PTC Therapeutics (PTCT) 10-Q 30 Apr 20 2020 Q1 Quarterly report Financial data

Cover

Cover - shares	3 Months Ended
	Mar. 31, 2020	Apr. 28, 2020
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Mar. 31, 2020
Document Transition Report	false
Entity File Number	001-35969
Entity Registrant Name	PTC Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3416587
Entity Address, Address Line One	100 Corporate Court
Entity Address, City or Town	South Plainfield,
Entity Address, State or Province	NJ
Entity Address, Postal Zip Code	07080
City Area Code	908
Local Phone Number	222-7000
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Title of 12(b) Security	Common Stock, $0.001 par value per share
Trading Symbol	PTCT
Security Exchange Name	NASDAQ
Entity Common Stock, Shares Outstanding		62,875,395
Entity Central Index Key	0001070081
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q1

Consolidated Balance Sheets (un

Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 123,287	$ 288,028
Marketable securities	472,572	398,535
Trade receivables, net	52,623	55,538
Inventory, net	19,133	19,285
Prepaid expenses and other current assets	24,307	17,898
Total current assets	691,922	779,284
Fixed assets, net	26,169	21,549
Intangible assets, net	705,294	710,500
Goodwill	82,341	82,341
Deposits and other assets	39,866	30,108
Total assets	1,545,592	1,623,782
Current liabilities:
Accounts payable and accrued expenses	145,386	159,276
Current portion of long-term debt	20,000	20,000
Deferred revenue	8,638	8,242
Other current liabilities	3,644	8,339
Deferred consideration payable	40,000	40,000
Total current liabilities	217,668	235,857
Deferred revenue- long term	1,768	3,415
Long-term debt	294,574	293,859
Contingent consideration payable	357,200	356,300
Deferred tax liability	130,862	130,862
Other long-term liabilities	14,786	9,159
Total liabilities	1,016,858	1,029,452
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 62,758,520 shares at March 31, 2020. Authorized 125,000,000 shares; issued and outstanding 61,935,870 shares at December 31, 2019.	62	62
Additional paid-in capital	1,834,061	1,795,351
Accumulated other comprehensive income	(1,985)	(10,584)
Accumulated deficit	(1,303,404)	(1,190,499)
Total stockholders’ equity	528,734	594,330
Total liabilities and stockholders’ equity	$ 1,545,592	$ 1,623,782

Consolidated Balance Sheets (_2

Consolidated Balance Sheets (unaudited) (Parenthetical) - $ / shares	Mar. 31, 2020	Dec. 31, 2019
Statement of Financial Position [Abstract]
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares (in shares)	125,000,000	125,000,000
Common stock, issued shares (in shares)	62,758,520	61,935,870
Common stock, outstanding shares (in shares)	62,758,520	61,935,870

Consolidated Statements of Oper

Consolidated Statements of Operations (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Revenues:
Revenue	$ 68,259	$ 53,583
Cost of Goods and Service, Excluding Amortization Of Intangible Assets	4,085	2,376
Operating expenses:
Amortization of acquired intangible assets	7,949	6,077
Research and development	90,107	52,566
Selling, general and administrative	58,209	40,544
Change in the fair value of deferred and contingent consideration	900	21,160
Total operating expenses	161,250	122,723
Loss from operations	(92,991)	(69,140)
Interest expense, net	(5,642)	(2,288)
Other expense, net	(13,832)	(109)
Loss before income tax expense	(112,465)	(71,537)
Income tax expense	(222)	(576)
Net loss attributable to common stockholders	$ (112,687)	$ (72,113)
Weighted-average shares outstanding:
Basic and diluted (in shares)	62,389,158	55,855,111
Net loss per share-basic and diluted (in dollars per share)
Net loss per share—basic and diluted (in dollars per share)	$ (1.81)	$ (1.29)
Net product revenue
Revenues:
Revenue	$ 68,196	$ 53,054
Collaboration and grant revenue
Revenues:
Revenue	$ 63	$ 529

