0001070081-21-000037 | 10-Q | XBRL Viewer

Cover - shares	9 Months Ended
Cover - shares	Sep. 30, 2021	Oct. 27, 2021
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2021
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 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 Common Stock, Shares Outstanding		70,697,900
Entity Central Index Key	0001070081
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2021
Document Fiscal Period Focus	Q3
Amendment Flag	false

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Current assets:
Cash and cash equivalents	$ 189,818	$ 208,812
Marketable securities	678,125	894,838
Trade receivables, net	96,645	69,929
Inventory, net	15,613	18,697
Prepaid expenses and other current assets	30,939	39,469
Total current assets	1,011,140	1,231,745
Fixed assets, net	46,354	33,831
Intangible assets, net	723,260	715,328
Goodwill	82,341	82,341
Operating lease ROU assets	78,699	84,410
Deposits and other assets	65,531	60,623
Total assets	2,007,325	2,208,278
Current liabilities:
Accounts payable and accrued expenses	252,329	242,168
Current portion of long-term debt	149,358
Deferred revenue		4,151
Operating lease liabilities- current	7,144	7,465
Finance lease liabilities- current	2,557	1,276
Liability for sale of future royalties - current	52,651	21,023
Other current liabilities	1,222	1,250
Total current liabilities	465,261	277,333
Long-term debt	281,604	309,145
Contingent consideration payable	252,000	240,400
Deferred tax liability	136,733	136,735
Operating lease liabilities- noncurrent	74,823	79,499
Finance lease liabilities- noncurrent	20,053	23,053
Liability for sale of future royalties- noncurrent	670,549	658,739
Other long-term liabilities	1,376	1,392
Total liabilities	1,902,399	1,726,296
Stockholders' equity:
Common stock, $0.001 par value. Authorized 250,000,000 shares; issued and outstanding 70,665,010 shares at September 30, 2021. Authorized 125,000,000 shares; issued and outstanding 69,718,096 shares at December 31, 2020	70	70
Additional paid-in capital	2,092,534	2,171,746
Accumulated other comprehensive loss	(32,961)	(60,957)
Accumulated deficit	(1,954,717)	(1,628,877)
Total stockholders' equity	104,926	481,982
Total liabilities and stockholders' equity	$ 2,007,325	$ 2,208,278

Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2021	Dec. 31, 2020
Statement of Financial Position [Abstract]
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares (in shares)	250,000,000	125,000,000
Common stock, issued shares (in shares)	70,665,010	69,718,096
Common stock, outstanding shares (in shares)	70,665,010	69,718,096

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Revenues:
Revenue	$ 138,743	$ 118,404	$ 373,364	$ 261,902
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible assets	6,539	4,667	23,001	14,056
Amortization of acquired intangible assets	14,383	9,630	38,411	26,309
Research and development	130,845	92,998	390,840	359,630
Selling, general and administrative	69,252	57,840	199,225	169,708
Change in the fair value of deferred and contingent consideration	10,800	8,400	11,600	16,980
Settlement of deferred and contingent consideration				10,613
Total operating expenses	231,819	173,535	663,077	597,296
Loss from operations	(93,076)	(55,131)	(289,713)	(335,394)
Interest expense, net	(21,802)	(21,039)	(63,520)	(32,060)
Other (expense) income, net	(18,782)	28,766	(26,499)	26,242
Loss before income tax expense	(133,660)	(47,404)	(379,732)	(341,212)
Income tax benefit (expense)	36	(22,288)	(904)	(22,594)
Net loss attributable to common stockholders	$ (133,624)	$ (69,692)	$ (380,636)	$ (363,806)
Weighted-average shares outstanding:
Basic and diluted (in shares)	70,585,938	67,641,171	70,397,846	65,068,281
Net loss per share-basic and diluted (in dollars per share)
Net loss per share-basic and diluted (in dollars per share)	$ (1.89)	$ (1.03)	$ (5.41)	$ (5.59)
Net product revenue
Revenues:
Revenue	$ 115,605	$ 82,708	$ 309,998	$ 226,143
Collaboration revenue
Revenues:
Revenue	10,011	35,000	30,018	35,063
Royalty revenue
Revenues:
Revenue	$ 13,127	$ 696	$ 33,348	$ 696

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Statement of Comprehensive Income [Abstract]
Net loss	$ (133,624)	$ (69,692)	$ (380,636)	$ (363,806)
Other comprehensive (loss) income:
Unrealized loss on marketable securities, net of tax of $0	(136)	(1,016)	(1,505)	1,639
Foreign currency translation gain (loss), net of tax of $0	13,262	(24,695)	29,501	(26,782)
Comprehensive loss	$ (120,498)	$ (95,403)	$ (352,640)	$ (388,949)

- Definition

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

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+ Details

Consolidated Statements of Comprehensive Loss (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Statement of Comprehensive Income [Abstract]
Unrealized loss on marketable securities, tax	$ 0	$ 0	$ 0	$ 0
Foreign currency translation gain, tax	$ 0	$ 0	$ 0	$ 0

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Common stock	Additional paid-in capital Cumulative Effect Adjustment	Additional paid-in capital	Accumulated other comprehensive income (loss)	Accumulated deficit Cumulative Effect Adjustment	Accumulated deficit	Cumulative Effect Adjustment	Total
Balance (in shares) at Dec. 31, 2019	61,935,870
Balance at the beginning of the period at Dec. 31, 2019	$ 62		$ 1,795,351	$ (10,584)		$ (1,190,499)		$ 594,330
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offerings (in shares)	542,470
Issuance of common stock related to equity offering	$ 1		28,091					28,092
Issuance of common stock related to acquisition (in shares)	845,364
Issuance of common stock related to acquisition	$ 1		42,868					42,869
Issuance of common stock related to rights exchange (in shares)	2,821,176
Issuance of common stock related to rights exchange	$ 3		150,525					150,528
Exercise of options (in shares)	1,426,026
Exercise of options	$ 1		32,986					32,987
Restricted stock vesting and issuance (in shares)	179,963
Issuance of common stock in connection with an employee stock purchase plan (in shares)	58,691
Issuance of common stock in connection with an employee stock purchase plan			2,406					2,406
Share-based compensation expense			48,909					48,909
Other						(218)		(218)
Net loss						(363,806)		(363,806)
Comprehensive income (loss)				(25,143)				(25,143)
Balance (in shares) at Sep. 30, 2020	67,809,560
Balance at the end of the period at Sep. 30, 2020	$ 68		2,101,136	(35,727)		(1,554,523)		510,954
Balance (in shares) at Jun. 30, 2020	67,240,679
Balance at the beginning of the period at Jun. 30, 2020	$ 67		2,067,274	(10,016)		(1,484,831)		572,494
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offerings (in shares)	173,956
Issuance of common stock related to equity offering			9,141					9,141
Exercise of options (in shares)	391,738
Exercise of options	$ 1		7,942					7,943
Restricted stock vesting and issuance (in shares)	3,187
Share-based compensation expense			16,779					16,779
Net loss						(69,692)		(69,692)
Comprehensive income (loss)				(25,711)				(25,711)
Balance (in shares) at Sep. 30, 2020	67,809,560
Balance at the end of the period at Sep. 30, 2020	$ 68		2,101,136	(35,727)		(1,554,523)		510,954
Balance (in shares) at Dec. 31, 2020	69,718,096
Balance at the beginning of the period at Dec. 31, 2020	$ 70	$ (175,236)	2,171,746	(60,957)	$ 54,796	(1,628,877)	$ (120,440)	481,982
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	574,230
Exercise of options			16,120					16,120
Restricted stock vesting and issuance (in shares)	299,563
Issuance of common stock in connection with an employee stock purchase plan (in shares)	73,121
Issuance of common stock in connection with an employee stock purchase plan			2,627					2,627
Share-based compensation expense			77,277					77,277
Net loss						(380,636)		(380,636)
Comprehensive income (loss)				27,996				27,996
Balance (in shares) at Sep. 30, 2021	70,665,010
Balance at the end of the period at Sep. 30, 2021	$ 70		2,092,534	(32,961)		(1,954,717)		104,926
Balance (in shares) at Jun. 30, 2021	70,559,330
Balance at the beginning of the period at Jun. 30, 2021	$ 70		2,063,687	(46,087)		(1,821,093)		196,577
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	98,288
Exercise of options			2,976					2,976
Restricted stock vesting and issuance (in shares)	7,392
Share-based compensation expense			25,871					25,871
Net loss						(133,624)		(133,624)
Comprehensive income (loss)				13,126				13,126
Balance (in shares) at Sep. 30, 2021	70,665,010
Balance at the end of the period at Sep. 30, 2021	$ 70		$ 2,092,534	$ (32,961)		$ (1,954,717)		$ 104,926

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Cash flows from operating activities
Net loss	$ (380,636)	$ (363,806)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	45,323	31,088
Non-cash operating lease expense	5,516	4,295
Non-cash finance lease amortization expense		41,382
Non-cash royalty revenue related to sale of future royalties	(14,317)	(299)
Non-cash interest expense on liability related to sale of future royalties	57,755	14,557
Change in valuation of deferred and contingent consideration	11,600	16,980
Settlement of deferred and contingent consideration		10,613
Non-cash stock consideration, acquisition		42,869
Unrealized (gain) loss on ClearPoint Equity Investments	(2,376)	(852)
Unrealized (gain) loss on ClearPoint convertible debt security	(2,054)	(633)
Unrealized gain on marketable securities - equity investments	(1,350)
Non-cash interest expense		16,678
Loss on disposal of asset		25
Amortization of premiums (discounts) on investments, net	4,052	(559)
Amortization of debt issuance costs	1,377	766
Share-based compensation expense	77,277	48,909
Unrealized foreign currency transaction losses (gains), net	33,280	(27,077)
Changes in operating assets and liabilities:
Inventory, net	2,476	390
Prepaid expenses and other current assets	8,161	(9,289)
Trade receivables, net	(28,625)	121
Deposits and other assets	(444)	(217)
Accounts payable and accrued expenses	8,888	54,390
Other liabilities	(4,340)	(4,096)
Deferred revenue	(4,055)	(5,940)
Net cash used in operating activities	(182,492)	(129,705)
Cash flows from investing activities
Purchases of fixed assets	(19,487)	(11,491)
Purchase of convertible debt security		(10,000)
Purchases of marketable securities - available for sale	(276,376)	(1,006,946)
Purchases of marketable securities - equity investments	(205,382)
Sale and redemption of marketable securities- available for sale	693,319	700,627
Sale and redemption of marketable securities - equity investments	740
Acquisition of product rights and licenses	(41,806)	(25,618)
Purchase of equity investment in ClearPoint	(100)
Net cash provided by (used in) investing activities	150,908	(353,428)
Cash flows from financing activities
Proceeds from exercise of options	16,120	32,987
Termination and exit fees related to payoff of secured term loan		(597)
Net proceeds from public offerings		28,092
Repayment of senior secured term loan		(28,333)
Payments on deferred consideration obligation		(38,100)
Proceeds from employee stock purchase plan	2,627	2,406
Payment of finance lease principal	(2,224)	(17,829)
Cash consideration received from Royalty Purchase Agreement		650,000
Net cash provided by (used in) financing activities	16,523	628,626
Effect of exchange rate changes on cash	(3,933)	449
Net decrease in cash and cash equivalents	(18,994)	145,942
Cash and cash equivalents, and restricted cash beginning of period	216,312	295,528
Cash and cash equivalents, and restricted cash end of period	197,318	441,470
Supplemental disclosure of cash information
Cash paid for interest	9,589	9,802
Cash paid for income taxes	5,527	1,562
Supplemental disclosure of non-cash investing and financing activity
Unrealized gain (loss) on marketable securities, net of tax	(1,505)	1,639
Right-of-use assets obtained in exchange for operating lease obligations		76,657
Right-of-use assets obtained in exchange for finance lease obligations		41,382
Acquisition of product rights and licenses	$ 19,154	13,786
Issuance of common stock related to rights exchange		$ 150,528

Summary of significant accounting policies

9 Months Ended

Sep. 30, 2021

Accounting Policies [Abstract]

Summary of significant accounting policies

2. Summary of significant accounting policies

The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2020 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on February 25, 2021 (the "2020 Form 10-K"). Selected significant accounting policies are discussed in further detail below.

Basis of presentation

The accompanying financial information as of September 30, 2021 and for the three and nine months ended September 30, 2021 and 2020 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. Certain prior period balances have been reclassified to conform to the current period presentation. These reclassifications did not have a material impact on the consolidated statements of operations, consolidated balance sheets, consolidated statements of cash flows, or notes to the consolidated financial statements. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2020 and notes thereto included in the 2020 Form 10-K.

In the opinion of management, the unaudited financial information as of September 30, 2021 and for the three and nine months ended September 30, 2021 and 2020 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders’ equity, and cash flows. The results of operations for the three and nine month periods ended September 30, 2021 are not necessarily indicative of the results to be expected for the year ended December 31, 2021 or for any other interim period or for any other future year.

Use of estimates

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

Restricted cash

Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the twelve-month period ended December 31, 2019 in connection with obligations under a facility lease for 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:


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2021		2020
Cash and cash equivalents	$	189,818	$	208,812
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	197,318	$	216,312

Marketable securities

The Company’s marketable securities consists of both debt securities and equity investments. The Company considers its investments in debt securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three month and nine month periods ended September 30, 2021, no allowance was recorded for credit losses.

Marketable securities that are equity investments are measured at fair value, as it is readily available, and as such are classified as Level 1 assets. Unrealized holding gains and losses for these equity investments are components of other (expense) income, net within the consolidated statement of operations.

Inventory and cost of product sales

Inventory

Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. Amounts related to clinical development programs and marketing efforts are immaterial.

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


	September 30, 2021		December 31, 2020
Raw materials	$	1,464	$	824
Work in progress		8,019		8,745
Finished goods		6,130		9,128
Total inventory	$	15,613	$	18,697

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. For the three and nine months ended September 30, 2021, the Company recorded inventory write-downs of $0.5 million and $2.2 million, respectively, primarily related to product approaching expiration. For the three and nine months ended September 30, 2020, inventory write-downs were immaterial. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2021 and 2020, 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, royalty payments associated with net product sales, and royalty payments to collaborative partners associated with royalty revenues and collaboration revenue related to milestones. Production costs are expensed as cost of product sales when the related products are sold or royalty revenues and collaboration revenue milestones are earned.

