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Cover - USD ($)	12 Months Ended
Cover - USD ($)	Dec. 31, 2019	Feb. 27, 2020	Jun. 28, 2019
Cover page.
Document Type	10-K
Document Annual Report	true
Document Period End Date	Dec. 31, 2019
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
Title of 12(b) Security	Common Stock, $0.001 par value per share
Trading Symbol	PTCT
Security Exchange Name	NASDAQ
Entity Well-Known Seasoned Issuer	Yes
Entity Voluntary Filers	No
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
Entity Public Float			$ 2,567,003,670
Entity Common Stock, Shares Outstanding		62,632,628
Documents Incorporated by Reference	DOCUMENTS INCORPORATED BY REFERENCE Part III of this Annual Report incorporates by reference information from the definitive Proxy Statement for the registrant’s 2020 Annual Meeting of Shareholders which is expected to be filed with the Securities and Exchange Commission not later than 120 days after the registrant’s fiscal year ended December 31, 2019
Entity Central Index Key	0001070081
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Cash and cash equivalents	$ 288,028	$ 169,498
Current assets:
Cash and cash equivalents	295,528	169,498
Marketable securities	398,535	58,088
Trade receivables, net	55,538	67,907
Inventory	19,285	16,117
Prepaid expenses and other current assets	17,898	9,247
Total current assets	779,284	320,857
Fixed assets, net	21,549	12,694
Intangible assets, net	710,500	701,031
Goodwill	82,341	82,341
Deposits and other assets	30,108	2,299
Total assets	1,623,782	1,119,222
Current liabilities:
Accounts payable and accrued expenses	159,276	128,199
Current portion of long-term debt	20,000	11,667
Deferred revenue	8,242	3,716
Other current liabilities	8,339	3,814
Deferred consideration payable- current	40,000	19,400
Total current liabilities	235,857	166,796
Deferred revenue- long-term	3,415	9,722
Long-term debt	293,859	141,347
Contingent consideration payable	356,300	310,240
Deferred consideration payable- long-term	0	18,300
Deferred tax liability	130,862	122,032
Other long-term liabilities	9,159	58
Total liabilities	1,029,452	768,495
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 61,935,870 shares at December 31, 2019. Authorized 125,000,000 shares; issued and outstanding 50,606,147 shares at December 31, 2018.	62	51
Additional paid-in capital	1,795,351	1,288,137
Accumulated other comprehensive (loss) income	(10,584)	1,462
Accumulated deficit	(1,190,499)	(938,923)
Total stockholders’ equity	594,330	350,727
Total liabilities and stockholders’ equity	$ 1,623,782	$ 1,119,222

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2019	Dec. 31, 2018
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)	61,935,870	50,606,147
Common stock, outstanding shares (in shares)	61,935,870	50,606,147

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Revenue	$ 306,980	$ 264,734	$ 194,392
Operating expenses:
Cost of Goods and Services Sold	12,135	12,670	4,577
Amortization of acquired intangible asset	27,650	22,877	15,380
Research and development	257,452	171,984	117,456
Selling, general and administrative	202,541	153,548	121,271
Change in the fair value of deferred and contingent consideration	48,360	19,340	0
Total operating expenses	548,138	380,419	258,684
Loss from operations	(241,158)	(115,685)	(64,292)
Interest expense, net	(12,491)	(12,554)	(12,094)
Other income (expense), net	13,723	129	(1,279)
Loss before income tax expense	(239,926)	(128,110)	(77,665)
Income tax (expense) benefit	(11,650)	29	(1,335)
Net loss attributable to common stockholders	$ (251,576)	$ (128,081)	$ (79,000)
Weighted-average shares outstanding:
Basic and diluted (in shares)	58,863,185	46,576,313	39,183,073
Net loss per share—basic and diluted (in dollars per share)	$ (4.27)	$ (2.75)	$ (2.02)
Net product revenue
Revenues:
Revenue	$ 291,306	$ 263,005	$ 174,066
Collaboration and grant revenue
Revenues:
Revenue	$ 15,674	$ 1,729	$ 20,326

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Statement of Comprehensive Income [Abstract]
Net loss	$ (251,576)	$ (128,081)	$ (79,000)
Other comprehensive loss:
Unrealized gain on marketable securities, net of tax	724	9	225
Foreign currency translation (loss) gain, net of tax	(12,770)	(2,516)	5,229
Comprehensive loss	$ (263,622)	$ (130,588)	$ (73,546)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common stock	Additional paid-in capital	Accumulated other comprehensive (loss) income	Accumulated deficit
Balance (in shares) at Dec. 31, 2016		34,169,410
Balance at the beginning of the period at Dec. 31, 2016	$ 119,583	$ 34	$ 856,142	$ (1,485)	$ (735,108)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to acquisition (in shares)		6,683,598
Issuance of common stock related to acquisition	75,191	$ 7	75,184
Exercise of options (in shares)		202,085
Exercise of options	2,182		2,182
Restricted stock vesting and issuance (in shares)		287,531
Restricted stock vesting and issuance	1	$ 1
Issuance of common stock in connection with an employee stock purchase plan (in shares)		269,771
Issuance of common stock in connection with an employee stock purchase plan	2,467		2,467
Share-based compensation expense	30,559		30,559
Net loss	(79,000)				(79,000)
Comprehensive loss	5,454			5,454
Balance (in shares) at Dec. 31, 2017		41,612,395
Balance at the end of the period at Dec. 31, 2017	156,437	$ 42	966,534	3,969	(814,108)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offerings (in shares)		4,600,000
Issuance of common stock related to equity offerings	117,916	$ 5	117,911
Issuance of common stock related to acquisition (in shares)		3,500,907
Issuance of common stock related to acquisition	155,860	$ 3	155,857
Exercise of options (in shares)		633,973
Exercise of options	10,868	$ 1	10,867
Restricted stock vesting and issuance (in shares)		119,691
Restricted stock vesting and issuance	0
Issuance of common stock in connection with an employee stock purchase plan (in shares)		139,181
Issuance of common stock in connection with an employee stock purchase plan	2,787		2,787
Share-based compensation expense	33,252		33,252
Receivable from Investor	929		929
Net loss	(128,081)				(128,081)
Comprehensive loss	(2,507)			(2,507)
Balance (in shares) at Dec. 31, 2018		50,606,147
Balance at the end of the period at Dec. 31, 2018	350,727	$ 51	1,288,137	1,462	(938,923)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offerings (in shares)		10,102,899
Issuance of common stock related to equity offerings	323,756	$ 10	323,746
Equity component of convertible notes, net	119,482		119,482
Exercise of options (in shares)		949,887
Exercise of options	18,276	$ 1	18,275
Restricted stock vesting and issuance	0
Issuance of common stock in connection with an employee stock purchase plan (in shares)		107,145
Issuance of common stock in connection with an employee stock purchase plan	3,577		3,577
Share-based compensation expense	42,134		42,134
Net loss	(251,576)				(251,576)
Comprehensive loss	(12,046)			(12,046)
Balance (in shares) at Dec. 31, 2019		61,935,870
Balance at the end of the period at Dec. 31, 2019	$ 594,330	$ 62	$ 1,795,351	$ (10,584)	$ (1,190,499)

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Cash flows from operating activities
Net loss	$ (251,576)	$ (128,081)	$ (79,000)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	32,180	26,087	17,682
Non-cash lease expense	3,709
Change in the fair value of deferred and contingent consideration	48,360	19,340	0
Unrealized gain on equity investment	(2,194)	0	0
Amortization of (discounts) premiums on investments, net	(1,922)	(433)	535
Amortization of debt issuance costs	694	524	433
Share-based compensation expense	42,134	33,252	30,559
Non-cash interest expense	12,027	7,518	6,755
Disposal of asset	312	2	5
Deferred income taxes	8,829	0	199
Unrealized foreign currency transaction gains, net	(11,619)	(59)	(459)
Changes in operating assets and liabilities:
Inventory, net	(3,456)	(5,823)	(6,454)
Prepaid expenses and other current assets	(8,835)	(1,609)	(1,784)
Trade receivables, net	11,525	(29,589)	(12,203)
Deposits and other assets	(17,923)	(1,093)	(544)
Accounts payable and accrued expenses	26,836	43,877	24,011
Other long-term liabilities	13,668	1,932	733
Deferred revenue	(1,388)	6,514	9,469
Net cash used in operating activities	(98,639)	(27,641)	(10,063)
Cash flows from investing activities
Purchases of fixed assets	(13,757)	(7,097)	(3,101)
Purchase of equity investment	(4,000)	0	0
Purchases of marketable securities	(494,068)	(68,614)	(81,368)
Sale & redemption of marketable securities	156,270	90,423	174,749
Acquisition of product rights	(31,682)	(8,433)	(77,163)
Business acquisition, net of cash acquired	0	(48,892)	0
Net cash (used in) provided by investing activities	(387,237)	(42,613)	13,117
Cash flows from financing activities
Proceeds from issuance of convertible notes	279,267	0	0
Proceeds from exercise of options	18,276	10,868	2,182
Proceeds from shares issued under employee stock purchase plan	3,577	2,787	2,468
Debt issuance costs related to secured term loan	0	0	(432)
Net proceeds from public offering	323,756	117,916	0
Proceeds from issuance of secured term loan	0	0	40,000
Repayment of senior secured term loan	(11,667)	0	0
Net cash provided by financing activities	613,209	131,571	44,218
Effect of exchange rate changes on cash	(1,303)	(3,611)	6,199
Net increase in cash and cash equivalents	126,030	57,706	53,471
Cash and cash equivalents, beginning of period	169,498	111,792	58,321
Cash and cash equivalents, and restricted cash end of period	295,528	169,498	111,792
Supplemental disclosure of cash information
Cash paid for interest	7,693	7,773	6,271
Cash paid for income taxes	2,109	1,583	1,101
Supplemental disclosures of non-cash information related to investing and financing activities
Unrealized gain on marketable securities	724	9	225
Right-of-use assets obtained in exchange for lease obligations	17,389	0	0
Acquisition of product rights and licenses	$ 11,434	$ 5,981	$ 0

The Company	12 Months Ended
The Company	Dec. 31, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	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, or 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. 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, or AADC, deficiency, or 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, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which it anticipates submitting to the U.S. Food and Drug Administration, or FDA, in the second quarter of 2020. In January 2020, the Company submitted a marketing authorization application, or 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 Medicinal Products for Human Use by the end of 2020. 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, or hATTR amyloidosis. Waylivra has received marketing authorization in the EU for the treatment of familial chylomicronemia syndrome, or FCS. The Company anticipates filing for marketing authorization for Waylivra with ANVISA in the second half of 2020. 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, or SMA Foundation. The lead compound in the SMA program is risdiplam (RG7916, RO7034067). Roche submitted an NDA for risdiplam to the FDA in the fourth quarter of 2019 and the Prescription Drug User Fee Act, or PDUFA, date for a decision by the FDA is May 24, 2020. Risdiplam is expected to be indicated in the United States for SMA type 1, 2 and 3 patients, if approved. Roche anticipates submitting an MAA for risdiplam in the EEA in mid-year 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. In 2020, the Company plans to initiate three trials in this platform with two unique compounds that regulate inflammation and oxidative stress. 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 July 2019 and is effective, unless extended, through August 5, 2020. 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, or 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 PTC’s appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company intends to follow the FDA’s recommendation and will collect, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, which the Company initiated in the fourth quarter of 2018. The Company expects that a potential re-submission of an NDA could occur in mid-year 2020. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework. On April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. The Transaction was completed pursuant to an asset purchase agreement, dated March 15, 2017, as amended on April 20, 2017, (the "Asset Purchase Agreement"), by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The Transaction was accounted for as an asset acquisition. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction. Upon the closing of the Transaction, the Company paid to Marathon total upfront consideration comprised of $75.0 million in cash, funded through cash on hand, and 6,683,598 shares of the Company’s common stock. The number of shares of common stock issued at closing was determined by dividing $65.0 million by the volume weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market (“Nasdaq”) for the 15 trading-day period ending on the third trading day immediately preceding the closing. Marathon will be entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset, and a single $50.0 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement. On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc., or Agilis, pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Merger Agreement”), by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and the Company's wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the "Merger"). Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of $49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on Nasdaq for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. Agilis equityholders may become entitled to receive contingent payments from the Company based on the achievement of certain development, regulatory and net sales milestones as well as based upon a percentage of net sales of certain products. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Upon the closing of the Asset Acquisition, the Company paid to BioElectron total upfront consideration of $10.0 million, funded with cash on hand, less (i) transaction expenses incurred by BioElectron, (ii) the amount of outstanding indebtedness of BioElectron including a $4.0 million loan advance to BioElectron plus accrued and unpaid interest thereon and (iii) $1.5 million held in an escrow account to secure potential indemnification obligations owed to the Company. 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. As of December 31, 2019, the Company had an accumulated deficit of approximately $1,190.5 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 8), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offering" of its common stock, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, 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 accounting policies

12 Months Ended

Dec. 31, 2019

Accounting Policies [Abstract]

Summary of significant accounting policies

Basis of presentation

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

Use of estimates

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

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 the Company’s 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- December 31, 2018		End of period- December 31, 2019
Cash and cash equivalents	$	169,498	$	288,028
Restricted cash included in deposits and other assets	—		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	169,498	$	295,528

Consolidation

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

Segment and geographic information

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

Cash equivalents

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

Marketable securities

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

Fixed assets

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



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

Concentration of credit risk

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

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



	December 31, 2019		December 31, 2018
Raw materials	$	874	$	1,431
Work in progress	9,652		9,324
Finished goods	8,759		5,362
Total inventory	$	19,285	$	16,117

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. The Company recorded a $0.4 million write down for the twelve month period ended December 31, 2019, primarily related to product approaching expiration. The Company recorded a $1.8 million inventory write down for the twelve month period ended December 31, 2018, primarily related to inventory labeling changes. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the twelve month periods ended December 31, 2019 and December 31, 2018, these amounts were immaterial.

Cost of product sales

Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales. Production costs are expensed as cost of product sales when the related products are sold.

Accumulated other comprehensive income (loss)

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

Revenue recognition

In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products (Topic 605) and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach, a practical expedient permitted under Topic 606, and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million, which was recorded on January 1, 2018 to the opening balance of accumulated deficit, related to the product sales of Emflaza. The ASC 606 transition adjustment recorded for Emflaza resulted in sales being recognized earlier than under Topic 605, as the deferred revenue recognition model (sell-through) is not allowed under Topic 606. The one-time adjustment

consisted of $3.9 million in deferred revenue offset by $0.6 million of variable consideration. The information presented for the periods prior to January 1, 2018 has not been adjusted and is reported under Topic 605.

Periods prior to January 1, 2018

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

Net product sales

Prior to the second quarter of 2017, the Company’s net product sales consisted of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with FASB ASC Subtopic 605-15, Revenue Recognition—Products.

The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and the Company’s third-party partner distributors. Revenue is recognized when risk of ownership has transferred. The Company’s third-party partner distributors act as intermediaries between the Company and end users and do not typically stock significant quantities of Translarna. The ultimate payor for Translarna is typically a government authority or institution or a third-party health insurer.

In May 2017, the Company began the commercialization of Emflaza in the U.S. The Company recorded product revenue related to the sales of Emflaza in the U.S. in accordance with ASC 605-15, when persuasive evidence of an arrangement exists, delivery has occurred and title of the product and associated risk of loss has passed to the customer, the price is fixed or determinable and collection from the customer has been reasonably assured. Due to the early stage of the product launch, the Company determined that it was not able to reliably make certain estimates, including returns, necessary to recognize product revenue upon shipment to distributors. As a result, the Company recorded net product revenue for Emflaza using a deferred revenue recognition model (sell-through). Under the deferred revenue model, the Company does not recognize revenue until Emflaza is shipped to the specialty pharmacy.

The Company records revenue net of estimated third-party discounts and rebates. Allowances are recorded as a reduction of revenue at the time revenues from product sales are recognized. These allowances are adjusted to reflect known changes in factors and may impact such allowances in the quarter those changes are known. For the year ended December 31, 2017, the Company recognized Translarna net sales of $145.2 million and Emflaza net sales of $28.8 million.

Collaboration and grant revenue

The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.

The Company evaluates all contingent consideration earned, such as a milestone payment, using the criteria as provided by ASC 605-28, Revenue Recognition—Milestone Method. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from its activities to achieve the milestone; (2) the milestone be related to past performance; and (3) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement. If these criteria are met then the contingent milestones can be considered a substantive milestone and will be recognized as revenue in the period that the milestone is achieved. The Company recognizes royalties as earned in accordance with the terms of various research and collaboration agreements. If not substantive, the contingent consideration is allocated to the existing units of accounting based on relative selling price and recognized following the same basis previously established for the associated unit of accounting.

The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.

Periods commencing January 1, 2018

The Company's net product revenue primarily consists of sales of Translarna in territories outside of the U.S. and sales of Emflaza in the U.S., both for the treatment of DMD.

Net product revenue

The Company'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 years ended December 31, 2019 and 2018, net product sales outside of the United States were $190.3 million and $171.0 million respectively, and net product sales in the United States were $101.0 million and $92.0 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.

Upon adoption of ASC Topic 606 on January 1, 2018, the Company elected the following practical expedients:


•	Portfolio Approach - the Company applied the Portfolio Approach to contract reviews within its identified revenue streams that have similar characteristics and the Company believes this approach would not differ materially than if applying ASC Topic 606 to each individual contract.


•	Significant Financing Component - the Company expects the period between when it transfers a promised good to a customer and when the customer pays for the good or service to be one year or less.


•	Immaterial Performance Obligations - the Company disregards promises deemed to be immaterial in the context of the contract.


•	Shipping and Handling Activities - the Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise.

Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Collaboration revenue

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.

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 $0.3 million as of December 31, 2019 and $0.7 million as of December 31, 2018. For the twelve months ended December 31, 2019, 2018, and 2017, bad debt expense was immaterial.

Research and development costs

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

Advance payments made for goods and services that will be used in future research and development activities are deferred if the contracted party has not yet performed the related activities. The amount deferred is then recognized as expense when the research and development activities are performed. The deferred research and development advance payments were $4.5 million and $2.4 million as of December 31, 2019 and 2018, respectively.

Fair value of financial instruments

The Company follows the fair value measurement rules, which provides guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes

the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority).