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Statement of Comprehensive Income [Abstract]
Net loss	$ (112,687)	$ (72,113)
Other comprehensive (loss) income:
Unrealized (loss) gain on marketable securities, net of tax	(63)	59
Foreign currency translation gain (loss), net of tax	8,662	(716)
Comprehensive loss	$ (104,088)	$ (72,770)

Consolidated Statements of Stoc

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common stock	Additional paid-in capital	AOCI Attributable to Parent	Accumulated deficit
Balance (in shares) at Dec. 31, 2018		50,606,147
Balance at the beginning of the period at Dec. 31, 2018	$ 350,727	$ 51	$ 1,288,137	$ 1,462	$ (938,923)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)		7,563,725
Issuance of common stock related to equity offerings	224,441	$ 7	224,434
Exercised (in shares)		80,826
Exercise of options	1,281		1,281
Restricted stock vesting and issuance, net (in shares)		168,092
Restricted stock vesting and issuance, net	0
Share-based compensation expense	9,263		9,263
Comprehensive income	(657)			(657)
Net loss	(72,113)				(72,113)
Balance (in shares) at Mar. 31, 2019		58,418,790
Balance at the end of the period at Mar. 31, 2019	512,942	$ 58	1,523,115	805	(1,011,036)
Balance (in shares) at Dec. 31, 2019		61,935,870
Balance at the beginning of the period at Dec. 31, 2019	594,330	$ 62	1,795,351	(10,584)	(1,190,499)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)		262,205
Issuance of common stock related to equity offerings	13,503	$ 0	13,503
Exercised (in shares)		379,684
Exercise of options	9,987	$ 0	9,987
Restricted stock vesting and issuance, net (in shares)		180,761
Restricted stock vesting and issuance, net	0
Share-based compensation expense	15,220		15,220
Other	(218)
Comprehensive income	8,599			8,599
Net loss	(112,687)
Balance (in shares) at Mar. 31, 2020		62,758,520
Balance at the end of the period at Mar. 31, 2020	$ 528,734	$ 62	$ 1,834,061	$ (1,985)	$ (1,303,404)

Consolidated Statements of Cash

Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Cash flows from operating activities
Net loss	$ (112,687)	$ (72,113)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	9,235	7,059
Non-cash lease expense	1,330	0
Change in valuation of deferred and contingent consideration	900	21,160
Unrealized loss on equity investment in Clearpoint	1,574	0
Unrealized loss on Clearpoint convertible debt security	2,799	0
Non-cash interest expense	5,459	1,982
Amortization of discounts on investments, net	(333)	(257)
Amortization of debt issuance costs	256	139
Share-based compensation expense	15,220	9,263
Unrealized foreign currency transaction losses, net	8,675	865
Changes in operating assets and liabilities:
Inventory	102	(334)
Prepaid expenses and other current assets	(6,675)	(191)
Trade receivables, net	2,346	20,786
Deposits and other assets	(5,819)	(10,754)
Accounts payable and accrued expenses	(4,000)	(28,653)
Other liabilities	1,264	8,065
Deferred revenue	(1,200)	574
Net cash used in operating activities	(81,554)	(42,409)
Cash flows from investing activities
Purchases of fixed assets	(6,023)	(2,865)
Purchase of convertible debt security	(10,000)	0
Purchases of marketable securities	(298,814)	(165,723)
Sale and redemption of marketable securities	224,997	18,090
Acquisition of product rights and licenses	(11,434)	0
Net cash used in investing activities	(101,274)	(150,498)
Cash flows from financing activities
Proceeds from exercise of options	9,987	1,281
Net proceeds from public offerings	13,503	224,441
Repayment of senior secured term loan	(5,000)	0
Net cash provided by financing activities	18,490	225,722
Effect of exchange rate changes on cash	(403)	(1,169)
Net increase in cash and cash equivalents	(164,741)	31,646
Cash and cash equivalents, and restricted cash beginning of period	295,528	169,498
Cash and cash equivalents, and restricted cash end of period	123,287
Supplemental disclosure of cash information
Cash paid for interest	4,878	3,111
Cash paid for income taxes	507	537
Supplemental disclosure of non-cash investing and financing activity
Unrealized (loss) gain on marketable securities, net of tax	(63)	59
Right-of-use assets obtained in exchange for lease obligations	22,642	11,314
Acquisition of product rights and licenses	$ 2,775	$ 0

