0001070081-22-000017 | 10-Q | XBRL Viewer

Fair value of financial instruments and investments - Marketable Securities, Balance Sheet Disclosures (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	$ 111,442	$ 221,611
Marketable securities, More Than 12 Months	133,378	155,074
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	27,281	75,279
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	72,783	131,606
Marketable securities, More Than 12 Months	111,217	136,077
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	4,100	8,724
Marketable securities, More Than 12 Months	6,072	6,574
Government obligations
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	7,278	6,002
Marketable securities, More Than 12 Months	$ 16,089	$ 12,423

Summary of significant accounting policies (Policies)

3 Months Ended

Mar. 31, 2022

Accounting Policies [Abstract]

Basis of presentation

The accompanying financial information as of March 31, 2022 and for the three months ended March 31, 2022 and 2021 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2021 and notes thereto included in the 2021 Form 10-K.

In the opinion of management, the unaudited financial information as of March 31, 2022 and for the three months ended March 31, 2022 and 2021 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 month period ended March 31, 2022 are not necessarily indicative of the results to be expected for the year ended December 31, 2022 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

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-
	March 31,		December 31,
	2022		2021
Cash and cash equivalents	$	144,178	$	189,718
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	151,678	$	197,218

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 periods ended March 31, 2022 and March 31, 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:


	March 31, 2022		December 31, 2021
Raw materials	$	1,501	$	1,418
Work in progress		8,070		7,721
Finished goods		5,710		6,717
Total inventory	$	15,281	$	15,856

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 month periods ended March 31, 2022 and 2021, the Company recorded inventory write-downs of $0.6 million and $1.4 million, respectively, primarily related to product approaching expiration. 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 month periods ended March 31, 2022 and 2021, 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 March 31, 2022 and 2021, net product sales outside of the United States were $81.2 million and $47.8 million, respectively, and net product sales in the United States were $48.6 million and $43.5 million, respectively, consisting solely of Emflaza. Translarna net revenues made up $79.2 million and $46.5 million of the net product sales outside of the United States for the three months ended March 30, 2022 and 2021, 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 Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“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 March 31, 2022 and 2021, the Company recognized $0.0 million and $20.0 million of collaboration revenue, respectively, related to the SMA License Agreement with Roche. The first commercial sale of Evrysdi in the EU was made in March 2021. This event triggered a $20.0 million milestone payment to the Company from Roche.

For the three months ended March 31, 2022 and 2021, the Company has recognized $18.9 million and $6.7 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 March 31, 2022 and 2021, no allowance was recorded for credit losses. The allowance for doubtful accounts was $0.1 million as of March 31, 2022 and $0.1 million as of December 31, 2021. Bad debt expense was immaterial for the three month periods ended March 31, 2022 and 2021.

Liability for sale of future royalties

On July 17, 2020, the Company, RPI, and, for the limited purposes set forth in the agreement, Royalty Pharma PLC, 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 License and Collaboration Agreement (the “SMA License Agreement”), dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation under the SMA program. In consideration for the sale of the Assigned Royalty Payments, RPI paid the Company $650.0 million in cash consideration. The Company has retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the SMA License Agreement, which milestone payments equal $300.0 million in the aggregate as of March 31, 2022. 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 is being amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The Company utilizes 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 a strain of novel coronavirus, COVID-19. The CARES Act includes modifications for net operating loss carryovers and carrybacks, limitations of business interest expense for tax, 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, the Coronavirus Response and Relief Supplemental Appropriations Act of 2021 – a $900 billion relief package to deliver the second round of economic stimulus for individuals, families, and businesses was signed into law. The bill provides relief through multiple measures and expands many of the provisions already put into place under the CARES Act. As of March 31, 2022, the Company expects that these provisions will not have a material impact. Tax provisions of the CARES Act also include the deferral of certain payroll taxes, relief for retaining employees, and other provisions. The relief for retaining employees was not material to the financial statements and the deferral of certain payroll taxes amounted to $1.3 million as of March 31, 2022, which is accrued in other current liabilities on the consolidated balance sheet.

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 March 31, 2022.

Starting in 2022, TCJA amendments to IRC Section 174 will no longer permit an immediate deduction for research and development (R&D) expenditures in the tax year that such costs are incurred. Instead, these IRC Section 174 development costs must now be capitalized and amortized over either a five- or 15-year period, depending on the location of the activities performed. The new amortization period begins with the midpoint of any taxable year that IRC Section 174 costs are first incurred, regardless of whether the expenditures were made prior to or after July 1, and runs until the midpoint of year five for activities conducted in the United States or year 15 in the case of development conducted on foreign soil. As a result of this tax law change, the Company recorded a federal and state tax provision for the three month period ended March 31, 2022, in the amount of $0.6 million and $2.6 million, respectively.

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.

On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc. (“Agilis”), pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Agilis Merger Agreement”), by and among the Company,

Agility Merger Sub, Inc., a Delaware corporation and the Company’s wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the “Agilis Merger”). The Company recorded a deferred tax liability in conjunction with the Agilis Merger of $122.0 million in 2018, related to the tax basis difference in the IPRD 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.

Leases - Supplemental lease terms (Details)	Mar. 31, 2022	Dec. 31, 2021
Leases
Weighted-average remaining lease terms - operating leases (years)	10 years 8 months 1 day	10 years 10 months 13 days
Weighted-average discount rate - operating leases	8.91%	8.91%
Weighted-average remaining lease terms - finance lease (years)	10 years 9 months	11 years
Weighted-average discount rate - finance lease	7.80%	7.80%

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Stock option plan
Share-based compensation expense	$ 26,589	$ 25,707
Unrecognized compensation cost	$ 251,800
Weighted average remaining service period for recognition of unrecognized compensation cost	2 years 7 months 13 days
Research and development
Stock option plan
Share-based compensation expense	$ 13,034	13,725
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 13,555	$ 11,982

Summary of significant accounting policies - Collaboration and Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Collaboration and royalty revenue
Revenue	$ 148,735	$ 117,942
Milestone payments received	50,000
Collaboration and grant revenue
Collaboration and royalty revenue
Revenue	7	20,007
Royalty revenue
Collaboration and royalty revenue
Revenue	18,896	6,655
SMA License Agreement \| Collaboration and grant revenue
Collaboration and royalty revenue
Revenue	0	20,000
SMA License Agreement \| Royalty revenue
Collaboration and royalty revenue
Revenue	$ 18,900	6,700
SMA License Agreement \| Sales Milestones
Collaboration and royalty revenue
Milestone payments received		$ 20,000

- 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

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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 244,820	$ 376,685
Contingent consideration payable	228,200	239,900
Recurring basis
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	13,477	14,525
ClearPoint convertible debt security	19,429	20,971
Recurring basis \| Quoted prices in active markets for identical assets (Level 1)
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	13,477	14,525
Recurring basis \| Significant other observable inputs (Level 2)
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint convertible debt security	19,429	20,971
Recurring basis \| Development and Regulatory Milestones
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	134,700	139,300
Recurring basis \| Development and Regulatory Milestones \| Significant unobservable inputs (Level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	134,700	139,300
Recurring basis \| Net Sales Milestones and Royalties
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	93,500	100,600
Recurring basis \| Net Sales Milestones and Royalties \| Significant unobservable inputs (Level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	93,500	100,600
Recurring basis \| Marketable securities
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	244,820	376,685
Marketable securities - equity investments	198,795	206,973
Recurring basis \| Marketable securities \| Quoted prices in active markets for identical assets (Level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - equity investments	198,795	206,973
Recurring basis \| Marketable securities \| Significant other observable inputs (Level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 244,820	$ 376,685

Net loss per share

3 Months Ended

Mar. 31, 2022

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 March 31,
	2022			2021
Numerator
Net loss	$	(126,726)		$	(128,642)
Denominator
Denominator for basic and diluted net loss per share		71,215,105			70,188,602
Net loss per share:
Basic and diluted	$	(1.78)	*	$	(1.83)	*

* In the three month periods ended March 31, 2022 and 2021, 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 March 31,
	2022	2021
Stock Options	11,751,713	10,989,202
Unvested restricted stock awards and units	2,514,981	1,494,638
Total	14,266,694	12,483,840

Commitments and contingencies

3 Months Ended

Mar. 31, 2022

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 made the first development milestone payment of $0.8 million to Wellcome Trust under the oncology platform funding agreement during 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 is 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. As of the three month period ended March 31, 2022, $14.0 million was owed and is classified as accounts payable and accrued expenses on the Company’s consolidated balance sheets. 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 received a $50.0 million sales-based milestone during the three month period ended March 31, 2022.

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 BioElectron 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 BioElectron 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, former 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 Tegsedi-Waylivra Agreement for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Pursuant to the Tegsedi-Waylivra 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 Tegsedi-Waylivra 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. The Company is not currently aware of any material legal proceedings against it.

Debt

3 Months Ended

Mar. 31, 2022

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 is being 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 utilizes the prospective method to account for subsequent changes in the estimated future payments to be made to RPI and updates 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 three month period ended March 31, 2022:


	Three Months Ended March 31,
Liability for sale of future royalties- (current and noncurrent)	2022
Beginning balance as of December 31, 2021	$	733,985
Less: Non-cash royalty revenue payable to RPI		(8,113)
Plus: Non-cash interest expense recognized		18,874
Ending balance	$	744,746
Effective interest rate as of March 31, 2022		10.1	%

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 of the 2026 Convertible Notes may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances:

●

during any calendar quarter commencing on or after December 31, 2019 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;

●

during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;

●

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

●

upon the occurrence of specified corporate events.

On or after March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company’s common stock or any combination thereof at the Company’s election.

The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.

The Company is not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically.

If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026

Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.

The 2026 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2026 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.

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	March 31, 2022		December 31, 2021
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(5,324)		(5,606)
Net carrying amount	$	282,176	$	281,894

As of March 31, 2022, the remaining contractual life of the 2026 Convertible Notes is approximately 4.5 years.

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



	Three Months Ended March 31,
	2022				2021
Contractual interest expense	$	1,069		$	1,069
Amortization of debt issuance costs		283			277
Total	$	1,352		$	1,346
Effective interest rate of the liability component		1.9	%		1.9	%

In April 2022, under the terms of the 2026 Convertible Notes Indenture, the Company paid additional interest on the 2026 Convertible Notes at a rate equal to 0.5% per annum, for a total interest payment of approximately $2.1 million, for the period beginning September 25, 2020 and ending March 14, 2022. This amount is not included in the table above, but was recorded as interest expense, net within the statement of operations for the three month period ended March 31, 2022.