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

•

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


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

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

Share-based compensation

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

The fair value of options is calculated using the Black-Scholes option pricing model to determine the fair value of stock options on the date of grant based on key assumptions such as expected volatility and expected term. The Company historically estimated the expected volatility of share options based on a historical volatility analysis of peers that were similar to the Company with respect to industry, stage of life cycle, size, and financial leverage. During the third quarter of 2019, the Company determined that it had sufficient stock volatility history to be able to estimate the expected volatility of its options. Accordingly, for the third and fourth quarters of 2019, the expected volatility of options was estimated based on the Company's historical stock volatility. The Company historically used the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. During the third quarter of 2019, the Company determined that it had sufficient exercise history to be able to estimate the expected term of its options. Accordingly, for the third and fourth quarters of 2019, the expected term of options was estimated based on the Company's historical exercise data. The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option. In connection with the adoption of ASU 2016-9, the Company made a policy election to continue its methodology for estimating its forfeiture rate.

Income taxes

On December 22, 2017, the U.S. government enacted the 2017 Tax Cuts and Jobs Act (the 2017 Tax Act), which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income (GILTI) provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended December 31, 2019.

In December 2017, the SEC staff issued Staff Accounting Bulletin No. 118, Income Tax Accounting Implications of the Tax Cuts and Jobs Act (SAB 118), which allowed the Company to record provisional amounts during a measurement period not

to extend beyond one year of the enactment date. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017. In the fourth quarter of 2018, the Company completed its analysis to determine the effect of the Tax Act and recorded no further adjustments.

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

The Company recorded a deferred tax liability in conjunction with the Merger, further discussed in Notes 1 and 3, of $122.0 million, related to the tax basis difference in the In-Process Research and Development, or IPR&D, indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful.

Foreign currency

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

Net (loss) income per share

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

Business combinations and asset acquisitions

The Company evaluates acquisitions of assets and other similar transactions to assess whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. If the screen is not met, further determination is required as to whether or not the Company has acquired inputs and processes that have the ability to create outputs, which would meet the requirements of a business. If determined to be a business combination, the Company accounts for the transaction under the acquisition method of accounting as indicated in ASU 2017-01, “Business Combinations”, which requires the acquiring entity in a business combination to recognize the fair value of all assets acquired, liabilities assumed, and any non-controlling interest in the acquiree and establishes the acquisition date as the fair value measurement point. Accordingly, the Company recognizes assets acquired and liabilities assumed in business combinations, including contingent assets and liabilities, and non-controlling interest in the acquiree based on the fair value estimates as of the date of acquisition. In accordance with ASC 805, the Company recognizes and measures goodwill as of the acquisition date, as the excess of the fair value of the consideration paid over the fair value of the identified net assets acquired.

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

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

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

Finite-lived intangible assets

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

Impairment of long-lived assets

The Company monitors its long-lived assets and finite-lived intangibles for indicators of impairment. If such indicators are present, the Company assesses the recoverability of affected assets by determining whether the carrying value of such assets is less than the sum of the undiscounted future cash flows of the assets. If such assets are found not to be recoverable, the Company measures the amount of such impairment by comparing the carrying value of the assets to the fair value of the assets, with the fair value generally determined based on the present value of the expected future cash flows associated with the assets. The Company believes that no impairment of long-lived assets exists as of December 31, 2019.

Indefinite-lived intangible assets

Indefinite-lived intangible assets consist of IPR&D. IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects 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. The Company performed a qualitative annual test for its indefinite-lived intangible assets as of October 1, 2019 and concluded that no impairment exists as of December 31, 2019.

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. As of December 31, 2019, the Company concluded that it continues to operate as one reporting unit. 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.The Company performed an annual test for goodwill as of October 1, 2019 and concluded that no impairment exists as of December 31, 2019.

Recent accounting pronouncements

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 will ASU 2016-13 and ASU 2019-11 effective January 1, 2020. The Company has completed its assessment of the effect of the adoption of ASU 2016-13 and ASU 2019-11on its consolidated financial statements and has the determined that the impact will be immaterial, as the Company has not historically had any material credit losses related to its accounts receivable or its available for sale debt securities. The Company will update its notes to the financial statements 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 will adopt this guidance January 1, 2020. The Company will update its notes to the financial statements with additional 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 will adopt this guidance January 1, 2020. The adoption is not expected to have a material impact on the Company’s consolidated financial statements and accompanying footnotes.

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 will adopt this guidance January 1, 2020. The adoption is not expected to have a material impact on the Company’s consolidated financial statements and accompanying footnotes.

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 principals 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 is currently planning to adopt this guidance when effective. The Company is assessing the impact of the adoption on the Company’s consolidated financial statements and accompanying footnotes.

Impact of recently adopted accounting pronouncements

In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)”. This standard requires organizations that lease assets with lease terms of more than 12 months to recognize assets and liabilities for the rights and obligations created by those leases on their balance sheets. The ASU also requires new qualitative and quantitative disclosures to help investors and other financial statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for public companies for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018, with early adoption permitted. Additionally, in March 2019, the FASB issued ASU 2019-01,"Leases (Topic 842): Codification Improvements”. ASU 2019-01 clarifies the transition guidance related to interim disclosures provided in the year of adoption. The Company adopted the new guidance on January 1, 2019 using the modified retrospective method. Prior period results were not adjusted and continue to be presented under Topic 840 based on the accounting standards originally in effect for such periods. As part of the adoption, the Company has elected to utilize practical expedients including the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed the Company to: 1) carry forward the historical determination of contracts as leases, lease classification and not reassess initial direct costs for historical lease arrangements, 2) not separate non-lease components from lease components and instead to account for each separate lease component and the non-lease components associated with that lease component as a single lease component (the Company elected to apply this practical expedient to all underlying asset classes), 3) not apply the recognition requirements in ASC 842 to short-term leases, and 4) not record an ROU asset or ROU liability for leases with an asset or liability balance that would be considered immaterial. Upon adoption, the Company recorded an operating lease liability with a corresponding operating lease ROU asset of $11.3 million. The adoption did not have a material impact on the consolidated results of operations, stockholder's equity, and cash flows for the twelve months ended December 31, 2019. As the Company is not a lessor, the aspects of the new guidance pertaining to lessors was not applicable for the Company.

In February 2018, the FASB issued ASU 2018-02, "Income Statement — Reporting Comprehensive Income (Topic 220): Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income". This standard permits the reclassification of tax effects stranded in other comprehensive income as a result of tax reform to retained earnings related to the change in federal tax rate in addition to other stranded effects that relate to the 2017 Tax Act but do not directly relate to the change in the federal rate. ASU 2018-02 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company adopted this guidance on January 1, 2019 and elected not to reclassify the tax effects in other comprehensive income related to the 2017 Tax Act, as these amounts were immaterial. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

In June 2018, the FASB issued ASU 2018-07, "Compensation — Stock Compensation (Topic 718), Improvements to Nonemployee Share-Based Payment Accounting". This standard expands the scope of ASC 718 to include share-based payments

granted to nonemployees in exchange for goods or services used or consumed in the entity’s own operations and supersedes the guidance in ASC 505-50. The ASU retains the existing cost attribution guidance, which requires entities to recognize compensation cost for nonemployee awards in the same period and in the same manner they would if they paid cash for the goods or services, but it moves the guidance to ASC 718. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company adopted this guidance on January 1, 2019. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

Acquisitions

12 Months Ended

Dec. 31, 2019

Business Combinations [Abstract]

Acquisitions

BioElectron Asset Acquisition

On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron pursuant to the Asset Acquisition Agreement by and between the Company and BioElectron, dated October 1, 2019. BioElectron was a private company with a pipeline focused on inflammatory and central nervous system (CNS) disorders. The lead program, PTC743, is pivotal trial ready for CNS disorders with substantial unmet need and significant commercial opportunity that are complementary to PTC’s existing pipeline.

Upon the closing of the Asset Acquisition, the Company paid to BioElectron total upfront consideration of $10.0 million , funded with cash on hand, less (i) transaction expenses incurred by BioElectron, (ii) the amount of outstanding indebtedness of BioElectron including a $4.0 million loan advance to BioElectron plus accrued and unpaid interest thereon and (iii) $1.5 million held in an escrow account to secure potential indemnification obligations owed to the Company. 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 contingent payments based on a percentage of net sales of certain products.

The Company concluded that the transaction included inputs and processes that did not constitute a business under the revised guidance of ASU 2017-01, which allows for a screen to evaluate if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. The Company determined that substantially all of the fair value is concentrated in PTC743 and accounted for the transaction as an asset acquisition under ASC 805-50.

The purchase price consisted of upfront consideration of $10.0 million in cash and approximately $0.5 million of acquisition costs, resulting in $10.5 million of total consideration transferred. As PTC743 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 asset of $10.0 million was expensed to research and development during the twelve month period ended December 31, 2019 and included within operating activities in the statement of cash flows. The remaining assets acquired and liabilities assumed were immaterial. Additionally, as noted above, BioElectron may be entitled to receive contingent milestone payment and contingent royalty payments. The Company will record the milestone and royalty payments if and when they become payable, in accordance with the applicable guidance. These payments will be capitalized and amortized over their expected useful lives.

Agilis Acquisition

On August 23, 2018, the Company completed its acquisition of Agilis pursuant to the Merger Agreement. Agilis was a privately-held biotechnology company advancing an innovative gene therapy platform for rare monogenic diseases that affect the central nervous system. Upon completion of the Merger, the Company acquired Agilis's lead product candidate, PTC-AADC, for the treatment of AADC deficiency, as well as three other gene therapies.

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 Nasdaq for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. The fair value of the stock on the acquisition date was determined to be $155.9 million.

Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2%-6%. The fair value of the contingent consideration payments at the acquisition date was estimated to be $290.5 million. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments mentioned above upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payments at the closing date was estimated to be $38.1 million. Refer to Footnote 4 for further fair value considerations.

The Company evaluated the acquisition of Agilis under ASU 2017-01, Business Combinations: Clarifying the Definition of a Business. Because the business contained both inputs and processes necessary to manage products and provide economic benefits directly to its owners and substantially all the value of the acquisition did not relate to a similar group of assets, it was determined that the acquisition represents a business combination. Therefore, the transaction has been accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the total purchase price of the acquisition is allocated to the net tangible and identifiable intangible assets acquired and liabilities assumed based on their fair values as of the date of acquisition.

The fair value of consideration totaled approximately $533.7 million summarized as follows:



	Fair Value
Cash consideration	$	49,221
Fair value of PTC common stock issued	155,860
Estimated fair value of deferred consideration payable	38,100
Estimated fair value of contingent consideration payable	290,500
Total consideration	$	533,681

The Company recorded the assets acquired and liabilities assumed as of the date of acquisition based on the information available at that time. The Company finalized its accounting for the Merger during the three month period ended December 31, 2018. The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of August 23, 2018, the measurement period adjustments recorded during the period from the acquisition date through December 31, 2018, and the final allocation of the purchase price as of December 31, 2018.



	Preliminary Allocation as of the acquisition date of August 23, 2018			Measurement Period Adjustments			Final Allocation as of December 31, 2018
Cash and cash equivalents	$	328		$	—		$	328
Prepaid expenses and other current assets	181			—			181
Fixed assets	153			—			153
Other assets	38			—			38
Intangible assets - IPR&D	480,000			96,500			576,500
Accounts payable and accrued expenses	(3,828		)	—			(3,828		)
Deferred tax liability	(115,200		)	(6,832		)	(122,032		)
Fair value of net assets acquired	$	361,672		$	89,668		$	451,340
Goodwill	100,309			(17,968		)	82,341
Total purchase price	$	461,981		$	71,700		$	533,681

The Company incurred approximately $1.7 million in acquisition related expenses which were included in selling, general and administrative expenses in the consolidated statement of operations as of December 31, 2018 . The results of Agilis’s operations have been included in the consolidated statements of operations beginning on the acquisition date of August 23, 2018. The net loss of Agilis included in the consolidated statement of operations for the period August 23, 2018 through December 31, 2018 was $8.7 million.

The fair value of the IPR&D was capitalized as of the acquisition date and accounted for as indefinite-lived intangible assets until disposition of the assets or completion or abandonment of the associated research and development efforts. Accordingly, during the development period after the completion of the acquisition, these assets will not be amortized into earnings; rather, these assets will be subject to periodic impairment testing. Upon successful completion of the development efforts, the useful lives of the IPR&D assets will be determined and the assets will be considered definite-lived intangible assets and amortized over their expected useful lives to cost of sales.

The goodwill recorded is the excess of the purchase price of the net assets acquired net of any deferred tax adjustments. The Company currently has a deferred tax liability for the indefinite lived IPR&D intangible assets, which have no tax basis and, therefore, will not result in a future tax deduction. The goodwill is not deductible for income tax purposes.

Pro-Forma Financial Information Associated with the Agilis Acquisition (Unaudited)

The following table summarizes certain supplemental pro forma financial information for the twelve-month periods ended December 31, 2018 and 2017 as if the Merger had occurred as of January 1, 2017. The unaudited pro-forma financial information for the twelve-month period ended December 31, 2018 reflects adjustments of $1.7 million related to acquisition fees that are non-recurring in nature. There were no adjustments related to the twelve-month period ended December 31, 2017.



	Twelve Months Ended December 31,
	2018			2017
Revenues	$	264,734		$	194,392
Net loss attributable to common stockholders	$	(138,083	)	$	(93,333	)

Emflaza Acquisition

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

Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction.

The Company concluded that the Transaction included inputs and processes that did not constitute a business under the revised guidance of ASU 2017-01, which allows for a screen to evaluate if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen is met, the transaction is accounted for as an asset acquisition. The Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and accounted for the Transaction as an asset acquisition under ASC 805-50.

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

Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone. In accordance with the guidance for an asset acquisition, the Company will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset. Refer to Note 18 for further details.

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



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



Purchase price	$	152,353

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

The Emflaza rights intangible asset is being amortized to cost of product sales over its expected useful life of approximately seven years. Given the inherent uncertainty of the Company's sales projections, the Company amortizes the asset on a straight line basis. Refer to Note 18 for further details.

Fair value of financial instruments and investments

12 Months Ended

Dec. 31, 2019

Fair Value Disclosures [Abstract]

Fair value of financial instruments and investments

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

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

In May 2019, the Company purchased $4.0 million of shares of ClearPoint Neuro, Inc.’s (“ClearPoint”) (formerly 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 year ended December 31,

2019, the Company recorded an unrealized gain of $2.2 million, which is a component of other (income) expense, net within the consolidated statement of operations. The fair value of the equity investment was $6.2 million as of December 31, 2019. 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.

The following represents the fair value using the hierarchy described in Note 2 for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of December 31, 2019 and 2018:



	December 31, 2019
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	398,535	$	—	$	398,535	$	—
Equity Investment	$	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 - Agilis	$	290,500	$	—	$	—	$	290,500
Contingent consideration payable- net sales milestones and royalties - Agilis	$	65,800	$	—	$	—	$	65,800



	December 31, 2018
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	58,088	$	—	$	58,088	$	—
Stock appreciation rights liability	$	3,814	$	—	$	—	$	3,814
Deferred consideration payable	$	37,700	$	—	$	37,700	$	—
Contingent consideration payable- development and regulatory milestones- Agilis	$	257,040	$	—	$	—	$	257,040
Contingent consideration payable- net sales milestones and royalties- Agilis	$	53,200	$	—	$	—	$	53,200

The Company uses the market approach to measure fair value for its financial assets. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The Company’s marketable securities investments classified as Level 2 primarily utilize broker quotes in a nonactive market to value these securities. No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the years ended December 31, 2019 and 2018.

The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2019 and 2018:



	December 31, 2019
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
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



	December 31, 2018
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	31,657	$	43	$	(1	)	$	31,699
Corporate debt securities	26,399		—		(10		)	26,389
Total	$	58,056	$	43	$	(11	)	$	58,088

Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. During the year ended December 31, 2019, the Company did not have any realized gains or losses from the sale of marketable securities. The cost of securities sold is based on the specific identification method. The Company evaluates investments with unrealized losses to determine if the losses are other than temporary. At December 31, 2019, the Company held securities with an unrealized loss position that were not considered to be other-than-temporarily impaired as the Company has the ability and intent to hold such investments until recovery of their amortized cost bases, which may be maturity. The Company has determined that it is not more likely than not that the Company will be required to sell the investments before such recovery.

In addition, the Company considered the financial condition, credit ratings and near-term prospects of the issuers, and the magnitude of the losses as compared to the cost and the length of time the investments have been in an unrealized loss position when determining if the losses are other than temporary.

The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2019 are as follows:



	December 31, 2019
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months				Total
	Unrealized losses			Fair Value		Unrealized losses		Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(20	)	$	71,779	$	—	$	—	$	(20	)	$	71,779
Asset-backed Securities	(8		)	24,211		—		—		(8		)	24,211
Total	$	(28	)	$	95,990	$	—	$	—	$	(28	)	$	95,990



	December 31, 2018
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Commercial paper	$	(1	)	$	1,993	$	—		$	—	$	(1	)	$	1,993
Corporate debt securities	(7		)	14,230		(3		)	10,087		(10		)	24,317
Total	$	(8	)	$	16,223	$	(3	)	$	10,087	$	(11	)	$	26,310

Marketable securities on the balance sheet at December 31, 2019 and 2018 mature as follows:



	December 31, 2019
	Less Than 12 Months		More Than 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



	December 31, 2018
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	31,699	$	—
Corporate debt securities	26,389		—
Total Marketable securities	$	58,088	$	—

The Company classifies all of its 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 3.0% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.5% 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 8. 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 December 31, 2019 and 2018 was $171.2 million and $146.6 million, respectively. The estimated fair value of the 2026 Convertible Notes at December 31, 2019 was $335.0 million.

The carrying amounts reported in the consolidated balance sheets for cash and cash equivalents, accounts receivable, accounts payable and borrowings under the credit and security agreement with MidCap Financial Trust and other financial institutions (as further discussed in Note 8) approximate fair value because of the immediate or short-term maturity of these financial instruments. The carrying amounts for the credit and security agreement approximate fair value based on market activity for other debt instruments with similar characteristics and comparable risk.

Deferred consideration payable

Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on the achievement of certain development milestones up to an aggregate maximum amount of $60.0

million and the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million. The Company is required to pay $40.0 million of development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payable at December 31, 2019 was $40.0 million. The Company did not apply a discount, as the milestones will be paid within one calendar year. Accordingly, as of December 31, 2019, the $40.0 million of the deferred consideration payable was classified as current on the balance sheet.

Level 3 valuation

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

The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss in the consolidated statements of operations. The fair value of the development and regulatory milestones are estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. The fair value of the net sales milestones and royalties is determined utilizing an option pricing model with Monte Carlo simulation to simulate a range of possible payment scenarios, and the average of the payments in these scenarios is then discounted to calculate present fair value.