Revenue recognition

Net product revenue

The Company’s net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of the product, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to product sales. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.

The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained. For the three months ended September 30, 2021 and 2020, net product sales outside of the United States were $68.5 million and $44.2 million, respectively. For the three months ended September 30, 2021 and 2020, net product sales in the United States were $47.1 million and $38.5 million, respectively, consisting solely of Emflaza. Translarna net revenues made up $67.2 million and $43.4 million of the net product sales outside of the United States for the three months ended September 30, 2021 and 2020, respectively. For the nine months ended September 30, 2021 and 2020, net product sales outside of the United States were $170.2 million and $124.0 million, respectively. For the nine months ended September 30, 2021 and 2020, net product sales in the United States, were $139.8 million and $102.1 million, respectively, consisting solely of Emflaza. Translarna net revenues made up $166.3 million and $122.7 million of the net product sales outside of the United States for the nine months ended September 30, 2021 and 2020, respectively.

In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. The Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Collaboration and royalty revenue

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

At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations.

For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance.

For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company’s control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes royalties from product sales at the later of when the related sales occur or when the performance obligation to which the royalty has been allocated has been satisfied. If it is probable that a significant revenue reversal will not occur, the Company will estimate the royalty payments using the most likely amount method.

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

For the three months ended September 30, 2021 and 2020, the Company recognized $10.0 million and $35.0 million of collaboration revenue, respectively, related to the SMA License Agreement with Roche. For the nine months ended September 30, 2021 and 2020, the Company recognized $30.0 million and $35.1 million of collaboration revenue, respectively, related to the SMA License Agreement with Roche.

For the three and nine months ended September 30, 2021, the Company has recognized $13.1 million and $33.3 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2020, the Company has recognized $0.7 million and $0.7 million of royalty revenue, respectively, related to Evrysdi.

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 Company also assesses whether an allowance for expected credit losses may be required which includes a review of the Company’s receivables portfolio, which are pooled on a customer basis or country basis. In making its assessment of whether an allowance for credit losses is required, the Company considers its historical experience with customers, current balances, levels of delinquency, regulatory and legal environments, and other relevant current and future forecasted economic conditions. For the three month periods ended September 30, 2021 and 2020, no allowance was recorded for credit losses. The allowance for doubtful accounts was $0.3 million as of September 30, 2021 and $0.1 million as of December 31, 2020. Bad debt expense was immaterial for the three and nine month periods ended September 30, 2021 and 2020.

Liability for sale of future royalties

On July 17, 2020, the Company entered into the Royalty Purchase Agreement. Pursuant to the Royalty Purchase Agreement, the Company sold to RPI 42.933% (the “Assigned Royalty Payment”) of the Company’s right to receive sales-based royalty payments (the “Royalty”) on worldwide net sales of Evrysdi and any other product developed pursuant to the SMA License Agreement. In consideration for the sale of the Assigned Royalty Payments, RPI paid the Company $650.0 million in cash consideration. The Company has retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the SMA License Agreement, which milestone payments equal $325.0 million in the aggregate as of September 30, 2021. The Royalty Purchase Agreement will terminate 60 days following the earlier of the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the SMA License Agreement and the date on which RPI has received $1.3 billion in respect of the Assigned Royalty Payments.

The cash consideration obtained pursuant to the Royalty Purchase Agreement is classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability will be amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The Company will utilize the prospective method to account for subsequent changes in the estimated future payments to be made to RPI. Refer to Note 9 for further details.

Indefinite-lived intangible assets

Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in

business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset acquired in a business combination. The Company utilizes the "income method” and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company’s outlook and market performance of the Company’s industry and recent and forecasted financial performance.

Goodwill

Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassess its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount.

Income Taxes

On March 27, 2020, the United States enacted the Coronavirus Aid, Relief, and Economic Security Act, referred to herein as the CARES Act, as a response to the economic uncertainty resulting from the pandemic caused by a strain of novel coronavirus, COVID-19. The CARES Act includes modifications for net operating loss carryovers and carrybacks, limitations of tax deductibility for net interest expense, immediate refund of alternative minimum tax (“AMT”) credit carryovers as well as a technical correction to the 2017 Tax Cuts and Jobs Act ("the 2017 Tax Act") for qualified improvement property. On December 27, 2020, additional COVID-19 relief provisions included in the Consolidated Appropriations Act, 2021, were signed into law. The new relief provisions include multiple measures and expands many of the provisions already put into place under the CARES Act. Tax provisions of the CARES Act also include the deferral of certain payroll taxes, relief for retaining employees, and other provisions. As of September 30, 2021, the Company expects that the relief for retaining employees was not material to the financial statements and the deferral of certain payroll taxes amounted to $2.5 million as of September 30, 2021, which is accrued in other current liabilities and other long-term liabilities on the consolidated balance sheets.

Additionally, the Organization for Economic Co-operation and Development (“OECD”), the European Community (“the EC”), and individual taxing jurisdictions where the Company and its affiliates do business have recently focused on issues related to the taxation of multinational corporations. The OECD has released its comprehensive plan to create an agreed set of international rules for fighting base erosion and profit shifting. In addition, the OECD, the EC and individual taxing jurisdictions are examining changes to how taxing rights should be allocated among countries considering the digital economy. As a result, the tax laws in the U.S. and other countries in which the Company and its affiliates do business could change on a prospective or retroactive basis and any such changes could materially adversely affect the Company’s business.

On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revised U.S. tax law by, among other provisions, lowering the U.S. federal statutory corporate 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-Taxed Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2021.

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 its acquisition of Agilis Biotherapeutics, Inc. (“Agilis”), pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Agilis Merger Agreement”), by and among the Company, Agility Merger Sub, Inc., Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the “Agilis Merger”) of $122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company’s policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful.

Leases

The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating and finance leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating and finance lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments.

Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases.

Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories.

A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates.

The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to

exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. See Note 3 Leases for additional information.

Impact of recently adopted accounting pronouncements

In August 2020, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2020-06, “Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity.” ASU 2020-06 simplifies the accounting for convertible instruments by removing certain separation models in Subtopic 470- 20, Debt—Debt with Conversion and Other Options, for convertible instruments. Under ASU 2020-06, the embedded conversion features no longer are separated from the host contract for convertible instruments with conversion features that are not required to be accounted for as derivatives under Topic 815, Derivatives and Hedging, or that do not result in substantial premiums accounted for as paid-in capital. Consequently, a convertible debt instrument will be accounted for as a single liability measured at its amortized cost and a convertible preferred stock will be accounted for as a single equity instrument measured at its historical cost, as long as no other features require bifurcation and recognition as derivatives. By removing those separation models, the interest rate of convertible debt instruments typically will be closer to the coupon interest rate when applying the guidance in Topic 835, Interest. The amendments under ASU 2020-06 also include revisions related to the derivatives scope exception for contracts in an entity’s own equity and earnings per share. The amendments under ASU 2020-06 are effective for public business entities that meet the definition of a SEC filer, excluding entities eligible to be smaller reporting companies as defined by the SEC, for fiscal years beginning after December 15, 2021, including interim periods within those fiscal years. For all other entities, the amendments are effective for fiscal years beginning after December 15, 2023, including interim periods within those fiscal years. Early adoption is permitted, but no earlier than fiscal years beginning after December 15, 2020, including interim periods within those fiscal years. The FASB specified that an entity should adopt the guidance as of the beginning of its annual fiscal year. The Company early adopted this guidance on January 1, 2021, utilizing the modified retrospective method. The Company now accounts for its Convertible Notes as single liabilities measured at amortized cost. As a result, the adoption of the guidance had a material impact on the consolidated financial statements and accompanying notes, resulting in adjustments of $175.2 million, $54.8 million, and $120.4 million to the opening balances of additional paid-in capital, retained earnings, and long term debt, respectively, as of January 1, 2021. Additionally, due to the adoption, the Company reversed the remaining balance of the deferred tax liability of $29.6 million which was initially recorded in connection with the Convertible Notes. Additionally, the Company increased the existing valuation allowance by $29.6 million as part of the adoption adjustment. The Company concluded that the adoption of the ASU did not change its prior valuation allowance conclusions. The Company has updated its debt note (Note 9) with additional and modified disclosures as required by the standard upon adoption.

Leases

9 Months Ended

Sep. 30, 2021

Leases

Leases

3. 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 and laboratory space in Bridgewater, New Jersey and office space in various countries for international employees primarily through workspace providers.

The Company also leases approximately 220,500 square feet of office, manufacturing and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”) pursuant to a Lease Agreement (the “Lease”) with Hopewell Campus Owner LLC (the “Landlord”). The rental term of the Lease commenced on July 1, 2020 and has an initial term of fifteen years (the “Initial Term”), with two consecutive ten year renewal periods, each at the Company’s option. The aggregate rent for the Initial Term will be approximately $111.5 million. The rental rate for the renewal periods will be 95% of the Prevailing Market Rate (as defined in the Lease) and determined at the time of the exercise of the renewal. The Company is also responsible for maintaining certain insurance and the payment of proportional taxes, utilities and common area operating expenses. The Lease contains customary events of default, representations, warranties and covenants.

Subject to the terms of the Lease, the Company has a right of first refusal to rent certain other space of the Campus, which would be triggered upon the Landlord’s issuance of a second round proposal or letter of intent to another tenant for such space. The Company also may seek to build a new separate building on the Campus, which may not contain less than 75,000 square feet (the “New Building”). Upon receipt of notice of the Company’s intention to build the New Building,

the Landlord may, in its sole discretion, construct and lease the New Building to the Company or enter into a ground lease with the Company permitting the Company to construct the New Building. Rent terms for the New Building would be determined based on the land value, construction and project costs subject to whether the Landlord or Company constructs the New Building.

On June 19, 2020, the Company entered into a commercial manufacturing service agreement for a term of 12.5 years with MassBiologics of the University of Massachusetts Medical School ("MassBio"). The agreement will expire on December 31, 2032 unless the Company terminates it with 24 months prior written notice to MassBio. Pursuant to the terms of the agreement, MassBio agreed to provide the Company with certain dedicated space for its gene therapy AADC program. The Company concluded that the agreement contains an embedded lease as the Company controls the use of the four dedicated rooms and the equipment therein. The agreement included guaranteed lease payments of $15.0 million at the onset of the agreement and $3.0 million annually thereafter. The present value of the guaranteed lease payments was determined to be $41.4 million, which exceeded the assessed fair value of the Company’s share of the building. Therefore, the Company determined that the agreement was a finance lease, for which the Company recorded a finance lease ROU asset and corresponding finance lease liability at the onset of the lease agreement. Given that the leased asset is designed for the production of PTC’s AADC program and would not have an alternate use outside the PTC gene therapy platform without incurring significant costs, the Company determined that the lease should be treated as research and development expense under ASC 730. Accordingly, the full $41.4 million relating to the finance lease ROU asset was written off and expensed to research and development during the twelve month period ending December 31, 2020. The remaining balance for the finance lease ROU asset related to this arrangement is $0 as of September 30, 2021 and as of December 31, 2020. As of September 30, 2021, the balance of the finance lease liabilities-current and finance lease liabilities-non-current are $2.6 million and $20.1 million, respectively, and are directly related to the Company’s MassBio agreement. As of December 31, 2020, the balance of the finance lease liabilities-current and finance lease liabilities non-current were $1.3 million and $23.1 million, respectively. Additionally, during the three and nine month periods ending September 30, 2021, the Company recorded finance lease costs of $0.4 million and $1.3 million related to interest on the lease liability, respectively; these costs were $0.5 million in both the three and nine month periods ending September 30, 2020.

The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s leases have remaining operating lease terms ranging from 0.3 years to 13.8 years and certain of the leases include renewal options to extend the lease for up to 10 years. Rent expense was $5.3 million and $5.2 million for the three month periods ended September 30, 2021 and 2020, respectively, and $15.9 million and $10.2 million for the nine month periods ended September 30, 2021 and 2020, respectively.

The components of operating lease expense were as follows:


	Three Months Ended		Three Months Ended		Nine Months Ended		Nine Months Ended
		September 30, 2021		September 30, 2020		September 30, 2021		September 30, 2020
Operating Lease Cost
Fixed lease cost	$	4,059	$	4,097	$	12,277	$	7,896
Variable lease cost		1,149		890		3,235		1,914
Short-term lease cost		122		175		405		340
Total operating lease cost	$	5,330	$	5,162	$	15,917	$	10,150

Total operating lease cost is a component of operating expenses on the consolidated statements of operations.

Supplemental balance sheet information related to leases was as follows:


	September 30, 2021		December 31, 2020
Operating lease ROU asset	$	78,699	$	84,410

Operating lease liabilities- current	$	7,144	$	7,465
Operating lease liabilities- noncurrent		74,823		79,499
Total operating lease liability	$	81,967	$	86,964


	September 30, 2021		December 31, 2020
Finance lease liabilities- current	$	2,557	$	1,276
Finance lease liabilities- noncurrent		20,053		23,053
Total finance lease liability	$	22,610	$	24,329

The Company did not enter into any new leases during the nine month period ended September 30, 2021. The decrease in the operating lease ROU asset primarily resulted from amortization of existing leases, along with the termination of several car leases and a Washington, DC office space during the nine month period ended September 30, 2021.

Supplemental lease term and discount rate information related to leases was as follows as of September 30, 2021 and December 31, 2020:


	September 30, 2021		December 31, 2020
Weighted-average remaining lease terms - operating leases (years)	11.07		11.49
Weighted-average discount rate - operating leases	8.92	%	8.86	%
Weighted-average remaining lease terms - finance lease (years)	11.25		12.00
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Supplemental cash flow information related to leases was as follows as of September 30, 2021 and 2020:


	Nine Months Ended September 30,
	2021		2020
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	10,254	$	5,611
Financing cash flows from finance lease		2,224		17,829
Operating cash flows from finance leases		776		171

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	—	$	76,657
Finance lease		—		41,382

Future minimum lease payments under non-cancelable leases as of September 30, 2021 were as follows:


	Operating Leases		Finance Lease
2021 (excludes the nine months ended September 30, 2021)	$	3,417	$	—
2022		13,235		3,000
2023		12,843		3,000
2024		12,150		3,000
2025 and thereafter		91,996		24,000
Total lease payments		133,641		33,000
Less: Imputed Interest expense		51,674		10,390
Total	$	81,967	$	22,610

In conjunction with the Asset Purchase Agreement by and between the Company and BioElectron Technology Corporation, dated October 1, 2019 (the “Asset Acquisition Agreement”), the Company acquired BioElectron’s lease in Mountainview, California. As substantially all of the fair value of the gross assets acquired was related to vatiquinone, the relative fair value allocated to the right of use asset and corresponding lease liability for the Mountainview lease was determined to be immaterial, and accordingly is not included in the tables above. The future minimum lease payments for the Mountainview lease as of September 30, 2021 are $0.5 million, and $1.4 million for the remainder of 2021 and for 2022, respectively, and $0 thereafter.

