
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue		35,000	100	35,100	100
Licensing And Collaboration Agreement | Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements		37,500		37,500			$ 135,000
Milestone payments received	$ 15,000
Licensing And Collaboration Agreement | Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements		325,000		325,000			$ 325,000
Milestone payments received	$ 20,000
Royalty revenue
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue		696	0	696	0
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue		38,500	22,900	102,100	68,300
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue		$ 44,200	$ 48,500	$ 124,000	$ 141,600

Revenue recognition - Performan

Revenue recognition - Performance Obligations (Details) - USD ($) $ in Millions	Sep. 30, 2020	Dec. 31, 2019
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Contract with Customer, Liability	$ 6	$ 11.7
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable		$ 11.7
Revenue, performance obligation, period		1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-07-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable	$ 6
Revenue, performance obligation, period	1 year

Intangible assets and goodwil_2

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended		9 Months Ended		12 Months Ended	25 Months Ended
	Dec. 31, 2019	May 31, 2019	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019	Dec. 31, 2019	Sep. 30, 2020	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life					7 years
Amortization of acquired intangible assets			$ 9,630	$ 7,025	$ 26,309	$ 19,677
Total allocation of IPR&D assets					576,500
Change in indefinite-lived intangibles								$ 0
Goodwill	$ 82,341		82,341		82,341		$ 82,341	$ 82,341
Research and development			92,998	$ 63,076	359,630	175,621
Changes in goodwill			$ 0		$ 0
Weighted Average
Finite-Lived Intangible Assets [Line Items]
Remaining amortization period					3 years 8 months 12 days
Akcea
Finite-Lived Intangible Assets [Line Items]
Upfront licensing fee					$ 12,000
Non-collaborative Arrangement Transactions | Akcea
Finite-Lived Intangible Assets [Line Items]
Milestone payments	$ 4,000	$ 6,000			$ 4,000		$ 6,000
Useful life					10 years
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Finite-Lived intangibles									$ 148,400
Milestone obligation payments made					$ 13,800	$ 7,400

Intangible assets and goodwil_3

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Sep. 30, 2020USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2020	$ 9,627
2021	38,506
2022	38,506
2023	38,506
2024 and thereafter	10,891
Total	$ 136,036

Subsequent events Narrative (De

Subsequent events Narrative (Details) $ in Millions	1 Months Ended
	Oct. 31, 2020USD ($)
Subsequent Event
Subsequent Event [Line Items]
Milestone payable to the company	$ 7.5