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuation for the SARs liability and the contingent consideration payables for the years ended December 31, 2019, and 2018:



	Level 3 liabilities
		SARs			Contingent consideration payable- development and regulatory milestones - Agilis			Contingent consideration payable- net sales milestones and royalties - Agilis
Beginning balance as of December 31, 2017		$	1,665		$	—		$	—
Additions		—			263,500			27,000
Change in fair value		4,140			(6,460		)	26,200
Payments		$	(1,991	)	$	—		$	—
Ending balance as of December 31, 2018		3,814			257,040			53,200
Additions		—			—			—
Change in fair value		3,187			33,460			12,600
Payments		(3,815		)	—			—
Ending balance as of December 31, 2019		$	3,186		$	290,500		$	65,800

The following significant unobservable inputs were used in the valuation of the SARs liability and the contingent consideration payables for the years ended December 31, 2019 and 2018:



	December 31, 2019
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$3,186	Option-pricing model	Volatility	28.93%
			Risk free interest rate	0.19%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$48.03
			Expected life	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
			Probabilities of success	25% - 94%
			Discount rates	2.2% - 4.7%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$65,800	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.5%
			Projected years of payments	2021 - 2038



	December 31, 2018
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$3,814	Option-pricing model	Volatility	46.53% - 59.59%
			Risk free interest rate	2.44% - 2.63%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$34.32
			Expected life	0.01 - 1.01 years
Contingent consideration payable- development and regulatory milestones	$257,040	Probability-adjusted discounted cash flow	Potential development and regulatory milestones	$0 - $555 million
			Probabilities of success	25% - 94%
			Discount rates	5.8% - 8.0%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$53,200	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.0%
			Projected years of payments	2021 - 2038

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.

- Definition

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

+ References + Details

Fixed assets

12 Months Ended

Dec. 31, 2019

Property, Plant and Equipment [Abstract]

Fixed assets

Fixed assets, net were as follows at December 31, 2019 and 2018:



	December 31,
	2019			2018
Leasehold improvements	$	5,039		$	2,384
Computer equipment and software	8,069			4,609
Furniture, fixtures, machinery and lab equipment	17,033			9,965
Assets in process	3,232			3,219
	33,373			20,177
Less accumulated depreciation and amortization	(11,824		)	(7,483		)
Total	$	21,549		$	12,694

Depreciation expense was approximately $4.7 million, $2.6 million, and $2.3 million for the years ended December 31, 2019, 2018, and 2017, respectively.

Leases (Notes)

12 Months Ended

Dec. 31, 2019

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 certain vehicles, lab equipment, and office equipment under operating leases. The Company’s operating leases have remaining lease terms ranging from 0.1 years to 6.5 years and certain of the leases include renewal options to extend the lease for up to 10 years. Rent expense was approximately $6.0 million, $2.7 million, and $2.2 million for the years ended December 31, 2019, 2018, and 2017.

The components of lease expense were as follows:



	Twelve Months Ended December 31, 2019
Operating Lease Cost
Fixed lease cost	$	4,929
Variable lease cost	694
Short-term lease cost	350
Total operating lease cost	$	5,973

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:



	December 31, 2019

Operating lease ROU asset	$	13,693

Operating lease liabilities- current	$	5,153
Operating lease liabilities- noncurrent	9,018
Total operating lease liability	$	14,171

Operating lease ROU asset is a component of deposits and other assets on the consolidated balance sheet. The current portion of operating lease liability is a component of other current liabilities on the consolidated balance sheet. The long term portion of operating lease liabilities is a component of other long term liabilities on the consolidated balance sheet.

Supplemental lease term and discount rate information related to leases was as follows:



	December 31, 2019

Weighted-average remaining lease terms - operating leases (years)	3.38
Weighted-average discount rate - operating leases	7.33	%

Supplemental cash flow information related to leases was as follows:



	Twelve Months Ended December 31, 2019
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	4,466
Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	17,389

Future minimum lease payments under non-cancelable leases as of December 31, 2019 were as follows:



	Operating Leases
2020	$	5,997
2021	4,144
2022	2,465
2023	1,931
2024 and thereafter	1,446
Total lease payments	15,983
Less: Imputed Interest	1,812
Total	$	14,171

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 PTC743, 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 are $1.8 million, $1.8 million, and $1.4 million for 2020, 2021, and 2022, respectively.

As of December 31, 2019, the Company had one operating lease that had not yet commenced, and accordingly, is not reflected in the tables above. On August 4, 2019, the Company and Bristol-Myers Squibb Company, (the “Landlord”), entered into a Lease Agreement (the “Lease”), relating to the lease of approximately 185,000 square feet of office, manufacturing and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”).

The rental term of the Lease is currently estimated to commence on July 1, 2020 (the “Commencement Date”). Upon the Commencement Date, the Lease has an initial term of 15 years (the “Initial Term”), with two consecutive 10 years renewal periods at the Company’s option.

The aggregate rent for the Initial Term will be approximately $88.1 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.

Accounts payable and accrued expenses

12 Months Ended

Dec. 31, 2019

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2019 and 2018 consist of the following:



	December 31,
	2019		2018
Employee compensation, benefits, and related accruals	$	38,889	$	27,629
Consulting and contracted research	12,969		11,267
Professional fees	3,562		5,574
Sales allowances and other related costs	41,155		29,417
Royalties and rebates	42,997		31,874
Accounts payable	10,324		6,001
Other	9,380		16,437
Total	$	159,276	$	128,199

Debt

12 Months Ended

Dec. 31, 2019

Debt Disclosure [Abstract]

Debt

2017 Credit Facility

In May 2017, the Company entered into a credit and security agreement (the "Credit Facility") with MidCap Financial Trust, a Delaware statutory trust (“MidCap”), as administrative agent and MidCap and certain other financial institutions as lenders thereunder (the “Credit Agreement”) that provides for a senior secured term loan facility of $60.0 million, of which $40.0 million was drawn by the Company on May 5, 2017. The Company’s ability to draw on the remaining $20.0 million under the senior secured term loan facility expired on December 31, 2018. The Company capitalized approximately $0.4 million of debt issuance costs, which were netted against the carrying value of the Credit Facility and will be amortized over the term of the Credit Facility using the effective interest rate method. As of December 31, 2019, the Company made loan repayments of $11.7 million on the Credit Facility. The remaining balance of the Credit Facility as of December 31, 2019 was $28.3 million, $20.0 million of which was classified as current portion of long term debt and $8.3 million was included within long term debt on the consolidated balance sheet.

Borrowings under the Credit Agreement bear interest at a rate per annum equal to LIBOR (with a LIBOR floor rate of 1.00%) plus 6.15%. The Company is obligated to make interest only payments (payable monthly in arrears) through April 30, 2019. Commencing on May 1, 2019 and continuing for the remaining twenty-four months of the facility, the Company will be required to make monthly interest payments and monthly principal payments. The principal payments are to be made based on straight-line amortization of the principal over the twenty-four month period. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier.

The Credit Facility is subject to certain financial covenants. As of December 31, 2019, the Company was in compliance with all required covenants.

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, which was exercised in full by the initial purchasers. 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 of the 2026 Convertible Notes 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.

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 is $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 term of the 2026 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 $25.3 million in connection with the 2026 Convertible Notes.

The 2026 Convertible Notes consist of the following:



Liability component	December 31, 2019
Principal	$	287,500
Less: Debt issuance costs	(4,567		)
Less: Debt discount, net(1)	(119,350		)
Net carrying amount	$	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 December 31, 2019, the remaining contractual life of the 2026 Convertible Notes is approximately 6.7 years.

The following table sets forth total interest expense recognized related to the 2026 Convertible Notes:



	Year ended December 31,
	2019
Contractual interest expense	$	1,220
Amortization of debt issuance costs	140
Amortization of debt discount	$	3,659
Total	$	5,019
Effective interest rate of the liability component	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 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 of the 2022 Convertible Notes 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 Convertible Notes Indenture) per $1,000 principal amount of Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;


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


•	upon the occurrence of specified corporate events.

On or after February 15, 2022, until the close of business on the business day immediately preceding the maturity date, holders may convert their 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 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 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 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.

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 term of the 2022 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 2022 Convertible Notes is $57.5 million and was recorded in additional paid-in capital.

In accounting for the transaction costs related to the issuance of the 2022 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year term of the Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the Notes.

The 2022 Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2019			2018
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(1,329		)	(1,746		)
Less: Debt discount, net (1)	(26,686		)	(35,054		)
Net carrying amount	$	121,985		$	113,200


(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 December 31, 2019, the remaining contractual life of the 2022 Convertible Notes is approximately 2.6 years.

The following table sets forth total interest expense recognized related to the 2022 Convertible Notes:



	Year ended December 31,
	2019			2018
Contractual interest expense	$	4,500		$	4,500
Amortization of debt issuance costs	417			375
Amortization of debt discount	8,368			7,518
Total	$	13,285		$	12,393
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure

12 Months Ended

Dec. 31, 2019

Stockholders' Equity Note [Abstract]

Capital structure

Common stock

In January 2019, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 7,563,725 shares of common stock under the registration statement at a public offering price of $30.20 per share, including 843,725 shares issued upon exercise by the underwriter of its option to purchase additional shares in February 2019. The Company received net proceeds of $224.2 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

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, pursuant to a registration statement on Form S-3. During the twelve month period ending December 31, 2019, the Company issued and sold an aggregate of 63,926 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $46.60 per share. The Company received net proceeds of $2.6 million after deducting agent discounts and commissions and other offering expenses payable by the Company.

In September 2019, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 2,475,248 shares of common stock under the registration statement at a public offering price of $40.40 per share. The offering included an option to purchase up to an additional 371,287 shares for a period of 30 days following the offering. This option was not exercised by the underwriter. The Company received net proceeds of $97.0 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

In April 2018, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 4,600,000 shares of common stock under the registration statement at a public offering price of $27.04 per share, including 600,000 shares issued upon exercise by the underwriters of their option to purchase additional shares. The Company received net proceeds of approximately $117.9 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

As of December 31, 2019, the Company’s number of authorized shares of common stock was 125,000,000.

Warrants

During the year ended December 31, 2019, all of the Company’s outstanding warrants expired, and the Company wrote off the remaining liability, which was immaterial. All of the Company’s outstanding warrants are classified as liabilities as of December 31, 2018 because they contain non-standard antidilution provisions. The fair value of the warrants as of December 31, 2018 was immaterial.

The following is a summary of the Company’s outstanding warrants as of December 31, 2018:



	Warrant shares	Exercise price		Expiration
Common stock	7,030	$	128	September 2019
Common stock	130	$	2,520	August 2019

Earnings per share

12 Months Ended

Dec. 31, 2019

Earnings Per Share [Abstract]

Earnings per share

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

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



	Year ended December 31,
	2019				2018				2017
Numerator
Net loss	$	(251,576	)		$	(128,081	)		$	(79,000	)
Denominator
Denominator for basic and diluted net loss per share	58,863,185				46,576,313				39,183,073
Net loss per share:
Basic and diluted	$	(4.27	)	*	$	(2.75	)	*	$	(2.02	)	*

* For the years ended December 31, 2019, 2018, and 2017, the Company experienced a net loss and therefore did not report any dilutive share impact.

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



	As of December 31,
	2019	2018	2017
Stock Options	11,054,439	8,534,358	6,448,642
Unvested restricted stock	642,419	571,479	393,011
Total	11,696,858	9,105,837	6,841,653

Stock award plan

12 Months Ended

Dec. 31, 2019

Share-based Payment Arrangement [Abstract]

Stock award plan

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

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

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

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of December 31, 2019, awards for 467,808 shares of common stock were available for issuance.

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

Inducement stock option awards

Pursuant to the Nasdaq inducement grant exception, during the year ended December 31, 2019, the Company issued options to purchase an aggregate of 1,675,075 shares of common stock to certain new hire employees at a weighted-average exercise price of $39.23 per share. An aggregate of 250,153 of options previously granted as inducement awards were forfeited during the year ended December 31, 2019 in connection with employee separations from the Company.

A summary of stock option activity is as follows:



	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2016	5,854,316		$	34.71
Granted	1,913,873		$	12.34
Exercised	(202,085	)	$	10.80
Forfeited	(1,117,462	)	$	33.65
Outstanding at December 31, 2017	6,448,642		$	29.00
Granted	3,181,623		$	26.64
Exercised	(633,973	)	$	18.61
Forfeited	(461,934	)	$	35.36
Outstanding at December 31, 2018	8,534,358		$	28.58
Granted	3,977,995		$	35.81
Exercised	(949,887	)	$	19.25
Forfeited	(518,527	)	$	35.27
Outstanding at December 31, 2019	11,043,939		$	31.67	7.34 years	$	192,350
Vested or expected to vest at December 31, 2019	5,370,703		$	31.62	8.83 years	$	88,165
Exercisable at December 31, 2019	5,242,221		$	31.37	5.70 years	$	98,781

The fair values of grants made in the years ended December 31, 2019, 2018 and 2017 were contemporaneously estimated on the date of grant using the following assumptions:



	2019	2018	2017
Risk-free interest rate	1.58% - 2.63%	2.25% - 3.10%	1.84% - 2.45%
Expected volatility	62% - 92%	64% - 90%	76% - 81%
Expected term	5.75 - 6.11 years	5.03 - 10.00 years	5.04 - 10.00 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the years ended December 31, 2019, 2018 and 2017 was $23.05, $17.48, and $8.45 per share, respectively.

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

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2018	571,479		$	17.61
Granted	306,549		$	32.97
Vested	(181,327	)	$	17.56
Forfeited	(54,282	)	$	23.14
Unvested at December 31, 2019	642,419		$	24.50

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

In May 2016, a total of 897,290 SARs were granted to non-executive employees (the 2016 SARs). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the period ending December 31, 2019, the Company recorded $3.2 million in compensation expense related to the 2016 SARs.

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (ESPP or the Plan) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Board. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six-month period through payroll withholdings and may purchase, at the end of the six-month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the period ending December 31, 2019, the Company recorded $1.3 million in compensation expense related to the ESPP.

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



			Year ended December 31,
	2019		2018		2017
Research and development	$	20,836	$	16,096	$	15,456
Selling, general and administrative	21,298		17,156		15,103
Total	$	42,134	$	33,252	$	30,559

As of December 31, 2019, there was approximately $111.5 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s Plans. This cost is expected to be recognized as compensation expense over the weighted average remaining service period of approximately 3.00 years.

Other comprehensive income (loss) and accumulated other comprehensive items

12 Months Ended

Dec. 31, 2019

Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]

Other comprehensive income (loss) and accumulated other comprehensive items

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

The following table summarizes other comprehensive income (loss) and the changes in accumulated other comprehensive items, by component, for the years ended December 31, 2019, 2018, and 2017, respectively.



	Unrealized (Losses)/Gains On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)
Other comprehensive income before reclassifications	225			5,229			5,454
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income	225			5,229			5,454
Balance at December 31, 2017	$	22		$	3,947		$	3,969
Other comprehensive income (loss) before reclassifications	9			(2,516		)	(2,507		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	9			(2,516		)	(2,507		)
Balance at December 31, 2018	$	31		$	1,431		$	1,462
Other comprehensive income (loss) before reclassifications	724			(12,770		)	(12,046		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	724			(12,770		)	(12,046		)
Balance at December 31, 2019	$	755		$	(11,339	)	$	(10,584	)

Revenue recognition	12 Months Ended
Revenue recognition	Dec. 31, 2019
Revenue from Contract with Customer [Abstract]
Revenue recognition	Revenue recognition Net product sales The Company views its operations and manages its business in one operating segment. During the twelve months ended December 31, 2019, 2018, and 2017, net product sales in the United States were $101.0 million, $92.0 million, and $28.8 million respectively, consisting solely of Emflaza, and net product sales not in the United States were $190.3 million, $171.0 million, and $145.2 million respectively, consisting of Translarna and Tegsedi. Three of the Company’s distributors each accounted for over 10% of the Company’s net product sales for the twelve months ended December 31, 2019, 2018, and 2017. The Company’s contract liabilities balances as of December 31, 2019 and 2018 were $11.7 million and $12.9 million, respectively. The Company did not have any contract assets for the twelve months ended December 31, 2019 and 2018. During the twelve months ended December 31, 2019 and 2018, the Company recognized revenues of $3.9 million and $0.0 million, respectively, related to amounts included in contract liability balance at the beginning of each period. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the twelve months ended December 31, 2019 and 2018. Remaining performance obligations Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of December 31, 2019 and 2018, the aggregate amount of transaction price allocated to remaining performance obligations relating to Translarna net product revenue was $11.7 million and $12.9 million, respectively. The Company expects to recognize revenue over the next one to two years as the specific timing for satisfying the performance obligations is contingent upon a number of factors, including customers’ needs and schedules. Collaboration revenue In November 2011, the Company and the Spinal Muscular Atrophy Foundation (SMA Foundation) entered into a licensing and collaboration agreement with F. Hoffman-La Roche Ltd and Hoffman- La Roche Inc. (collectively, Roche) for a spinal muscular atrophy program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s spinal muscular atrophy program, which includes three compounds currently in preclinical development, as well as potential back-up compounds. The Company received a nonrefundable upfront cash payment of $30.0 million during the research term, which was terminated effective December 31, 2014, after which Roche provided the Company with funding, based on an agreed- upon full-time equivalent rate, for an agreed-upon number of full- time equivalent employees that the Company contributed to the research program. The Company identified two material promises in the collaboration agreement, the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises were bundled into one distinct performance obligation. As a result, the Company deferred the $30.0 million upfront payment which was recognized over the estimated performance period of two years, which was the contracted research period. As of adoption of ASC Topic 606 on January 1, 2018, all performance obligations had been satisfied and the balance of the remaining deferred upfront payment was fully recognized. Under the agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of certain sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. In August 2013, a lead development compound, RG7800, was selected to move into IND-enabling studies, which triggered a milestone payment to the Company from Roche of $10.0 million. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2013. In January 2014, the Company announced the initiation of a Phase 1 clinical program in its SMA collaboration with Roche and the SMA Foundation which triggered a $7.5 million milestone payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its SMA collaboration with Roche and the SMA Foundation which triggered a $10.0 million payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014. In October 2017, the Company announced that the Sunfish, a two-part clinical trial in pediatric and adult type 2 and type 3 SMA initiated in the fourth quarter of 2016 with Roche and SMA Foundation, had transitioned into the pivotal second part of its study. The achievement of this milestone triggered a $20.0 million payment to the Company from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2017. In November 2019, the Company announced the filing of an NDA in the United States, which triggered a $15.0 million payment to the Company from Roche. Under ASC Topic 606, the acceptance of the NDA filing by the FDA resolved the uncertainty of whether the milestone was probable of being achieved, and the Company recorded it as collaboration revenue for the year ended December 31, 2019. The remaining potential research and development event milestones that can be received as of December 31, 2019 is $72.5 million. The remaining potential sales milestones as of December 31, 2019 is $325.0 million upon achievement of certain sales events. In addition, the Company is eligible to receive up to double digit royalties on worldwide annual net sales of a commercial product. For the twelve months ended December 31, 2019, 2018, and 2017, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $15.2 million, $0.2 million, and $20.3 million, respectively.