Fair value of financial instruments and marketable securities

9 Months Ended

Sep. 30, 2021

Fair Value Disclosures [Abstract]

Fair value of financial instruments and marketable securities

4. Fair value of financial instruments and marketable securities

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

●

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

●

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

●

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

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

In May 2019, the Company purchased $4.0 million of shares of ClearPoint Neuro, Inc.’s ("ClearPoint"), formerly known as MRI Interventions, Inc., common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with ClearPoint, a publicly traded medical device company. In February 2021, the Company purchased $0.1 million of shares of ClearPoint’s common stock, at a purchase price of $23.50 per share, in connection with ClearPoint’s underwritten public offering of common stock. The Company determined that the May 2019 and February 2021 ClearPoint equity investments (collectively, the “ClearPoint Equity Investments”) represent financial instruments, and therefore, are recorded at fair value, which is readily determinable. The ClearPoint Equity Investments are components of deposits and other assets on the consolidated balance sheet. During the three and nine month periods ended September 30, 2021, the Company recorded an unrealized loss of $1.7 million and an unrealized gain of $2.4 million on the ClearPoint Equity Investments, respectively. During the three and nine month periods ended September 30, 2020, the Company recorded unrealized gains of $2.5 million and $0.9 million, respectively. These unrealized gains and losses are components of other (expense) income, net within the consolidated statement of operations. The fair value of the ClearPoint Equity Investments was $23.0 million and $20.5 million as of September 30, 2021 and December 31, 2020, respectively. The Company classifies the ClearPoint Equity Investments as Level 1 assets within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted.

In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that the Company can convert into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three and nine month periods ended September 30, 2021, the Company recorded an unrealized loss of $2.3 million and an unrealized gain of $2.1 million, respectively. During the three and nine month periods ended September 30, 2020, the Company recorded unrealized gains of $1.4 million and $0.6 million, respectively. These unrealized gains and losses are components of other (expense) income, net within the consolidated statement of operations. The fair value of the convertible debt security was $31.3 million and $29.3 million as of September 30, 2021 and December 31, 2020, respectively. The

convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the ClearPoint Equity Investments and the convertible debt security, no other items included in deposits and other assets on the consolidated balance sheets are fair valued.

In February 2021, the Company invested $200.0 million in two mutual funds. In August 2021, the Company made a $5.4 million investment into a third mutual fund that is denominated in a foreign currency. All of these are equity investments and are classified as marketable securities on the Company’s consolidated balance sheets. These equity investments are reported at fair value, as it is readily available, and as such are classified as Level 1 assets. Unrealized holding gains and losses for these equity investments are included as components of other (expense) income, net within the consolidated statement of operations. For the three and nine month periods ended September 30, 2021, the Company had $0.7 million and $1.4 million unrealized net gains relating to the equity investments still held at the reporting date, respectively. For the three and nine month periods ended September 30, 2021, the Company had redemptions of $0.7 million and $0.7 million, respectively. For the three and nine month periods ended September 30, 2021, the Company had $0.2 million and $0.2 million foreign currency unrealized losses relating to these equity investments.

Fair value of marketable securities that are classified as available for sale debt securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining available for sale debt securities, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices.

The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2021 and December 31, 2020:


	September 30, 2021
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	472,338	$	—	$	472,338	$	—
Marketable securities - equity investments	$	205,787	$	205,787	$	—	$	—
ClearPoint Equity Investments	$	22,979	$	22,979	$	—	$	—
ClearPoint convertible debt security	$	31,306	$	—	$	31,306	$	—
Contingent consideration payable- development and regulatory milestones	$	140,200	$	—	$	—	$	140,200
Contingent consideration payable- net sales milestones and royalties	$	111,800	$	—	$	—	$	111,800


	December 31, 2020
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	894,838	$	—	$	894,838	$	—
ClearPoint Equity Investments	$	20,503	$	20,503	$	—	$	—
ClearPoint convertible debt security	$	29,252	$	—	$	29,252	$	—
Contingent consideration payable- development and regulatory milestones	$	139,200	$	—	$	—	$	139,200
Contingent consideration payable- net sales milestones and royalties	$	101,200	$	—	$	—	$	101,200

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2021 and December 31, 2020.

The following is a summary of marketable securities accounted for as available for sale debt securities at September 30, 2021 and December 31, 2020:


	September 30, 2021
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	109,890	$	20	$	—	$	109,910
Corporate debt securities		281,467		351		(37)		281,781
Asset-backed securities		20,704		45		(1)		20,748
Government obligations		59,883		20		(4)		59,899
Total	$	471,944	$	436	$	(42)	$	472,338


	December 31, 2020
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	276,855	$	19	$	(37)	$	276,837
Corporate debt securities		474,030		1,658		(29)		475,659
Asset-backed securities		28,681		210		(3)		28,888
Government obligations		113,372		88		(6)		113,454
Total	$	892,938	$	1,975	$	(75)	$	894,838

For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. For the three and nine month periods ended September 30, 2021, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three and nine month periods ended September 30, 2021 and 2020, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity.

For the three and nine month periods ended September 30, 2021, the Company had $0.0 million and $0.7 million realized gains from the sale of available for sale debt securities, respectively. For the three and nine month periods ended September 30, 2020, the Company had $0.3 million and $0.5 million realized gains from the sale of available for sale debt securities, respectively. Realized gains and losses are reported as a component of interest expense, net in the consolidated statement of operations.

The unrealized losses and fair values of available for sale debt securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2021 are as follows:


	September 30, 2021
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities		(37)		78,272		—		—		(37)		78,272
Asset-backed securities		(1)		499		—		—		(1)		499
Government obligations		(4)		19,926		—		—		(4)		19,926
Total	$	(42)	$	98,697	$	—	$	—	$	(42)	$	98,697

The unrealized losses and fair values of available for sale debt securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2020 are as follows:


	December 31, 2020
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(37)		129,630		—		—		(37)		129,630
Corporate debt securities		(29)		102,426		—		—		(29)		102,426
Asset-backed securities		(3)		1,830		—		—		(3)		1,830
Government obligations		(6)		27,084		—		—		(6)		27,084
Total	$	(75)	$	260,970	$	—	$	—	$	(75)	$	260,970

Available for sale debt securities at September 30, 2021 and December 31, 2020 mature as follows:


	September 30, 2021
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	109,910	$	—
Corporate debt securities		154,067		127,714
Asset-backed securities		8,881		11,867
Government obligations		49,608		10,291
Total	$	322,466	$	149,872


	December 31, 2020
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	276,837	$	—
Corporate debt securities		240,139		235,520
Asset-backed securities		6,363		22,525
Government obligations		65,524		47,930
Total	$	588,863	$	305,975

The Company classifies all of its marketable securities as current as they are all either available for sale debt securities or equity investments and are available for current operations.

Convertible senior notes

In August 2015, the Company issued $150.0 million of 3.00% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.50% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,” together with the “2022 Convertible Notes,” the “Convertible Notes”). The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the 2022 Convertible Notes at September 30, 2021 and December 31, 2020 was $155.5 million and $193.2 million, respectively. The estimated fair value of the 2026 Convertible Notes at September 30, 2021 and December 31, 2020 was $294.9 million and $394.9 million, respectively.

Level 3 valuation

The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of deferred and contingent consideration on the consolidated statements of operations. The fair value of the development and regulatory milestones is estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. At September 30, 2021, the weighted average discount rate for the development and regulatory milestones was 3.3% and the

weighted average probability of success was 42%. The fair value of the net sales milestones and royalties is determined utilizing an option pricing model with Monte Carlo simulation to simulate a range of possible payment scenarios, and the average of the payments in these scenarios is then discounted to calculate present fair value. At September 30, 2021, the weighted average discount rate for the net sales milestones and royalties was 11.0% and the weighted average probability of success for the net sales milestones was 48%.

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the contingent consideration payable for the periods ended September 30, 2021 and September 30, 2020:


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2020	$	139,200	$	101,200
Additions		—		—
Change in fair value		1,000		10,600
Payments		—		—
Ending balance as of September 30, 2021	$	140,200	$	111,800


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2019	$	290,500	$	65,800
Additions		—		—
Change in fair value		(13,120)		30,100
Payments		—		—
Rights Exchange settlement		(139,180)		—
Ending balance as of September 30, 2020	$	138,200	$	95,900

The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended September 30, 2020 and December 31, 2020:


	September 30, 2021
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$140,200	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 1.6% - 4.7% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$111,800	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 94% 2% - 6% 11.0% 2022 - 2040


	December 31, 2020
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$139,200	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 2.2% - 4.5% 2021 - 2028
Contingent considerable payable- net sales milestones and royalties	$101,200	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 94% 2% - 6% 11.5% 2022 - 2040

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

Accounts payable and accrued expenses

9 Months Ended

Sep. 30, 2021

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

5. Accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2021 and December 31, 2020 consist of the following:


	September 30,		December 31,
	2021		2020
Employee compensation, benefits, and related accruals	$	39,367	$	53,291
Income tax payable		—		4,315
Consulting and contracted research		22,553		18,250
Professional fees		5,174		3,614
Sales allowance		60,980		54,327
Sales rebates		67,056		63,774
Royalties		27,928		16,575
Accounts payable		21,462		18,665
Other		7,809		9,357
Total	$	252,329	$	242,168

Capitalization

9 Months Ended

Sep. 30, 2021

Stockholders' Equity Note [Abstract]

Capitalization

6. Capitalization

In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. During the three and nine month periods ending September 30, 2020, the Company issued and sold an aggregate of 173,956 and 542,470 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $54.39 and $53.37 per share, respectively. During the three and nine month periods ending September 30, 2020, the Company received net proceeds of $9.1 million and $28.1 million, respectively, after deducting underwriting discounts and commissions and other offering expenses payable by the Company. No shares were sold during the three and nine month periods ending September 30, 2021. The remaining shares of the Company’s common stock available to be issued and sold, under the At the Market Offering, have an aggregate offering price of up to $93.0 million as of September 30, 2021.

In June 2021, the Company filed a Certificate of Amendment to its Restated Certificate of Incorporation, which increased the number of authorized shares of the Company’s common stock from 125,000,000 to 250,000,000 shares.

Net loss per share

9 Months Ended

Sep. 30, 2021

Earnings Per Share [Abstract]

Net loss per share

7. Net loss per share

Basic and diluted net loss per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Potentially dilutive securities were excluded from the diluted calculation because their effect would be anti-dilutive.

The following tables set forth the computation of basic and diluted net loss per share:


	Three Months Ended September 30,						Nine Months Ended September 30,
	2021			2020			2021			2020
Numerator
Net loss	$	(133,624)		$	(69,692)		$	(380,636)		$	(363,806)
Denominator
Denominator for basic and diluted net loss per share		70,585,938			67,641,171			70,397,846			65,068,281
Net loss per share:
Basic and diluted	$	(1.89)	*	$	(1.03)	*	$	(5.41)	*	$	(5.59)	*

* In the three and nine months ended September 30, 2021 and 2020, the Company experienced a net loss and therefore did not report any dilutive share impact.

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


	As of September 30,
	2021	2020
Stock Options	10,882,081	11,528,241
Unvested restricted stock awards and units	1,536,265	961,795
Total	12,418,346	12,490,036

Stock award plan

9 Months Ended

Sep. 30, 2021

Share-based Payment Arrangement [Abstract]

Stock award plan

8. Stock award plan

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of September 30, 2021, awards for 930,840 shares of common stock are available for issuance under the 2013 Long Term Incentive Plan.

There are no additional shares of common stock available for issuance under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan or 2013 Stock Incentive Plan.

In January 2020, the Company’s Board of Directors approved the 2020 Inducement Stock Incentive Plan. The 2020 Inducement Stock Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards for up to an aggregate of 1,000,000 shares of common stock. Any grants made under the 2020 Inducement Stock Incentive Plan must be made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company’s new hires’ employment compensation. In December 2020, the Company’s Board of Directors approved an additional 1,000,000 shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan. As of September 30, 2021, awards for 857,693 shares of common stock are available for issuance under the 2020 Inducement Stock Incentive Plan.

From January 1, 2021 through September 30, 2021, the Company issued a total of 2,403,484 stock options to various employees. Of those, 309,095 were inducement grants for non-statutory stock options, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

A summary of stock option activity is as follows:


				Weighted-
		Weighted-		average		Aggregate
		average		remaining		intrinsic
	Number of	exercise		contractual		value(in
	options	price		term		thousands)

Outstanding at December 31, 2020	9,663,677	$	38.72
Granted	2,403,484		62.21
Exercised	(574,230)		28.11
Forfeited/Cancelled	(610,850)		52.52
Outstanding at September 30, 2021	10,882,081	$	43.70	7.16	years	$	39,772
Vested or Expected to vest at September 30, 2021	4,802,564	$	50.12	8.47	years	$	6,311
Exercisable at September 30, 2021	5,585,904	$	37.32	5.88	years	$	33,232

The fair value of grants made in the nine months ended September 30, 2021 was contemporaneously estimated on the date of grant using the following assumptions:


		Nine months ended
		September 30, 2021
Risk-free interest rate		0.51%-1.05%
Expected volatility		77.53%-88.61%
Expected term		5.5 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine month period ended September 30, 2021 was $43.75 per share.

The expected term of options was estimated based on the Company’s historical exercise data and the expected volatility of options was estimated based on the Company’s historical stock volatility. The risk-free rate of the options was based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.