Summary of significant accounti

Summary of significant accounting policies	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Summary of significant accounting policies	Summary of significant accounting policies The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2019 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 2, 2020 (the " 2019 Form 10-K"). Additional significant accounting policies adopted during the three month period ended March 31, 2020 are discussed in further detail below. Basis of presentation The accompanying financial information as of March 31, 2020 and for the three months ended March 31, 2020 and 2019 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2019 and notes thereto included in the 2019 Form 10-K. In the opinion of management, the unaudited financial information as of March 31, 2020 and for the three months ended March 31, 2020 and 2019 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders' equity, and cash flows. The results of operations for the three month period ended March 31, 2020 are not necessarily indicative of the results to be expected for the year ended December 31, 2020 or for any other interim period or for any other future year. Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, valuation procedures for convertible notes, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. Restricted cash Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the twelve-month period ended December 31, 2019 in connection with obligations under a facility lease for our leased biologics manufacturing facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million , is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows: Beginning of period- December 31, 2019 End of period- March 31, 2020 Cash and cash equivalents $ 288,028 $ 123,287 Restricted cash included in deposits and other assets 7,500 7,500 Total Cash, cash equivalents and restricted cash per statement of cash flows $ 295,528 $ 130,787 Marketable securities The Company considers securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security's amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three-month period ended March 31, 2020 , no allowance was recorded for credit losses. Inventory and cost of product sales Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. Amounts related to clinical development programs and marketing efforts are immaterial. The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2020 December 31, 2019 Raw materials $ 871 $ 874 Work in progress 9,482 9,652 Finished goods 8,780 8,759 Total inventory $ 19,133 $ 19,285 The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. For the three month period ended March 31, 2020 , the Company recorded a $0.2 million inventory write-down, primarily related to product approaching expiration. No write downs were recorded for the three month period ended March 31, 2019 . Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three month periods ended March 31, 2020 and 2019 , these amounts were immaterial. Cost of product sales Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales. Production costs are expensed as cost of product sales when the related products are sold. Revenue recognition Net product revenue The Company's net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of the product, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to product sales. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month. The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained. For the three months ended March 31, 2020 and 2019 , net product sales outside of the United States were $40.7 million and $35.3 million respectively, and net product sales in the United States were $27.5 million and $17.8 million respectively. In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. The Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense. Collaboration revenue The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events. At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations. For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance. For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company's control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities. Allowance for doubtful accounts The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends. The allowance for doubtful accounts was $0.2 million as of March 31, 2020 and $0.3 million as of December 31, 2019 . Bad debt expense was immaterial for the three -month periods ended March 31, 2020 and 2019 . For the three-month period ended March 31, 2020 , no allowance was recorded for credit losses. Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset acquired in a business combination. The Company utilizes the "income method”, and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company's outlook and market performance of the Company's industry and recent and forecasted financial performance. Goodwill Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassess its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount. Income Taxes O n 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"), referred to herein as the U.S. Tax Act, for qualified improvement property. As of March 31, 2020, the Company expects that these provisions will not have a material impact. Tax provisions of the Act also include the deferral of certain payroll taxes, relief for retaining employees, and other provisions. The Company is evaluating the impact of the Act and currently expects to benefit from the deferral of certain payroll taxes and retention credit through the end of calendar year 2020. The ultimate impact of the CARES Act may differ from this estimate due to changes in interpretations and guidance that may be issued and actions the Company may take in response to the CARES Act. The Company will continue to assess the impact that various provisions will have on its business. On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended March 31, 2020 . Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized. The Company recorded a deferred tax liability in conjunction with the Merger of $ 122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful. 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 leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments. Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases. Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories. A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates. The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. See Note 3 Leases for additional information. Impact of recently adopted accounting pronouncements In December 2019, the FASB issued ASU 2019-12,"Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes”. ASU 2019-12 simplifies the accounting for income taxes by removing certain exceptions to the general principals in Topic 740. The amendments also improve consistent application of and simplify GAAP for other areas of Topic 740 by clarifying and amending the existing guidance. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2020. For all other entities, it is effective for annual periods beginning after December 15, 2021 and interim periods in annual periods beginning after December 15, 2022. Early adoption is permitted, including adoption in any interim period. The Company early adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments - Credit Losses, which expands the scope of the practical expedient that allows entities to exclude the accrued interest component of amortized cost from various disclosures required by ASC 326 to also include certain disclosures required by ASC 320. Entities that elect to apply the practical expedient must disclose the total amount of accrued interest that they exclude from their disclosures of amortized cost. The amendments have the same effective dates as ASU 2016-13 (Topic 326) for entities that have not yet adopted that standard. The Company adopted ASU 2016-13 and ASU 2019-11 effective January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its accounting policy for marketable securities within this footnote as well as its fair value footnote (Note 4) with additional disclosures as required by the standard upon adoption. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820), Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". This standard eliminates certain disclosure requirements for fair value measurements for all entities, requires public entities to disclose certain new information and modifies some disclosure requirements. The new guidance is effective for all entities for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years. An entity is permitted to early adopt either the entire standard or only the provisions that eliminate or modify requirements. Entities can elect to early adopt in interim periods, including periods for which they have not yet issued financial statements or made their financial statements available for issuance. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its fair value footnote (Note 4) with additional and modified disclosures as required by the standard upon adoption. In August 2018, the FASB issued ASU 2018-15,"Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract". ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In November 2018, the FASB issued ASU 2018-18,"Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606”. ASU 2018-18 provides guidance on whether certain transactions between collaborative arrangement participants should be accounted for with revenue under Topic 606. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