Income taxes

12 Months Ended

Dec. 31, 2019

Income Tax Disclosure [Abstract]

Income taxes

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2019, 2018, and 2017:



	2019			2018			2017
Domestic	$	(231,915	)	$	(68,461	)	$	(54,588	)
Foreign	(8,011		)	(59,649		)	(23,077		)
Total	$	(239,926	)	$	(128,110	)	$	(77,665	)

The Income Tax Provision consisted of the following for the years ended December 31, 2019, 2018 and 2017:



	2019			2018			2017
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(61		)	(38		)	(6		)
Foreign	(2,041		)	(669		)	(1,131		)
Deferred:
U.S. Federal	—			—			(198		)
U.S. State and Local	(8,812		)	—			—
Foreign	(736		)	736			—
Total tax benefit (expense)	$	(11,650	)	$	29		$	(1,335	)

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



	December 31,
	2019		2018		2017
Federal income tax provision at statutory rate	21.00	%	21.00	%	34.00	%
State income tax provision, net of federal benefit	1.08		0.05		(1.01	)
Permanent differences	(6.17	)	(6.41	)	(8.48	)
Research and development	4.38		6.49		19.53
Change in valuation allowances	(35.49	)	2.20		29.10
Change in deferred tax assets	15.89		(14.22	)	(64.12	)
Foreign tax rate differential	(1.88	)	(9.10	)	(10.33	)
Benefit allocated from other comprehensive income	—		—		(0.26	)
Tax rate change	(3.67	)	—		—
Other	—		0.01		(0.15	)
Effective income tax rate	(4.86	)%	0.02	%	(1.72	)%

Accounting for income taxes under U.S. GAAP requires that individual tax-paying entities of the company offset all deferred tax liabilities and assets within each particular tax jurisdiction and present them as a noncurrent deferred tax liability or asset. Amounts in different tax jurisdictions cannot be offset against each other. The noncurrent deferred income tax asset is recorded within deposits and other assets on the balance sheet. The amount of deferred income taxes are as follows:



	2019			2018
Assets:
Noncurrent deferred income taxes	$	—		$	736
Liabilities:
Noncurrent deferred income taxes	(130,862		)	(122,032		)
Deferred income taxes - net	$	(130,862	)	$	(121,296	)

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2019 and 2018 are as follows:



	2019			2018
Deferred tax assets:
Accrued expense	$	2,588		$	714
Amortization	78,291			5,148
Depreciation	991			1,601
Federal tax credits	99,421			89,070
State tax credits	6,489			5,473
Federal net operating losses	91,010			62,159
State net operating losses	1,360			165
Foreign net operating losses	1,056			736
Capitalized research and development costs	1,274			2,093
Share based compensation and other	16,425			21,411
Other comprehensive loss	1,512			—
Total gross deferred tax assets	300,417			188,570
Less valuation allowance	(267,131		)	(180,481		)
Total deferred tax assets, net of valuation allowance	$	33,286		$	8,089
Deferred tax liabilities:
Convertible debt	$	(33,286	)	$	(7,353	)
Indefinite lived intangible	(130,862		)	(122,032		)
Total gross deferred tax liabilities	(164,148		)	(129,385		)
Net deferred tax assets (liabilities)	$	(130,862	)	$	(121,296	)

At December 31, 2019 and 2018, the Company recorded valuation allowance against its net deferred tax assets of approximately $267.1 million and $180.5 million, respectively. The change in the valuation allowance during the years ended December 31, 2019 and 2018 was approximately $86.7 million and $2.8 million, respectively. A valuation allowance has been recorded since, in the judgment of management, these assets are not more likely than not to be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during periods in which those temporary differences and carryforwards become deductible or are utilized. As of December 31, 2019, the Company incurred approximately $433.3 million, $224.4 million, $8.4 million of federal, state, and foreign net operating loss carryforwards, respectively. As a result of the adoption of ASU 2016-09, the Company no longer excludes tax benefits that arose directly from equity compensation in excess of compensation recognized for financial reporting in its U.S. federal and U.S. state net operating loss carryforwards.

During 2018, the Company acquired IPR&D as part of the acquisition of Agilis. This asset is currently considered an indefinite-lived intangible with no related book amortization and tested for impairment, annually. As the IPR&D has no tax basis and is an indefinite-lived intangible, the deferred tax liability created at the time of acquisition is not considered positive evidence of future income and is presented as a deferred tax liability in the balance sheet.

As of December 31, 2019, research and development credit carryforwards for federal and state purposes are approximately $14.2 million and $6.2 million, respectively. In addition, the Orphan Drug Credit Carryover available as of December 31, 2019 is approximately $85.2 million. As a result of U.S. tax reform legislation, federal net operating losses generated in 2018 carryforward indefinitely, however, the Company has federal net operating losses that pre-date U.S. tax reform legislation which begin to expire in 2021 and federal credit carryforwards that begin to expire in 2019. State net operating loss carryforwards begin to expire in 2030, and the state credit carryforwards began to expire in 2016. Sections 382 and 383 of the Internal Revenue Code of 1986 subject the future utilization of net operating losses and certain other tax attributes, such as research and development tax credits, to an annual limitation in the event of certain ownership changes, as defined. The Company has undergone an ownership change

and has determined that a “change in ownership” as defined by IRC Section 382 of the Internal Revenue Code of 1986, as amended, and the rules and regulations promulgated thereunder, did occur in June of 2013. Accordingly, about $231.5 million of the Company’s NOL carryforwards are limited and the Company can only use $16.7 million for the first five years from the ownership change and $5.7 million per year going forward. Therefore, $169.2 million of the NOL’s will be freed up over the next 20 years and $62.3 million are expected to expire unused which are not included in the deferred tax assets listed above. In summary, including the NOLs expected to expire, there are $495.7 million of NOLs available, out of which $231.5 million are limited by IRC Section 382. At December 31, 2019, there is $333.2 million available for immediate use and an additional $5.7 million will free up in 2020.

The income tax expense for the years ended December 31, 2019 and 2018 differed from the amounts computed by applying the U.S. federal income tax rate of 21% to loss before tax expense as a result of changes in state effective tax rates, foreign taxes, nondeductible expenses, tax credits generated, true up of net operating loss carryforwards, and increase in the Company’s valuation allowance. The Company applies the elements of FASB ASC 740-10 regarding accounting for uncertainty in income taxes. This clarifies the accounting for uncertainty in income taxes recognized in financial statements and required impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. As of December 31, 2019 the Company did not have any unrecognized tax benefits and has not accrued any interest or penalties through 2019. The Company does not expect to have any unrecognized tax benefits within the next twelve months. The Company’s policy is to recognize interest and penalties related to tax matters within the income tax provision. Tax years beginning in 2014 are generally subject to examination by taxing authorities, although net operating losses from all years are subject to examinations and adjustments for at least three years following the year in which the attributes are used. The Company concluded in 2018 the examination from the United States Internal Revenue Service for tax year 2014 noting adjustments to the U.S. federal net operating loss carryforwards and research and development credit carryforwards. The Company is currently under a tax audit in Switzerland for tax years 2014 through 2018. Although the outcome of tax audits is always uncertain, the company does not expect any adjustment to result for these years as of December 31, 2019.

For all years through December 31, 2016, the Company generated research credits but has not conducted a study to document the qualified activities. This study may result in an adjustment to the Company’s research and development credit carryforwards; however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the deferred tax asset established for the research and development credit carryforwards and the valuation allowance.

As a result of U.S. tax reform legislation, distributions of profits from non-U.S. subsidiaries are not expected to cause a significant incremental U.S. tax impact in the future. However, distributions may be subject to non-U.S. withholding taxes if profits are distributed from certain jurisdictions. U.S. federal income taxes have not been provided on undistributed earnings of our international subsidiaries as it is our intention to reinvest any earnings into the respective subsidiaries. It is not practicable to estimate the amount of tax that might be payable if some or all of such earnings were to be repatriated due to the legal structure and complexity of U.S. and local tax laws. As of December 31, 2019 and December 31, 2018 there are no undistributed earnings.

The Company has completed its accounting for the income tax effects of U.S. tax reform legislation and included measurement period adjustments in 2018. As a result of the reduction in the U.S. corporate income tax rate, the Company revalued its ending net deferred tax assets as of December 31, 2017. In the fourth quarter of 2018, the Company completed its analysis to determine the effect of the Tax Act and recorded no further adjustments.

PTC Therapeutics International Limited (PTC International) and PTC Therapeutics Holdings Corp. Limited (PTC Bermuda) entered into an intra-entity asset transfer on October 1, 2019, for which PTC Bermuda sold beneficial rights to the Translarna Intellectual Properly to PTC International in exchange for an interest-free loan note of $556.7 million. No deferred tax asset was recognized for the excess of PTC International’s tax basis over the carrying amount in the consolidated financial statements because the Company provided for a valuation allowance on its deferred tax assets.

Commitments and contingencies	12 Months Ended
Commitments and contingencies	Dec. 31, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and contingencies Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited (Wellcome Trust) for the research and development of small molecule compounds in connection with its oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company made the first development milestone payment of $0.8 million to Wellcome Trust under the oncology program funding agreement during the second quarter of 2016. Additional milestone payments up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement. The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single- digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon its payment to the SMA Foundation of a specified amount. Pursuant to the Asset Purchase Agreement with 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 may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2%-6%. The Company is 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. 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. The Company also has a Collaboration and License Agreement with Akcea Therapeutics, Inc. ("Akcea") for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million. 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. 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. During the twelve months ended December 31, 2019, the Company entered into a purchase commitments with Aldevron, LLC to secure good manufacturing practices capacity for the Company’s gene therapy portfolio. As of December 31, 2019, the commitment was for $6.9 million, which will be paid in fiscal year 2020. 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. The Company is not currently aware of any material legal proceedings against it.

Geographic information

12 Months Ended

Dec. 31, 2019

Segments, Geographical Areas [Abstract]

Geographic information

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



	Year Ended December 31, 2019
	United States		Non-US		Total
Total assets	$	1,508,055	$	115,727	$	1,623,782
Property and equipment, net	$	19,656	$	1,893	$	21,549
Revenue	$	116,676	$	190,304	$	306,980



	Year Ended December 31, 2018
	United States		Non-US		Total
Total assets	$	1,013,977	$	105,245	$	1,119,222
Property and equipment, net	$	10,497	$	2,197	$	12,694
Revenue	$	93,694	$	171,040	$	264,734

401(k) plan	12 Months Ended
401(k) plan	Dec. 31, 2019
Retirement Benefits [Abstract]
401(k) plan	401(k) plan The Company maintains a 401(k) plan for its employees. Employee contributions are voluntary. The Company may match employee contributions in amounts to be determined at the Company’s sole discretion. The Company provided an 100%, 92% and 84% matching contribution for up to the first 6% of each contributing employee’s base salary contributions for the years ended December 31, 2019, 2018 and 2017, respectively. The Company made matching contributions to the 401(k) plan and recorded expense of approximately $3.5 million, $2.2 million and $1.6 million for the years ended December 31, 2019, 2018 and 2017, respectively.

Intangible assets and goodwill

12 Months Ended

Dec. 31, 2019

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 will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset. For the twelve month period ended December 31, 2019 and 2018, milestones payments of $27.1 million and $14.4 million were recorded, respectively. These payments are being amortized over the remaining useful life of the Emflaza rights asset on a straight line basis. As of December 31, 2019, a milestone payable to Marathon of $11.4 million was recorded on the balance sheet within accounts payable and accrued expenses.

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 twelve month periods ended December 31, 2019, 2018, and 2017, the Company recognized amortization expense of $27.7 million, $22.9 million, and $15.4 million respectively, related to the Emflaza rights, Waylivra, and Tegsedi intangible assets, resulting in accumulated amortization of $65.9 million as of December 31, 2019. The estimated future amortization of the Emflaza rights, Waylivra, and Tegsedi intangible assets is expected to be as follows:



	As of December 31, 2019
2020	$	31,139
2021	31,139
2022	31,139
2023	31,139
2024 and thereafter	9,444
Total	$	134,000

The weighted average remaining amortization period of the definite-lived intangibles as of December 31, 2019 was 4.5 years.

Indefinite-lived intangibles

In connection with the acquisition of the Company’s gene therapy platform from Agilis (Note 3), the Company acquired rights to PTC-AADC, for the treatment of AADC deficiency. AADC deficiency is a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. The 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. The Company performed a qualitative annual impairment test for its indefinite-lived intangible assets as of October 1, 2019 and concluded that no impairment exists as of December 31, 2019.

Goodwill

As a result of the Merger on August 23, 2018, the Company recorded $82.3 million of goodwill, which included a measurement period adjustment of $18.0 million recorded during the three month period ended December 31, 2018. This adjustment was related to the finalization of the fair values assigned to the intangible assets and corresponding deferred tax liability, the contingent consideration, and the deferred consideration. Refer to Note 3 for further details. There have been no changes to the balance of goodwill since the date of the Merger. Accordingly, the goodwill balance as of December 31, 2018 and 2019 was $82.3 million. The Company performed an annual impairment test for goodwill as of October 1, 2019 and concluded that no impairment exists as of December 31, 2019.

Collaboration and Licensing Agreement

On August 1, 2018, the Company entered into a Collaboration and License Agreement with Akcea for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million and a second payment of $6.0 million that was paid after Waylivra received regulatory approval from the the EMA in May 2019. The Company evaluated the agreement under the guidance in ASC 730 and concluded that the acquired rights to commercialize the products had no alternative future use as of the date of the Merger. Accordingly, the $12.0 million was charged to research and development expense in the consolidated statements of operations for the twelve month period ended December 31, 2018. As denoted above, the $6.0 million milestone payment to Akcea upon regulatory approval of Waylivra from the EMA was recorded as an intangible asset in 2019 as the product was now approved and thus capable of providing future benefit.

Subsequent events	12 Months Ended
Subsequent events	Dec. 31, 2019
Subsequent Events [Abstract]
Subsequent events	Subsequent events The Company has evaluated all subsequent events and transactions through the filing date. There were no material events that impacted the audited consolidated financial statements or disclosures.

Selected quarterly financial data (Unaudited)

12 Months Ended

Dec. 31, 2019

Quarterly Financial Information Disclosure [Abstract]

Selected quarterly financial data (Unaudited)

The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2019 and 2018 are as follows:



	For the quarters ending (1)
	March 31			June 30			September 30			December 31
2019:
Net product revenue	$	53,054		$	85,476		$	71,369		$	81,407
Collaboration and grant revenue	529			46			47			15,052
Operating expenses	122,723			124,280			131,891			169,243
Loss income from operations	(69,140		)	(38,758		)	(60,475		)	(72,784		)
Net loss	(72,113		)	(41,789		)	(59,997		)	(77,677		)
Basic and diluted net loss per common share(1)	$	(1.29	)	$	(0.75	)	$	(1.06	)	$	(1.37	)
2018:
Net product revenue	$	55,981		$	68,170		$	53,021		$	85,833
Collaboration and grant revenue	81			573			570			505
Operating expenses	72,805			74,317			101,821			131,476
Loss from operations	(16,743		)	(5,574		)	(48,230		)	(45,138		)
Net loss	(19,263		)	(9,520		)	(50,969		)	(48,330		)
Basic and diluted net loss per common share(1)	$	(0.46	)	$	(0.21	)	$	(1.06	)	$	0.96

(1)

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

Summary of significant accounting policies (Policies)

12 Months Ended

Dec. 31, 2019

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Restricted Cash

Consolidation

Segment and geographic information

Cash equivalents

Marketable securities

Fixed assets

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



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

Concentration of credit risk

Inventory and cost of product sales

Inventory

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



	December 31, 2019		December 31, 2018
Raw materials	$	874	$	1,431
Work in progress	9,652		9,324
Finished goods	8,759		5,362
Total inventory	$	19,285	$	16,117

Cost of product sales

Accumulated other comprehensive income (loss)

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

Revenue recognition

Periods prior to January 1, 2018

Net product sales

Collaboration and grant revenue

Periods commencing January 1, 2018

The Company's net product revenue primarily consists of sales of Translarna in territories outside of the U.S. and sales of Emflaza in the U.S., both for the treatment of DMD.

Net product revenue

Upon adoption of ASC Topic 606 on January 1, 2018, the Company elected the following practical expedients:


•	Portfolio Approach - the Company applied the Portfolio Approach to contract reviews within its identified revenue streams that have similar characteristics and the Company believes this approach would not differ materially than if applying ASC Topic 606 to each individual contract.


•	Significant Financing Component - the Company expects the period between when it transfers a promised good to a customer and when the customer pays for the good or service to be one year or less.


•	Immaterial Performance Obligations - the Company disregards promises deemed to be immaterial in the context of the contract.


•	Shipping and Handling Activities - the Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise.

Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Collaboration revenue

service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.

Allowance for doubtful accounts

Research and development costs

Fair value of financial instruments

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 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.

Share-based compensation

Income taxes

Foreign currency

Net (loss) income per share

Business combinations and asset acquisitions

Finite-lived intangible assets

Impairment of long-lived assets

Indefinite-lived intangible assets

Goodwill

Recent accounting pronouncements

Impact of recently adopted accounting pronouncements

Summary of significant accounting policies (Tables)

12 Months Ended

Dec. 31, 2019

Accounting Policies [Abstract]

Schedule of reconciliation cash



	Beginning of period- December 31, 2018		End of period- December 31, 2019
Cash and cash equivalents	$	169,498	$	288,028
Restricted cash included in deposits and other assets	—		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	169,498	$	295,528

Schedule of estimated useful life of related assets

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



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

Schedule of inventory

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



	December 31, 2019		December 31, 2018
Raw materials	$	874	$	1,431
Work in progress	9,652		9,324
Finished goods	8,759		5,362
Total inventory	$	19,285	$	16,117

Acquisitions (Tables)

12 Months Ended

Dec. 31, 2019

Business Combinations [Abstract]

Schedule of Business Acquisitions

The fair value of consideration totaled approximately $533.7 million summarized as follows:



	Fair Value
Cash consideration	$	49,221
Fair value of PTC common stock issued	155,860
Estimated fair value of deferred consideration payable	38,100
Estimated fair value of contingent consideration payable	290,500
Total consideration	$	533,681

Preliminary Allocation and Purchase Consideration

The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of August 23, 2018, the measurement period adjustments recorded during the period from the acquisition date through December 31, 2018, and the final allocation of the purchase price as of December 31, 2018.