Restricted Stock Awards and Restricted Stock Units—Restricted stock awards and restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock awards and restricted stock units, which have been determined based upon the market value of the Company’s shares on the grant date, are expensed over the vesting period. From January 1, 2021 through September 30, 2021, the Company issued a total of 994,603 restricted stock units to various employees. Of those, 107,085 were inducement grants for restricted stock units, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

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


	Restricted Stock Awards and Units
		Weighted
		Average
		Grant
	Number of	Date
	Shares	Fair Value
Unvested at December 31, 2020	982,058	$	41.78
Granted	994,603		63.15
Vested	(326,519)		35.49
Forfeited	(113,877)		57.95
Unvested at September 30, 2021	1,536,265	$	55.76

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (as amended, “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 Company’s Board of Directors. In June 2021, the Plan was amended to increase the total number of shares available for purchase under the Plan from one million shares to two 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 three and nine month periods ended September 30, 2021, the Company recorded $0.5 million and $1.8 million, respectively, in compensation expense related to the ESPP.

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


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Research and development	$	13,048	$	9,220	$	40,216	$	25,961
Selling, general and administrative		12,823		7,559		37,061		22,948
Total	$	25,871	$	16,779	$	77,277	$	48,909

As of September 30, 2021, there was approximately $226.3 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the 2009 Equity and Long Term Incentive Plan, the 2013 Long Term Incentive Plan and equity awards made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 2.71 years.

Debt

9 Months Ended

Sep. 30, 2021

Debt Disclosure [Abstract]

Debt

9. Debt

Liability for sale of future royalties

In July 2020, the Company entered into the Royalty Purchase Agreement. As RPI’s interest is explicitly limited, the $650.0 million cash consideration was classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability will be amortized using the effective interest method over the life of the arrangement, in accordance with ASC 470 and ASC 835. The initial annual effective interest rate was determined to be 11.0%. The Company will utilize the

prospective method to account for subsequent changes in the estimated future payments to be made to RPI and will update the effective interest rate on a quarterly basis. Issuance costs related to the transaction were determined to be immaterial.

The following table shows the activity within the “liability for sale of future royalties- current” and “liability for sale of future royalties- noncurrent” accounts for the nine month period ended September 30, 2021:


	Nine Months Ended September 30,
Liability for sale of future royalties- (current and noncurrent)	2021
Beginning balance as of December 31, 2020	$	679,762
Less: Non-cash royalty revenue payable to RPI		(14,317)
Plus: Non-cash interest expense recognized		57,755
Ending balance	$	723,200
Effective interest rate as of September 30, 2021		11	%

Non-cash interest expense is recorded in the statement of operations within “Interest expense, net”.

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 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.

Prior to the adoption of ASU 2020-06, the Company accounted for the 2026 Convertible Notes as a liability and equity component where the carrying value of the liability component was valued based on a similar instrument. In accounting for the issuance of the 2026 Convertible Notes, the Company separated the 2026 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that did 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, was amortized to interest expense over the seven-year term of the 2026 Convertible Notes. The equity component was not re-measured as long as it continued to meet the conditions for equity classification. The equity component recorded at issuance related to the 2026 Convertible Notes was $123.0 million and was recorded in additional paid-in capital.

In accounting for the transaction costs related to the issuance of the 2026 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2026 Convertible Notes based on their relative values. Transaction costs attributable to the liability component were amortized to interest expense over the seven-year term of the 2026 Convertible Notes, and transaction costs attributable to the equity component were 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.

Effective January 1, 2021 the Company adopted ASU 2020-06. After adoption, the Company now accounts for the 2026 Convertible Notes as a single liability measured at amortized cost. As the equity component is no longer required to be split into a separate component, the Company recorded an adjustment for the initial $123.0 million that was allocated to additional paid in capital and $16.1 million of life to date interest expense recorded as amortization of debt discount. Additionally, the net deferred tax liability recorded for the 2026 Convertible Notes was reversed. The principal amount of the liability over its carrying amount is amortized to interest expense over the seven-year term of the 2026 Convertible Notes. Since the 2026 Convertible Notes are classified as a single liability, there is no debt discount required to be amortized.

The 2026 Convertible Notes consist of the following:


Liability component	September 30, 2021		December 31, 2020
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(5,896)		(4,058)
Less: Debt discount, net(1)		—		(106,065)
Net carrying amount	$	281,604	$	177,377

(1)	Included in the consolidated balance sheets within convertible senior notes (due 2026) and amortized to interest expense over the remaining life of the 2026 Convertible Notes using the effective interest rate method.

As of September 30, 2021, the remaining contractual life of the 2026 Convertible Notes is approximately 5.0 years.

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



	Three Months Ended September 30,						Nine Months Ended September 30,
	2021				2020		2021				2020
Contractual interest expense	$	1,081		$	1,081		$	3,217		$	3,223
Amortization of debt issuance costs		283			127			839			374
Amortization of debt discount		—			3,313			—			9,786
Total	$	1,364		$	4,521		$	4,056		$	13,383
Effective interest rate of the liability component		1.9	%		10.2	%		1.9	%		10.2	%

2022 Convertible Notes

In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.00% convertible senior notes due 2022. The 2022 Convertible Notes bear cash interest at a rate of 3.00% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The 2022 Convertible Notes will mature on August 15, 2022, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $145.4 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.

The 2022 Convertible Notes are governed by an indenture (the "2022 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2022 Convertible Notes Trustee").

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

●

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

●

during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2022 Convertible Notes Indenture) per $1,000 principal amount of 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;

●

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

●

upon the occurrence of specified corporate events.

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

The conversion rate for the 2022 Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.

The Company was not permitted to redeem the 2022 Convertible Notes prior to August 20, 2018. As of August 20, 2018, the Company may redeem for cash all or any portion of the 2022 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2022 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2022 Convertible Notes, which means that the Company is not required to redeem or retire the 2022 Convertible Notes periodically. There have been no redemptions to date.

If the Company undergoes a “fundamental change” (as defined in the 2022 Convertible Notes Indenture), subject to certain conditions, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.

The 2022 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2022 Convertible Notes Indenture contains customary events of default with respect to the 2022 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2022 Convertible Notes when due and payable) occurring and continuing, the 2022 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2022 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2022 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2022 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2022 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2022 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.

Prior to the adoption of ASU 2020-06, the Company accounted for the 2022 Convertible Notes as a liability and equity component where the carrying value of the liability component was valued based on a similar instrument. In accounting for the issuance of the 2022 Convertible Notes, the Company separated the 2022 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that did 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, was amortized to interest expense over the seven-year term of the 2022 Convertible Notes. The equity component was not re-measured as long as it continued to meet the conditions for equity classification. The equity component recorded at issuance related to the 2022 Convertible Notes was $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 2022 Convertible Notes based on their relative values. Transaction costs attributable to the liability component were amortized to interest expense over the seven-year term of the 2022 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the 2022 Convertible Notes.

Effective January 1, 2021 the Company adopted ASU 2020-06. After adoption, the Company now accounts for the 2022 Convertible Notes as a single liability measured at amortized cost. As the equity component is no longer required to be split into a separate component, the Company recorded an adjustment for the initial $57.5 million that was allocated to additional paid in capital and $38.7 million of life to date interest expense recorded as amortization of debt discount. Additionally, the net deferred tax liability recorded for the 2022 Convertible Notes was reversed. The principal amount of the liability over its carrying amount is amortized to interest expense over the seven-year term of the 2022 Convertible Notes. Since the 2022 Convertible Notes are classified as a single liability, there is no debt discount required to be amortized.

The 2022 Convertible Notes consist of the following:




Liability component	September 30, 2021		December 31, 2020
Principal	$	150,000	$	150,000
Less: Debt issuance costs		(642)		(865)
Less: Debt discount, net (1)		—		(17,372)
Net carrying amount	$	149,358	$	131,763

(1)	Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the 2022 Convertible Notes using the effective interest rate method.

As of September 30, 2021, the remaining contractual life of the 2022 Convertible Notes is approximately 0.9 years.

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



	Three Months Ended September 30,						Nine Months Ended September 30,
	2021			2020			2021			2020
Contractual interest expense	$	1,134		$	1,131		$	3,375		$	3,375
Amortization of debt issuance costs		182			118			538			343
Amortization of debt discount		—			2,372			—			6,892
Total	$	1,316		$	3,621		$	3,913		$	10,610
Effective interest rate of the liability component		3.5	%		11.0	%		3.5	%		11.0	%

Commitments and contingencies

9 Months Ended

Sep. 30, 2021

Commitments and Contingencies Disclosure [Abstract]

Commitments and contingencies

10. Commitments and contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company’s oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement.

The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single-digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, with respect to collaboration products the Company outlicenses, including Evrysdi, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon the Company’s payment to the SMA Foundation of an aggregate of $52.5 million.

Pursuant to the asset purchase agreement ("Asset Purchase Agreement") between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC) (“Marathon”), Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone.

Pursuant to the Agilis Merger Agreement, Agilis equityholders were previously entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2%-6%. The Company was required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Agilis Merger, regardless of whether the applicable milestones have been achieved.

Pursuant to the terms of a Rights Exchange Agreement, by and among the Company, the Rightholders set forth therein, and, for the limited purposes set forth therein, Shareholder Representatives Services LLC, dated as of April 29, 2020 (the “Rights Exchange Agreement”), the former equityholders of Agilis (the “Participating Rightholders”) canceled and forfeited their rights under the Agilis Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments that would have been due upon the passing of the second anniversary of the closing of the Agilis Merger, regardless of whether the milestones are achieved.

The Rights Exchange Agreement has no effect on the Agilis Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightholders’ rights to receive $211.6 million, in the aggregate, of the milestone payments described above. As a result, all other rights and obligations under the Agilis Merger Agreement remain in effect pursuant to their terms, including the Company’s obligation to pay up to an aggregate maximum amount of $20.0 million

upon the achievement of certain development milestones (representing the remaining portion of potential development milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement while excluding the remaining $2.4 million milestone payment that was due and paid upon the passing of the second anniversary of the closing of the Agilis Merger), up to an aggregate maximum amount of $361.0 million upon the achievement of certain regulatory milestones (representing the remaining portion of potential regulatory milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement), up to a maximum aggregate amount of $150.0 million upon the achievement of certain net sales milestones and a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% to 6%, pursuant to the terms of the Agilis Merger Agreement.

Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products.

Subject to the terms and conditions of the Censa Merger Agreement, Censa securityholders may become entitled to receive contingent payments from the Company based on (i) the achievement of certain development and regulatory milestones up to an aggregate maximum amount of $217.5 million for PTC923’s two most advanced programs and receipt of a priority review voucher from the FDA as set forth in the Censa Merger Agreement, (ii) $109.0 million in development and regulatory milestones for each additional indication of PTC923, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $160.0 million, (iv) a percentage of annual net sales during specified terms, ranging from single to low double digits of the applicable net sales threshold amount, and (v) any sublicense fees paid to the Company in consideration of any sublicense of Censa’s intellectual property to commercialize PTC923, on a country-by-country basis, which contingent payment shall equal to a mid-double digit percentage of any such sublicense fees. Pursuant to the Censa Merger Agreement, the Company has the option to pay the initial $30.0 million development milestone, for the completion of enrollment of a Phase 3 clinical trial for PTC923 for PKU, if achieved, in cash or shares of the Company’s common stock.

The Company also has the Akcea Collaboration and License Agreement for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the Akcea Collaboration and License Agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million. In 2019, a $6.0 million milestone was paid upon receipt of regulatory approval of Waylivra from the EMA and a $4.0 million milestone was paid upon regulatory approval of Tegsedi from ANVISA, the Brazilian health regulatory authority. In addition, a $4.0 million milestone was paid upon receipt of regulatory approval for Waylivra from ANVISA in August 2021. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement.

The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur. Additionally, the Company has royalty payments associated with Translarna and Emflaza product net sales, payable quarterly or annually in accordance with the terms of the related agreements.

From time to time in the ordinary course of its business, the Company is subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in the Company’s clinical trials or otherwise gain access to its product candidates. The Company is not currently aware of any material legal proceedings against it.

Revenue recognition

9 Months Ended

Sep. 30, 2021

Revenue from Contract with Customer [Abstract]

Revenue recognition

11. Revenue recognition

Net product sales

The Company views its operations and manages its business in one operating segment.

During the three months ended September 30, 2021 and 2020, net product sales in the United States were $47.1 million and $38.5 million, respectively, consisting solely of Emflaza, and net product sales outside of the United States were $68.5 million and $44.2 million, respectively, consisting of Translarna, Tegsedi, and Waylivra. Translarna net revenues made up $67.2 million and $43.4 million of the net product sales outside of the United States for the three months ended September 30, 2021 and 2020, respectively. For the three months ended September 30, 2021 and 2020, the Company had a total of two and two distributors, respectively, that each accounted for over 10% of the Company’s net product sales.

During the nine months ended September 30, 2021 and 2020, net product sales in the United States were $139.8 million and $102.1 million, respectively, consisting solely of Emflaza, and net product sales outside of the United States were $170.2 million and $124.0 million, respectively, consisting of Translarna, Tegsedi, and Waylivra. Translarna net revenues made up $166.3 million and $122.7 million of the net product sales outside of the United States for the nine months ended September 30, 2021 and 2020, respectively. For the nine months ended September 30, 2021 and 2020, the Company had a total of two and two distributors, respectively, that each accounted for over 10% of the Company's net product sales.

As of September 30, 2021, the Company does not have a contract liabilities balance. As of December 31, 2020, the Company’s contract liabilities balance was $4.2 million. The Company did not have any contract assets as of September 30, 2021 and as of December 31, 2020. During the three month period ended September 30, 2021, the Company did not recognize any revenue related to the amounts included in the contract liability balance at the beginning of the period. For the nine month period ended September 30, 2021, the Company recognized $4.0 million of revenue related to the amounts included in the contract liability balance at the beginning of the period. During the three and nine month periods ended September 30, 2020, the Company recognized $2.0 million and $6.0 million of revenue, respectively, related to the amounts included in the contract liability balance at the beginning of the period. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine month periods ending September 30, 2021 and 2020.

Remaining performance obligations

Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of September 30, 2021 the Company does not have any remaining performance obligations relating to Translarna net product revenue. As of December 31, 2020, the aggregate amount of the transaction price allocated to the remaining performance obligations relating to Translarna net product revenue was $4.2 million.

Collaboration and Royalty revenue

In November 2011, the Company and the SMA Foundation entered into the SMA License Agreement with Roche. Under the terms of the SMA License Agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program.

The Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product.

The SMA program currently has one approved product, Evrysdi™ (risdiplam), which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. As of September 30, 2021, the Company does not have any remaining research and development event milestones that can be received. The final research and development milestone of $10.0 million was received in August 2021 for the first commercial sale of Evrysdi in Japan. The remaining potential sales milestones that can be received is $325.0 million.