The Company

The Company	3 Months Ended
	Mar. 31, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-driven global biopharmaceutical company focused on the discovery, development and commercialization of clinically-differentiated medicines that provide benefits to patients with rare disorders. The Company’s ability to globally commercialize products is the foundation that drives its continued investment in a robust diversified pipeline of transformative medicines and its mission to provide access to best-in-class treatments for patients who have an unmet medical need. The Company’s strategy is to bring best-in-class therapies with differentiated clinical benefit to patients affected by rare disorders and to leverage its global commercial infrastructure to maximize value for its patients and other stakeholders. The Company has two products, Translarna ™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna has marketing authorization in the European Economic Area (the “EEA”) for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged 2 years and older and in Brazil for the treatment of nmDMD in ambulatory patients aged 5 years and older, subject to annual renewal and other conditions. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. The Company has a pipeline of gene therapy product candidates for rare monogenic diseases that affect the central nervous system (“CNS”) including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC deficiency, a rare CNS disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. The Company is preparing a biologics license application, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which it anticipates submitting to the United States Food and Drug Administration, or FDA, in the second half of 2020. In January 2020, the Company submitted a marketing authorization application, or MAA, to the European Medicines Agency (“EMA”) for PTC-AADC for the treatment of AADC deficiency in the EEA, and the Company expects an opinion from the Committee for Medicinal Products for Human Use by the end of 2020. The Company holds the rights for the commercialization of Tegsedi™ (inotersen) and Waylivra™ (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to the Company’s Collaboration and License Agreement with Akcea Therapeutics, Inc. (“Akcea”). Tegsedi has received marketing authorization in the United States, the European Union (the “EU”) and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis, or hATTR amyloidosis. Waylivra has received marketing authorization in the EU for the treatment of familial chylomicronemia syndrome, or FCS. The Company anticipates filing for marketing authorization for Waylivra with ANVISA, the Brazilian health regulatory authority, in the second half of 2020. The Company also has a spinal muscular atrophy ("SMA") collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc., referred to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. The lead compound in the SMA program is risdiplam (RG7916, RO7034067). Roche submitted an NDA for risdiplam to the FDA in the fourth quarter of 2019. In April 2020, the FDA extended the Prescription Drug User Fee Act ("PDUFA") date for a decision from May 24, 2020 to August 24, 2020 as a result of additional data that Roche submitted, including comprehensive data from the Sunfish part 2 study. Risdiplam is expected to be indicated in the United States for SMA type 1, 2 and 3 patients, if approved. Roche anticipates submitting an MAA for risdiplam in the EEA in mid-year 2020. On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, including certain compounds that the Company has begun to develop as part of its Bio-e platform, (the “Asset Acquisition”) pursuant to an Asset Purchase Agreement by and between the Company and BioElectron, dated October 1, 2019 (the “Asset Acquisition Agreement”). The transaction was accounted for as an asset acquisition. In 2020, the Company plans to initiate three trials in this platform with two unique compounds that regulate inflammation and oxidative stress. In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas, including rare diseases and oncology. The Company’s marketing authorization for Translarna in the EEA is subject to annual review and renewal by the European Commission following reassessment by the EMA of the benefit-risk balance of the authorization, which the Company refers to as the annual EMA reassessment. This marketing authorization is further subject to the specific obligation to conduct and submit the results of a multi-center, randomized, double-blind, 18-month, placebo-controlled trial, followed by an 18-month open-label extension, according