	Preliminary Allocation as of the acquisition date of August 23, 2018			Measurement Period Adjustments			Final Allocation as of December 31, 2018
Cash and cash equivalents	$	328		$	—		$	328
Prepaid expenses and other current assets	181			—			181
Fixed assets	153			—			153
Other assets	38			—			38
Intangible assets - IPR&D	480,000			96,500			576,500
Accounts payable and accrued expenses	(3,828		)	—			(3,828		)
Deferred tax liability	(115,200		)	(6,832		)	(122,032		)
Fair value of net assets acquired	$	361,672		$	89,668		$	451,340
Goodwill	100,309			(17,968		)	82,341
Total purchase price	$	461,981		$	71,700		$	533,681



Purchase price	$	152,353

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

Business Acquisition, Pro Forma Information



	Twelve Months Ended December 31,
	2018			2017
Revenues	$	264,734		$	194,392
Net loss attributable to common stockholders	$	(138,083	)	$	(93,333	)

Schedule of Purchase Price

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



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

Fair value of financial instruments and investments (Tables)

12 Months Ended

Dec. 31, 2019

Fair Value Disclosures [Abstract]

Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis



	December 31, 2019
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	398,535	$	—	$	398,535	$	—
Equity Investment	$	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 - Agilis	$	290,500	$	—	$	—	$	290,500
Contingent consideration payable- net sales milestones and royalties - Agilis	$	65,800	$	—	$	—	$	65,800



	December 31, 2018
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	58,088	$	—	$	58,088	$	—
Stock appreciation rights liability	$	3,814	$	—	$	—	$	3,814
Deferred consideration payable	$	37,700	$	—	$	37,700	$	—
Contingent consideration payable- development and regulatory milestones- Agilis	$	257,040	$	—	$	—	$	257,040
Contingent consideration payable- net sales milestones and royalties- Agilis	$	53,200	$	—	$	—	$	53,200

Summary of marketable securities accounted for as available-for-sale securities

The following is a summary of marketable securities accounted for as available-for-sale securities at December 31, 2019 and 2018:



	December 31, 2019
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
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



	December 31, 2018
	Amortized Cost		Gross Unrealized					Fair Value
			Gross Unrealized
			Gains		Losses
Commercial paper	$	31,657	$	43	$	(1	)	$	31,699
Corporate debt securities	26,399		—		(10		)	26,389
Total	$	58,056	$	43	$	(11	)	$	58,088

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



	December 31, 2019
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months				Total
	Unrealized losses			Fair Value		Unrealized losses		Fair Value		Unrealized losses			Fair Value
Corporate debt securities	$	(20	)	$	71,779	$	—	$	—	$	(20	)	$	71,779
Asset-backed Securities	(8		)	24,211		—		—		(8		)	24,211
Total	$	(28	)	$	95,990	$	—	$	—	$	(28	)	$	95,990



	December 31, 2018
	Securities in an unrealized loss position less than 12 months					Securities in an unrealized loss position greater than 12 months					Total
	Unrealized losses			Fair Value		Unrealized losses			Fair Value		Unrealized losses			Fair Value
Commercial paper	$	(1	)	$	1,993	$	—		$	—	$	(1	)	$	1,993
Corporate debt securities	(7		)	14,230		(3		)	10,087		(10		)	24,317
Total	$	(8	)	$	16,223	$	(3	)	$	10,087	$	(11	)	$	26,310

Schedule of marketable securities on the balance sheet

Marketable securities on the balance sheet at December 31, 2019 and 2018 mature as follows:



	December 31, 2019
	Less Than 12 Months		More Than 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



	December 31, 2018
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	31,699	$	—
Corporate debt securities	26,389		—
Total Marketable securities	$	58,088	$	—

Fair value of the Company's Level 3 valuation for warrant liability



	Level 3 liabilities
		SARs			Contingent consideration payable- development and regulatory milestones - Agilis			Contingent consideration payable- net sales milestones and royalties - Agilis
Beginning balance as of December 31, 2017		$	1,665		$	—		$	—
Additions		—			263,500			27,000
Change in fair value		4,140			(6,460		)	26,200
Payments		$	(1,991	)	$	—		$	—
Ending balance as of December 31, 2018		3,814			257,040			53,200
Additions		—			—			—
Change in fair value		3,187			33,460			12,600
Payments		(3,815		)	—			—
Ending balance as of December 31, 2019		$	3,186		$	290,500		$	65,800

The following significant unobservable inputs were used in the valuation of the SARs liability and the contingent consideration payables for the years ended December 31, 2019 and 2018:



	December 31, 2019
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$3,186	Option-pricing model	Volatility	28.93%
			Risk free interest rate	0.19%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$48.03
			Expected life	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
			Probabilities of success	25% - 94%
			Discount rates	2.2% - 4.7%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$65,800	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.5%
			Projected years of payments	2021 - 2038



	December 31, 2018
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$3,814	Option-pricing model	Volatility	46.53% - 59.59%
			Risk free interest rate	2.44% - 2.63%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$34.32
			Expected life	0.01 - 1.01 years
Contingent consideration payable- development and regulatory milestones	$257,040	Probability-adjusted discounted cash flow	Potential development and regulatory milestones	$0 - $555 million
			Probabilities of success	25% - 94%
			Discount rates	5.8% - 8.0%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$53,200	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.0%
			Projected years of payments	2021 - 2038

Fixed assets (Tables)

12 Months Ended

Dec. 31, 2019

Property, Plant and Equipment [Abstract]

Schedule of fixed assets, net

Fixed assets, net were as follows at December 31, 2019 and 2018:



	December 31,
	2019			2018
Leasehold improvements	$	5,039		$	2,384
Computer equipment and software	8,069			4,609
Furniture, fixtures, machinery and lab equipment	17,033			9,965
Assets in process	3,232			3,219
	33,373			20,177
Less accumulated depreciation and amortization	(11,824		)	(7,483		)
Total	$	21,549		$	12,694

Leases (Tables)

12 Months Ended

Dec. 31, 2019

Leases [Abstract]

Lease, cost

The components of lease expense were as follows:



	Twelve Months Ended December 31, 2019
Operating Lease Cost
Fixed lease cost	$	4,929
Variable lease cost	694
Short-term lease cost	350
Total operating lease cost	$	5,973

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:



	December 31, 2019

Operating lease ROU asset	$	13,693

Operating lease liabilities- current	$	5,153
Operating lease liabilities- noncurrent	9,018
Total operating lease liability	$	14,171

Supplemental lease term and discount rate information related to leases was as follows:



	December 31, 2019

Weighted-average remaining lease terms - operating leases (years)	3.38
Weighted-average discount rate - operating leases	7.33	%

Supplemental cash flow information related to leases was as follows:



	Twelve Months Ended December 31, 2019
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	4,466
Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	17,389

Lessee payments

Future minimum lease payments under non-cancelable leases as of December 31, 2019 were as follows:



	Operating Leases
2020	$	5,997
2021	4,144
2022	2,465
2023	1,931
2024 and thereafter	1,446
Total lease payments	15,983
Less: Imputed Interest	1,812
Total	$	14,171

Accounts payable and accrued expenses (Tables)

12 Months Ended

Dec. 31, 2019

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses

Accounts payable and accrued expenses at December 31, 2019 and 2018 consist of the following:



	December 31,
	2019		2018
Employee compensation, benefits, and related accruals	$	38,889	$	27,629
Consulting and contracted research	12,969		11,267
Professional fees	3,562		5,574
Sales allowances and other related costs	41,155		29,417
Royalties and rebates	42,997		31,874
Accounts payable	10,324		6,001
Other	9,380		16,437
Total	$	159,276	$	128,199

Debt (Tables)

12 Months Ended

Dec. 31, 2019

Debt Disclosure [Abstract]

Summary of convertible notes

The following table sets forth total interest expense recognized related to the 2026 Convertible Notes:



	Year ended December 31,
	2019
Contractual interest expense	$	1,220
Amortization of debt issuance costs	140
Amortization of debt discount	$	3,659
Total	$	5,019
Effective interest rate of the liability component	10.2		%

he 2026 Convertible Notes consist of the following:



Liability component	December 31, 2019
Principal	$	287,500
Less: Debt issuance costs	(4,567		)
Less: Debt discount, net(1)	(119,350		)
Net carrying amount	$	163,583

The 2022 Convertible Notes consist of the following:



	Year ended December 31,
Liability component	2019			2018
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(1,329		)	(1,746		)
Less: Debt discount, net (1)	(26,686		)	(35,054		)
Net carrying amount	$	121,985		$	113,200

(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.

Summary of interest expense recognized related to the Convertible Notes

The following table sets forth total interest expense recognized related to the 2022 Convertible Notes:



	Year ended December 31,
	2019			2018
Contractual interest expense	$	4,500		$	4,500
Amortization of debt issuance costs	417			375
Amortization of debt discount	8,368			7,518
Total	$	13,285		$	12,393
Effective interest rate of the liability component	11.0		%	11.0		%

Capital structure (Tables)

12 Months Ended

Dec. 31, 2019

Stockholders' Equity Note [Abstract]

Summary of the Company's outstanding warrants

The following is a summary of the Company’s outstanding warrants as of December 31, 2018:



	Warrant shares	Exercise price		Expiration
Common stock	7,030	$	128	September 2019
Common stock	130	$	2,520	August 2019

Earnings per share (Tables)

12 Months Ended

Dec. 31, 2019

Earnings Per Share [Abstract]

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

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



	Year ended December 31,
	2019				2018				2017
Numerator
Net loss	$	(251,576	)		$	(128,081	)		$	(79,000	)
Denominator
Denominator for basic and diluted net loss per share	58,863,185				46,576,313				39,183,073
Net loss per share:
Basic and diluted	$	(4.27	)	*	$	(2.75	)	*	$	(2.02	)	*

* For the years ended December 31, 2019, 2018, and 2017, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding



	As of December 31,
	2019	2018	2017
Stock Options	11,054,439	8,534,358	6,448,642
Unvested restricted stock	642,419	571,479	393,011
Total	11,696,858	9,105,837	6,841,653

Stock award plan (Tables)

12 Months Ended

Dec. 31, 2019

Share-based Payment Arrangement [Abstract]

Summary of stock option activity

A summary of stock option activity is as follows:



	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2016	5,854,316		$	34.71
Granted	1,913,873		$	12.34
Exercised	(202,085	)	$	10.80
Forfeited	(1,117,462	)	$	33.65
Outstanding at December 31, 2017	6,448,642		$	29.00
Granted	3,181,623		$	26.64
Exercised	(633,973	)	$	18.61
Forfeited	(461,934	)	$	35.36
Outstanding at December 31, 2018	8,534,358		$	28.58
Granted	3,977,995		$	35.81
Exercised	(949,887	)	$	19.25
Forfeited	(518,527	)	$	35.27
Outstanding at December 31, 2019	11,043,939		$	31.67	7.34 years	$	192,350
Vested or expected to vest at December 31, 2019	5,370,703		$	31.62	8.83 years	$	88,165
Exercisable at December 31, 2019	5,242,221		$	31.37	5.70 years	$	98,781

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

The fair values of grants made in the years ended December 31, 2019, 2018 and 2017 were contemporaneously estimated on the date of grant using the following assumptions:



	2019	2018	2017
Risk-free interest rate	1.58% - 2.63%	2.25% - 3.10%	1.84% - 2.45%
Expected volatility	62% - 92%	64% - 90%	76% - 81%
Expected term	5.75 - 6.11 years	5.03 - 10.00 years	5.04 - 10.00 years

Summary of information on the Company's restricted stock

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
Unvested at December 31, 2018	571,479		$	17.61
Granted	306,549		$	32.97
Vested	(181,327	)	$	17.56
Forfeited	(54,282	)	$	23.14
Unvested at December 31, 2019	642,419		$	24.50

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



			Year ended December 31,
	2019		2018		2017
Research and development	$	20,836	$	16,096	$	15,456
Selling, general and administrative	21,298		17,156		15,103
Total	$	42,134	$	33,252	$	30,559

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

12 Months Ended

Dec. 31, 2019

Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]

Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items



	Unrealized (Losses)/Gains On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2016	$	(203	)	$	(1,282	)	$	(1,485	)
Other comprehensive income before reclassifications	225			5,229			5,454
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income	225			5,229			5,454
Balance at December 31, 2017	$	22		$	3,947		$	3,969
Other comprehensive income (loss) before reclassifications	9			(2,516		)	(2,507		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	9			(2,516		)	(2,507		)
Balance at December 31, 2018	$	31		$	1,431		$	1,462
Other comprehensive income (loss) before reclassifications	724			(12,770		)	(12,046		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive income (loss)	724			(12,770		)	(12,046		)
Balance at December 31, 2019	$	755		$	(11,339	)	$	(10,584	)

Income taxes (Tables)

12 Months Ended

Dec. 31, 2019

Income Tax Disclosure [Abstract]

Schedule of Income before Income Tax, Domestic and Foreign

The loss from operations before tax (expense) benefit consisted of the following for the years ended December 31, 2019, 2018, and 2017:



	2019			2018			2017
Domestic	$	(231,915	)	$	(68,461	)	$	(54,588	)
Foreign	(8,011		)	(59,649		)	(23,077		)
Total	$	(239,926	)	$	(128,110	)	$	(77,665	)

Components of Income Tax Provision

The Income Tax Provision consisted of the following for the years ended December 31, 2019, 2018 and 2017:



	2019			2018			2017
Current:
U.S. Federal	$	—		$	—		$	—
U.S. State and Local	(61		)	(38		)	(6		)
Foreign	(2,041		)	(669		)	(1,131		)
Deferred:
U.S. Federal	—			—			(198		)
U.S. State and Local	(8,812		)	—			—
Foreign	(736		)	736			—
Total tax benefit (expense)	$	(11,650	)	$	29		$	(1,335	)

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

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



	December 31,
	2019		2018		2017
Federal income tax provision at statutory rate	21.00	%	21.00	%	34.00	%
State income tax provision, net of federal benefit	1.08		0.05		(1.01	)
Permanent differences	(6.17	)	(6.41	)	(8.48	)
Research and development	4.38		6.49		19.53
Change in valuation allowances	(35.49	)	2.20		29.10
Change in deferred tax assets	15.89		(14.22	)	(64.12	)
Foreign tax rate differential	(1.88	)	(9.10	)	(10.33	)
Benefit allocated from other comprehensive income	—		—		(0.26	)
Tax rate change	(3.67	)	—		—
Other	—		0.01		(0.15	)
Effective income tax rate	(4.86	)%	0.02	%	(1.72	)%

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

The significant components of the Company’s deferred tax assets and liabilities at December 31, 2019 and 2018 are as follows:



	2019			2018
Deferred tax assets:
Accrued expense	$	2,588		$	714
Amortization	78,291			5,148
Depreciation	991			1,601
Federal tax credits	99,421			89,070
State tax credits	6,489			5,473
Federal net operating losses	91,010			62,159
State net operating losses	1,360			165
Foreign net operating losses	1,056			736
Capitalized research and development costs	1,274			2,093
Share based compensation and other	16,425			21,411
Other comprehensive loss	1,512			—
Total gross deferred tax assets	300,417			188,570
Less valuation allowance	(267,131		)	(180,481		)
Total deferred tax assets, net of valuation allowance	$	33,286		$	8,089
Deferred tax liabilities:
Convertible debt	$	(33,286	)	$	(7,353	)
Indefinite lived intangible	(130,862		)	(122,032		)
Total gross deferred tax liabilities	(164,148		)	(129,385		)
Net deferred tax assets (liabilities)	$	(130,862	)	$	(121,296	)

Geographic information (Tables)

12 Months Ended

Dec. 31, 2019

Segments, Geographical Areas [Abstract]

Summary of financial information based on geographical location

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



	Year Ended December 31, 2019
	United States		Non-US		Total
Total assets	$	1,508,055	$	115,727	$	1,623,782
Property and equipment, net	$	19,656	$	1,893	$	21,549
Revenue	$	116,676	$	190,304	$	306,980



	Year Ended December 31, 2018
	United States		Non-US		Total
Total assets	$	1,013,977	$	105,245	$	1,119,222
Property and equipment, net	$	10,497	$	2,197	$	12,694
Revenue	$	93,694	$	171,040	$	264,734

Intangible assets and goodwill (Tables)

12 Months Ended

Dec. 31, 2019

Goodwill and Intangible Assets Disclosure [Abstract]

Future amortization expense

The estimated future amortization of the Emflaza rights, Waylivra, and Tegsedi intangible assets is expected to be as follows:



	As of December 31, 2019
2020	$	31,139
2021	31,139
2022	31,139
2023	31,139
2024 and thereafter	9,444
Total	$	134,000

Selected quarterly financial data (Tables)

12 Months Ended

Dec. 31, 2019

Quarterly Financial Information Disclosure [Abstract]

Summary of quarterly data



	For the quarters ending (1)
	March 31			June 30			September 30			December 31
2019:
Net product revenue	$	53,054		$	85,476		$	71,369		$	81,407
Collaboration and grant revenue	529			46			47			15,052
Operating expenses	122,723			124,280			131,891			169,243
Loss income from operations	(69,140		)	(38,758		)	(60,475		)	(72,784		)
Net loss	(72,113		)	(41,789		)	(59,997		)	(77,677		)
Basic and diluted net loss per common share(1)	$	(1.29	)	$	(0.75	)	$	(1.06	)	$	(1.37	)
2018:
Net product revenue	$	55,981		$	68,170		$	53,021		$	85,833
Collaboration and grant revenue	81			573			570			505
Operating expenses	72,805			74,317			101,821			131,476
Loss from operations	(16,743		)	(5,574		)	(48,230		)	(45,138		)
Net loss	(19,263		)	(9,520		)	(50,969		)	(48,330		)
Basic and diluted net loss per common share(1)	$	(0.46	)	$	(0.21	)	$	(1.06	)	$	0.96

(1)