For the three months ended September 30, 2021 and 2020, the Company recognized collaboration revenue related to the SMA License Agreement of $10.0 million and $35.0 million, respectively. For the nine months ended September 30, 2021 and 2020, the Company recognized collaboration revenue related to the SMA License Agreement of $30.0 million and $35.1 million, respectively.

In addition to research and development and sales milestones, the Company is eligible to receive up to double-digit royalties on worldwide annual net sales of a commercial product under the SMA License Agreement. For the three and nine months ended September 30, 2021, the Company has recognized $13.1 million and $33.3 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2020, the company recognized $0.7 million and $0.7 million of royalty revenue, respectively, related to Evrysdi.

- Definition

The entire disclosure of revenue from contract with customer to transfer good or service and to transfer nonfinancial asset. Includes, but is not limited to, disaggregation of revenue, credit loss recognized from contract with customer, judgment and change in judgment related to contract with customer, and asset recognized from cost incurred to obtain or fulfill contract with customer. Excludes insurance and lease contracts.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-URI http://asc.fasb.org/topic&trid=49130388

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130551-203045

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 13
-Subparagraph (b)(2)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130556-203045

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 12
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130554-203045

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130550-203045

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 12
-Subparagraph (e)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130554-203045

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 12
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130554-203045

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 12
-Subparagraph (d)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130554-203045

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130558-203045

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 12
-Subparagraph (c)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130554-203045

+ Details

Intangible assets and goodwill

9 Months Ended

Sep. 30, 2021

Goodwill and Intangible Assets Disclosure [Abstract]

Intangible assets and goodwill

12. Intangible assets and goodwill

Definite-lived intangibles

On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to the Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. In accordance with ASU 2017-01, the Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and as such accounted for the transaction as an asset acquisition under ASC 805-50 and recorded an intangible asset of $148.4 million, which is being amortized to cost of product sales over its expected useful life of approximately seven years on a straight line basis.

Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In accordance with the guidance for an asset acquisition, the Company records the milestone payment when it becomes payable to Marathon and increases the cost basis for the Emflaza rights intangible asset. For the three months ended September 30, 2021 and 2020, milestone payments of $16.8 million and $13.0 million were recorded, respectively. For the nine months ended September 30, 2021 and 2020, milestone payments of $42.8 million and $28.0 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 September 30, 2021, a milestone payable to Marathon of $19.2 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. In December 2019, the Company made a $4.0 million milestone payment to Akcea upon regulatory approval of Tegsedi from ANVISA. Both payments were recorded as intangible assets and are being amortized to cost of product sales over their expected useful life of approximately ten years on a straight line basis. Additionally, in August 2021, the Company made a $4.0 million milestone payment to Akcea upon regulatory approval of Waylivra from ANVISA. In accordance with the guidance for an asset acquisition, the Company recorded the milestone payment when it became payable to Akcea, and it increased the cost basis for the Waylivra intangible asset. This payment is being amortized to cost of product sales over the expected remaining useful life of the Waylivra asset 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 and Tegsedi. 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 and Tegsedi intangible assets, respectively.

For the three months ended September 30, 2021 and 2020, the Company recognized amortization expense of $14.4 million and $9.6 million, respectively, related to the Emflaza rights, Waylivra, and Tegsedi intangible assets. For the nine months ended September 30, 2021 and 2020, the Company recognized amortization expense of $38.4 million and $26.3 million,

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


	As of September 30, 2021
2021	$	14,413
2022		57,650
2023		57,650
2024		9,905
2025 and thereafter		7,142
Total	$	146,760

The weighted average remaining amortization period of the definite-lived intangibles as of September 30, 2021 is 2.9 years.

Indefinite-lived intangibles

In connection with the acquisition of the Company’s gene therapy platform from Agilis, the Company acquired rights to PTC-AADC, for the treatment of AADC deficiency. AADC deficiency is a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. The gene therapy platform also includes an asset targeting Friedreich ataxia, a rare and life-shortening neurodegenerative disease caused by a single defect in the FXN gene which causes reduced production of the frataxin protein. Additionally, the gene therapy platform includes two other programs targeting CNS disorders, including Angelman syndrome, a rare, genetic, neurological disorder characterized by severe developmental delays.

In accordance with the acquisition method of accounting, the Company allocated the acquisition cost for the Agilis 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 Agilis Merger.

Goodwill

As a result of the Agilis Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. There were no changes to the recorded value of goodwill for the three and nine month periods ended September 30, 2021.

Subsequent events

9 Months Ended

Sep. 30, 2021

Subsequent Events [Abstract]

Subsequent events

13. Subsequent events

The Company has evaluated subsequent events and transactions through the filing date. There were no material events that impacted the consolidated financial statements or disclosures.

Summary of significant accounting policies (Policies)

9 Months Ended

Sep. 30, 2021

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Restricted Cash

Restricted cash


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2021		2020
Cash and cash equivalents	$	189,818	$	208,812
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	197,318	$	216,312

Marketable securities

Inventory and cost of product sales

Inventory

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


	September 30, 2021		December 31, 2020
Raw materials	$	1,464	$	824
Work in progress		8,019		8,745
Finished goods		6,130		9,128
Total inventory	$	15,613	$	18,697

Cost of product sales

Revenue recognition

Net product revenue

Collaboration and royalty revenue

Allowance for doubtful accounts

Liability for sale of future royalties

Indefinite-lived intangible assets

Goodwill

Income Taxes

Leases

Impact of recently adopted accounting pronouncements

Summary of significant accounting policies (Tables)

9 Months Ended

Sep. 30, 2021

Accounting Policies [Abstract]

Reconciliation of cash


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2021		2020
Cash and cash equivalents	$	189,818	$	208,812
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	197,318	$	216,312

Schedule of Inventory


	September 30, 2021		December 31, 2020
Raw materials	$	1,464	$	824
Work in progress		8,019		8,745
Finished goods		6,130		9,128
Total inventory	$	15,613	$	18,697

Leases - (Tables)

9 Months Ended

Sep. 30, 2021

Leases

Schedule of lease costs


	Three Months Ended		Three Months Ended		Nine Months Ended		Nine Months Ended
		September 30, 2021		September 30, 2020		September 30, 2021		September 30, 2020
Operating Lease Cost
Fixed lease cost	$	4,059	$	4,097	$	12,277	$	7,896
Variable lease cost		1,149		890		3,235		1,914
Short-term lease cost		122		175		405		340
Total operating lease cost	$	5,330	$	5,162	$	15,917	$	10,150


	September 30, 2021		December 31, 2020
Weighted-average remaining lease terms - operating leases (years)	11.07		11.49
Weighted-average discount rate - operating leases	8.92	%	8.86	%
Weighted-average remaining lease terms - finance lease (years)	11.25		12.00
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Schedule of supplemental balance sheet information related to leases


	September 30, 2021		December 31, 2020
Operating lease ROU asset	$	78,699	$	84,410

Operating lease liabilities- current	$	7,144	$	7,465
Operating lease liabilities- noncurrent		74,823		79,499
Total operating lease liability	$	81,967	$	86,964


	September 30, 2021		December 31, 2020
Finance lease liabilities- current	$	2,557	$	1,276
Finance lease liabilities- noncurrent		20,053		23,053
Total finance lease liability	$	22,610	$	24,329

Schedule of supplemental cash flow information related to leases


	Nine Months Ended September 30,
	2021		2020
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	10,254	$	5,611
Financing cash flows from finance lease		2,224		17,829
Operating cash flows from finance leases		776		171

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	—	$	76,657
Finance lease		—		41,382

Schedule of future lease payments - Operating leases


	Operating Leases		Finance Lease
2021 (excludes the nine months ended September 30, 2021)	$	3,417	$	—
2022		13,235		3,000
2023		12,843		3,000
2024		12,150		3,000
2025 and thereafter		91,996		24,000
Total lease payments		133,641		33,000
Less: Imputed Interest expense		51,674		10,390
Total	$	81,967	$	22,610

Schedule of future lease payments - Finance leases


	Operating Leases		Finance Lease
2021 (excludes the nine months ended September 30, 2021)	$	3,417	$	—
2022		13,235		3,000
2023		12,843		3,000
2024		12,150		3,000
2025 and thereafter		91,996		24,000
Total lease payments		133,641		33,000
Less: Imputed Interest expense		51,674		10,390
Total	$	81,967	$	22,610

Fair value of financial instruments and marketable securities - (Tables)

9 Months Ended

Sep. 30, 2021

Fair Value Disclosures [Abstract]

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


	September 30, 2021
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	472,338	$	—	$	472,338	$	—
Marketable securities - equity investments	$	205,787	$	205,787	$	—	$	—
ClearPoint Equity Investments	$	22,979	$	22,979	$	—	$	—
ClearPoint convertible debt security	$	31,306	$	—	$	31,306	$	—
Contingent consideration payable- development and regulatory milestones	$	140,200	$	—	$	—	$	140,200
Contingent consideration payable- net sales milestones and royalties	$	111,800	$	—	$	—	$	111,800


	December 31, 2020
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	894,838	$	—	$	894,838	$	—
ClearPoint Equity Investments	$	20,503	$	20,503	$	—	$	—
ClearPoint convertible debt security	$	29,252	$	—	$	29,252	$	—
Contingent consideration payable- development and regulatory milestones	$	139,200	$	—	$	—	$	139,200
Contingent consideration payable- net sales milestones and royalties	$	101,200	$	—	$	—	$	101,200

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


	September 30, 2021
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	109,890	$	20	$	—	$	109,910
Corporate debt securities		281,467		351		(37)		281,781
Asset-backed securities		20,704		45		(1)		20,748
Government obligations		59,883		20		(4)		59,899
Total	$	471,944	$	436	$	(42)	$	472,338


	December 31, 2020
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	276,855	$	19	$	(37)	$	276,837
Corporate debt securities		474,030		1,658		(29)		475,659
Asset-backed securities		28,681		210		(3)		28,888
Government obligations		113,372		88		(6)		113,454
Total	$	892,938	$	1,975	$	(75)	$	894,838

Summary of unrealized losses and fair values of available-for-sale debt securities in a continuous unrealized loss position


	September 30, 2021
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities		(37)		78,272		—		—		(37)		78,272
Asset-backed securities		(1)		499		—		—		(1)		499
Government obligations		(4)		19,926		—		—		(4)		19,926
Total	$	(42)	$	98,697	$	—	$	—	$	(42)	$	98,697


	December 31, 2020
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(37)		129,630		—		—		(37)		129,630
Corporate debt securities		(29)		102,426		—		—		(29)		102,426
Asset-backed securities		(3)		1,830		—		—		(3)		1,830
Government obligations		(6)		27,084		—		—		(6)		27,084
Total	$	(75)	$	260,970	$	—	$	—	$	(75)	$	260,970

Schedule of marketable securities on the balance sheet


	September 30, 2021
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	109,910	$	—
Corporate debt securities		154,067		127,714
Asset-backed securities		8,881		11,867
Government obligations		49,608		10,291
Total	$	322,466	$	149,872


	December 31, 2020
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	276,837	$	—
Corporate debt securities		240,139		235,520
Asset-backed securities		6,363		22,525
Government obligations		65,524		47,930
Total	$	588,863	$	305,975

Summary of changes in the fair value of the Company's Level 3 valuation for contingent consideration payable


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2020	$	139,200	$	101,200
Additions		—		—
Change in fair value		1,000		10,600
Payments		—		—
Ending balance as of September 30, 2021	$	140,200	$	111,800


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2019	$	290,500	$	65,800
Additions		—		—
Change in fair value		(13,120)		30,100
Payments		—		—
Rights Exchange settlement		(139,180)		—
Ending balance as of September 30, 2020	$	138,200	$	95,900

Fair Value Measurement Inputs and Valuation Techniques


	September 30, 2021
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$140,200	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 1.6% - 4.7% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$111,800	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 94% 2% - 6% 11.0% 2022 - 2040


	December 31, 2020
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$139,200	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 2.2% - 4.5% 2021 - 2028
Contingent considerable payable- net sales milestones and royalties	$101,200	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 94% 2% - 6% 11.5% 2022 - 2040

Accounts payable and accrued expenses - (Tables)

9 Months Ended

Sep. 30, 2021

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses


	September 30,		December 31,
	2021		2020
Employee compensation, benefits, and related accruals	$	39,367	$	53,291
Income tax payable		—		4,315
Consulting and contracted research		22,553		18,250
Professional fees		5,174		3,614
Sales allowance		60,980		54,327
Sales rebates		67,056		63,774
Royalties		27,928		16,575
Accounts payable		21,462		18,665
Other		7,809		9,357
Total	$	252,329	$	242,168

Net loss per share - (Tables)

9 Months Ended

Sep. 30, 2021

Earnings Per Share [Abstract]

Schedule of computation of basic and diluted net loss available to common stockholders


	Three Months Ended September 30,						Nine Months Ended September 30,
	2021			2020			2021			2020
Numerator
Net loss	$	(133,624)		$	(69,692)		$	(380,636)		$	(363,806)
Denominator
Denominator for basic and diluted net loss per share		70,585,938			67,641,171			70,397,846			65,068,281
Net loss per share:
Basic and diluted	$	(1.89)	*	$	(1.03)	*	$	(5.41)	*	$	(5.59)	*

* In the three and nine months ended September 30, 2021 and 2020, 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 September 30,
	2021	2020
Stock Options	10,882,081	11,528,241
Unvested restricted stock awards and units	1,536,265	961,795
Total	12,418,346	12,490,036

Stock award plan - (Tables)

9 Months Ended

Sep. 30, 2021

Share-based Payment Arrangement [Abstract]

Summary of stock option activity


				Weighted-
		Weighted-		average		Aggregate
		average		remaining		intrinsic
	Number of	exercise		contractual		value(in
	options	price		term		thousands)

Outstanding at December 31, 2020	9,663,677	$	38.72
Granted	2,403,484		62.21
Exercised	(574,230)		28.11
Forfeited/Cancelled	(610,850)		52.52
Outstanding at September 30, 2021	10,882,081	$	43.70	7.16	years	$	39,772
Vested or Expected to vest at September 30, 2021	4,802,564	$	50.12	8.47	years	$	6,311
Exercisable at September 30, 2021	5,585,904	$	37.32	5.88	years	$	33,232

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


		Nine months ended
		September 30, 2021
Risk-free interest rate		0.51%-1.05%
Expected volatility		77.53%-88.61%
Expected term		5.5 years