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

●

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

●

during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 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.

As of 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 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 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	March 31, 2022		December 31, 2021
Principal	$	150,000	$	150,000
Less: Debt issuance costs		(279)		(460)
Net carrying amount	$	149,721	$	149,540

As of March 31, 2022, the remaining contractual life of the 2022 Convertible Notes is approximately 0.4 years.

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



	Three Months Ended March 31,
	2022			2021
Contractual interest expense	$	1,110		$	1,110
Amortization of debt issuance costs		181			175
Total	$	1,291		$	1,285
Effective interest rate of the liability component		3.5	%		3.5	%

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021	Dec. 31, 2021
Accounting Policies [Abstract]
Raw materials	$ 1,501		$ 1,418
Work in progress	8,070		7,721
Finished goods	5,710		6,717
Total inventory	15,281		$ 15,856
Inventory write-down	$ 600	$ 1,400

Accounts payable and accrued expenses - (Tables)

3 Months Ended

Mar. 31, 2022

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses


	March 31,		December 31,
	2022		2021
Employee compensation, benefits, and related accruals	$	29,485	$	55,733
Income tax payable		4,549		1,287
Consulting and contracted research		28,391		26,434
Professional fees		5,013		3,547
Sales allowance		63,109		61,662
Sales rebates		57,680		68,770
Royalties		30,670		35,679
Accounts payable		18,365		23,033
Other		9,259		12,639
Total	$	246,521	$	288,784

Debt - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands		3 Months Ended
	Jul. 17, 2020	Mar. 31, 2022
Debt Disclosure [Abstract]
Proceeds from sale of future royalties	$ 650,000
Beginning balance		$ 733,985
Less: Non-cash royalty revenue payable to RPI		(8,113)
Plus: non-cash interest expense recognized		18,874
Ending balance		$ 744,746
Effective interest rate of the liability component	11.00%	10.10%

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands		1 Months Ended			3 Months Ended			12 Months Ended	43 Months Ended
	Apr. 20, 2017	Aug. 31, 2021	Dec. 31, 2019	May 31, 2019	Mar. 31, 2022	Mar. 31, 2021	Dec. 31, 2018	Dec. 31, 2019	Mar. 31, 2022	Dec. 31, 2021	Apr. 29, 2020	Aug. 23, 2018
Finite-Lived Intangible Assets
Milestone payments received					$ 50,000				$ 50,000
Amortization of intangible assets					23,473	$ 11,278
Total allocation of IPR&D assets					576,500
Change in indefinite-lived intangibles									0
Accrued royalties					30,670				30,670	$ 35,679
Goodwill					82,341				82,341	$ 82,341
Changes in goodwill									0
Tegsedi
Finite-Lived Intangible Assets
Royalty payments					$ 400	0
Accrued royalties						500
Weighted Average [Member]
Finite-Lived Intangible Assets
Remaining amortization period					2 years 2 months 12 days
Akcea
Finite-Lived Intangible Assets
Milestone payments		$ 4,000
Agilis
Finite-Lived Intangible Assets
Development milestone payments which the entity is obligated to pay					$ 40,000				40,000		$ 40,000
Goodwill												$ 82,300
Goodwill adjustment							$ 18,000
Agilis Merger Agreement
Finite-Lived Intangible Assets
Development milestone payments which the entity is obligated to pay					50,000				50,000
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					62,100	$ 8,900
Useful life	7 years
Emflaza asset acquisition \| Accounts payable and accrued expenses
Finite-Lived Intangible Assets
Milestone payable					$ 12,100				$ 12,100

Summary of significant accounting policies - Narrative (Details) $ in Thousands			3 Months Ended
	Jul. 17, 2020 USD ($)	Dec. 22, 2017	Mar. 31, 2022 USD ($) segment	Mar. 31, 2021 USD ($)	Dec. 31, 2021 USD ($)	Dec. 31, 2018 USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of Credit			$ 7,500
Term for letter of credit (in years)			5 years
Number of operating segments \| segment			1
Allowance for credit loss			$ 0
Increase in allowance for credit losses			0	$ 0
Allowance for doubtful accounts receivable			100		$ 100
Revenue			148,735	117,942
Deferred payroll taxes provided for under CARES Act			1,300
Cash consideration received from Royalty Purchase Agreement	$ 650,000
Income taxes
Federal income tax statutory rate		21.00%
Federal income tax provision - IRC Section 174 R&D Expenses			600
State income tax provision - IRC Section 174 R&D Expenses			$ 2,600
Minimum
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Term for letter of credit (in years)			5 years
Agilis
Income taxes
Deferred tax liability						$ 122,000
Fifth Anniversary
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of Credit			$ 3,800
Net product revenue
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			129,832	91,280
Net product revenue \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			81,200	47,800
Emflaza \| United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			48,600	43,500
Translarna \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue			$ 79,200	$ 46,500

Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2022	Dec. 31, 2021
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	250,000,000
Common stock, issued shares (in shares)	71,337,041	70,828,226
Common stock, outstanding shares (in shares)	71,337,041	70,828,226

Revenue recognition - Performance Obligations (Details) - USD ($)	Mar. 31, 2022	Dec. 31, 2021
Revenue from Contract with Customer [Abstract]
Remaining performance obligations	$ 0	$ 0

Fair value of financial instruments and investments - Fair Value Liabilities Measured (Details) - Agilis - Commitments $ in Thousands	Mar. 31, 2022 USD ($)	Dec. 31, 2021 USD ($)	Mar. 31, 2021 USD ($)	Dec. 31, 2020 USD ($)
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Minimum
Fair Value Valuation Inputs
Potential milestones	$ 0	$ 0
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 381,000	$ 381,000
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.25	0.25
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.94	0.94
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.42
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.038	0.017
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.061	0.047
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.051
Development and Regulatory Milestones \| Significant unobservable inputs (Level 3)
Fair Value Valuation Inputs
Fair value	$ 134,700	$ 139,300	$ 139,300	$ 139,200
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Minimum
Fair Value Valuation Inputs
Potential milestones	0	0
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 150,000	$ 150,000
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.25	0.25
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.94	0.94
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.48
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.02	0.02
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.06	0.06
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Measurement Input, Discount Rate
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.120	0.110
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Measurement Input, Discount Rate \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.120
Net Sales Milestones and Royalties \| Significant unobservable inputs (Level 3)
Fair Value Valuation Inputs
Fair value	$ 93,500	$ 100,600	$ 101,200	$ 101,200

Consolidated Statements of Comprehensive Loss (Parenthetical) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Statement of Comprehensive Income [Abstract]
Unrealized loss on marketable securities, tax	$ 0	$ 0
Foreign currency translation gain, tax	$ 0	$ 0

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

3 Months Ended

Mar. 31, 2022

Fair Value Disclosures [Abstract]

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


	March 31, 2022
			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	$	244,820	$	—	$	244,820	$	—
Marketable securities - equity investments	$	198,795	$	198,795	$	—	$	—
ClearPoint Equity Investments	$	13,477	$	13,477	$	—	$	—
ClearPoint convertible debt security	$	19,429	$	—	$	19,429	$	—
Contingent consideration payable- development and regulatory milestones	$	134,700	$	—	$	—	$	134,700
Contingent consideration payable- net sales milestones and royalties	$	93,500	$	—	$	—	$	93,500


	December 31, 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	$	376,685	$	—	$	376,685	$	—
Marketable securities - equity investments	$	206,973	$	206,973	$	—	$	—
ClearPoint Equity Investments	$	14,525	$	14,525	$	—	$	—
ClearPoint convertible debt security	$	20,971	$	—	$	20,971	$	—
Contingent consideration payable- development and regulatory milestones	$	139,300	$	—	$	—	$	139,300
Contingent consideration payable- net sales milestones and royalties	$	100,600	$	—	$	—	$	100,600

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


	March 31, 2022
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	27,292		—		(11)		27,281
Corporate debt securities		187,121		18		(3,139)		184,000
Asset-backed securities		10,202		7		(37)		10,172
Government obligations		23,720		5		(358)		23,367
Total	$	248,335	$	30	$	(3,545)	$	244,820


	December 31, 2021
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	75,275		5		(1)	$	75,279
Corporate debt securities		268,246		81		(644)		267,683
Asset-backed securities		15,287		16		(5)		15,298
Government obligations		18,479		5		(59)		18,425
Total	$	377,287	$	107	$	(709)	$	376,685

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


	March 31, 2022
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(11)		27,281		—		—		(11)		27,281
Corporate debt securities		(2,996)		174,146		(143)		4,876		(3,139)		179,022
Asset-backed securities		(37)		8,435		—		—		(37)		8,435
Government obligations		(358)		18,056		—		—		(358)		18,056
Total	$	(3,402)	$	227,918	$	(143)	$	4,876	$	(3,545)	$	232,794


	December 31, 2021
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(1)		12,992		—		—		(1)		12,992
Corporate debt securities		(608)		217,540		(36)		4,985		(644)		222,525
Asset-backed securities		(5)		10,786		—		—		(5)		10,786
Government obligations		(59)		15,483		—		—		(59)		15,483
Total	$	(673)	$	256,801	$	(36)	$	4,985	$	(709)	$	261,786

Schedule of marketable securities on the balance sheet


	March 31, 2022
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	27,281	$	—
Corporate debt securities		72,783		111,217
Asset-backed securities		4,100		6,072
Government obligations		7,278		16,089
Total	$	111,442	$	133,378


	December 31, 2021
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	75,279	$	—
Corporate debt securities		131,606		136,077
Asset-backed securities		8,724		6,574
Government obligations		6,002		12,423
Total	$	221,611	$	155,074

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, 2021	$	139,300	$	100,600
Additions		—		—
Change in fair value		(4,600)		(7,100)
Payments		—		—
Ending balance as of March 31, 2022	$	134,700	$	93,500


	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		100		—
Payments		—		—
Ending balance as of March 31, 2021	$	139,300	$	101,200

Fair Value Measurement Inputs and Valuation Techniques


	March 31, 2022
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$134,700	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 3.8% - 6.1% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$93,500	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% 12.0% 2023 - 2040


	December 31, 2021
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$139,300	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 1.7% - 4.7% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$100,600	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% 2023 - 2040

Net loss per share - (Tables)

3 Months Ended

Mar. 31, 2022

Earnings Per Share [Abstract]

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


	Three Months Ended March 31,
	2022			2021
Numerator
Net loss	$	(126,726)		$	(128,642)
Denominator
Denominator for basic and diluted net loss per share		71,215,105			70,188,602
Net loss per share:
Basic and diluted	$	(1.78)	*	$	(1.83)	*