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

The Company (Details) - USD ($) $ in Thousands				1 Months Ended
The Company (Details) - USD ($) $ in Thousands	Oct. 25, 2019	Aug. 23, 2018	Apr. 20, 2017	Aug. 31, 2014	Dec. 31, 2019	Sep. 30, 2019	Dec. 31, 2018	Aug. 31, 2015
Minimum age of ambulatory patient				5 years
Accumulated deficit					$ (1,190,499)		$ (938,923)
Convertible Senior Notes, 1.5%, Due September 15, 2026 \| Convertible debt
Interest rate					1.50%	1.50%
3.00% Convertible senior notes due 2022 \| Convertible debt
Interest rate								3.00%
Marathon Pharmaceuticals, LLC \| Non-collaborative Arrangement Transactions
Cash consideration			$ 75,000
Equity interest issued or issuable, number of shares (in shares)			6,683,598
Numerator for calculation of number of shares of equity interests issued to acquire entity			$ 65,000
Trading day period			15 days
Development milestone payment obligations			$ 50,000
Agilis
Cash consideration		$ 49,221
Equity interest issued or issuable, 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 payment obligations		$ 40,000			$ 40,000
Agilis \| Non-collaborative Arrangement Transactions
Development milestone payment obligations		$ 40,000			40,000
Maximum \| Agilis
Development milestone payment obligations					60,000
Net sales milestones					150,000
Maximum \| BioElectron
Development milestone payment obligations					200,000
BioElectron
Cash consideration	$ 10,000
Development milestone payment obligations					$ 200,000
Loan advance	4,000
Escrow deposit disbursements related to property acquisition	1,500
BioElectron \| Maximum
Net sales milestones	$ 200,000

Summary of significant accounting policies - Narrative (Details)	12 Months Ended
	Dec. 31, 2019 USD ($) segment	Dec. 31, 2018 USD ($)	Dec. 31, 2017 USD ($)	Jan. 01, 2019 USD ($)	Aug. 23, 2018 USD ($)	Jan. 01, 2018 USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit	$ 7,500,000
Term for letter of credit (in years)	5 years
Number of operating segments \| segment	1
Number of reporting units \| segment	1
Inventory write-down	$ 400,000	$ 1,800,000
Operating lease ROU asset	13,693,000			$ 11,300,000
Accumulated deficit	(1,190,499,000)	(938,923,000)
ASC 606 Adjustment	3,900,000
Allowance for doubtful accounts	300,000	700,000
Deferred research and development advance payments	$ 4,500,000	$ 2,400,000
Federal income tax provision at statutory rate	21.00%	21.00%	34.00%
Impairment of long-lived assets	$ 0
Operating lease, liability	14,171,000			$ 11,300,000
Agilis
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Deferred tax liability	122,000,000.0	$ 122,032,000			$ 115,200,000
Difference between Revenue Guidance in Effect before and after Topic 606
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Accumulated deficit						$ 3,300,000
Variable consideration of accounting principle	600,000
Fifth Anniversary
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit	$ 3,800,000
Term for letter of credit (in years)	5 years
Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Net product sales	$ 190,300,000	171,000,000.0	$ 145,200,000
United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Net product sales	$ 101,000,000.0	$ 92,000,000.0	$ 28,800,000

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Cash and cash equivalents	$ 288,028	$ 169,498
Restricted cash included in deposits and other assets	7,500	0
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 295,528	$ 169,498	$ 111,792	$ 58,321

Summary of significant accounting policies - Fixed Assets (Details)	12 Months Ended
	Dec. 31, 2019
Computer equipment and software
Fixed assets
Estimated useful life	3 years
Furniture, fixtures, machinery and lab equipment
Fixed assets
Estimated useful life	7 years

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Accounting Policies [Abstract]
Raw materials	$ 874	$ 1,431
Work in progress	9,652	9,324
Finished goods	8,759	5,362
Total inventory	$ 19,285	$ 16,117

Acquisitions - Narrative (Details) - USD ($) $ in Thousands				4 Months Ended	12 Months Ended
Acquisitions - Narrative (Details) - USD ($) $ in Thousands	Oct. 25, 2019	Aug. 23, 2018	Apr. 20, 2017	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Finite-Lived Intangible Assets [Line Items]
Research and development					$ 257,452	$ 171,984	$ 117,456
Contingent consideration payable				$ 310,240	$ 356,300	310,240
Issuance of common stock related to acquisition						155,860	75,191
Useful life					7 years
BioElectron
Finite-Lived Intangible Assets [Line Items]
Payments for asset acquisitions	$ 10,000
Loan advance	4,000
Escrow deposit disbursements related to property acquisition	1,500
Research and development					$ 10,000
Acquisition costs	500
Acquisition Costs, Cumulative					10,500
Cash consideration	10,000
Development milestone payment obligations					200,000
Intellectual Property \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Payments for asset acquisitions			$ 75,000
Acquisition costs			$ (2,163)
Issuance of common stock related to acquisition (in shares)			6,683,598
Issuance of common stock related to acquisition			$ 75,190
Useful life			7 years
Non-collaborative Arrangement Transactions \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration			$ 75,000
Numerator for calculation of number of shares of equity interests issued to acquire entity			$ 65,000
Trading day period			15 days
Development milestone payment obligations			$ 50,000
Agilis
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 49,221
Numerator for calculation of number of shares of equity interests issued to acquire entity		$ 150,000
Trading day period		10 days
Fair value of PTC common stock issued		$ 155,860
Development milestone payment obligations		40,000			40,000
Estimated fair value of contingent consideration payable		290,500
Estimated fair value of deferred consideration payable		38,100
Total consideration		533,681
Estimated fair value of contingent consideration payable						1,700
Loss of acquire since acquisition date				$ 8,700
Net loss attributable to common stockholders						(138,083)	$ (93,333)
Agilis \| Non-collaborative Arrangement Transactions
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations		$ 40,000			40,000
Acquisition-related Costs \| Agilis
Finite-Lived Intangible Assets [Line Items]
Net loss attributable to common stockholders						$ 1,700
Maximum \| BioElectron
Finite-Lived Intangible Assets [Line Items]
Net sales milestones	$ 200,000
Maximum \| Agilis
Finite-Lived Intangible Assets [Line Items]
Net sales milestones					$ 150,000
Percentage of annual net sales					6.00%
Development milestone payment obligations					$ 60,000
Priority review voucher amount					$ 535,000
Minimum \| Agilis
Finite-Lived Intangible Assets [Line Items]
Percentage of annual net sales					2.00%
Common stock
Finite-Lived Intangible Assets [Line Items]
Issuance of common stock related to acquisition (in shares)						3,500,907	6,683,598
Issuance of common stock related to acquisition						$ 3	$ 7

Acquisitions - Schedule of Business Acquisitions (Details) - USD ($) $ in Thousands			12 Months Ended
	Oct. 25, 2019	Aug. 23, 2018	Dec. 31, 2018	Dec. 31, 2019
Agilis
Business Acquisition [Line Items]
Cash consideration		$ 49,221
Fair value of PTC common stock issued		155,860
Estimated fair value of deferred consideration payable		38,100
Estimated fair value of contingent consideration payable			$ 1,700
Total consideration		$ 533,681
BioElectron
Business Acquisition [Line Items]
Cash consideration	$ 10,000
Acquisition Costs, Cumulative				$ 10,500

Acquisitions - Preliminary Allocation of purchase price (Details) - USD ($) $ in Thousands		3 Months Ended	4 Months Ended
	Aug. 23, 2018	Dec. 31, 2018	Dec. 31, 2018	Dec. 31, 2019
Finite-Lived Intangible Assets [Line Items]
Goodwill		$ 82,341	$ 82,341	$ 82,341
Goodwill adjustment		18,000
Agilis
Finite-Lived Intangible Assets [Line Items]
Total consideration	$ 533,681
Cash and cash equivalents	328	328	328
Prepaid expenses and other current assets	181	181	181
Fixed assets	153	153	153
Other assets	38	38	38
Accounts payable and accrued expenses	(3,828)	(3,828)	(3,828)
Deferred tax liability	(115,200)	(122,032)	(122,032)	(122,000)
Deferred tax liability adjustment			(6,832)
Fair value of net assets acquired	361,672	451,340	451,340
Fair value of net assets acquired adjustment			89,668
Goodwill	100,309	82,341	82,341	$ 82,300
Goodwill adjustment			(17,968)
Total purchase price	461,981	533,681	533,681
Total purchase price adjustment			71,700
In Process Research and Development [Member] \| Agilis
Finite-Lived Intangible Assets [Line Items]
Intangible assets	$ 480,000	$ 576,500	576,500
Intangibles adjustment			$ 96,500

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

Acquisitions - Schedule of purchase price (Details) - USD ($) $ in Thousands		12 Months Ended
	Apr. 20, 2017	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Finite-Lived Intangible Assets [Line Items]
Cash consideration		$ 31,682	$ 8,433	$ 77,163
Fair value of PTC common stock issued to Marathon (6,683,598 shares)			$ 155,860	$ 75,191
Intellectual Property \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 75,000
Fair value of PTC common stock issued to Marathon (6,683,598 shares)	75,190
Acquisition costs	2,163
Total consideration transferred	$ 152,353

Acquisitions - Total Purchase Consideration (Details) $ in Thousands	Apr. 20, 2017 USD ($)
Marathon Pharmaceuticals, LLC
Business Acquisition [Line Items]
Inventory	$ 3,980
Intellectual Property \| Marathon Pharmaceuticals, LLC
Business Acquisition [Line Items]
Purchase price	152,353
Emflaza asset acquisition
Business Acquisition [Line Items]
Emflaza rights	$ 148,373

Fair value of financial instruments and investments - Narrative (Details)	12 Months Ended
	Dec. 31, 2019 USD ($) $ / shares	Dec. 31, 2018 USD ($) $ / shares	Dec. 31, 2017 USD ($)	Sep. 30, 2019 USD ($)	May 31, 2019 USD ($) $ / shares	Aug. 23, 2018 USD ($)	Apr. 30, 2018 $ / shares	Aug. 31, 2015 USD ($)
Financial assets and liabilities measured at fair value on recurring basis
Share price (in USD per share) \| $ / shares							$ 27.04
Unrealized (gains) losses of MRI investment	$ 2,194,000	$ 0	$ 0
Investment In MRI	6,200,000
Marketable securities	398,535,000	58,088,000
Contingent consideration payable	356,300,000	310,240,000
Deferred consideration payable- current	40,000,000	19,400,000
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						$ 150,000,000.0
Interest rate								3.00%
Debt instrument	171,200,000	146,600,000
Convertible Senior Notes, 1.5%, Due September 15, 2026 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal	$ 287,500,000			$ 287,500,000
Interest rate	1.50%			1.50%
Debt instrument	$ 335,000,000.0
Stock Appreciation Rights (SARs)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable- net sales milestones and royalties	$ 3,186,000	$ 3,814,000
Stock Appreciation Rights (SARs) \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input \| $ / shares	6.76	6.76
Stock Appreciation Rights (SARs) \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input \| $ / shares	30.86	30.86
Stock Appreciation Rights (SARs) \| Volatility \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input	0.2893	0.4653
Stock Appreciation Rights (SARs) \| Volatility \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input		0.5959
Stock Appreciation Rights (SARs) \| Risk free interest rate \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input	0.0019	0.0244
Stock Appreciation Rights (SARs) \| Risk free interest rate \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input		0.0263
Stock Appreciation Rights (SARs) \| Expected life \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input	0.01	0.01
Stock Appreciation Rights (SARs) \| Expected life \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Measurement input	1.01	1.01
Common stock \| Stock Appreciation Rights (SARs) \| Fair value of common stock
Financial assets and liabilities measured at fair value on recurring basis
Measurement input \| $ / shares	48.03	34.32
Fair Value, Measurements, Recurring \| Fair Value, Inputs, Level 2
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 398,535,000	$ 58,088,000
Deferred consideration payable	40,000,000	37,700,000
Stock appreciation rights liability	0	0
Contingent consideration payable		0
Contingent consideration payable- net sales milestones and royalties		0
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	40,000,000.0					$ 40,000,000.0
Deferred consideration payable						38,100,000
Agilis \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	60,000,000.0
Priority review voucher amount	535,000,000.0
Agilis \| Fair Value, Measurements, Recurring \| Fair Value, Inputs, Level 2
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	0
Contingent consideration payable- net sales milestones and royalties	0
Non-collaborative Arrangement Transactions \| Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payment obligations	40,000,000.0					$ 40,000,000.0
Total \| Fair Value, Measurements, Recurring
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	398,535,000	58,088,000
Deferred consideration payable	40,000,000	37,700,000
Stock appreciation rights liability	3,186,000	3,814,000
Contingent consideration payable		257,040,000
Contingent consideration payable- net sales milestones and royalties		$ 53,200,000
Total \| Agilis \| Fair Value, Measurements, Recurring
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	290,500,000
Contingent consideration payable- net sales milestones and royalties	65,800,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Purchase investment					$ 4,000,000.0
Share price (in USD per share) \| $ / shares					$ 3.10
Unrealized (gains) losses of MRI investment	$ 2,200,000

Fair value of financial instruments and investments - Schedule of financial assets and liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Aug. 23, 2018
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	$ 398,535	$ 58,088
Contingent consideration payable	356,300	310,240
Fair Value, Measurements, Recurring \| Total
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	398,535	58,088
Equity Investment	6,194
Stock appreciation rights liability	3,186	3,814
Deferred consideration payable	40,000	37,700
Contingent consideration payable		257,040
Contingent consideration payable- net sales milestones and royalties		53,200
Fair Value, Measurements, Recurring \| Quoted prices in active markets for identical assets (level 1)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0	0
Equity Investment	6,194
Stock appreciation rights liability	0	0
Deferred consideration payable	0	0
Contingent consideration payable		0
Contingent consideration payable- net sales milestones and royalties		0
Fair Value, Measurements, Recurring \| Significant other observable inputs (level 2)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	398,535	58,088
Equity Investment	0
Stock appreciation rights liability	0	0
Deferred consideration payable	40,000	37,700
Contingent consideration payable		0
Contingent consideration payable- net sales milestones and royalties		0
Fair Value, Measurements, Recurring \| Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Marketable securities	0	0
Equity Investment	0
Stock appreciation rights liability	3,186	3,814
Deferred consideration payable	0	0
Contingent consideration payable		257,040
Agilis
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Deferred consideration payable			$ 38,100
Agilis \| Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable- net sales milestones and royalties	65,800
Agilis \| Fair Value, Measurements, Recurring \| Total
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable	290,500
Contingent consideration payable- net sales milestones and royalties	65,800
Agilis \| Fair Value, Measurements, Recurring \| Quoted prices in active markets for identical assets (level 1)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable	0
Contingent consideration payable- net sales milestones and royalties	0
Agilis \| Fair Value, Measurements, Recurring \| Significant other observable inputs (level 2)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable	0
Contingent consideration payable- net sales milestones and royalties	0
Agilis \| Fair Value, Measurements, Recurring \| Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable	$ 290,500
BioElectron \| Fair Value, Measurements, Recurring \| Significant unobservable inputs (level 3)
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Contingent consideration payable- net sales milestones and royalties		$ 53,200

Fair value of financial instruments and investments - Marketable Securities, Unrealized Gains (Losses) (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Marketable securities accounted for as available-for-sale securities
Amortized Cost	$ 397,776	$ 58,056
Gross Unrealized Gains	787	43
Gross Unrealized Losses	(28)	(11)
Fair Value	398,535	58,088
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	157,936	31,657
Gross Unrealized Gains	162	43
Gross Unrealized Losses	0	(1)
Fair Value	158,098	31,699
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	188,778	26,399
Gross Unrealized Gains	576	0
Gross Unrealized Losses	(20)	(10)
Fair Value	189,334	$ 26,389
Asset-backed securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	51,062
Gross Unrealized Gains	49
Gross Unrealized Losses	(8)
Fair Value	$ 51,103

Fair value of financial instruments and investments - Available-for-sale securities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	$ (28)	$ (8)
Fair Value	95,990	16,223
Unrealized losses	0	(3)
Fair Value	0	10,087
Unrealized losses	(28)	(11)
Fair Value	95,990	26,310
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Unrealized losses		(1)
Fair Value		1,993
Unrealized losses		0
Fair Value		0
Unrealized losses		(1)
Fair Value		1,993
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	(20)	(7)
Fair Value	71,779	14,230
Unrealized losses	0	(3)
Fair Value	0	10,087
Unrealized losses	(20)	(10)
Fair Value	71,779	$ 24,317
Asset-backed Securities
Debt Securities, Available-for-sale [Line Items]
Unrealized losses	(8)
Fair Value	24,211
Unrealized losses	0
Fair Value	0
Unrealized losses	(8)
Fair Value	$ 24,211

Fair value of financial instruments and investments - Marketable Securities, Balance Sheet Disclosures (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Marketable securities on the balance sheet
Less Than 12 Months	$ 342,418	$ 58,088
More Than 12 Months	56,117	0
Commercial paper
Marketable securities on the balance sheet
Less Than 12 Months	158,098	31,699
More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Less Than 12 Months	139,596	26,389
More Than 12 Months	49,738	$ 0
Asset-backed Securities
Marketable securities on the balance sheet
Less Than 12 Months	44,724
More Than 12 Months	$ 6,379

Fair value of financial instruments and investments - Summary of changes in the fair value of the Company's Level 3 valuation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	$ 3,814
Ending balance	3,186	$ 3,814
Significant unobservable inputs (level 3) \| Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability
Beginning balance	3,814	1,665
Additions	0	0
Change in fair value	3,187	4,140
Payments	(3,815)	(1,991)
Ending balance	3,186	3,814
Significant unobservable inputs (level 3) \| Agilis
Changes in the fair value of warrant liability
Ending balance	65,800
Liability, Development and Regulatory Milestone \| Agilis
Changes in the fair value of warrant liability
Beginning balance	257,040
Ending balance	290,500	257,040
Liability, Development and Regulatory Milestone \| Significant unobservable inputs (level 3) \| BioElectron \| Commitments
Changes in the fair value of warrant liability
Beginning balance	257,040	0
Additions	0	263,500
Change in fair value	33,460	(6,460)
Payments	0	0
Ending balance	290,500	257,040
Liability, Net Sales Milestones and Royalties \| Agilis
Changes in the fair value of warrant liability
Beginning balance	53,200
Ending balance	65,800	53,200
Liability, Net Sales Milestones and Royalties \| Significant unobservable inputs (level 3) \| BioElectron
Changes in the fair value of warrant liability
Beginning balance	53,200	0
Additions	0	27,000
Change in fair value	12,600	26,200
Payments	0	0
Ending balance	$ 65,800	$ 53,200