Summary of information on the Company's restricted stock


	Restricted Stock Awards and Units
		Weighted
		Average
		Grant
	Number of	Date
	Shares	Fair Value
Unvested at December 31, 2020	982,058	$	41.78
Granted	994,603		63.15
Vested	(326,519)		35.49
Forfeited	(113,877)		57.95
Unvested at September 30, 2021	1,536,265	$	55.76

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


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Research and development	$	13,048	$	9,220	$	40,216	$	25,961
Selling, general and administrative		12,823		7,559		37,061		22,948
Total	$	25,871	$	16,779	$	77,277	$	48,909

Debt - (Tables)

9 Months Ended

Sep. 30, 2021

Debt Instrument, Redemption [Line Items]

Summary of liability for sale of future royalties


	Nine Months Ended September 30,
Liability for sale of future royalties- (current and noncurrent)	2021
Beginning balance as of December 31, 2020	$	679,762
Less: Non-cash royalty revenue payable to RPI		(14,317)
Plus: Non-cash interest expense recognized		57,755
Ending balance	$	723,200
Effective interest rate as of September 30, 2021		11	%

1.50% Convertible senior notes due 2026

Debt Instrument, Redemption [Line Items]

Summary of convertible notes


Liability component	September 30, 2021		December 31, 2020
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(5,896)		(4,058)
Less: Debt discount, net(1)		—		(106,065)
Net carrying amount	$	281,604	$	177,377

Summary of interest expense recognized related to the Convertible Notes



	Three Months Ended September 30,						Nine Months Ended September 30,
	2021				2020		2021				2020
Contractual interest expense	$	1,081		$	1,081		$	3,217		$	3,223
Amortization of debt issuance costs		283			127			839			374
Amortization of debt discount		—			3,313			—			9,786
Total	$	1,364		$	4,521		$	4,056		$	13,383
Effective interest rate of the liability component		1.9	%		10.2	%		1.9	%		10.2	%

3.00% Convertible senior notes due 2022

Debt Instrument, Redemption [Line Items]

Summary of convertible notes




Liability component	September 30, 2021		December 31, 2020
Principal	$	150,000	$	150,000
Less: Debt issuance costs		(642)		(865)
Less: Debt discount, net (1)		—		(17,372)
Net carrying amount	$	149,358	$	131,763

Summary of interest expense recognized related to the Convertible Notes



	Three Months Ended September 30,						Nine Months Ended September 30,
	2021			2020			2021			2020
Contractual interest expense	$	1,134		$	1,131		$	3,375		$	3,375
Amortization of debt issuance costs		182			118			538			343
Amortization of debt discount		—			2,372			—			6,892
Total	$	1,316		$	3,621		$	3,913		$	10,610
Effective interest rate of the liability component		3.5	%		11.0	%		3.5	%		11.0	%

Intangible assets and goodwill - (Tables)

9 Months Ended

Sep. 30, 2021

Goodwill and Intangible Assets Disclosure [Abstract]

Future amortization expense


	As of September 30, 2021
2021	$	14,413
2022		57,650
2023		57,650
2024		9,905
2025 and thereafter		7,142
Total	$	146,760

The Company (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020	Sep. 30, 2019	Aug. 31, 2015
Long-term debt
Retained earnings (accumulated deficit)	$ (1,954,717)	$ (1,628,877)
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Interest rate ( as a percent )	1.50%		1.50%
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Interest rate ( as a percent )				3.00%

Summary of significant accounting policies - Narrative (Details) $ in Thousands			3 Months Ended		9 Months Ended
	Jul. 17, 2020 USD ($)	Dec. 22, 2017	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2021 USD ($) segment	Sep. 30, 2020 USD ($)	Dec. 31, 2020 USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of Credit			$ 7,500		$ 7,500
Term for letter of credit (in years)					5 years
Number of operating segments \| segment					1
Allowance for credit loss			0		$ 0
Increase in allowance for credit losses			0	$ 0
Allowance for doubtful accounts receivable			300		300		$ 100
Revenue			138,743	118,404	373,364	$ 261,902
Deferred payroll taxes provided for under CARES Act					2,500
Cash consideration received from Royalty Purchase Agreement	$ 650,000					650,000
Federal income tax statutory rate		21.00%
Deferred tax liability			122,000		$ 122,000
Minimum
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Term for letter of credit (in years)					5 years
Fifth Anniversary
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of Credit			3,800		$ 3,800
Net product revenue
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			115,605	82,708	309,998	226,143
Net product revenue \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			68,500	44,200	170,200	124,000
Emflaza \| United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			47,100	38,500	139,800	102,100
Translarna \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			$ 67,200	$ 43,400	$ 166,300	$ 122,700

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020	Sep. 30, 2020	Dec. 31, 2019
Accounting Policies [Abstract]
Cash and cash equivalents	$ 189,818	$ 208,812
Restricted cash included in deposits and other assets	7,500	7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 197,318	$ 216,312	$ 441,470	$ 295,528

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2021	Dec. 31, 2020
Accounting Policies [Abstract]
Raw materials	$ 1,464	$ 1,464	$ 824
Work in progress	8,019	8,019	8,745
Finished goods	6,130	6,130	9,128
Total inventory	15,613	15,613	$ 18,697
Inventory write-down	$ 500	$ 2,200

Summary of significant accounting policies - Collaboration and Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Collaboration and royalty revenue
Revenue	$ 138,743	$ 118,404	$ 373,364	$ 261,902
Collaboration revenue
Collaboration and royalty revenue
Revenue	10,011	35,000	30,018	35,063
Royalty revenue
Collaboration and royalty revenue
Revenue	13,127	696	33,348	696
SMA License Agreement \| Collaboration revenue
Collaboration and royalty revenue
Revenue	10,000	35,000	30,000	35,100
SMA License Agreement \| Royalty revenue
Collaboration and royalty revenue
Revenue	$ 13,100	$ 700	$ 33,300	$ 700

- Definition

Amount, excluding tax collected from customer, of revenue from satisfaction of performance obligation by transferring promised good or service to customer. Tax collected from customer is tax assessed by governmental authority that is both imposed on and concurrent with specific revenue-producing transaction, including, but not limited to, sales, use, value added and excise.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 30
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8906-108599

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 40
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e9031-108599

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 41
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e9038-108599

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 32
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8933-108599

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 32
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8933-108599

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 4
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130543-203045

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 22
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8736-108599

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 22
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8736-108599

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 42
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e9054-108599

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 606
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=121604090&loc=SL49130545-203045

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 924
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SAB Topic 11.L)
-URI http://asc.fasb.org/extlink&oid=6472922&loc=d3e499488-122856

+ Details

Summary of significant accounting policies - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands		9 Months Ended
	Jul. 17, 2020	Sep. 30, 2020	Sep. 30, 2021
Assigned royalty payments
Cash consideration received from Royalty Purchase Agreement	$ 650,000	$ 650,000
Assigned royalty payment, retained percentage	57.067%
Remaining potential milestones that can be achieved			$ 325,000
Royalty Purchase Agreement \| Assigned Royalty Payments
Assigned royalty payments
Assigned royalty payment, percentage	42.933%
Cash consideration received from Royalty Purchase Agreement	$ 650,000
Royalty purchase agreement, termination period	60 days
Royalty purchase agreement, payment maximum	$ 1,300,000

Summary of significant accounting policies - Adoption of ASU 2020-06 (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Jun. 30, 2021	Dec. 31, 2020	Sep. 30, 2020	Jun. 30, 2020	Dec. 31, 2019
Stockholders equity	$ 104,926	$ 196,577	$ 481,982	$ 510,954	$ 572,494	$ 594,330
Long-term debt	281,604		309,145
Cumulative Effect Adjustment
Stockholders equity			(120,440)
Long-term debt			120,400
Deferred tax liability - convertible debt			(29,600)
Deferred tax valuation allowance			29,600
Additional paid-in capital
Stockholders equity	2,092,534	2,063,687	2,171,746	2,101,136	2,067,274	1,795,351
Additional paid-in capital \| Cumulative Effect Adjustment
Stockholders equity			(175,236)
Accumulated deficit
Stockholders equity	$ (1,954,717)	$ (1,821,093)	(1,628,877)	$ (1,554,523)	$ (1,484,831)	$ (1,190,499)
Accumulated deficit \| Cumulative Effect Adjustment
Stockholders equity			$ 54,796

- Definition

Total of all stockholders' equity (deficit) items, net of receivables from officers, directors, owners, and affiliates of the entity which are attributable to the parent. The amount of the economic entity's stockholders' equity attributable to the parent excludes the amount of stockholders' equity which is allocable to that ownership interest in subsidiary equity which is not attributable to the parent (noncontrolling interest, minority interest). This excludes temporary equity and is sometimes called permanent equity.

+ References + Details

Leases - Narrative (Details) $ in Thousands		3 Months Ended		9 Months Ended		12 Months Ended
Leases - Narrative (Details) $ in Thousands	Jun. 19, 2020 USD ($) room	Sep. 30, 2021 USD ($) ft² lease item	Sep. 30, 2020 USD ($)	Sep. 30, 2021 USD ($) ft² lease item	Sep. 30, 2020 USD ($)	Dec. 31, 2020 USD ($)
Leases
Number of operating leases \| lease		3		3
Operating lease, expense		$ 5,300	$ 5,200	$ 15,900	$ 10,200
Finance lease liabilities- current		2,557		2,557		$ 1,276
Finance lease liabilities- noncurrent		20,053		20,053		23,053
Aggregate rent, Initial term		133,641		133,641
2021 (excludes the nine months ended September 30, 2021)		3,417		3,417
2022		13,235		13,235
Finance Lease, Right-of-Use Asset		0		0
Research and development		130,845	92,998	390,840	359,630
MassBio
Leases
Finance lease cost		$ 400	$ 500	$ 1,300	$ 500
Written notice required for early lease termination	24 months
Number of dedicated rooms provided for gene therapy AADC program \| room	4
Guaranteed lease payment due at onset of the lease agreement	$ 15,000
Guaranteed lease payments due annually	3,000
Present value of guaranteed lease payments	$ 41,400
Finance lease, term of contract	12 years 6 months
Research and development						$ 41,400
Minimum
Leases
Operating lease, term of contract		3 months 18 days		3 months 18 days
Maximum
Leases
Operating lease, term of contract		13 years 9 months 18 days		13 years 9 months 18 days
Renewal Term		10 years		10 years
New Building \| Minimum
Leases
Area of real estate property \| ft²		75,000		75,000
Hopewell Campus
Leases
Operating lease, term of contract		15 years		15 years
Area of real estate property \| ft²		220,500		220,500
Renewal Term		10 years		10 years
Number of renewable terms \| item		2		2
Aggregate rent, Initial term		$ 111,500		$ 111,500
Percent of market rate		95.00%		95.00%
Mountainview
Leases
2021 (excludes the nine months ended September 30, 2021)		$ 500		$ 500
2022		1,400		1,400
Thereafter		$ 0		$ 0

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Leases - Lease costs (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Leases
Fixed lease cost	$ 4,059	$ 4,097	$ 12,277	$ 7,896
Variable lease cost	1,149	890	3,235	1,914
Short-term lease cost	122	175	405	340
Total operating lease cost	$ 5,330	$ 5,162	$ 15,917	$ 10,150

Leases - Balance sheet (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Leases
Operating lease ROU assets	$ 78,699	$ 84,410
Operating lease liabilities- current	7,144	7,465
Operating lease liabilities- noncurrent	74,823	79,499
Total operating lease liability	81,967	86,964
Finance lease liabilities- current	2,557	1,276
Finance lease liabilities- noncurrent	20,053	23,053
Total finance lease liability	$ 22,610	$ 24,329

Leases - Supplemental lease terms (Details)	Sep. 30, 2021	Dec. 31, 2020
Leases
Weighted-average remaining lease terms - operating leases (years)	11 years 25 days	11 years 5 months 26 days
Weighted-average discount rate - operating leases	8.92%	8.86%
Weighted-average remaining lease terms - finance lease (years)	11 years 3 months	12 years
Weighted-average discount rate - finance lease	7.80%	7.80%

Leases - Cash flow (Details) - USD ($) $ in Thousands	9 Months Ended
Leases - Cash flow (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Sep. 30, 2020
Leases
Operating cash flows from operating leases	$ 10,254	$ 5,611
Financing cash flows from finance lease	2,224	17,829
Operating cash flows from finance leases	$ 776	171
Right-of-use assets obtained in exchange for operating lease obligations		76,657
Right-of-use assets obtained in exchange for finance lease obligations		$ 41,382

Leases - Lease payments (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Operating leases
2021 (excludes the nine months ended September 30, 2021)	$ 3,417
2022	13,235
2023	12,843
2024	12,150
2025 and thereafter	91,996
Total lease payments	133,641
Less: Imputed Interest expense	51,674
Total	81,967	$ 86,964
Finance leases
2022	3,000
2023	3,000
2024	3,000
2025 and thereafter	24,000
Total lease payments	33,000
Less: Imputed Interest expense	10,390
Total	$ 22,610	$ 24,329