* In the three month periods ended March 31, 2022 and 2021, 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 March 31,
	2022	2021
Stock Options	11,751,713	10,989,202
Unvested restricted stock awards and units	2,514,981	1,494,638
Total	14,266,694	12,483,840

Accounts payable and accrued expenses

3 Months Ended

Mar. 31, 2022

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

5. Accounts payable and accrued expenses

Accounts payable and accrued expenses at March 31, 2022 and December 31, 2021 consist of the following:


	March 31,		December 31,
	2022		2021
Employee compensation, benefits, and related accruals	$	29,485	$	55,733
Income tax payable		4,549		1,287
Consulting and contracted research		28,391		26,434
Professional fees		5,013		3,547
Sales allowance		63,109		61,662
Sales rebates		57,680		68,770
Royalties		30,670		35,679
Accounts payable		18,365		23,033
Other		9,259		12,639
Total	$	246,521	$	288,784

Fair value of financial instruments and investments - Marketable Securities, Unrealized Gains (Losses) (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021	Dec. 31, 2021
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 248,335		$ 377,287
Gross Unrealized, Gain	30		107
Gross Unrealized, Loss	(3,545)		(709)
Fair Value	244,820		376,685
Write downs of available for sale debt securities	0
Increase in allowance for credit losses	0	$ 0
Realized gain (loss) from sale of marketable securities	(100)	$ 700
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	27,292		75,275
Gross Unrealized, Gain	0		5
Gross Unrealized, Loss	(11)		(1)
Fair Value	27,281		75,279
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	187,121		268,246
Gross Unrealized, Gain	18		81
Gross Unrealized, Loss	(3,139)		(644)
Fair Value	184,000		267,683
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	10,202		15,287
Gross Unrealized, Gain	7		16
Gross Unrealized, Loss	(37)		(5)
Fair Value	10,172		15,298
Government obligations
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	23,720		18,479
Gross Unrealized, Gain	5		5
Gross Unrealized, Loss	(358)		(59)
Fair Value	$ 23,367		$ 18,425

Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Current assets:
Cash and cash equivalents	$ 144,178	$ 189,718
Marketable securities	443,615	583,658
Trade and royalty receivables, net	141,288	110,455
Inventory, net	15,281	15,856
Prepaid expenses and other current assets	29,647	54,681
Total current assets	774,009	954,368
Fixed assets, net	59,088	52,585
Intangible assets, net	763,665	724,841
Goodwill	82,341	82,341
Operating lease ROU assets	76,093	77,421
Deposits and other assets	44,395	46,500
Total assets	1,799,591	1,938,056
Current liabilities:
Accounts payable and accrued expenses	246,521	288,784
Current portion of long-term debt	149,721	149,540
Operating lease liabilities- current	7,369	7,273
Finance lease liabilities- current	1,772	3,000
Liability for sale of future royalties - current	69,943	59,291
Other current liabilities	1,450	1,460
Total current liabilities	476,776	509,348
Long-term debt	282,176	281,894
Contingent consideration payable	228,200	239,900
Deferred tax liability	137,110	137,110
Operating lease liabilities- noncurrent	72,432	73,619
Finance lease liabilities- noncurrent	18,675	20,053
Liability for sale of future royalties- noncurrent	674,803	674,694
Total liabilities	1,890,172	1,936,618
Stockholders' (deficit) equity:
Common stock, $0.001 par value. Authorized 250,000,000 shares; issued and outstanding 71,337,041 shares at March 31, 2022. Authorized 250,000,000 shares; issued and outstanding 70,828,226 shares at December 31, 2021	71	71
Additional paid-in capital	2,152,639	2,123,606
Accumulated other comprehensive loss	(18,608)	(24,282)
Accumulated deficit	(2,224,683)	(2,097,957)
Total stockholders' (deficit) equity	(90,581)	1,438
Total liabilities and stockholders' equity	$ 1,799,591	$ 1,938,056

Revenue recognition - Net Product Sales (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2022 USD ($) segment Distributor	Mar. 31, 2021 USD ($) Distributor	Dec. 31, 2021 USD ($)
Net product sales
Number of operating segments \| segment	1
Revenue	$ 148,735	$ 117,942
Number of distributors \| Distributor	2	2
Contract with customer, liability	$ 0		$ 0
Performance obligations satisfied in period	$ 0	$ 2,100
Minimum
Net product sales
Percentage of net product sales threshold	10.00%	10.00%
Net product revenue
Net product sales
Revenue	$ 129,832	$ 91,280
Net product revenue \| Non-US
Net product sales
Revenue	81,200	47,800
Emflaza \| United States
Net product sales
Revenue	48,600	43,500
Translarna \| Non-US
Net product sales
Revenue	$ 79,200	$ 46,500

The Company (Details) $ in Thousands	3 Months Ended
The Company (Details) $ in Thousands	Mar. 31, 2022 USD ($) product	Dec. 31, 2021 USD ($)	Sep. 30, 2019	Aug. 31, 2015
Long-term debt
Number of products \| product	2
Retained earnings (accumulated deficit) \| $	$ (2,224,683)	$ (2,097,957)
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%

- Definition

The cumulative amount of the reporting entity's undistributed earnings or deficit.

+ References + Details

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended			3 Months Ended
	Dec. 31, 2020	Jun. 30, 2016	May 31, 2013	Mar. 31, 2022	Mar. 31, 2021	Apr. 30, 2022	Jun. 30, 2021	May 31, 2021	Jan. 31, 2020
Stock option plan
Share-based compensation expense				$ 26,589	$ 25,707
Unrecognized compensation cost				$ 251,800
Weighted average remaining service period for recognition of unrecognized compensation cost				2 years 7 months 13 days
Unvested restricted stock
Stock option plan
Granted (in shares)				1,490,190
Forfeited (in shares)				68,570
Stock option
Stock option plan
Granted (in shares)				1,275,830
Forfeited (in shares)				199,511
Expected dividend yield (as a percent)				0.00%
Weighted average grant date fair value (in dollars per share)				$ 23.92
Employee Stock [Member]
Stock option plan
Number of shares authorized (in shares)							2,000,000	1,000,000
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit		5.00%
Share-based compensation expense				$ 500
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
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				922,076
2020 Inducement Stock Incentive Plan
Stock option plan
Number of shares authorized (in shares)						1,300,000
Vesting period				4 years
2020 Inducement Stock Incentive Plan \| Maximum
Stock option plan
Expiration period				10 years
2020 Inducement Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance				823,211
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
Stockholder's specified ownership percentage				10.00%
Inducement grants for non-statutory stock options (in shares)				18,255
2020 Inducement Stock Incentive Plan \| Stock option \| Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date				100.00%
2020 Inducement Stock Incentive Plan \| Stock option \| Maximum
Stock option plan
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date				110.00%
2020 Inducement Stock Incentive Plan \| Restricted stock units
Stock option plan
Granted (in shares)				10,675

Intangible assets and goodwill

3 Months Ended

Mar. 31, 2022

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. Marathon received a $50.0 million sales-based milestone during the three month period ended March 31, 2022. For the three months ended March 31, 2022 and 2021, total milestone payments of $62.1 million and $8.9 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 March 31, 2022, a milestone payable to Marathon of $12.1 million was recorded on the balance sheet within accounts payable and accrued expenses.

Pursuant to the Tegsedi-Waylivra 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 Tegsedi-Waylivra 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 March 31, 2022, a royalty payment of $0.4 million was recorded for Tegsedi. No royalty payment was recorded for the three months ended March 31, 2021. As of March 31, 2022, a royalty payable of $0.5 million was recorded on the balance sheet within accounts payable and accrued expenses.

For the three months ended March 31, 2022 and 2021, the Company recognized amortization expense of $23.5 million and $11.3 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 March 31, 2022
2022	$	70,475
2023		93,966
2024		16,041
2025		1,542
2026 and thereafter		5,140
Total	$	187,164

The weighted average remaining amortization period of the definite-lived intangibles as of March 31, 2022 is 2.2 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, which included a measurement period adjustment of $18.0 million recorded during the three month period ended December 31, 2018. This adjustment was related to the finalization of the fair values assigned to the intangible assets and corresponding deferred

tax liability, the contingent consideration, and the deferred consideration. There have been no changes to the balance of goodwill since the date of the Agilis Merger. Accordingly, the goodwill balance as of March 31, 2022 is $82.3 million.

Summary of significant accounting policies

3 Months Ended

Mar. 31, 2022

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, 2021 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on February 22, 2022 (the "2021 Form 10-K"). Selected significant accounting policies are discussed in further detail below.

Basis of presentation

Use of estimates

Restricted cash


	End of			Beginning of
	period-		period-
	March 31,		December 31,
	2022		2021
Cash and cash equivalents	$	144,178	$	189,718
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	151,678	$	197,218

Marketable securities

Inventory and cost of product sales

Inventory

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


	March 31, 2022		December 31, 2021
Raw materials	$	1,501	$	1,418
Work in progress		8,070		7,721
Finished goods		5,710		6,717
Total inventory	$	15,281	$	15,856

Cost of product sales

Revenue recognition

Net product revenue

Collaboration and royalty revenue

For the three months ended March 31, 2022 and 2021, the Company has recognized $18.9 million and $6.7 million of royalty revenue, respectively, related to Evrysdi.

Allowance for doubtful accounts

Liability for sale of future royalties

Indefinite-lived intangible assets

Goodwill

Income Taxes

Leases

Leases - Cash flow (Details) - USD ($) $ in Thousands	3 Months Ended
Leases - Cash flow (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Mar. 31, 2021
Leases
Operating cash flows from operating leases	$ 3,411	$ 3,406
Financing cash flows from finance lease	1,276	2,224
Operating cash flows from finance leases	1,724	776
Right-of-use assets obtained in exchange for operating lease obligations	$ 587	$ 13

Fair value of financial instruments and marketable securities

3 Months Ended

Mar. 31, 2022

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 month period ended March 31, 2022, the Company recorded an unrealized loss of $1.0 million. During the three month period ended March 31, 2021, the Company recorded an unrealized gain of $6.8 million. 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 $13.5 million and $14.5 million as of March 31, 2022 and December 31, 2021, 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 month period ended March 31, 2022, the Company recorded an unrealized loss of $1.5 million. During the three month period ended March 31, 2021, the Company recorded an unrealized gain of $7.9 million. 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 $19.4 million and $21.0 million as of March 31, 2022 and December 31, 2021, 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 and $4.6 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 month periods ended March 31, 2022 and 2021, the Company had $6.5 million and $0.3 million of unrealized net losses relating to the equity investments still held at the reporting date, respectively. For the three month periods ended March 31, 2022 and 2021 the Company had redemptions of $2.4 million and $0.0 million, respectively. For the three month periods ended March 31, 2022 and 2021, the Company had foreign currency unrealized gains relating to these equity investments of $0.7 million and $0.0 million, respectively.