Fixed assets (Details) - USD ($) $ in Thousands	12 Months Ended
Fixed assets (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Fixed assets
Gross fixed assets	$ 33,373	$ 20,177
Less accumulated depreciation and amortization	(11,824)	(7,483)
Net fixed assets	21,549	12,694
Depreciation	4,700	2,600	$ 2,300
Leasehold improvements
Fixed assets
Gross fixed assets	5,039	2,384
Computer equipment and software
Fixed assets
Gross fixed assets	8,069	4,609
Furniture, fixtures, machinery and lab equipment
Fixed assets
Gross fixed assets	17,033	9,965
Assets in process
Fixed assets
Gross fixed assets	$ 3,232	$ 3,219

Leases - Narrative (Details) $ in Thousands	12 Months Ended
Leases - Narrative (Details) $ in Thousands	Dec. 31, 2019 USD ($) ft² operating_lease Term	Dec. 31, 2018 USD ($)	Dec. 31, 2017 USD ($)	Jan. 01, 2019 USD ($)
Lessee, Lease, Description [Line Items]
2020	$ 5,997
Number of operating leases \| operating_lease	3
Term of Contract ( in years )	15 years
Rent expense	$ 6,000	$ 2,700	$ 2,200
Area of real estate property \| ft²	185,000
Weighted-average remaining lease terms - operating leases (years)	3 years 4 months 17 days
Operating lease ROU asset	$ 13,693			$ 11,300
Lease not yet commenced \| operating_lease	1
Total	$ 14,171			$ 11,300
Renewal Term ( in years )	10 years
Aggregate rent, Initial term	$ 15,983
Percent of market rate	95.00%
2021	$ 4,144
2022	$ 2,465
Minimum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	1 month 6 days
Maximum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	6 years 6 months
New Building
Lessee, Lease, Description [Line Items]
Number of terms \| Term	2
Renewal Term ( in years )	10 years
The Campus
Lessee, Lease, Description [Line Items]
Aggregate rent, Initial term	$ 88,100
BioElectron
Lessee, Lease, Description [Line Items]
2020	1,800
2021	1,800
2022	$ 1,400

Leases - Lease costs (Details) - USD ($) $ in Thousands	12 Months Ended
Leases - Lease costs (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Jan. 01, 2019
Leases [Abstract]
Fixed lease cost	$ 4,929
Variable lease cost	694
Short-term lease cost	350
Total operating lease cost	5,973
Assets and Liabilities, Lessee [Abstract]
Operating lease ROU asset	13,693			$ 11,300
Operating lease liabilities- current	5,153
Operating lease liabilities- noncurrent	9,018
Total operating lease liability	$ 14,171			$ 11,300
Weighted-average remaining lease terms - operating leases (years)	3 years 4 months 17 days
Weighted-average discount rate - operating leases ( as a percent)	7.33%
Operating cash flows from operating leases	$ 4,466
Right-of-use assets obtained in exchange for lease obligations	$ 17,389	$ 0	$ 0

Leases - Lease payments (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Jan. 01, 2019
Leases [Abstract]
2020	$ 5,997
2021	4,144
2022	2,465
2023	1,931
2024 and thereafter	1,446
Total lease payments	15,983
Less: Imputed Interest	1,812
Total	$ 14,171	$ 11,300

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 38,889	$ 27,629
Consulting and contracted research	12,969	11,267
Professional fees	3,562	5,574
Sales allowances and other related costs	41,155	29,417
Royalties and rebates	42,997	31,874
Accounts payable	10,324	6,001
Other	9,380	16,437
Accounts payable and accrued expenses	$ 159,276	$ 128,199

Debt - 2017 Credit Facility (Details) - USD ($)		1 Months Ended	12 Months Ended
Debt - 2017 Credit Facility (Details) - USD ($)	May 05, 2017	May 31, 2017	Dec. 31, 2019	Dec. 31, 2018
Long-term debt
Long-term debt			$ 293,859,000	$ 141,347,000
Current portion of long-term debt			20,000,000	$ 11,667,000
MidCap Financial Trust
Long-term debt
Line of credit facility, maximum borrowing capacity		$ 60,000,000.0
Proceeds from lines of credit	$ 40,000,000.0
Additional capacity available		20,000,000.0
Debt issuance costs, line of credit arrangements		$ 400,000
Repayments of debt			11,700,000
Interest payment period		24 months
Net carrying amount			28,300,000
Long-term debt			20,000,000.0
Current portion of long-term debt			$ 8,300,000
MidCap Financial Trust \| LIBOR
Long-term debt
Floor interest rate		1.00%
Basis spread on variable rate		6.15%

Debt - 2026 Convertible Notes (Details)		1 Months Ended		12 Months Ended
Debt - 2026 Convertible Notes (Details)	Dec. 31, 2019 USD ($) $ / shares	Sep. 30, 2019 USD ($) day	Aug. 31, 2015 USD ($) day $ / shares	Dec. 31, 2019 USD ($) $ / shares	Dec. 31, 2018 USD ($)
Long-term debt
Debt instrument additional mount available for repurchase				$ 37,500,000
Equity component of convertible notes, net				119,482,000
Convertible debt \| Convertible Senior Notes, 1.5%, Due September 15, 2026
Long-term debt
Debt instrument	$ 287,500,000	$ 287,500,000		$ 287,500,000
Interest rate	1.50%	1.50%		1.50%
Net proceeds from issuance of convertible notes				$ 279,300,000
Conversion ratio		19.0404
Conversion price per share \| $ / shares	$ 52.52			$ 52.52
Equity component of convertible notes, net		$ 123,000,000.0
Net deferred tax liability in connection with convertible notes	$ 25,300,000			$ 25,300,000
Term of the convertible notes	6 years 8 months 12 days
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Debt instrument	$ 150,000,000		$ 150,000,000.0	$ 150,000,000	$ 150,000,000
Interest rate			3.00%
Net proceeds from issuance of convertible notes			$ 145,400,000
Consecutive trading days, period \| day			30
Stock price trigger		130.00%	130.00%
Trading days, number \| day		20	20
Business days, period		5 days	5 days
Consecutive trading-day period		5 days	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%		98.00%	98.00%
Conversion ratio			17.7487
Conversion price per share \| $ / shares			$ 56.34
Convertible instruments principal and unpaid interest payable upon events of default		100.00%	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%	25.00%
Net deferred tax liability in connection with convertible notes			$ 22,300,000
Term of the convertible notes			7 years
Convertible debt \| 3.00% Convertible senior notes due 2022 \| Redemption on or after August 20, 2018
Long-term debt
Consecutive trading days, period \| day		30	30
Stock price trigger		130.00%	130.00%
Trading days, number \| day		19	19
Redemption price		100.00%	100.00%
Debt instrument, cumulative sinking fund payments	$ 0			$ 0

Debt - 2015 Convertible Notes (Details)	1 Months Ended		12 Months Ended
Debt - 2015 Convertible Notes (Details)	Sep. 30, 2019 day	Aug. 31, 2015 USD ($) day $ / shares	Dec. 31, 2019 USD ($)	Dec. 31, 2018 USD ($)
Long-term debt
Additional paid-in capital			$ 1,795,351,000	$ 1,288,137,000
3.00% Convertible senior notes due 2022 \| Convertible debt
Long-term debt
Debt instrument		$ 150,000,000.0	$ 150,000,000	150,000,000
Interest rate		3.00%
Net proceeds from issuance of convertible notes		$ 145,400,000
Trading days, number \| day	20	20
Consecutive trading days, period \| day		30
Stock price trigger	130.00%	130.00%
Business days, period	5 days	5 days
Consecutive trading-day period	5 days	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%	98.00%
Conversion ratio		17.7487
Conversion price per share \| $ / shares		$ 56.34
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default	25.00%	25.00%
Convertible instruments principal and unpaid interest payable upon events of default	100.00%	100.00%
Term of the convertible notes		7 years
Additional paid-in capital			$ 57,500,000
Net deferred tax liability in connection with convertible notes		$ 22,300,000
Debt instrument			$ 171,200,000	$ 146,600,000
Remaining amortization period			2 years 7 months 6 days
3.00% Convertible senior notes due 2022 \| Convertible debt \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| day	19	19
Consecutive trading days, period \| day	30	30
Stock price trigger	130.00%	130.00%
Redemption price	100.00%	100.00%

Debt - Summary of convertible notes (Details) - Convertible debt - USD ($)	Dec. 31, 2019	Sep. 30, 2019	Dec. 31, 2018	Aug. 31, 2015
Convertible Senior Notes, 1.5%, Due September 15, 2026
Long-term debt
Principal	$ 287,500,000	$ 287,500,000
Less: Debt issuance costs	(4,567,000)
Less: Debt discount, net	(119,350,000)
Net carrying amount	163,583,000
3.00% Convertible senior notes due 2022
Long-term debt
Principal	150,000,000		$ 150,000,000	$ 150,000,000.0
Less: Debt issuance costs	(1,329,000)		(1,746,000)
Less: Debt discount, net	(26,686,000)		(35,054,000)
Net carrying amount	$ 121,985,000		$ 113,200,000

Debt - Summary of Interest Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Long-term debt
Amortization of debt issuance costs	$ 694	$ 524	$ 433
Convertible debt \| Convertible Senior Notes, 1.5%, Due September 15, 2026
Long-term debt
Contractual interest expense	1,220
Amortization of debt issuance costs	140
Amortization of debt discount	3,659
Total	$ 5,019
Effective interest rate of the liability component	10.20%
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 4,500	4,500
Amortization of debt issuance costs	417	375
Amortization of debt discount	8,368	7,518
Total	$ 13,285	$ 12,393
Effective interest rate of the liability component	11.00%	11.00%

Capital structure - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended				3 Months Ended	12 Months Ended
	Sep. 30, 2019	Aug. 31, 2019	Jan. 31, 2019	Apr. 30, 2018	Sep. 30, 2019	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Capital structure
Common stock, issued and sold (in shares)	2,475,248		7,563,725		63,926
Net proceeds from sale of stock	$ 97,000		$ 224,200		$ 2,600
Sale price (in USD per share)	$ 46.60		$ 30.20		$ 46.60
Issuance of common stock related to equity offering (in shares)				4,600,000
Share price (in USD per share)				$ 27.04
Net proceeds from public offering				$ 117,900		$ 323,756	$ 117,916	$ 0
Common stock, authorized shares (in shares)						125,000,000	125,000,000
Common stock
Capital structure
Sale price (in USD per share)	$ 40.40				$ 40.40
Common stock, authorized shares (in shares)						125,000,000
Over-Allotment Option
Capital structure
Common stock, issued and sold (in shares)	371,287		843,725
Issuance of common stock related to equity offering (in shares)				600,000
Maximum
Capital structure
Net proceeds from sale of stock		$ 125,000

Earnings per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Numerator
Net loss	$ (77,677)	$ (59,997)	$ (41,789)	$ (72,113)	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ (251,576)	$ (128,081)	$ (79,000)
Denominator
Denominator for basic and diluted net loss per share (in shares)									58,863,185	46,576,313	39,183,073
Net loss per share:
Basic and diluted (in dollars per share)									$ (4.27)	$ (2.75)	$ (2.02)

- Definition

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 220
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04(19))
-URI http://asc.fasb.org/extlink&oid=116637232&loc=SL114874131-224263

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=117326831&loc=d3e1337-109256

Reference 3: http://www.xbrl.org/2003/role/exampleRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 55
-Paragraph 52
-URI http://asc.fasb.org/extlink&oid=117327953&loc=d3e4984-109258

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03(21))
-URI http://asc.fasb.org/extlink&oid=116634182&loc=SL114868664-224227

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22694-107794

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=117326831&loc=d3e1252-109256

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 220
-Section S99
-Paragraph 1
-Subparagraph (SX 210.9-04(23))
-URI http://asc.fasb.org/extlink&oid=116637391&loc=SL114874048-224260

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 60B
-Subparagraph (d)
-URI http://asc.fasb.org/extlink&oid=117326831&loc=SL5780133-109256

+ Details

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

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

Earnings per share - Antidilutive (Details) - shares	12 Months Ended
Earnings per share - Antidilutive (Details) - shares	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded from calculation (in shares)	11,696,858	9,105,837	6,841,653
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded from calculation (in shares)	11,054,439	8,534,358	6,448,642
Unvested restricted stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded from calculation (in shares)	642,419	571,479	393,011

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended			12 Months Ended
	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Stock option plan
Share-based compensation expense					$ 42,134	$ 33,252	$ 30,559
Unrecognized compensation cost					$ 111,500
Weighted average remaining service period for recognition of unrecognized compensation cost					3 years
Unvested restricted stock
Stock option plan
Options granted (in shares)					306,549
Stock option
Stock option plan
Granted (in shares)					3,977,995	3,181,623	1,913,873
Forfeited (in shares)					518,527	461,934	1,117,462
Expected dividend yield					0.00%	0.00%	0.00%
Weighted average grant date fair value (in dollars per share)					$ 23.05	$ 17.48	$ 8.45
Stock option \| Minimum
Stock option plan
Vesting period					3 years
Stock option \| Maximum
Stock option plan
Vesting period					4 years
Stock Appreciation Rights (SARs)
Stock option plan
Granted (in shares)			897,290
Vesting period			4 years
Share-based compensation expense					$ 3,200
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)					1,000,000,000,000
Award requisite service period					6 months
Purchase price of common stock					85.00%
Employee stock purchase plan, voting percentage limit		5.00%
Share-based compensation expense					$ 1,300
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan \| Unvested restricted stock
Stock option plan
Options granted (in shares)	735,324
2013 Stock Incentive Plan \| Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)				0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan \| Stock option
Stock option plan
Stockholder's specified ownership percentage					10.00%
Expiration period					10 years
2009 Equity and Long Term Incentive Plan \| Stock option \| Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date					100.00%
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date					110.00%
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)				122,296
2013 Long Term Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)					467,808
Number of shares subject to outstanding awards (in shares)				3,040,444
Annual increase in the number of shares on the first day of the fiscal year (in shares)				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Inducement grant plan \| Stock option
Stock option plan
Options granted (in shares)					1,675,075
Granted (in dollars per share)					$ 39.23
Forfeited (in shares)					250,153

Stock award plan - Stock Option Activity (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Number of options
Outstanding at the beginning of the period (in shares)	8,534,358	6,448,642	5,854,316
Granted (in shares)	3,977,995	3,181,623	1,913,873
Exercised (in shares)	(949,887)	(633,973)	(202,085)
Forfeited (in shares)	(518,527)	(461,934)	(1,117,462)
Outstanding at the end of the period (in shares)	11,043,939	8,534,358	6,448,642
Vested or expected to vest at the end of the period (in shares)	5,370,703
Exercisable at the end of the period (in shares)	5,242,221
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 28.58	$ 29.00	$ 34.71
Granted (in dollars per share)	35.81	26.64	12.34
Exercised (in dollars per share)	19.25	18.61	10.80
Forfeited (in dollars per share)	35.27	35.36	33.65
Outstanding at the end of the period (in dollars per share)	31.67	$ 28.58	$ 29.00
Vested or expected to vest at the end of the period (in dollars per share)	31.62
Exercisable at the end of the period (in dollars per share)	$ 31.37
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 4 months 2 days
Vested or expected to vest at the end of the period	8 years 9 months 29 days
Exercisable at the end of the period	5 years 8 months 12 days
Aggregate intrinsic value
Outstanding at the end of the period (in dollars)	$ 192,350
Vested or expected to vest at the end of the period (in dollars)	88,165
Exercisable at the end of the period (in dollars)	$ 98,781

Stock award plan - Assumptions Used (Details) - Stock option	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Minimum
Valuation assumptions
Risk-free interest rate	1.84%	1.58%	2.25%
Expected volatility	76.00%	62.00%	64.00%
Expected term	5 years 14 days	5 years 9 months	5 years 10 days
Maximum
Valuation assumptions
Risk-free interest rate	2.45%	2.63%	3.10%
Expected volatility	81.00%	92.00%	90.00%
Expected term	10 years	6 years 1 month 10 days	10 years

Stock award plan - Restricted Stock Activity (Details) - Unvested restricted stock	12 Months Ended
	Dec. 31, 2019 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	571,479
Granted (in shares) \| shares	306,549
Vested (in shares) \| shares	(181,327)
Forfeited (in shares) \| shares	(54,282)
Balance at the end of the period (in shares) \| shares	642,419
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 17.61
Granted (in dollars per share) \| $ / shares	32.97
Vested (in dollars per share) \| $ / shares	17.56
Forfeited (in dollars per share) \| $ / shares	23.14
Balance at the end of the period (in dollars per share) \| $ / shares	$ 24.50

Stock award plan - Share-based Compensation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 42,134	$ 33,252	$ 30,559
Research and development
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	20,836	16,096	15,456
Selling, general and administrative
Share-based compensation expense recorded in the statement of operations
Share-based compensation expense	$ 21,298	$ 17,156	$ 15,103

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	$ 350,727	$ 156,437	$ 119,583
Other comprehensive income (loss) before reclassifications	(12,046)	(2,507)	5,454
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(12,046)	(2,507)	5,454
Balance at the end of the period	594,330	350,727	156,437
Unrealized (Losses)/Gains On Marketable Securities, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	31	22	(203)
Other comprehensive income (loss) before reclassifications	724	9	225
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	724	9	225
Balance at the end of the period	755	31	22
Foreign Currency Translation
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	1,431	3,947	(1,282)
Other comprehensive income (loss) before reclassifications	(12,770)	(2,516)	5,229
Amounts reclassified from other comprehensive items	0	0	0
Other comprehensive income (loss)	(12,770)	(2,516)	5,229
Balance at the end of the period	(11,339)	1,431	3,947
Total Accumulated Other Comprehensive Items
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at the beginning of the period	1,462	3,969	(1,485)
Balance at the end of the period	$ (10,584)	$ 1,462	$ 3,969

Revenue recognition - Narrative (Details) $ in Millions	1 Months Ended						12 Months Ended
Revenue recognition - Narrative (Details) $ in Millions	Nov. 30, 2019 USD ($)	Oct. 31, 2017 USD ($)	Nov. 30, 2014 USD ($)	Jan. 31, 2014 USD ($)	Aug. 31, 2013 USD ($)	Nov. 30, 2011 USD ($) compound	Dec. 31, 2019 USD ($) segment Number_Distributor	Dec. 31, 2018 USD ($) deliverable	Dec. 31, 2017 USD ($)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of operating segments \| segment							1
Number of distributors \| Number_Distributor							3
Percentage of net product sales							10.00%
Contract with customer, liability							$ 11.7	$ 12.9
Performance obligations satisfied in current period							3.9	0.0
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product sales							101.0	92.0	$ 28.8
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product sales							190.3	171.0	145.2
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligations satisfied in current period	$ 15.0	$ 20.0	$ 10.0	$ 7.5	$ 10.0
Additions						$ 30.0
Revenue, remaining performance obligation, amount						$ 30.0
Revenue, remaining performance obligation, expected timing of satisfaction, period						2 years
Revenue							15.2	$ 0.2	$ 20.3
Collaborative Arrangement \| Roche And Sma Foundation
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements number of compounds in preclinical development \| compound						3
Collaborative arrangements number of significant deliverables \| deliverable								2
Research And Development Event Milestones \| Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, remaining milestone, potential achievements							72.5
Revenue recognition, milestone, potential achievements							135.0
Potential net sales milestones \| Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements							$ 325.0