Fair value of financial instruments and marketable securities - Narrative (Details)	1 Months Ended			3 Months Ended		9 Months Ended
	Aug. 31, 2021 USD ($)	Feb. 28, 2021 USD ($) fund $ / shares	Jan. 31, 2020 USD ($) $ / shares	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($) shares	Dec. 31, 2020 USD ($)	Apr. 29, 2020	Sep. 30, 2019 USD ($) $ / shares	May 31, 2019 USD ($) $ / shares	Aug. 31, 2015 USD ($) $ / shares
Financial assets and liabilities measured at fair value on recurring basis
Write downs of available for sale debt securities				$ 0		$ 0
Realized gain (loss) from sale of marketable securities				0.0	$ 300,000	700,000	$ 500,000
Increase in allowance for credit losses				0	0	0	0
Unrealized gain (loss) on ClearPoint Equity Investment				(1,700,000)	2,500,000	2,376,000	852,000
Marketable securities - equity investments				23,000,000.0		23,000,000.0		$ 20,500,000
Purchase of convertible debt investment			$ 10,000,000.0				10,000,000
Conversion price per share (in dollars per share) \| $ / shares			$ 6.00
Debt instrument, convertible, period			5 years
Unrealized loss				2,300,000			600,000
Unrealized gain on convertible note					1,400,000	2,100,000
Fair value of convertible debt				31,300,000		31,300,000		29,300,000
Purchase of marketable securities - equity investments	$ 5,400,000	$ 200,000,000.0				205,382,000
Number of mutual funds invested in \| fund		2
Redemption of marketable securities- equity investments				700,000		740,000
Unrealized gain on marketable securities - equity investments				700,000		1,400,000
Unrealized foreign currency losses on equity investments				200,000		200,000
Transfers of assets measured between Level 1, Level 2, and Level 3				0		0		0
Non-cash stock consideration, acquisition							42,869,000
Operating Expenses				231,819,000	173,535,000	663,077,000	597,296,000
Business Combination, Contingent Consideration Arrangements, Change in Amount of Contingent Consideration, Asset				(10,800,000)	$ (8,400,000)	(11,600,000)	$ (16,980,000)
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Issuance of common stock related to rights exchange (in shares) \| shares							2,821,176
3.00% Convertible senior notes due 2022 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal				150,000,000		150,000,000		150,000,000				$ 150,000,000.0
Interest rate ( as a percent )												3.00%
Fair value of convertible notes				155,500,000		155,500,000		193,200,000
Conversion price per share (in dollars per share) \| $ / shares												$ 56.34
1.50% Convertible senior notes due 2026 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal				$ 287,500,000		$ 287,500,000		287,500,000		$ 287,500,000
Interest rate ( as a percent )				1.50%		1.50%				1.50%
Fair value of convertible notes				$ 294,900,000		$ 294,900,000		394,900,000
Conversion price per share (in dollars per share) \| $ / shares										$ 52.52
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay				$ 40,000,000.0		$ 40,000,000.0
Agilis \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Product sales (as a percent)				2.00%		2.00%			2.00%
Agilis \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Product sales (as a percent)				6.00%		6.00%			6.00%
Development milestone payments which the entity is obligated to pay				$ 60,000,000.0		$ 60,000,000.0
Priority review voucher amount						535,000,000.0
Net sales amount				150,000,000.0		150,000,000.0
Recurring basis
Financial assets and liabilities measured at fair value on recurring basis
Fair value of convertible debt				$ 31,306,000		$ 31,306,000		$ 29,252,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Shares purchased		$ 100,000									$ 4,000,000.0
Share price (in USD per share) \| $ / shares		$ 23.50									$ 3.10
Development and Regulatory Milestone \| Probability of Success \| Weighted Average \| Contingent Consideration Payable
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement				42		42
Development and Regulatory Milestone \| Agilis \| Measurement Input, Discount Rate \| Weighted Average \| Contingent Consideration Payable
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement				3.3		3.3
Net Sales Milestones and Royalties \| Probability of Success \| Weighted Average \| Contingent Consideration Payable
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement				48		48
Net Sales Milestones and Royalties \| Agilis \| Measurement Input, Discount Rate \| Contingent Consideration Payable
Financial assets and liabilities measured at fair value on recurring basis
Rights Exchange settlement				0.110		0.110

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 472,338	$ 894,838
Marketable securities - equity investments	23,000	20,500
ClearPoint convertible debt security	31,300	29,300
Contingent consideration payable	252,000	240,400
Recurring basis
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	22,979	20,503
ClearPoint convertible debt security	31,306	29,252
Recurring basis \| Level 1
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	22,979	20,503
Recurring basis \| Level 2
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint convertible debt security	31,306	29,252
Recurring basis \| Development and Regulatory Milestone
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	140,200	139,200
Recurring basis \| Development and Regulatory Milestone \| Level 3
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	140,200	139,200
Recurring basis \| Net Sales Milestones and Royalties
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	111,800	101,200
Recurring basis \| Net Sales Milestones and Royalties \| Level 3
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	111,800	101,200
Recurring basis \| Marketable securities
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	472,338	894,838
Marketable securities - equity investments	205,787
Recurring basis \| Marketable securities \| Level 1
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - equity investments	205,787
Recurring basis \| Marketable securities \| Level 2
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 472,338	$ 894,838

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 471,944	$ 892,938
Gross Unrealized, Gain	436	1,975
Gross Unrealized, Loss	(42)	(75)
Fair Value	472,338	894,838
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	109,890	276,855
Gross Unrealized, Gain	20	19
Gross Unrealized, Loss	0	(37)
Fair Value	109,910	276,837
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	281,467	474,030
Gross Unrealized, Gain	351	1,658
Gross Unrealized, Loss	(37)	(29)
Fair Value	281,781	475,659
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	20,704	28,681
Gross Unrealized, Gain	45	210
Gross Unrealized, Loss	(1)	(3)
Fair Value	20,748	28,888
Government obligations
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	59,883	113,372
Gross Unrealized, Gain	20	88
Gross Unrealized, Loss	(4)	(6)
Fair Value	$ 59,899	$ 113,454

Fair value of financial instruments and marketable securities - Unrealized Loss Positions (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2021	Dec. 31, 2020
Unrealized losses
Securities in an unrealized loss position less than 12 months	$ (42)	$ (42)	$ (75)
Total	(42)	(42)	(75)
Fair Value
Securities in an unrealized loss position less than 12 months	98,697	98,697	260,970
Total	98,697	98,697	260,970
Write downs of available for sale debt securities	0	0
Commercial paper
Unrealized losses
Securities in an unrealized loss position less than 12 months			(37)
Total			(37)
Fair Value
Securities in an unrealized loss position less than 12 months			129,630
Total			129,630
Corporate debt securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(37)	(37)	(29)
Total	(37)	(37)	(29)
Fair Value
Securities in an unrealized loss position less than 12 months	78,272	78,272	102,426
Total	78,272	78,272	102,426
Asset-backed securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(1)	(1)	(3)
Total	(1)	(1)	(3)
Fair Value
Securities in an unrealized loss position less than 12 months	499	499	1,830
Total	499	499	1,830
Government obligations
Unrealized losses
Securities in an unrealized loss position less than 12 months	(4)	(4)	(6)
Total	(4)	(4)	(6)
Fair Value
Securities in an unrealized loss position less than 12 months	19,926	19,926	27,084
Total	$ 19,926	$ 19,926	$ 27,084

Fair value of financial instruments and marketable securities - Marketable securities (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 322,466	$ 588,863
Total Marketable securities, More Than 12 Months	149,872	305,975
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	109,910	276,837
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	154,067	240,139
Total Marketable securities, More Than 12 Months	127,714	235,520
Asset-backed securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	8,881	6,363
Total Marketable securities, More Than 12 Months	11,867	22,525
Government obligations
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	49,608	65,524
Total Marketable securities, More Than 12 Months	$ 10,291	$ 47,930

Fair value of financial instruments and marketable securities - Fair Value Measurement Inputs and Valuation Techniques (Details) - Level 3 $ in Thousands	9 Months Ended
	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)
Contingent Consideration Payable
Level 3 roll forward
Beginning Balance	$ 139,200	$ 290,500
Additions	0	0
Change in fair value	1,000	(13,120)
Payments	0	$ 0
Rights Exchange settlement		(139,180)
Ending Balance	140,200	$ 138,200
Net Sales Milestones and Royalties \| Agilis
Level 3 roll forward
Beginning Balance	101,200	65,800
Additions	0	0
Change in fair value	10,600	30,100
Payments	0	$ 0
Rights Exchange settlement		0
Ending Balance	111,800	$ 95,900
Net Sales Milestones and Royalties \| Agilis \| Contingent Consideration Payable
Level 3 roll forward
Beginning Balance	101,200
Ending Balance	$ 111,800

Fair value of financial instruments and investments - Fair Value Liabilities Measured (Details) $ in Thousands	Sep. 30, 2021 USD ($)	Dec. 31, 2020 USD ($)	Sep. 30, 2020 USD ($)	Dec. 31, 2019 USD ($)
Level 3 \| Contingent Consideration Payable
Fair Value Valuation Inputs
Fair value	$ 140,200	$ 139,200	$ 138,200	$ 290,500
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Minimum
Fair Value Valuation Inputs
Potential milestones	0	0
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 381,000	$ 381,000
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.25	0.25
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.94	0.94
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.016	0.022
Agilis \| Development and Regulatory Milestone \| Contingent Consideration Payable \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.047	0.045
Agilis \| Development and Regulatory Milestone \| Level 3 \| Contingent Consideration Payable
Fair Value Valuation Inputs
Fair value	$ 140,200	$ 139,200
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Minimum
Fair Value Valuation Inputs
Potential milestones	0	0
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 150,000	$ 150,000
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.25	0.25
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.94	0.94
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.02	0.02
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.06	0.06
Agilis \| Net Sales Milestones and Royalties \| Contingent Consideration Payable \| Valuation Technique, Option Pricing Model \| Measurement Input, Discount Rate
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.110	0.115
Agilis \| Net Sales Milestones and Royalties \| Level 3
Fair Value Valuation Inputs
Fair value	$ 111,800	$ 101,200	$ 95,900	$ 65,800
Agilis \| Net Sales Milestones and Royalties \| Level 3 \| Contingent Consideration Payable
Fair Value Valuation Inputs
Fair value	$ 111,800	$ 101,200

Accounts payable and accrued expenses - Narrative (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 39,367	$ 53,291
Income tax payable		4,315
Consulting and contracted research	22,553	18,250
Professional fees	5,174	3,614
Sales allowance	60,980	54,327
Sales rebates	67,056	63,774
Royalties	27,928	16,575
Accounts payable	21,462	18,665
Other	7,809	9,357
Accounts payable and accrued expenses	$ 252,329	$ 242,168

Capitalization - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Aug. 31, 2019	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Jun. 30, 2021	Dec. 31, 2020
Warrants
Net consideration received on transaction			$ 9,100		$ 28,100
Number of shares issued in transaction (in shares)		0	173,956	0	542,470
Issuance of common stock related to acquisition					$ 42,869
Common stock, authorized shares (in shares)		250,000,000		250,000,000		250,000,000	125,000,000
Maximum
Warrants
Net consideration received on transaction	$ 125,000
Value of remaining shares available to be issued and sold in transaction		$ 93,000		$ 93,000
Weighted Average
Warrants
Sale of stock, weighted average price per share (in USD per share)		$ 54.39		$ 53.37

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Numerator
Net loss	$ (133,624)	$ (69,692)	$ (380,636)	$ (363,806)
Denominator
Denominator for basic and diluted net loss per share (in shares)	70,585,938	67,641,171	70,397,846	65,068,281
Net loss per share:
Basic and diluted (in dollars per share)	$ (1.89)	$ (1.03)	$ (5.41)	$ (5.59)

- Definition

Amount, after deduction of tax, noncontrolling interests, dividends on preferred stock and participating securities; of income (loss) available to common shareholders.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22595-107794

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=121326447&loc=d3e1448-109256

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 11
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22694-107794

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=121326447&loc=d3e1377-109256

Reference 5: 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 6: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 22
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8736-108599

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 11
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22694-107794

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 60B
-Subparagraph (c)
-URI http://asc.fasb.org/extlink&oid=121326447&loc=SL5780133-109256

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 32
-Subparagraph (f)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8933-108599

Reference 10: http://www.xbrl.org/2003/role/exampleRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 31
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8924-108599

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 30
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8906-108599

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22583-107794

Reference 13: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 32
-Subparagraph (c)
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8933-108599

+ Details

Net loss per share - Antidilutive (Details) - shares	9 Months Ended
Net loss per share - Antidilutive (Details) - shares	Sep. 30, 2021	Sep. 30, 2020
Net loss per share
Total shares excluded from calculation (in shares)	12,418,346	12,490,036
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	10,882,081	11,528,241
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	1,536,265	961,795

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended			3 Months Ended		9 Months Ended
	Dec. 31, 2020	Jun. 30, 2016	May 31, 2013	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Jun. 30, 2021	May 31, 2021	Jan. 31, 2020
Stock option plan
Share-based compensation expense				$ 25,871	$ 16,779	$ 77,277	$ 48,909
Restricted stock
Stock option plan
Grants in period (in shares)						994,603
Stock option
Stock option plan
Granted (in shares)						2,403,484
Expected dividend yield (as a percent)						0.00%
Weighted average grant date fair value (in dollars per share)						$ 43.75
1998 Employee, Director, and Consultant Stock Option Plan, 2009 Equity and Long-term Incentive Plan, and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance				0		0
1998 Employee, Director, and Consultant Stock Option Plan, 2009 Equity and Long-term Incentive Plan, and 2013 Stock Incentive Plan \| Common stock \| Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)			3,040,444
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance			122,296
2013 Long Term Incentive Plan \| Minimum
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number			2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year			4.00%
2013 Long Term Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance				930,840		930,840
2020 Inducement Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance				857,693		857,693
Number of additional shares authorized (in shares)	1,000,000
2020 Inducement Stock Incentive Plan \| Common stock \| Maximum
Stock option plan
Number of shares authorized (in shares)										1,000,000
2020 Inducement Stock Incentive Plan \| Stock option
Stock option plan
Inducement grants for non-statutory stock options (in shares)						309,095
2020 Inducement Stock Incentive Plan \| Restricted stock units
Stock option plan
Grants in period (in shares)						107,085
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)								2,000,000	1,000,000
Share-based compensation expense				$ 500		$ 1,800
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit		5.00%

Stock award plan - Share Base Compensation (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2021
Number of options
Outstanding at the beginning of the period (in shares)	9,663,677
Granted (in shares)	2,403,484
Exercised (in shares)	(574,230)
Forfeited/Cancelled (in shares)	(610,850)
Outstanding at the end of the period (in shares)	10,882,081
Vested or Expected to vest at the end of the period (in shares)	4,802,564
Exercisable at the end of the period (in shares)	5,585,904
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 38.72
Granted (in dollars per share)	62.21
Exercised (in dollars per share)	28.11
Forfeited/Cancelled (in dollars per share)	52.52
Outstanding at the end of the period (in dollars per share)	43.70
Vested or Expected to vest at the end of the period (in dollars per share)	50.12
Exercisable at the end of the period (in dollars per share)	$ 37.32
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 1 month 28 days
Vested or Expected to vest at the end of the period	8 years 5 months 19 days
Exercisable at the end of the period	5 years 10 months 17 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars)	$ 39,772
Vested or Expected to vest at the end of the period (in dollars)	6,311
Exercisable at the end of the period (in dollars)	$ 33,232
Valuation assumptions
Expected term (in years)	5 years 6 months
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	0.51%
Expected volatility (as a percent)	77.53%
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	1.05%
Expected volatility (as a percent)	88.61%