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 March 31, 2022 and December 31, 2021:


	March 31, 2022
			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	$	244,820	$	—	$	244,820	$	—
Marketable securities - equity investments	$	198,795	$	198,795	$	—	$	—
ClearPoint Equity Investments	$	13,477	$	13,477	$	—	$	—
ClearPoint convertible debt security	$	19,429	$	—	$	19,429	$	—
Contingent consideration payable- development and regulatory milestones	$	134,700	$	—	$	—	$	134,700
Contingent consideration payable- net sales milestones and royalties	$	93,500	$	—	$	—	$	93,500


	December 31, 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	$	376,685	$	—	$	376,685	$	—
Marketable securities - equity investments	$	206,973	$	206,973	$	—	$	—
ClearPoint Equity Investments	$	14,525	$	14,525	$	—	$	—
ClearPoint convertible debt security	$	20,971	$	—	$	20,971	$	—
Contingent consideration payable- development and regulatory milestones	$	139,300	$	—	$	—	$	139,300
Contingent consideration payable- net sales milestones and royalties	$	100,600	$	—	$	—	$	100,600

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended March 31, 2022 and December 31, 2021.

The following is a summary of marketable securities accounted for as available for sale debt securities at March 31, 2022 and December 31, 2021:


	March 31, 2022
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	27,292		—		(11)		27,281
Corporate debt securities		187,121		18		(3,139)		184,000
Asset-backed securities		10,202		7		(37)		10,172
Government obligations		23,720		5		(358)		23,367
Total	$	248,335	$	30	$	(3,545)	$	244,820


	December 31, 2021
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	75,275		5		(1)	$	75,279
Corporate debt securities		268,246		81		(644)		267,683
Asset-backed securities		15,287		16		(5)		15,298
Government obligations		18,479		5		(59)		18,425
Total	$	377,287	$	107	$	(709)	$	376,685

For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. For the three month period ended March 31, 2022, 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 basis, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three month periods ended March 31, 2022 and 2021, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity.

For the three month period ended March 31, 2022, the Company had $0.1 million realized losses from the sale of available for sale debt securities. For the three month period ended March 31, 2021, the Company had $0.7 million realized gains from the sale of available for sale debt securities. 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 March 31, 2022 are as follows:


	March 31, 2022
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(11)		27,281		—		—		(11)		27,281
Corporate debt securities		(2,996)		174,146		(143)		4,876		(3,139)		179,022
Asset-backed securities		(37)		8,435		—		—		(37)		8,435
Government obligations		(358)		18,056		—		—		(358)		18,056
Total	$	(3,402)	$	227,918	$	(143)	$	4,876	$	(3,545)	$	232,794

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, 2021 are as follows:


	December 31, 2021
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Commercial paper	$	(1)		12,992		—		—		(1)		12,992
Corporate debt securities		(608)		217,540		(36)		4,985		(644)		222,525
Asset-backed securities		(5)		10,786		—		—		(5)		10,786
Government obligations		(59)		15,483		—		—		(59)		15,483
Total	$	(673)	$	256,801	$	(36)	$	4,985	$	(709)	$	261,786

Available for sale debt securities at March 31, 2022 and December 31, 2021 mature as follows:


	March 31, 2022
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	27,281	$	—
Corporate debt securities		72,783		111,217
Asset-backed securities		4,100		6,072
Government obligations		7,278		16,089
Total	$	111,442	$	133,378


	December 31, 2021
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	75,279	$	—
Corporate debt securities		131,606		136,077
Asset-backed securities		8,724		6,574
Government obligations		6,002		12,423
Total	$	221,611	$	155,074

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 March 31, 2022 and December 31, 2021 was $155.7 million and $158.3 million, respectively. The estimated fair value of the 2026 Convertible notes at March 31, 2022 and December 31, 2021 was $287.5 million and $305.3 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 March 31, 2022, the weighted average discount rate for the development and regulatory milestones was 5.1% 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 March 31, 2022, the weighted average discount rate for the net sales milestones and royalties was 12.0% and the weighted average probability of success for the net sales milestones was 48%.

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the contingent consideration payable for the periods ended March 31, 2022 and March 31, 2021:


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2021	$	139,300	$	100,600
Additions		—		—
Change in fair value		(4,600)		(7,100)
Payments		—		—
Ending balance as of March 31, 2022	$	134,700	$	93,500


	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		100		—
Payments		—		—
Ending balance as of March 31, 2021	$	139,300	$	101,200

The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended March 31, 2022 and December 31, 2021:


	March 31, 2022
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$134,700	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 3.8% - 6.1% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$93,500	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% 12.0% 2023 - 2040


	December 31, 2021
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$139,300	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $381 million 25% - 94% 1.7% - 4.7% 2022 - 2028
Contingent considerable payable- net sales milestones and royalties	$100,600	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% 2023 - 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

Debt - Convertible Notes (Details) - USD ($)	Mar. 31, 2022	Dec. 31, 2021	Jan. 01, 2021	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	(279,000)	(460,000)
Net carrying amount	149,721,000	149,540,000
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	(5,324,000)	(5,606,000)
Net carrying amount	$ 282,176,000	$ 281,894,000

- Definition

Amount, after unamortized (discount) premium and debt issuance costs, of long-term debt. Includes, but not limited to, notes payable, bonds payable, debentures, mortgage loans and commercial paper. Excludes capital lease obligations.

+ References + Details

Fair value of financial instruments and investments - Summary of changes in the fair value of the Company's Level 3 valuation (Details) - Significant unobservable inputs (Level 3) - Agilis - Commitments - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Development and Regulatory Milestones
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	$ 139,300	$ 139,200
Additions	0	0
Change in fair value	(4,600)	100
Rights Exchange settlement	0	0
Ending Balance	134,700	139,300
Net Sales Milestones and Royalties
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	100,600	101,200
Additions	0	0
Change in fair value	(7,100)	0
Rights Exchange settlement	0	0
Ending Balance	$ 93,500	$ 101,200

Summary of significant accounting policies (Tables)

3 Months Ended

Mar. 31, 2022

Accounting Policies [Abstract]

Reconciliation of cash


	End of			Beginning of
	period-		period-
	March 31,		December 31,
	2022		2021
Cash and cash equivalents	$	144,178	$	189,718
Restricted cash included in deposits and other assets		7,500		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	151,678	$	197,218

Schedule of Inventory


	March 31, 2022		December 31, 2021
Raw materials	$	1,501	$	1,418
Work in progress		8,070		7,721
Finished goods		5,710		6,717
Total inventory	$	15,281	$	15,856

Consolidated Statements of Stockholders' (Deficit) Equity - USD ($) $ in Thousands	Common stock	Additional paid-in capital Cumulative Effect Adjustment	Additional paid-in capital	AOCI Attributable to Parent	Accumulated deficit Cumulative Effect Adjustment	Accumulated deficit	Cumulative Effect Adjustment	Total
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)	415,783
Exercise of options			11,755					11,755
Restricted stock vesting and issuance (in shares)	272,026
Share-based compensation expense			25,707					25,707
Net loss						(128,642)		(128,642)
Comprehensive income (loss)				22,214				22,214
Balance (in shares) at Mar. 31, 2021	70,405,905
Balance at the end of the period at Mar. 31, 2021	$ 70		2,033,972	(38,743)		(1,702,723)		292,576
Balance (in shares) at Dec. 31, 2021	70,828,226
Balance at the beginning of the period at Dec. 31, 2021	$ 71		2,123,606	(24,282)		(2,097,957)		1,438
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	97,188
Exercise of options			2,444					2,444
Restricted stock vesting and issuance (in shares)	411,627
Share-based compensation expense			26,589					26,589
Net loss						(126,726)		(126,726)
Comprehensive income (loss)				5,674				5,674
Balance (in shares) at Mar. 31, 2022	71,337,041
Balance at the end of the period at Mar. 31, 2022	$ 71		$ 2,152,639	$ (18,608)		$ (2,224,683)		$ (90,581)

- Definition

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

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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.

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+ Details

Capitalization

3 Months Ended

Mar. 31, 2022

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. No shares were sold during the three month periods ended March 31, 2022 and 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 March 31, 2022.

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

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+ Details

Capitalization - Narrative (Details) - Sales Agreement - USD ($) $ in Millions	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021	Aug. 31, 2019
Common stock
Number of shares issued in transaction (in shares)	0	0
Maximum
Common stock
Value of shares available to be issued and sold in transaction			$ 125.0
Aggregate value of remaining shares to be issued and sold	$ 93.0

Stock award plan - Stock Option Activity (Details) - Stock option $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2022 USD ($) $ / shares shares
Number of options
Outstanding at the beginning of the period (in shares) \| shares	10,772,582
Granted (in shares) \| shares	1,275,830
Exercised (in shares) \| shares	(97,188)
Forfeited/Cancelled (in shares) \| shares	(199,511)
Outstanding at the end of the period (in shares) \| shares	11,751,713
Vested or Expected to vest at the end of the period (in shares) \| shares	4,497,327
Exercisable at the end of the period (in shares) \| shares	6,763,376
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share) \| $ / shares	$ 43.66
Granted (in dollars per share) \| $ / shares	38.10
Exercised (in dollars per share) \| $ / shares	25.15
Forfeited/Cancelled (in dollars per share) \| $ / shares	49.92
Outstanding at the end of the period (in dollars per share) \| $ / shares	43.11
Vested or Expected to vest at the end of the period (in dollars per share) \| $ / shares	48.04
Exercisable at the end of the period (in dollars per share) \| $ / shares	$ 39.44
Weighted- average remaining contractual term
Outstanding at the end of the period	6 years 11 months 19 days
Vested or Expected to vest at the end of the period	8 years 6 months 14 days
Exercisable at the end of the period	5 years 9 months 14 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars) \| $	$ 38,075
Vested or Expected to vest at the end of the period (in dollars) \| $	2,127
Exercisable at the end of the period (in dollars) \| $	$ 35,859

Stock award plan

3 Months Ended

Mar. 31, 2022

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 March 31, 2022, awards for 922,076 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 March 31, 2022, awards for 823,211 shares of common stock were available for issuance under the 2020 Inducement Stock Incentive Plan. In April 2022, the Company’s Board of Directors approved a reduction in the total number of shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan to 1,300,000 shares.