Revenue recognition Recenue recognition - Roche and SMA Foundation (Details) $ in Thousands	1 Months Ended						12 Months Ended
	Nov. 30, 2019 USD ($)	Oct. 31, 2017 USD ($)	Nov. 30, 2014 USD ($)	Jan. 31, 2014 USD ($)	Aug. 31, 2013 USD ($)	Nov. 30, 2011 USD ($) compound	Dec. 31, 2019 USD ($)	Dec. 31, 2018 USD ($) deliverable	Dec. 31, 2017 USD ($)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligations satisfied in current period							$ 3,900	$ 0
Revenue							306,980	264,734	$ 194,392
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Additions						$ 30,000
Performance obligations satisfied in current period	$ 15,000	$ 20,000	$ 10,000	$ 7,500	$ 10,000
Revenue							15,200	$ 200	20,300
Revenue, remaining performance obligation, amount						$ 30,000
Collaborative Arrangement \| Roche And Sma Foundation
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements number of compounds in preclinical development \| compound						3
Collaborative arrangements number of significant deliverables \| deliverable								2
Research And Development Event Milestones \| Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements							135,000
Potential net sales milestones \| Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements							325,000
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product sales							101,000	$ 92,000	28,800
Revenue							116,676	93,694
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product sales							190,300	171,000	$ 145,200
Revenue							$ 190,304	$ 171,040

Revenue recognition Revenue recognition - Remaining performance obligation (Details) - Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01	Dec. 31, 2019
Minimum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, remaining performance obligation, expected timing of satisfaction, period	1 year
Maximum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, remaining performance obligation, expected timing of satisfaction, period	2 years

Income taxes - Narrative (Details) - USD ($) $ in Thousands	12 Months Ended
Income taxes - Narrative (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Operating loss carryforwards
Valuation allowance	$ 267,131	$ 180,481
Valuation allowance, deferred tax asset, increase (decrease)	86,700	$ 2,800
Deferred Tax Assets, Operating Loss Carryforwards	231,500
Deferred Tax Assets, Operating Loss Carryforwards, Limited by IRC Section 382	231,500
Orphan drug credit carryover	85,200
Operating loss carryforwards, not subject to expiration	169,200
Operating loss carryforwards, subject to expiration	62,300
Operating loss carryforwards for immediate use	333,200
Operating loss carryforwards in next twelve months	$ 5,700
Federal income tax provision at statutory rate	21.00%	21.00%	34.00%
Uncertain tax position	$ 0
First five years from ownership change
Operating loss carryforwards
Net operating loss carryforwards	16,700
After five years
Operating loss carryforwards
Net operating loss carryforwards	5,700
Federal
Operating loss carryforwards
Net operating loss carryforwards	433,300
Research and development credit carryforwards	14,200
Operating Loss Carryforwards, Available	495,700
State
Operating loss carryforwards
Net operating loss carryforwards	224,400
Research and development credit carryforwards	6,200
Foreign Tax Authority
Operating loss carryforwards
Net operating loss carryforwards	$ 8,400

Income taxes - Loss from operations before tax (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Domestic	$ (231,915)	$ (68,461)	$ (54,588)
Foreign	(8,011)	(59,649)	(23,077)
Total	$ (239,926)	$ (128,110)	$ (77,665)

Income taxes - Provision for Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Current:
U.S. Federal	$ 0	$ 0	$ 0
U.S. State and Local	(61)	(38)	(6)
Foreign	(2,041)	(669)	(1,131)
Deferred:
U.S. Federal	0	0	(198)
U.S. State and Local	(8,812)	0	0
Foreign	(736)	736	0
Total tax benefit (expense)	$ (11,650)	$ 29	$ (1,335)

Income taxes - Tax Rate Reconciliation (Details)	12 Months Ended
Income taxes - Tax Rate Reconciliation (Details)	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Reconciliation of the U.S. statutory income tax rate to the entity's effective tax rate
Federal income tax provision at statutory rate	21.00%	21.00%	34.00%
State income tax provision, net of federal benefit	1.08%	0.05%	(1.01%)
Permanent differences	(6.17%)	(6.41%)	(8.48%)
Research and development	4.38%	6.49%	19.53%
Change in valuation allowances	(35.49%)	2.20%	29.10%
Change in deferred tax assets	0.1589	(0.1422)	(0.6412)
Foreign tax rate differential	(1.88%)	(9.10%)	(10.33%)
Benefit allocated from other comprehensive income	0.00%	0.00%	(0.26%)
Effective Income Tax Rate Reconciliation, change in deferred tax liabilities, intangible assets, Percent	(3.67%)	0.00%	0.00%
Other	0.00%	0.01%	(0.15%)
Effective income tax rate	(4.86%)	0.02%	(1.72%)

Income taxes - Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Income Tax Disclosure [Abstract]
Deferred Income Taxes and Other Assets, Noncurrent	$ 0	$ 736
Deferred tax assets:
Accrued expense	2,588	714
Amortization	78,291	5,148
Depreciation	991	1,601
Federal tax credits	99,421	89,070
State tax credits	6,489	5,473
Federal net operating losses	91,010	62,159
State net operating losses	1,360	165
Foreign net operating losses	1,056	736
Capitalized research and development costs	1,274	2,093
Share based compensation and other	16,425	21,411
Other comprehensive loss	1,512	0
Total gross deferred tax assets	300,417	188,570
Less valuation allowance	(267,131)	(180,481)
Total deferred tax assets, net of valuation allowance	33,286	8,089
Deferred tax liabilities:
Convertible debt	(33,286)	(7,353)
Indefinite lived intangible	(130,862)	(122,032)
Total gross deferred tax liabilities	(164,148)	(129,385)
Net deferred tax assets (liabilities)	$ (130,862)	$ (121,296)

Income taxes - IP transfer intercompany loan (Details) $ in Millions	Dec. 31, 2019 USD ($)
Loans Payable
Certain Loans Acquired in Transfer Not Accounted for as Debt Securities Acquired During Period [Line Items]
Intercompany Loans, Description	$ 556.7

Commitments and contingencies - Narrative (Details) - USD ($) $ in Thousands		1 Months Ended	12 Months Ended
	Apr. 20, 2017	May 31, 2019	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Aug. 23, 2018	Jun. 30, 2016
Other contingencies
Useful life			7 years
Purchase obligation			$ 6,900
Amortization of acquired intangible asset			27,650	$ 22,877	$ 15,380
Akcea
Other contingencies
Upfront licensing fee		$ 6,000		12,000
Milestone, potential achievements, regulatory approval			4,000
Collaborative Arrangement \| Wellcome trust limited
Other contingencies
Development milestone payment obligations			$ 22,400				$ 800
Non-collaborative Arrangement Transactions \| Marathon Pharmaceuticals, LLC
Other contingencies
Development milestone payment obligations	$ 50,000
Non-collaborative Arrangement Transactions \| Akcea
Other contingencies
Useful life			10 years
Milestone, potential achievements, regulatory approval		$ 6,000	$ 4,000
Emflaza asset acquisition
Other contingencies
Emflaza rights	$ 148,373
Milestone, potential achievements, regulatory approval			27,100	$ 14,400
Marathon Pharmaceuticals, LLC
Other contingencies
Development milestone payment obligations			11,400
Agilis
Other contingencies
Development milestone payment obligations			40,000			$ 40,000
Agilis \| Non-collaborative Arrangement Transactions
Other contingencies
Development milestone payment obligations			40,000			$ 40,000
Maximum \| Akcea
Other contingencies
Milestone, potential achievements, regulatory approval			4,000
Maximum \| Agilis
Other contingencies
Development milestone payment obligations			60,000
Priority review voucher amount			535,000
Net sales milestones			$ 150,000
Percentage of annual net sales			6.00%
Maximum \| BioElectron
Other contingencies
Development milestone payment obligations			$ 200,000
Minimum \| Agilis
Other contingencies
Percentage of annual net sales			2.00%
Intellectual Property
Other contingencies
Accumulated amortization			$ 65,900
Intellectual Property \| Marathon Pharmaceuticals, LLC
Other contingencies
Useful life	7 years

Geographic information (Details) $ in Thousands	12 Months Ended
Geographic information (Details) $ in Thousands	Dec. 31, 2019 USD ($) segment	Dec. 31, 2018 USD ($)	Dec. 31, 2017 USD ($)
Segments, Geographical Areas [Abstract]
Number of operating segments \| segment	1
Segment Reporting Information [Line Items]
Total assets	$ 1,623,782	$ 1,119,222
Property and equipment, net	21,549	12,694
Revenue	306,980	264,734	$ 194,392
United States
Segment Reporting Information [Line Items]
Total assets	1,508,055	1,013,977
Property and equipment, net	19,656	10,497
Revenue	116,676	93,694
Non-US
Segment Reporting Information [Line Items]
Total assets	115,727	105,245
Property and equipment, net	1,893	2,197
Revenue	$ 190,304	$ 171,040

401(k) plan (Details) - USD ($) $ in Millions	12 Months Ended
401(k) plan (Details) - USD ($) $ in Millions	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Retirement Benefits [Abstract]
Matching contribution (as a percent of total salary)	100.00%	92.00%	84.00%
Percentage of employee's base salary, matched by employer	6.00%
Expense recorded	$ 3.5	$ 2.2	$ 1.6

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended	4 Months Ended	12 Months Ended
	May 31, 2019	Dec. 31, 2018	Dec. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Aug. 23, 2018	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life				7 years
Amortization of acquired intangible asset				$ 27,650	$ 22,877	$ 15,380
Finite-Lived Intangible Assets, Remaining Amortization Period				4 years 6 months
Goodwill		$ 82,341	$ 82,341	$ 82,341	82,341
Goodwill adjustment		18,000
Akcea
Finite-Lived Intangible Assets [Line Items]
Milestone, potential achievements, regulatory approval				$ 4,000
Upfront licensing fee	$ 6,000				12,000
Non-collaborative Arrangement Transactions \| Akcea
Finite-Lived Intangible Assets [Line Items]
Useful life				10 years
Milestone, potential achievements, regulatory approval	$ 6,000			$ 4,000
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Intangibles assets of Emflaza								$ 148,373
Milestone, potential achievements, regulatory approval		14,400	14,400	27,100	14,400
Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations				11,400
Agilis
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations				40,000			$ 40,000
Goodwill		82,341	82,341	82,300	82,341		100,309
Goodwill adjustment			(17,968)
Agilis \| Non-collaborative Arrangement Transactions
Finite-Lived Intangible Assets [Line Items]
Development milestone payment obligations				40,000			40,000
Intellectual Property
Finite-Lived Intangible Assets [Line Items]
Accumulated amortization				$ 65,900
In Process Research and Development [Member] \| Agilis
Finite-Lived Intangible Assets [Line Items]
Intangible assets, other than goodwill		$ 576,500	$ 576,500		$ 576,500		$ 480,000

Intangible assets and goodwill - Future Amortization (Details) - Marathon Pharmaceuticals, LLC - Intellectual Property $ in Thousands	Dec. 31, 2019 USD ($)
Finite-Lived Intangible Assets [Line Items]
2020	$ 31,139
2021	31,139
2022	31,139
2023	31,139
2024 and thereafter	9,444
Total	$ 134,000

Selected quarterly financial data (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Disaggregation of Revenue [Line Items]
Revenue									$ 306,980	$ 264,734	$ 194,392
Operating expenses	$ 169,243	$ 131,891	$ 124,280	$ 122,723	$ 131,476	$ 101,821	$ 74,317	$ 72,805	548,138	380,419	258,684
Loss from operations	(72,784)	(60,475)	(38,758)	(69,140)	(45,138)	(48,230)	(5,574)	(16,743)	(241,158)	(115,685)	(64,292)
Net loss attributable to common stockholders	$ (77,677)	$ (59,997)	$ (41,789)	$ (72,113)	$ (48,330)	$ (50,969)	$ (9,520)	$ (19,263)	$ (251,576)	$ (128,081)	$ (79,000)
Basic and diluted net loss per common share (in dollars per share)	$ (1.37)	$ (1.06)	$ (0.75)	$ (1.29)	$ 0.96	$ (1.06)	$ (0.21)	$ (0.46)	$ (4.27)	$ (2.75)	$ (2.02)
Net product revenue
Disaggregation of Revenue [Line Items]
Revenue	$ 81,407	$ 71,369	$ 85,476	$ 53,054	$ 85,833	$ 53,021	$ 68,170	$ 55,981	$ 291,306	$ 263,005	$ 174,066
Collaboration and grant revenue
Disaggregation of Revenue [Line Items]
Revenue	$ 15,052	$ 47	$ 46	$ 529	$ 505	$ 570	$ 573	$ 81	$ 15,674	$ 1,729	$ 20,326

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Label	Element	Value
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000
Common Stock [Member]
Stock Issued During Period, Shares, Restricted Stock Award, Net of Forfeitures	us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardNetOfForfeitures	169,792
Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000

Fair value of financial instruments and investments - Fair Value Liabilities Measured (Details) $ in Thousands	Dec. 31, 2019 USD ($) $ / shares	Dec. 31, 2018 USD ($) $ / shares	Dec. 31, 2017 USD ($)
Stock Appreciation Rights (SARs)
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	$ 3,186	$ 3,814
Minimum \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input \| $ / shares	6.76	6.76
Minimum \| Volatility \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input	0.2893	0.4653
Minimum \| Risk free interest rate \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input	0.0019	0.0244
Minimum \| Expected life \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input	0.01	0.01
Maximum \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input \| $ / shares	30.86	30.86
Maximum \| Volatility \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input		0.5959
Maximum \| Risk free interest rate \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input		0.0263
Maximum \| Expected life \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Measurement input	1.01	1.01
Significant unobservable inputs (level 3) \| Stock Appreciation Rights (SARs)
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	$ 3,186	$ 3,814	$ 1,665
Significant unobservable inputs (level 3) \| Agilis
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	65,800
Liability, Development and Regulatory Milestone \| Agilis
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	290,500	257,040
Liability, Development and Regulatory Milestone \| Agilis \| Minimum \| Potential development and regulatory milestones \| Commitments
Fair value of warrant liability
Milestone		$ 0
Liability, Development and Regulatory Milestone \| Agilis \| Minimum \| Potential net sales milestones \| Commitments
Fair value of warrant liability
Milestone	$ 0
Liability, Development and Regulatory Milestone \| Agilis \| Minimum \| Probabilities of success \| Commitments
Fair value of warrant liability
Measurement input	0.25	0.25
Liability, Development and Regulatory Milestone \| Agilis \| Minimum \| Potential percentage of net sales for royalties \| Commitments
Fair value of warrant liability
Measurement input	0.02
Liability, Development and Regulatory Milestone \| Agilis \| Minimum \| Discount rate \| Commitments
Fair value of warrant liability
Measurement input		0.058
Liability, Development and Regulatory Milestone \| Agilis \| Maximum \| Potential development and regulatory milestones \| Commitments
Fair value of warrant liability
Milestone		$ 555,000
Liability, Development and Regulatory Milestone \| Agilis \| Maximum \| Potential net sales milestones \| Commitments
Fair value of warrant liability
Milestone	$ 150,000
Liability, Development and Regulatory Milestone \| Agilis \| Maximum \| Probabilities of success \| Commitments
Fair value of warrant liability
Measurement input	0.89	0.94
Liability, Development and Regulatory Milestone \| Agilis \| Maximum \| Potential percentage of net sales for royalties \| Commitments
Fair value of warrant liability
Measurement input	0.06
Liability, Development and Regulatory Milestone \| Agilis \| Maximum \| Discount rate \| Commitments
Fair value of warrant liability
Measurement input		0.080
Liability, Development and Regulatory Milestone \| Significant unobservable inputs (level 3) \| BioElectron \| Commitments
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	$ 290,500	$ 257,040	0
Liability, Net Sales Milestones and Royalties \| Agilis
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	$ 65,800	$ 53,200
Liability, Net Sales Milestones and Royalties \| Agilis \| Discount rate \| Commitments
Fair value of warrant liability
Measurement input	0.145	0.140
Liability, Net Sales Milestones and Royalties \| Agilis \| Minimum \| Potential development and regulatory milestones \| Commitments
Fair value of warrant liability
Milestone	$ 0
Liability, Net Sales Milestones and Royalties \| Agilis \| Minimum \| Potential net sales milestones \| Commitments
Fair value of warrant liability
Milestone		$ 0
Liability, Net Sales Milestones and Royalties \| Agilis \| Minimum \| Probabilities of success \| Commitments
Fair value of warrant liability
Measurement input	0.25	0.25
Liability, Net Sales Milestones and Royalties \| Agilis \| Minimum \| Potential percentage of net sales for royalties \| Commitments
Fair value of warrant liability
Measurement input		0.02
Liability, Net Sales Milestones and Royalties \| Agilis \| Minimum \| Discount rate \| Commitments
Fair value of warrant liability
Measurement input	0.022
Liability, Net Sales Milestones and Royalties \| Agilis \| Maximum \| Potential development and regulatory milestones \| Commitments
Fair value of warrant liability
Milestone	$ 555,000
Liability, Net Sales Milestones and Royalties \| Agilis \| Maximum \| Potential net sales milestones \| Commitments
Fair value of warrant liability
Milestone		$ 150,000
Liability, Net Sales Milestones and Royalties \| Agilis \| Maximum \| Probabilities of success \| Commitments
Fair value of warrant liability
Measurement input	0.94	0.89
Liability, Net Sales Milestones and Royalties \| Agilis \| Maximum \| Potential percentage of net sales for royalties \| Commitments
Fair value of warrant liability
Measurement input		0.06
Liability, Net Sales Milestones and Royalties \| Agilis \| Maximum \| Discount rate \| Commitments
Fair value of warrant liability
Measurement input	0.047
Liability, Net Sales Milestones and Royalties \| Significant unobservable inputs (level 3) \| BioElectron
Fair value of warrant liability
Contingent consideration payable- net sales milestones and royalties	$ 65,800	$ 53,200	$ 0