Stock award plan - Restricted Stock (Details) - Restricted stock	9 Months Ended
	Sep. 30, 2021 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	982,058
Granted (in shares) \| shares	994,603
Vested (in shares) \| shares	(326,519)
Forfeited (in shares) \| shares	(113,877)
Balance at the end of the period (in shares) \| shares	1,536,265
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 41.78
Granted (in dollars per share) \| $ / shares	63.15
Vested (in dollars per share) \| $ / shares	35.49
Forfeited (in dollars per share) \| $ / shares	57.95
Balance at the end of the period (in dollars per share) \| $ / shares	$ 55.76

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Stock option plan
Share-based compensation expense	$ 25,871	$ 16,779	$ 77,277	$ 48,909
Unrecognized compensation cost	226,300		$ 226,300
Weighted average remaining service period for recognition of unrecognized compensation cost			2 years 8 months 15 days
Research and development
Stock option plan
Share-based compensation expense	13,048	9,220	$ 40,216	25,961
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 12,823	$ 7,559	$ 37,061	$ 22,948

Debt - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands		9 Months Ended
	Jul. 17, 2020	Sep. 30, 2021	Sep. 30, 2020
Debt Disclosure [Abstract]
Proceeds from sale of future royalties	$ 650,000		$ 650,000
Beginning balance		$ 679,762
Less: Non-cash royalty revenue payable to RPI		(14,317)
Plus: non-cash interest expense recognized		57,755
Ending balance		$ 723,200
Effective interest rate of the liability component	11.00%	11.00%

Debt - Narrative (Details)		1 Months Ended		3 Months Ended	9 Months Ended
Debt - Narrative (Details)	Jan. 01, 2021 USD ($)	Sep. 30, 2019 USD ($) D $ / shares	Aug. 31, 2015 USD ($) D $ / shares	Sep. 30, 2020 USD ($)	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)	Dec. 31, 2020 USD ($)	Jan. 31, 2020 $ / shares
Long-term debt
Long-term debt					$ 281,604,000		$ 309,145,000
Current portion of long-term debt					149,358,000
Conversion price per share (in dollars per share) \| $ / shares								$ 6.00
Additional paid-in capital					2,092,534,000		2,171,746,000
1.50% Convertible senior notes due 2026
Long-term debt
Term of the convertible notes	7 years
Debt discount to be amortized	$ 0
3.00% Convertible senior notes due 2022
Long-term debt
Term of the convertible notes	7 years
Debt discount to be amortized	$ 0
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Net carrying amount					281,604,000		177,377,000
Debt principal amount		$ 287,500,000			$ 287,500,000		287,500,000
Debt instrument additional amount available for repurchase		$ 37,500,000
Interest rate ( as a percent )		1.50%			1.50%
Net proceeds from issuance of convertible notes		$ 279,300,000
Trading days, number \| D		20
Consecutive trading days, period \| D		30
Stock price trigger		130.00%
Business days, period		5 days
Consecutive trading-day period		5 days
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day		98.00%
Conversion ratio		19.0404
Conversion price per share (in dollars per share) \| $ / shares		$ 52.52
Convertible instruments principal and unpaid interest payable upon events of default		100.00%
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default		25.00%
Term of the convertible notes		7 years	7 years		5 years
Equity component of convertible notes, net		$ 123,000,000.0
Amortization of debt discount				$ 3,313,000		$ 9,786,000
Debt discount to be amortized							106,065,000
Net deferred tax liability in connection with convertible notes					$ 25,300,000
Fair value of convertible notes					294,900,000		394,900,000
Convertible debt \| 1.50% Convertible senior notes due 2026 \| Redemption on or after September 20, 2023
Long-term debt
Trading days, number \| D		19
Consecutive trading days, period \| D		30
Stock price trigger		130.00%
Redemption price as percent of principal amount		100.00%
Sinking fund		$ 0
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Net carrying amount					149,358,000		131,763,000
Debt principal amount			$ 150,000,000.0		150,000,000		150,000,000
Interest rate ( as a percent )			3.00%
Net proceeds from issuance of convertible notes			$ 145,400,000
Trading days, number \| D			20
Stock price trigger			130.00%
Business days, period			5 days
Consecutive trading-day period			5 days
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day			98.00%
Conversion ratio			17.7487
Conversion price per share (in dollars per share) \| $ / shares			$ 56.34
Convertible instruments principal and unpaid interest payable upon events of default			100.00%
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default			25.00%
Term of the convertible notes			7 years
Equity component of convertible notes, net			$ 57,500,000
Amortization of debt discount				$ 2,372,000		$ 6,892,000
Debt discount to be amortized							17,372,000
Net deferred tax liability in connection with convertible notes			$ 22,300,000
Fair value of convertible notes					$ 155,500,000		193,200,000
Remaining contractual life of the convertible notes					10 months 24 days
Convertible debt \| 3.00% Convertible senior notes due 2022 \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| D			19
Consecutive trading days, period \| D			30
Stock price trigger			130.00%
Redemption price as percent of principal amount			100.00%
Sinking fund			$ 0
Cumulative Effect Adjustment
Long-term debt
Long-term debt							$ 120,400,000
Cumulative Effect Adjustment \| 1.50% Convertible senior notes due 2026
Long-term debt
Additional paid-in capital	(123,000,000.0)
Amortization of debt discount	16,100,000
Cumulative Effect Adjustment \| 3.00% Convertible senior notes due 2022
Long-term debt
Additional paid-in capital	(57,500,000)
Amortization of debt discount	$ 38,700,000

Debt - Convertible Notes (Details) - USD ($)	Sep. 30, 2021	Jan. 01, 2021	Dec. 31, 2020	Sep. 30, 2019	Aug. 31, 2015
3.00% Convertible senior notes due 2022
Long-term debt
Less: Debt discount, net		$ 0
3.00% Convertible senior notes due 2022 \| Convertible debt
Long-term debt
Principal	$ 150,000,000		$ 150,000,000		$ 150,000,000.0
Less: Debt issuance costs	(642,000)		(865,000)
Less: Debt discount, net			(17,372,000)
Net carrying amount	149,358,000		131,763,000
1.50% Convertible senior notes due 2026
Long-term debt
Less: Debt discount, net		$ 0
1.50% Convertible senior notes due 2026 \| Convertible debt
Long-term debt
Principal	287,500,000		287,500,000	$ 287,500,000
Less: Debt issuance costs	(5,896,000)		(4,058,000)
Less: Debt discount, net			(106,065,000)
Net carrying amount	$ 281,604,000		$ 177,377,000

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Debt - Interest Expense (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Jul. 17, 2020
Long-term debt
Amortization of debt issuance costs			$ 1,377	$ 766
Effective interest rate of the liability component	11.00%		11.00%		11.00%
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 1,134	$ 1,131	$ 3,375	3,375
Amortization of debt issuance costs	182	118	538	343
Amortization of debt discount		2,372		6,892
Total	$ 1,316	$ 3,621	$ 3,913	$ 10,610
Effective interest rate of the liability component	3.50%	11.00%	3.50%	11.00%
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 1,081	$ 1,081	$ 3,217	$ 3,223
Amortization of debt issuance costs	283	127	839	374
Amortization of debt discount		3,313		9,786
Total	$ 1,364	$ 4,521	$ 4,056	$ 13,383
Effective interest rate of the liability component	1.90%	10.20%	1.90%	10.20%

Commitments and contingencies - Narrative (Details) - USD ($) $ in Millions			1 Months Ended			9 Months Ended	12 Months Ended
	Jun. 29, 2020	Apr. 29, 2020	Aug. 31, 2021	Dec. 31, 2019	May 31, 2019	Sep. 30, 2021	Dec. 31, 2019	May 29, 2020	Apr. 20, 2017	Jun. 30, 2016
Akcea
Other Commitments
Upfront licensing fee						$ 12.0
Milestone payments			$ 4.0
Akcea \| Maximum
Other Commitments
Milestone payments						4.0
Censa
Other Commitments
Asset acquisition, development and regulatory milestones								$ 109.0
Asset acquisition, initial milestone								30.0
Censa \| Maximum
Other Commitments
Asset acquisition, milestone, amount								217.5
Asset acquisition, net sales milestone								$ 160.0
Agilis Merger Agreement \| Marathon Pharmaceuticals, LLC
Other Commitments
Development milestone payments which the entity is obligated to pay									$ 50.0
Agilis Merger Agreement \| Akcea
Other Commitments
Milestone payments				$ 4.0	$ 6.0	4.0	$ 6.0
SMA License Agreement \| Maximum
Other Commitments
Potential royalty payments due on net product sales						52.5
Agilis
Other Commitments
Development milestone payments which the entity is obligated to pay						40.0
Development milestone obligation payments made						$ 2.4
Agilis \| Minimum
Other Commitments
Product sales (as a percent)		2.00%				2.00%
Agilis \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay						$ 60.0
Priority review voucher amount						535.0
Net sales amount						$ 150.0
Product sales (as a percent)		6.00%				6.00%
Development milestone payment obligations, net of cancellation and forfeiture						$ 20.0
Agilis \| Rights Exchange Agreement
Other Commitments
Contingent liability cancellation and forfeiture of potential milestone payments						174.0
Development milestone payment obligations, cancellation and forfeiture						37.6
Contingent liability, cancellation and forfeiture	$ 211.6
Agilis \| Rights Exchange Agreement \| Maximum
Other Commitments
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture		$ 361.0
BioElectron \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay						200.0
Net product revenue \| Wellcome Trust
Other Commitments
Development milestone payments which the entity is obligated to pay										$ 0.8
Net product revenue \| Wellcome Trust \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay						$ 22.4

Revenue recognition - Narrative (Details)	1 Months Ended	3 Months Ended		9 Months Ended
Revenue recognition - Narrative (Details)	Aug. 31, 2021 USD ($)	Sep. 30, 2021 USD ($) Distributor	Sep. 30, 2020 USD ($) Distributor	Sep. 30, 2021 USD ($) segment Distributor	Sep. 30, 2020 USD ($) Distributor	Dec. 31, 2020 USD ($)	Nov. 30, 2011 USD ($)
Revenue recognition
Number of operating segments \| segment				1
Number of distributors \| Distributor		2	2	2	2
Contract with customer, liability		$ 0		$ 0		$ 4,200,000
Contract with customer, asset		0		0		$ 0
Performance obligations satisfied in period			$ 2,000,000.0	4,000,000.0	$ 6,000,000.0
Deferred consideration payable		0		0
Remaining potential milestones that can be achieved		325,000,000.0		325,000,000.0
Revenue		$ 138,743,000	$ 118,404,000	$ 373,364,000	$ 261,902,000
Minimum
Revenue recognition
Percentage of net product sales threshold		10.00%	10.00%	10.00%	10.00%
Net product revenue
Revenue recognition
Revenue		$ 115,605,000	$ 82,708,000	$ 309,998,000	$ 226,143,000
Net product revenue \| Non-US
Revenue recognition
Revenue		68,500,000	44,200,000	170,200,000	124,000,000.0
Emflaza \| United States
Revenue recognition
Revenue		47,100,000	38,500,000	139,800,000	102,100,000
Translarna \| Non-US
Revenue recognition
Revenue		67,200,000	43,400,000	166,300,000	122,700,000
Collaboration revenue
Revenue recognition
Revenue		10,011,000	35,000,000	30,018,000	35,063,000
Royalty revenue
Revenue recognition
Revenue		13,127,000	696,000	33,348,000	696,000
SMA License Agreement \| Collaboration revenue
Revenue recognition
Revenue		10,000,000.0	35,000,000.0	30,000,000.0	35,100,000
SMA License Agreement \| Royalty revenue
Revenue recognition
Revenue		13,100,000	700,000	33,300,000	700,000
SMA License Agreement \| Roche And SMA Foundation \| Collaboration revenue
Revenue recognition
Revenue		10,000,000.0	$ 35,000,000.0	30,000,000.0	$ 35,100,000
Research And Development Event Milestones \| SMA License Agreement
Revenue recognition
Milestone payments received	$ 10,000,000.0
Research And Development Event Milestones \| SMA License Agreement \| Maximum
Revenue recognition
Remaining potential milestones that can be achieved							$ 135,000,000.0
Sales Milestones \| SMA License Agreement
Revenue recognition
Remaining potential milestones that can be achieved		$ 325,000,000.0		$ 325,000,000.0
Sales Milestones \| SMA License Agreement \| Maximum
Revenue recognition
Remaining potential milestones that can be achieved							$ 325,000,000.0

Revenue recognition - Performance Obligations (Details) - USD ($)	Sep. 30, 2021	Dec. 31, 2020
Remaining Performance Obligation
Deferred consideration payable	$ 0
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Remaining Performance Obligation
Deferred consideration payable		$ 4,200,000
Revenue, performance obligation, period		9 months

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands		1 Months Ended			3 Months Ended		9 Months Ended		12 Months Ended	37 Months Ended
	Apr. 20, 2017	Aug. 31, 2021	Dec. 31, 2019	May 31, 2019	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Dec. 31, 2019	Sep. 30, 2021	Dec. 31, 2020	Aug. 23, 2018
Finite-Lived Intangible Assets
Amortization of acquired intangible assets					$ 14,383	$ 9,630	$ 38,411	$ 26,309
Total allocation of IPR&D assets							576,500
Change in indefinite-lived intangibles										$ 0
Goodwill					82,341		82,341			82,341	$ 82,341	$ 82,300
Changes in goodwill					0		$ 0
Weighted Average
Finite-Lived Intangible Assets
Remaining amortization period							2 years 10 months 24 days
Akcea
Finite-Lived Intangible Assets
Milestone payments		$ 4,000
Agilis Merger Agreement \| Akcea
Finite-Lived Intangible Assets
Milestone payments			$ 4,000	$ 6,000			$ 4,000		$ 6,000
Useful life			10 years
Emflaza asset acquisition
Finite-Lived Intangible Assets
Finite-lived intangibles	$ 148,400
Milestone obligation payments recorded					16,800	$ 13,000	42,800	$ 28,000
Useful life	7 years
Emflaza asset acquisition \| Accounts payable and accrued expenses
Finite-Lived Intangible Assets
Milestone payable					$ 19,200		$ 19,200			$ 19,200

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Sep. 30, 2021 USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2021	$ 14,413
2022	57,650
2023	57,650
2024	9,905
2025 and thereafter	7,142
Total	$ 146,760