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

From January 1, 2022 through March 31, 2022, the Company issued a total of 1,275,830 stock options to various employees. Of those, 18,255 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, 2021	10,772,582	$	43.66
Granted	1,275,830		38.10
Exercised	(97,188)		25.15
Forfeited/Cancelled	(199,511)		49.92
Outstanding at March 31, 2022	11,751,713	$	43.11	6.97	years	$	38,075
Vested or Expected to vest at March 31, 2022	4,497,327	$	48.04	8.54	years	$	2,127
Exercisable at March 31, 2022	6,763,376	$	39.44	5.79	years	$	35,859

The fair value of grants made in the three months ended March 31, 2022 was contemporaneously estimated on the date of grant using the following assumptions:


		Three months ended
		March 31, 2022
Risk-free interest rate		1.55%
Expected volatility		73.56%
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 three months ended March 31, 2022 was $23.92 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. For the three month period ended March 31, 2022, the Company issued a total of 1,490,190 restricted stock units to various employees. Of those, 10,675 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, 2021	1,519,831	$	55.43
Granted	1,490,190		38.10
Vested	(426,470)		51.26
Forfeited	(68,570)		48.45
Unvested at March 31, 2022	2,514,981	$	46.06

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 months ended March 31, 2022, the Company recorded $0.5 million in compensation expense related to the ESPP.

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


	Three Months Ended March 31,
	2022		2021
Research and development	$	13,034	$	13,725
Selling, general and administrative		13,555		11,982
Total	$	26,589	$	25,707

As of March 31, 2022, there was approximately $251.8 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 2.62 years.

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Mar. 31, 2022 USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2022	$ 70,475
2023	93,966
2024	16,041
2025	1,542
2026 and thereafter	5,140
Total	$ 187,164

Leases

3 Months Ended

Mar. 31, 2022

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 March 31, 2022 and as of December 31, 2021. As of March 31, 2022, the balance of the finance lease liabilities-current and finance lease liabilities-non-current are $1.8 million and $18.7 million, respectively, and are directly related to the Company’s MassBio agreement. As of December 31, 2021, the balance of the finance lease liabilities-current and finance lease liabilities-non current were $3.0 million and $20.1 million, respectively. Additionally, the Company recorded finance lease costs of $0.4 million related to interest on the lease liability during both the three month period ending March 31, 2022, and the three month period ending March 31, 2021.

The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s leases have remaining operating lease terms ranging from 0.1 years to 13.3 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 $5.4 million for the three month periods ended March 31, 2022 and 2021, respectively.

The components of operating lease expense were as follows:


	Three Months Ended		Three Months Ended
		March 31, 2022		March 31, 2021
Operating Lease Cost
Fixed lease cost	$	4,126	$	4,104
Variable lease cost		1,076		1,093
Short-term lease cost		74		164
Total operating lease cost	$	5,276	$	5,361

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

The Company entered into one new lease, an office in Tokyo, Japan, during the three months ended March 31, 2022; this new Japan lease did not have a material impact on the consolidated financial statements.

Supplemental lease term and discount rate information related to leases was as follows as of March 31, 2022 and December 31, 2021:


	March 31, 2022		December 31, 2021
Weighted-average remaining lease terms - operating leases (years)	10.67		10.87
Weighted-average discount rate - operating leases	8.91	%	8.91	%
Weighted-average remaining lease terms - finance lease (years)	10.75		11.00
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Supplemental cash flow information related to leases was as follows as of March 31, 2022 and 2021:


	Three Months Ended March 31,
	2022		2021
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	3,411	$	3,406
Financing cash flows from finance lease		1,276		2,224
Operating cash flows from finance leases		1,724		776

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	587	$	13

Future minimum lease payments under non-cancelable leases as of March 31, 2022 were as follows:


	Operating Leases		Finance Lease
2022 (excludes the three months ended March 31, 2022)	$	10,154	$	—
2023		13,298		3,000
2024		12,619		3,000
2025		11,231		3,000
2026 and thereafter		80,769		21,000
Total lease payments		128,071		30,000
Less: Imputed Interest expense		48,270		9,553
Total	$	79,801	$	20,447

In conjunction with the Asset Purchase Agreement by and between the Company and BioElectron Technology Corporation, dated October 1, 2019 (the “BioElectron 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 March 31, 2022 are $0.9 million for the remainder of 2022 and $0 thereafter.

Accounts payable and accrued expenses - Narrative (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 29,485	$ 55,733
Income tax payable	4,549	1,287
Consulting and contracted research	28,391	26,434
Professional fees	5,013	3,547
Sales allowance	63,109	61,662
Sales rebates	57,680	68,770
Royalties	30,670	35,679
Accounts payable	18,365	23,033
Other	9,259	12,639
Accounts payable and accrued expenses	$ 246,521	$ 288,784

Fair value of financial instruments and investments - Available-for-sale securities (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position less than 12 months - Unrealized losses	$ (3,402)	$ (673)
Securities in an unrealized loss position less than 12 months - Fair Value	227,918	256,801
Securities in an unrealized loss position greater than 12 months - Unrealized losses	(143)	(36)
Securities in an unrealized loss position greater than 12 months - Fair Value	4,876	4,985
Total - Unrealized losses	(3,545)	(709)
Total - Fair Value	232,794	261,786
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position less than 12 months - Unrealized losses	(11)	(1)
Securities in an unrealized loss position less than 12 months - Fair Value	27,281	12,992
Total - Unrealized losses	(11)	(1)
Total - Fair Value	27,281	12,992
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position less than 12 months - Unrealized losses	(2,996)	(608)
Securities in an unrealized loss position less than 12 months - Fair Value	174,146	217,540
Securities in an unrealized loss position greater than 12 months - Unrealized losses	(143)	(36)
Securities in an unrealized loss position greater than 12 months - Fair Value	4,876	4,985
Total - Unrealized losses	(3,139)	(644)
Total - Fair Value	179,022	222,525
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position less than 12 months - Unrealized losses	(37)	(5)
Securities in an unrealized loss position less than 12 months - Fair Value	8,435	10,786
Total - Unrealized losses	(37)	(5)
Total - Fair Value	8,435	10,786
Government obligations
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position less than 12 months - Unrealized losses	(358)	(59)
Securities in an unrealized loss position less than 12 months - Fair Value	18,056	15,483
Total - Unrealized losses	(358)	(59)
Total - Fair Value	$ 18,056	$ 15,483

Leases - (Tables)

3 Months Ended

Mar. 31, 2022

Leases

Schedule of lease costs


	Three Months Ended		Three Months Ended
		March 31, 2022		March 31, 2021
Operating Lease Cost
Fixed lease cost	$	4,126	$	4,104
Variable lease cost		1,076		1,093
Short-term lease cost		74		164
Total operating lease cost	$	5,276	$	5,361


	March 31, 2022		December 31, 2021
Weighted-average remaining lease terms - operating leases (years)	10.67		10.87
Weighted-average discount rate - operating leases	8.91	%	8.91	%
Weighted-average remaining lease terms - finance lease (years)	10.75		11.00
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Schedule of supplemental cash flow information related to leases


	Three Months Ended March 31,
	2022		2021
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	3,411	$	3,406
Financing cash flows from finance lease		1,276		2,224
Operating cash flows from finance leases		1,724		776

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	587	$	13

Schedule of future lease payments - Operating leases


	Operating Leases		Finance Lease
2022 (excludes the three months ended March 31, 2022)	$	10,154	$	—
2023		13,298		3,000
2024		12,619		3,000
2025		11,231		3,000
2026 and thereafter		80,769		21,000
Total lease payments		128,071		30,000
Less: Imputed Interest expense		48,270		9,553
Total	$	79,801	$	20,447

Schedule of future lease payments - Finance leases


	Operating Leases		Finance Lease
2022 (excludes the three months ended March 31, 2022)	$	10,154	$	—
2023		13,298		3,000
2024		12,619		3,000
2025		11,231		3,000
2026 and thereafter		80,769		21,000
Total lease payments		128,071		30,000
Less: Imputed Interest expense		48,270		9,553
Total	$	79,801	$	20,447

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	3 Months Ended
	Mar. 31, 2022 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	1,519,831
Granted (in shares) \| shares	1,490,190
Vested (in shares) \| shares	(426,470)
Forfeited (in shares) \| shares	(68,570)
Balance at the end of the period (in shares) \| shares	2,514,981
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 55.43
Granted (in dollars per share) \| $ / shares	38.10
Vested (in dollars per share) \| $ / shares	51.26
Forfeited (in dollars per share) \| $ / shares	48.45
Balance at the end of the period (in dollars per share) \| $ / shares	$ 46.06

Revenue recognition

3 Months Ended

Mar. 31, 2022

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 March 31, 2022 and 2021, net product sales in the United States were $48.6 million and $43.5 million, respectively, consisting solely of Emflaza, and net product sales outside of the United States were $81.2 million and $47.8 million, respectively, consisting of Translarna, Tegsedi, and Waylivra. Translarna net revenues made up $79.2 million and $46.5 million of the net product sales outside of the United States for the three months ended March 31, 2022 and 2021, respectively. For the three months ended March 31, 2022 and 2021, 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 March 31, 2022 and December 31, 2021, the Company did not have any contract liabilities or assets. For the three month period ended March 31, 2022, 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 three month period ended March 31, 2021, the Company recognized $2.1 million of revenue, 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 month periods ending March 31, 2022 and 2021.

Remaining performance obligations

Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of March 31, 2022 and December 31, 2021 the Company does not have any remaining performance obligations relating to Translarna net product revenue.

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.

Under the SMA License Agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of 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, which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. As of March 31, 2022, the Company does not have any remaining research and development event milestones that can be received. The remaining potential sales milestones that can be received is $300.0 million.

For the three months ended March 31, 2022 and 2021, the Company recognized $0.0 million and $20.0 million, respectively, related to the SMA License Agreement with Roche. The first commercial sale of Evrysdi in the EU was made in March 2021. This event triggered a $20.0 million milestone payment to the Company from Roche for the three months ended March 31, 2021.