to an agreed protocol, in order to confirm the efficacy and safety of Translarna. The final report on the trial and open-label extension is to be submitted by the Company to the EMA by the end of the third quarter of 2022. The Company refers to the trial and open-label extension together as Study 041. The marketing authorization in the EEA was last renewed in July 2019 and is effective, unless extended, through August 5, 2020. The renewal was based on the Company’s commitment to conduct Study 041 and the totality of the clinical data available from its trials and studies of Translarna for the treatment of nmDMD, including the safety and efficacy results of the Phase 2b and Phase 3 clinical trials. The primary efficacy endpoint was not achieved in either trial within the pre-specified level of statistical significance. In February 2020, the Company submitted a marketing authorization renewal request to the EMA. Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application, or NDA, over protest with the FDA, for which the FDA granted a standard review. In October 2017, the Office of Drug Evaluation I of the FDA issued a complete response letter for the NDA, stating that it was unable to approve the application in its current form. In response, the Company filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied the Company's appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company intends to follow the FDA’s recommendation and will collect, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, which the Company initiated in the fourth quarter of 2018. The Company expects that data for Study 045 will be available in the third quarter of 2020 followed by a potential re-submission of an NDA thereafter. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework. On April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. The Transaction was completed pursuant to an asset purchase agreement, dated March 15, 2017, as amended on April 20, 2017, (the "Asset Purchase Agreement"), by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The Transaction was accounted for as an asset acquisition. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction. Upon the closing of the Transaction, the Company paid to Marathon total upfront consideration comprised of $75.0 million in cash, funded through cash on hand, and 6,683,598 shares of the Company’s common stock. The number of shares of common stock issued at closing was determined by dividing $65.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Stock Market for the 15 trading-day period ending on the third trading day immediately preceding the closing. 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, and a single $50.0 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement. On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc., or Agilis, pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Merger Agreement”), by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and the Company's wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the "Merger"). Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of $49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. Agilis equityholders may become entitled to receive contingent payments from the Company based on the achievement of certain development, regulatory and net sales milestones as well as based upon a percentage of net sales of certain products. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Upon the closing of the Asset Acquisition, the Company paid to BioElectron total upfront consideration of $10.0 million , funded with cash on hand, less (i) transaction expenses incurred by BioElectron, (ii) the amount of outstanding indebtedness of BioElectron including a $4.0 million loan advance to BioElectron plus accrued and unpaid interest thereon and (iii) $1.5 million held in an escrow account to secure potential indemnification obligations owed to the Company. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products. As of March 31, 2020 , the Company had an accumulated deficit of approximately $1,303.4 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 10), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offerings" of its common stock, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates. Since 2014, the Company has also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and since May 2017, the Company has generated revenue from net sales of Emflaza for the treatment of DMD in the United States. The Company expects that cash flows from the sales of its products, together with the Company's cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