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 months ended March 31, 2022, the Company has recognized $18.9 million of royalty revenue, related to Evrysdi. For the three months ended March 31, 2021, the Company has recognized $6.7 million of royalty revenue 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=123351226&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=123351226&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=123351226&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=123351226&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=123351226&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=123351226&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=123351226&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=123351226&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=123351226&loc=SL49130554-203045

+ Details

Intangible assets and goodwill - (Tables)

3 Months Ended

Mar. 31, 2022

Goodwill and Intangible Assets Disclosure [Abstract]

Future amortization expense


	As of March 31, 2022
2022	$	70,475
2023		93,966
2024		16,041
2025		1,542
2026 and thereafter		5,140
Total	$	187,164

Leases - Lease payments (Details) $ in Thousands	Mar. 31, 2022 USD ($)
Operating leases
2022 (excludes the three months ended March 31, 2022)	$ 10,154
2023	13,298
2024	12,619
2025	11,231
2026 and thereafter	80,769
Total lease payments	128,071
Less: Imputed Interest expense	48,270
Total	79,801
Finance leases
2023	3,000
2024	3,000
2025	3,000
2026 and thereafter	21,000
Total lease payments	30,000
Less: Imputed Interest expense	9,553
Total	$ 20,447

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Numerator
Net loss - Basic	$ (126,726)	$ (128,642)
Net loss - Diluted	$ (126,726)	$ (128,642)
Denominator
Basic	71,215,105	70,188,602
Diluted	71,215,105	70,188,602
Net loss per share:
Basic	$ (1.78)	$ (1.83)
Diluted	$ (1.78)	$ (1.83)

- Definition

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+ References + Details

Commitments and contingencies - Narrative (Details) - USD ($) $ in Thousands		1 Months Ended			3 Months Ended	12 Months Ended
	Apr. 29, 2020	Aug. 31, 2021	Dec. 31, 2019	May 31, 2019	Mar. 31, 2022	Dec. 31, 2019	Dec. 31, 2021	May 29, 2020	Jun. 30, 2016
Other Commitments
Accrued royalties					$ 30,670		$ 35,679
Akcea
Other Commitments
Upfront licensing fee					12,000
Milestone payments		$ 4,000
Akcea \| Maximum
Other Commitments
Milestone payments		$ 4,000
Censa
Other Commitments
Asset acquisition, development and regulatory milestones								$ 109,000
Asset acquisition, initial milestone								30,000
Censa \| Maximum
Other Commitments
Asset acquisition, milestone, amount								217,500
Asset acquisition, net sales milestone								$ 160,000
Agilis Merger Agreement
Other Commitments
Development milestone payments which the entity is obligated to pay					50,000
Agilis Merger Agreement \| Akcea
Other Commitments
Milestone payments			$ 4,000	$ 6,000	4,000	$ 6,000
SMA License Agreement
Other Commitments
Accrued royalties					14,000
SMA License Agreement \| Maximum
Other Commitments
Potential royalty payments due on net product sales					52,500
Agilis
Other Commitments
Development milestone payments which the entity is obligated to pay	$ 40,000				40,000
Development milestone obligation payments made					$ 2,400
Agilis \| Minimum
Other Commitments
Product sales (as a percent)					2.00%
Agilis \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay					$ 60,000
Priority review voucher amount					535,000
Net sales amount					$ 150,000
Product sales (as a percent)					6.00%
Development milestone payment obligations, net of cancellation and forfeiture					$ 20,000
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture					361,000
Agilis \| Rights Exchange Agreement
Other Commitments
Contingent liability cancellation and forfeiture of potential milestone payments	174,000
Development milestone payment obligations, cancellation and forfeiture	37,600
Contingent liability, cancellation and forfeiture	$ 211,600
BioElectron \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay					200,000
Net product revenue \| Wellcome trust
Other Commitments
Development milestone payments which the entity is obligated to pay									$ 800
Net product revenue \| Wellcome trust \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay					$ 22,400

Stock award plan - Assumptions Used (Details) - Stock option	3 Months Ended
	Mar. 31, 2022
Valuation assumptions
Risk-free interest rate (as a percent)	1.55%
Expected volatility (as a percent)	73.56%
Expected term (in years)	5 years 6 months

The Company

3 Months Ended

Mar. 31, 2022

Organization, Consolidation and Presentation of Financial Statements [Abstract]

The Company

1. The Company

PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-driven global biopharmaceutical company focused on the discovery, development and commercialization of clinically differentiated medicines that provide benefits to patients with rare disorders. PTC’s ability to innovate to identify new therapies and to globally commercialize products is the foundation that drives investment in a robust and diversified pipeline of transformative medicines. PTC’s mission is to provide access to best-in-class treatments for patients who have few or no treatment options. PTC’s strategy is to leverage its strong scientific and clinical expertise and global commercial infrastructure to bring therapies to patients. PTC believes that this allows it to maximize value for all of its stakeholders.

PTC has a portfolio pipeline that includes several commercial products and product candidates in various stages of development, including clinical, pre-clinical and research and discovery stages, focused on the development of new treatments for multiple therapeutic areas for rare diseases.

The Company has two products, Translarna™ (ataluren) and Emflaza® (deflazacort), for the treatment of Duchenne muscular dystrophy (“DMD”), a rare, life threatening disorder. Translarna has marketing authorization in the European Economic Area (the “EEA”) for the treatment of nonsense mutation Duchenne muscular dystrophy (“nmDMD”) in ambulatory patients aged 2 years and older and in Russia for the treatment of nmDMD in patients aged two years and older. In July 2020, the European Commission approved the removal of the statement “efficacy has not been demonstrated in non-ambulatory patients” from the indication statement for Translarna. Translarna also has marketing authorization in Brazil for the treatment of nmDMD in ambulatory patients two years and older and for continued treatment of patients that become non-ambulatory. Emflaza is approved in the United States for the treatment of DMD in patients two years and older.

The Company holds the rights for the commercialization of Tegsedi® (inotersen) and Waylivra® (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to the Collaboration and License Agreement (the “Tegsedi-Waylivra Agreement”), dated August 1, 2018, by and between the Company and Akcea Therapeutics, Inc. (“Akcea”), a subsidiary of Ionis Pharmaceuticals, Inc. Tegsedi has received marketing authorization in the United States, the European Union (the “EU”) and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis (“hATTR amyloidosis”). The Company began to make commercial sales of Tegsedi for the treatment of hATTR amyloidosis in Brazil in the second quarter of 2022 and it continues to make Tegsedi available in certain other countries within Latin America and the Caribbean through early access programs (“EAP Programs”). In August 2021, ANVISA, the Brazilian health regulatory authority, approved Waylivra as the first treatment for familial chylomicronemia syndrome (“FCS”) in Brazil, and the Company has initiated its commercial launch in Brazil while continuing to make Waylivra available in certain other countries within Latin America and the Caribbean through EAP Programs. Waylivra has also received marketing authorization in the EU for the treatment of FCS. Additionally, the Company submitted an application to ANVISA in December 2021 for the approval of Waylivra for the treatment of familial partial lipodystrophy, and it expects a regulatory decision on approval in the second half of 2022.

The Company also has a spinal muscular atrophy (“SMA”) collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc. (referred to collectively as “Roche”) and the Spinal Muscular Atrophy Foundation (“SMA Foundation”). The SMA program has one approved product, Evrysdi® (risdiplam), which was approved by the United States Food and Drug Administration (“FDA”) in August 2020 for the treatment of SMA in adults and children two months and older and by the European Commission in March 2021 for the treatment of 5q SMA in patients two months and older with a clinical diagnosis of SMA Type 1, Type 2 or Type 3 or with one to four SMN2 copies. Evrysdi also received marketing authorization for the treatment of SMA in Brazil in October 2020 and Japan in June 2021. In January 2022, the FDA granted priority review of a supplemental new drug application for Evrysdi to expand the indication to include pre-symptomatic infants under two months old with SMA and a regulatory decision on approval is expected in May 2022. In

addition to the Company’s SMA program, the Company’s splicing platform also includes PTC518, which is being developed for the treatment of Huntington’s disease (“HD”). The Company announced the results from its Phase 1 study of PTC518 in healthy volunteers in September 2021 demonstrating dose-dependent lowering of huntingtin messenger ribonucleic acid and protein levels, that PTC518 efficiently crosses the blood brain barrier at significant levels and that PTC518 was well tolerated. The Company initiated a Phase 2 study of PTC518 for the treatment of HD in the first quarter of 2022, which consists of an initial 12-week placebo-controlled phase focused on safety, pharmacology and pharmacodynamic effects followed by a nine-month placebo-controlled phase focused on PTC518 biomarker effect. The Company expects results from the initial 12-week phase of the Phase 2 study by the end of 2022.

The Company has a pipeline of gene therapy product candidates for rare monogenic diseases that affect the central nervous system (“CNS”) including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase (“AADC”) deficiency (“AADC deficiency”), a rare CNS disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. In January 2020, the Company submitted a marketing authorization application (“MAA”) for PTC-AADC for the treatment of AADC deficiency in the EEA to the European Medicines Agency (“EMA”). In April 2022, the Company completed the Scientific Advisory Group and Oral Explanation meetings for PTC-AADC with the EMA’s Committee for Advanced Therapies. We expect an opinion from the Committee for Medicinal Products for Human Use (“CHMP”) in May 2022. The Company is also preparing a biologics license application (“BLA”) for PTC-AADC for the treatment of AADC deficiency in the United States. In response to discussions with the FDA, the Company intends to provide additional information concerning the use of the commercial cannula for PTC-AADC in young patients. The Company expects to submit a BLA to the FDA in the third quarter of 2022.

The Company’s Bio-e platform consists of small molecule compounds that target oxidoreductase enzymes that regulate oxidative stress and inflammatory pathways central to the pathology of a number of CNS diseases. The two most advanced molecules in the Company’s Bio-e platform are vatiquinone and PTC857. The Company initiated a registration-directed Phase 2/3 placebo-controlled trial of vatiquinone in children with mitochondrial disease associated seizures in the third quarter of 2020. The Company previously experienced delays in enrolling this trial due to the COVID-19 pandemic and anticipates results from this trial to be available in the fourth quarter of 2022 The Company also initiated a registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich ataxia in the fourth quarter of 2020 and anticipates results from this trial to be available in the second quarter of 2023. In the third quarter of 2021, the Company completed a Phase 1 trial in healthy volunteers to evaluate the safety and pharmacology of PTC857. PTC857 was found to be well-tolerated with no reported serious adverse events while demonstrating predictable pharmacology. The Company initiated a Phase 2 trial of PTC857 for amyotrophic lateral sclerosis in the first quarter of 2022.

The most advanced molecule in the Company’s metabolic platform is PTC923, an oral formulation of synthetic sepiapterin, a precursor to intracellular tetrahydrobiopterin, which is a critical enzymatic cofactor involved in metabolism and synthesis of numerous metabolic products, for orphan diseases. The Company initiated a registration-directed Phase 3 trial for PTC923 for phenylketonuria (“PKU”) in the third quarter of 2021 and expects results from this trial to be available by the end of 2022.

The Company also has two oncology agents that are in clinical development, unesbulin and emvododstat. The Company completed its Phase 1 trials evaluating unesbulin in leiomyosarcoma (“LMS”) and diffuse intrinsic pontine glioma (“DIPG”) in the fourth quarter of 2021. The Company initiated a registration-directed Phase 2/3 trial of unesbulin for the treatment of LMS in the first quarter of 2022, and it expects to initiate a registration-directed Phase 2 trial of unesbulin for the treatment of DIPG in the third quarter of 2022. The Company completed its Phase 1 trial evaluating emvododstat in acute myelogenous leukemia (“AML”), in the fourth quarter of 2021. The Company expects to provide further updates regarding its emvododstat program at a later date.

In June 2020, the Company initiated a Phase 2/3 clinical trial evaluating the efficacy and safety of emvododstat in patients hospitalized with COVID-19. In February 2021, the Company announced the completion of the first stage of the Phase 2/3 trial. The Company expects results from this trial to be available in the second quarter of 2022.

In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas for rare diseases.

The Company’s marketing authorization for Translarna in the EEA is subject to annual review and renewal by the European Commission following reassessment by the EMA of the benefit-risk balance of the authorization, which the Company refers to as the annual EMA reassessment. The marketing authorization in the EEA was last renewed in June 2021 and is effective, unless extended, through August 5, 2022. In February 2022, the Company submitted a marketing authorization renewal request to the EMA and, in April 2022, the CHMP issued an opinion recommending the renewal. This marketing authorization is further subject to the specific obligation to conduct and submit the results of a multi-center, randomized, double-blind, 18-month, placebo-controlled trial, followed by an 18-month open-label extension, according to an agreed protocol, in order to confirm the efficacy and safety of Translarna. The Company refers to the trial and open-label extension together as Study 041. The Company anticipates reporting results from the placebo-controlled trial by the end of the second quarter of 2022 after data analysis is completed. The Company then expects to submit a report on the placebo-controlled trial and the open-label extension data that has been collected to date to the EMA by the end of the third quarter of 2022, as required.

Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application (“NDA”) over protest with the FDA, for which the FDA granted a standard review. In October 2017, the Office of Drug Evaluation I of the FDA issued a complete response letter for the NDA, stating that it was unable to approve the application in its current form. In response, the Company filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied PTC’s appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company followed the FDA’s recommendation and collected, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, and announced the results of Study 045 in February 2021. Study 045 did not meet its pre-specified primary endpoint. The Company anticipates reporting results from the placebo-controlled trial of Study 041 by the end of the second quarter of 2022 after data analysis is completed, and subject to a positive outcome in that study, the Company expects to re-submit the NDA.

As of March 31, 2022, the Company had an accumulated deficit of approximately $2,224.7 million. The Company has financed its operations to date primarily through the private offerings in September 2019 of 1.50% convertible senior notes due 2026 and in August 2015 of 3.00% convertible senior notes due 2022 (see Note 9), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offering" of its common stock, its initial public offering of common stock in June 2013, proceeds from the Royalty Purchase Agreement dated as of July 17, 2020, by and among the Company, RPI 2019 Intermediate Finance Trust (“RPI”), and, solely for the limited purposes set forth therein, Royalty Pharma PLC (the “Royalty Purchase Agreement”) (see Note 2), private placements of its convertible preferred stock, collaborations, bank and institutional lender debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates. Since 2014, the Company has also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and since May 2017, the Company has generated revenue from net sales of Emflaza for the treatment of DMD in the United States. The Company has also relied on revenue associated with milestone and royalty payments from Roche pursuant to the License and Collaboration Agreement (the “SMA License Agreement”) dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation, under its SMA program. The Company expects that cash flows from the sales of its products, together with the Company’s cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Revenues:
Revenue	$ 148,735	$ 117,942
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible assets	10,135	9,104
Amortization of intangible assets	23,473	11,278
Research and development	140,078	134,513
Selling, general and administrative	73,271	61,095
Change in the fair value of deferred and contingent consideration	(11,700)	100
Total operating expenses	235,257	216,090
Loss from operations	(86,522)	(98,148)
Interest expense, net	(23,514)	(19,159)
Other expense, net	(11,855)	(10,884)
Loss before income tax expense	(121,891)	(128,191)
Income tax expense	(4,835)	(451)
Net loss attributable to common stockholders	$ (126,726)	$ (128,642)
Weighted-average shares outstanding:
Basic	71,215,105	70,188,602
Diluted	71,215,105	70,188,602
Net loss per share-basic and diluted (in dollars per share)
Basic	$ (1.78)	$ (1.83)
Diluted	$ (1.78)	$ (1.83)
Net product revenue
Revenues:
Revenue	$ 129,832	$ 91,280
Collaboration revenue
Revenues:
Revenue	7	20,007
Royalty revenue
Revenues:
Revenue	$ 18,896	$ 6,655

Subsequent events

3 Months Ended

Mar. 31, 2022

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 - Reconciliation of cash (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021	Mar. 31, 2021	Dec. 31, 2020
Accounting Policies [Abstract]
Cash and cash equivalents	$ 144,178	$ 189,718
Restricted cash included in deposits and other assets	7,500	7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 151,678	$ 197,218	$ 154,132	$ 216,312

Leases - Narrative (Details) $ in Thousands		3 Months Ended		12 Months Ended
Leases - Narrative (Details) $ in Thousands	Jun. 19, 2020 USD ($) room	Mar. 31, 2022 USD ($) ft² item lease	Mar. 31, 2021 USD ($)	Dec. 31, 2020 USD ($)	Dec. 31, 2021 USD ($)
Leases
Number of operating leases \| lease		3
Number of new leases entered into during the period. \| lease		1
Operating lease, expense		$ 5,300	$ 5,400
Finance lease liabilities- current		1,772			$ 3,000
Finance lease liabilities- noncurrent		18,675			$ 20,053
Aggregate rent, Initial term		128,071
2022 (excludes the three months ended March 31, 2022)		10,154
2023		13,298
Finance Lease, Right-of-Use Asset		0
Research and development		140,078	134,513
MassBio
Leases
Finance lease cost		$ 400	$ 400
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		1 month 6 days
Maximum
Leases
Operating lease, term of contract		13 years 3 months 18 days
Renewal Term		10 years
New Building \| Minimum
Leases
Area of real estate property \| ft²		75,000
Hopewell Campus
Leases
Operating lease, term of contract		15 years
Area of real estate property \| ft²		220,500
Renewal Term		10 years
Number of renewable terms \| item		2
Aggregate rent, Initial term		$ 111,500
Percent of market rate		95.00%
Mountain View
Leases
2022 (excludes the three months ended March 31, 2022)		$ 900
Thereafter		$ 0

Fair value of financial instruments and marketable securities - Narrative (Details)	1 Months Ended				3 Months Ended
	Aug. 31, 2021 USD ($)	Feb. 28, 2021 USD ($) fund $ / shares	Jan. 31, 2020 USD ($) $ / shares	May 31, 2019 USD ($) $ / shares	Mar. 31, 2022 USD ($)	Mar. 31, 2021 USD ($)	Dec. 31, 2021 USD ($)	Apr. 29, 2020 USD ($)	Sep. 30, 2019 USD ($)	Aug. 31, 2015 USD ($)
Financial assets and liabilities measured at fair value on recurring basis
Write downs of available for sale debt securities					$ 0
Realized gain (loss) from sale of marketable securities					(100,000)	$ 700,000
Increase in allowance for credit losses					0	0
Purchase of equity investments						100,000
Unrealized gain (loss) on ClearPoint Equity Investment					(1,049,000)	6,764,000
Purchase of convertible note					39,035,000	141,985,000
Unrealized gain (loss) on convertible note					(1,542,000)	7,858,000
Purchase of marketable securities - equity investments						200,000,000
Redemption of marketable securities- equity investments					2,423,000
Transfers of assets measured between Level 1, Level 2, and Level 3					0		$ 0
Operating Expenses					235,257,000	216,090,000
Business Combination, Contingent Consideration Arrangements, Change in Amount of Contingent Consideration, Asset					11,700,000	(100,000)
3.00% Convertible senior notes due 2022 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal					150,000,000		150,000,000			$ 150,000,000.0
Interest rate ( as a percent )										3.00%
Fair value of convertible notes					155,700,000		158,300,000
1.50% Convertible senior notes due 2026 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal					$ 287,500,000		287,500,000		$ 287,500,000
Interest rate ( as a percent )					1.50%				1.50%
Fair value of convertible notes					$ 287,500,000		305,300,000
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%
Agilis \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Product sales (as a percent)					6.00%
Development milestone payments which the entity is obligated to pay					$ 60,000,000.0
Priority review voucher amount					535,000,000.0
Net sales amount					150,000,000.0
Non-collaborative Arrangement Transactions
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay					50,000,000.0
Recurring basis
Financial assets and liabilities measured at fair value on recurring basis
Fair value of convertible debt					19,429,000		20,971,000
ClearPoint equity investment
Financial assets and liabilities measured at fair value on recurring basis
Purchase of equity investments		$ 100,000		$ 4,000,000.0
Share price (in USD per share) \| $ / shares		$ 23.50		$ 3.10
Unrealized gain (loss) on ClearPoint Equity Investment					(1,000,000.0)	6,800,000
Marketable securities - equity investments					13,500,000		14,500,000
ClearPoint convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Purchase of convertible debt investment			$ 10,000,000.0
Conversion price - convertible note \| $ / shares			$ 6.00
Unrealized gain (loss) on convertible note					(1,500,000)	7,900,000
Fair value of convertible debt					19,400,000		$ 21,000,000.0
Mutual Funds
Financial assets and liabilities measured at fair value on recurring basis
Purchase of marketable securities - equity investments		$ 200,000,000.0
Number of mutual funds invested in \| fund		2
Redemption of marketable securities- equity investments					2,400,000	0.0
Unrealized loss on marketable securities - equity investments					6,500,000	300,000
Unrealized foreign currency transaction losses, net					$ 700,000	$ (0.0)
Mutual Fund, Purchase One
Financial assets and liabilities measured at fair value on recurring basis
Purchase of marketable securities - equity investments	$ 5,400,000
Mutual Fund, Purchase Two
Financial assets and liabilities measured at fair value on recurring basis
Purchase of marketable securities - equity investments	$ 4,600,000

Net loss per share - Antidilutive (Details) - shares	3 Months Ended
Net loss per share - Antidilutive (Details) - shares	Mar. 31, 2022	Mar. 31, 2021
Net loss per share
Total shares excluded from calculation (in shares)	14,266,694	12,483,840
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	11,751,713	10,989,202
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	2,514,981	1,494,638

Revenue recognition - Collaboration and Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021	Nov. 30, 2011
Collaboration and royalty revenue
Remaining potential milestones that can be achieved	$ 300,000
Milestone payments received	50,000
Revenue	148,735	$ 117,942
Collaboration revenue
Collaboration and royalty revenue
Revenue	7	20,007
Royalty revenue
Collaboration and royalty revenue
Revenue	18,896	6,655
SMA License Agreement \| Collaboration revenue
Collaboration and royalty revenue
Revenue	0	20,000
SMA License Agreement \| Royalty revenue
Collaboration and royalty revenue
Revenue	18,900	6,700
SMA License Agreement \| Roche And Sma Foundation \| Collaboration revenue
Collaboration and royalty revenue
Revenue	0	20,000
Research And Development Event Milestones \| SMA License Agreement
Collaboration and royalty revenue
Milestone payments received		20,000
Sales Milestones \| SMA License Agreement
Collaboration and royalty revenue
Remaining potential milestones that can be achieved	$ 300,000
Milestone payments received		$ 20,000
Maximum \| Research And Development Event Milestones \| SMA License Agreement
Collaboration and royalty revenue
Remaining potential milestones that can be achieved			$ 135,000
Maximum \| Sales Milestones \| SMA License Agreement
Collaboration and royalty revenue
Remaining potential milestones that can be achieved			$ 325,000

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended
Leases - Lease costs (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Mar. 31, 2021
Leases
Fixed lease cost	$ 4,126	$ 4,104
Variable lease cost	1,076	1,093
Short-term lease cost	74	164
Total operating lease cost	$ 5,276	$ 5,361

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Cash flows from operating activities
Net loss	$ (126,726)	$ (128,642)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	26,314	13,587
Non-cash operating lease expense	1,908	1,819
Non-cash royalty revenue related to sale of future royalties	(8,113)	(2,858)
Non-cash interest expense on liability related to sale of future royalties	18,874	18,080
Change in valuation of deferred and contingent consideration	(11,700)	100
Unrealized loss (gain) on ClearPoint Equity Investments	1,049	(6,764)
Unrealized loss (gain) on ClearPoint convertible debt security	1,542	(7,858)
Unrealized gain on marketable securities - equity investments	6,477	302
Amortization of premiums on investments, net	887	1,359
Amortization of debt issuance costs	464	452
Share-based compensation expense	26,589	25,707
Disposal of asset	79
Unrealized foreign currency transaction losses, net	2,135	24,691
Changes in operating assets and liabilities:
Inventory, net	350	1,963
Prepaid expenses and other current assets	25,118	15,605
Trade and royalty receivables, net	(28,372)	(25,010)
Deposits and other assets	(510)	136
Accounts payable and accrued expenses	(30,680)	(28,756)
Other liabilities	(3,089)	(1,916)
Deferred revenue		(2,154)
Net cash used in operating activities	(97,404)	(100,157)
Cash flows from investing activities
Purchases of fixed assets	(9,312)	(5,669)
Purchases of marketable securities - available for sale	(39,035)	(141,985)
Purchases of marketable securities - equity investments		(200,000)
Sale and redemption of marketable securities- available for sale	167,101	392,093
Sale and redemption of marketable securities - equity investments	2,423
Acquisition of product rights and licenses	(72,134)	(14,192)
Purchase of equity investment in ClearPoint		(100)
Net cash provided by investing activities	49,043	30,147
Cash flows from financing activities
Proceeds from exercise of options	2,444	11,755
Payment of finance lease principal	(1,276)	(2,224)
Net cash provided by financing activities	1,168	9,531
Effect of exchange rate changes on cash	1,653	(1,701)
Net decrease in cash and cash equivalents	(45,540)	(62,180)
Cash and cash equivalents, and restricted cash beginning of period	197,218	216,312
Cash and cash equivalents, and restricted cash end of period	151,678	154,132
Supplemental disclosure of cash information
Cash paid for interest	6,130	5,182
Cash paid for income taxes	1,987	687
Supplemental disclosure of non-cash investing and financing activity
Unrealized loss on marketable securities, net of tax	(2,913)	(1,294)
Right-of-use assets obtained in exchange for operating lease obligations	587	13
Acquisition of product rights and licenses	$ 12,589	$ 8,870

Debt - Narrative (Details)		1 Months Ended		3 Months Ended		6 Months Ended
Debt - Narrative (Details)	Jan. 01, 2021 USD ($)	Sep. 30, 2019 USD ($) D $ / shares	Aug. 31, 2015 USD ($) D $ / shares	Mar. 31, 2022 USD ($)	Mar. 31, 2021 USD ($)	Mar. 14, 2021 USD ($)	Dec. 31, 2021 USD ($)
Long-term debt
Long-term debt				$ 282,176,000			$ 281,894,000
Current portion of long-term debt				149,721,000			149,540,000
Additional paid-in capital				2,152,639,000			2,123,606,000
1.50% Convertible senior notes due 2026
Long-term debt
Term of the convertible notes	7 years
Debt discount to be amortized	$ 0
Incremental interest rate per annum						0.50%
Interest expense				1,352,000	$ 1,346,000	$ 2,100,000
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				282,176,000			281,894,000
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	4 years 6 months
Equity component of convertible notes, net		$ 123,000,000.0
Net deferred tax liability in connection with convertible notes				$ 25,300,000
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				149,721,000			149,540,000
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
Net deferred tax liability in connection with convertible notes			$ 22,300,000
Remaining contractual life of the convertible notes				4 months 24 days
Interest expense				$ 1,291,000	$ 1,285,000
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%
Redemptions of convertible notes				$ 0
Sinking fund			$ 0
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

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Statement of Comprehensive Income [Abstract]
Net loss	$ (126,726)	$ (128,642)
Other comprehensive (loss) income:
Unrealized loss on marketable securities, net of tax of $0	(2,913)	(1,294)
Foreign currency translation gain (loss), net of tax of $0	8,587	23,508
Comprehensive loss	$ (121,052)	$ (106,428)

- Definition

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

+ References

+ Details

Summary of significant accounting policies - Liability for Sale of Future Royalties (Details) - USD ($) $ in Millions	Jul. 17, 2020	Mar. 31, 2022
Assigned royalty payments
Cash consideration received from Royalty Purchase Agreement	$ 650.0
Assigned royalty payment, retained percentage	57.067%
Remaining potential milestones that can be achieved		$ 300.0
Royalty Purchase Agreement \| Assigned Royalty Payments
Assigned royalty payments
Assigned royalty payment, percentage	42.933%
Cash consideration received from Royalty Purchase Agreement	$ 650.0
Royalty purchase agreement, termination period	60 days
Royalty purchase agreement, payment maximum	$ 1,300.0

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
Debt - Interest Expense (Details) - USD ($) $ in Thousands	Mar. 31, 2022	Mar. 31, 2021	Mar. 14, 2021	Jul. 17, 2020
Long-term debt
Amortization of debt issuance costs	$ 464	$ 452
Effective interest rate of the liability component	10.10%			11.00%
1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 1,069	1,069
Amortization of debt issuance costs	283	277
Total	$ 1,352	$ 1,346	$ 2,100
Effective interest rate of the liability component	1.90%	1.90%
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 1,110	$ 1,110
Amortization of debt issuance costs	181	175
Total	$ 1,291	$ 1,285
Effective interest rate of the liability component	3.50%	3.50%

Debt - (Tables)

3 Months Ended

Mar. 31, 2022

Debt Instrument, Redemption [Line Items]

Summary of liability for sale of future royalties


	Three Months Ended March 31,
Liability for sale of future royalties- (current and noncurrent)	2022
Beginning balance as of December 31, 2021	$	733,985
Less: Non-cash royalty revenue payable to RPI		(8,113)
Plus: Non-cash interest expense recognized		18,874
Ending balance	$	744,746
Effective interest rate as of March 31, 2022		10.1	%

1.50% Convertible senior notes due 2026

Debt Instrument, Redemption [Line Items]

Summary of convertible notes



Liability component	March 31, 2022		December 31, 2021
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(5,324)		(5,606)
Net carrying amount	$	282,176	$	281,894

Summary of interest expense recognized related to the Convertible Notes



	Three Months Ended March 31,
	2022				2021
Contractual interest expense	$	1,069		$	1,069
Amortization of debt issuance costs		283			277
Total	$	1,352		$	1,346
Effective interest rate of the liability component		1.9	%		1.9	%

3.00% Convertible senior notes due 2022

Debt Instrument, Redemption [Line Items]

Summary of convertible notes




Liability component	March 31, 2022		December 31, 2021
Principal	$	150,000	$	150,000
Less: Debt issuance costs		(279)		(460)
Net carrying amount	$	149,721	$	149,540

Summary of interest expense recognized related to the Convertible Notes



	Three Months Ended March 31,
	2022			2021
Contractual interest expense	$	1,110		$	1,110
Amortization of debt issuance costs		181			175
Total	$	1,291		$	1,285
Effective interest rate of the liability component		3.5	%		3.5	%

Stock award plan - (Tables)

3 Months Ended

Mar. 31, 2022

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, 2021	10,772,582	$	43.66
Granted	1,275,830		38.10
Exercised	(97,188)		25.15
Forfeited/Cancelled	(199,511)		49.92
Outstanding at March 31, 2022	11,751,713	$	43.11	6.97	years	$	38,075
Vested or Expected to vest at March 31, 2022	4,497,327	$	48.04	8.54	years	$	2,127
Exercisable at March 31, 2022	6,763,376	$	39.44	5.79	years	$	35,859

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


		Three months ended
		March 31, 2022
Risk-free interest rate		1.55%
Expected volatility		73.56%
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, 2021	1,519,831	$	55.43
Granted	1,490,190		38.10
Vested	(426,470)		51.26
Forfeited	(68,570)		48.45
Unvested at March 31, 2022	2,514,981	$	46.06

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


	Three Months Ended March 31,
	2022		2021
Research and development	$	13,034	$	13,725
Selling, general and administrative		13,555		11,982
Total	$	26,589	$	25,707