Leases

Leases	3 Months Ended
	Mar. 31, 2020
Leases [Abstract]
Leases	Leases The Company leases office space in South Plainfield, New Jersey for its principal office under three noncancelable operating leases through May 2022 and August 2024, in addition to office space in various countries for international employees primarily through workspace providers. The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s operating leases have remaining lease terms ranging from 0.1 years to 7.2 years and certain of the leases include renewal options to extend the lease for up to 10 years . Rent expense was approximately $2.4 million and $1.0 million for the three month periods ended March 31, 2020 and 2019. The components of lease expense were as follows: Three Months Ended March 31, 2020 Three Months Ended March 31, 2019 Operating Lease Cost Fixed lease cost $ 2,118 $ 812 Variable lease cost 228 143 Short-term lease cost 77 53 Total operating lease cost $ 2,423 $ 1,008 Total operating lease cost is a component of operating expenses on the consolidated statements of operations. Supplemental balance sheet information related to leases was as follows: March 31, 2020 December 31, 2019 Operating lease ROU asset $ 17,671 $ 13,693 Operating lease liabilities- current $ 3,589 $ 5,153 Operating lease liabilities- noncurrent 14,645 9,018 Total operating lease liability $ 18,234 $ 14,171 Operating lease ROU asset is a component of deposits and other assets on the consolidated balance sheets. The current portion of operating lease liability is a component of other current liabilities on the consolidated balance sheets. The long term portion of operating lease liabilities is a component of other long term liabilities on the consolidated balance sheets. Supplemental lease term and discount rate information related to leases was as follows as of March 31, 2020 and 2019: March 31, 2020 March 31, 2019 Weighted-average remaining lease terms - operating leases (years) 5.35 4.71 Weighted-average discount rate - operating leases 7.34 % 7.02 % Supplemental cash flow information related to leases was as follows as of March 31, 2020 and 2019: Three Months Ended March 31, 2020 Three Months Ended March 31, 2019 Cash paid for amounts included in the measurement of lease liabilities: Operating cash flows from operating leases $ 1,971 $ 732 Right-of-use assets obtained in exchange for lease obligations: Operating leases $ 22,642 $ 11,314 Future minimum lease payments under non-cancelable leases as of March 31, 2020 were as follows: Operating Leases 2020 (excludes the three-months ended March 31, 2020) $ 3,543 2021 4,372 2022 3,846 2023 3,435 2024 and thereafter 6,900 Total lease payments 22,096 Less: Imputed Interest 3,862 Total $ 18,234 In conjunction with the Asset Acquisition, the Company acquired BioElectron’s lease in Mountainview, California. As substantially all of the fair value of the gross assets acquired was related to PTC743, the relative fair value allocated to the right of use asset and corresponding lease liability for the Mountainview lease was determined to be immaterial, and accordingly is not included in the tables above. The future minimum lease payments for the Mountainview lease as of March 31, 2020 are $ 1.3 million , $1.8 million , and $1.4 million for 2020, 2021 and 2022, respectively. As of March 31, 2020 , the Company had two operating leases that had not yet commenced, and accordingly, are not reflected in the tables above. On March 20, 2020, the Company entered into a lease agreement with COE Bridgewater LLC relating to the lease of office and laboratory space located in Bridgewater, New Jersey. This lease will replace the Company's existing lease on the property beginning on May 1, 2020 and will include additional rental property of approximately 59,000 square feet. Additional obligations stem from the occupancy of the additional space which has not yet commenced as of March 31, 2020. On August 4, 2019, the Company and Bristol-Myers Squibb Company, (the “Landlord”), entered into a Lease Agreement (the “Lease”), relating to the lease of approximately 185,000 square feet of office, manufacturing and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”). On March 25, 2020, the Company entered into an amendment increasing the rented space to approximately 220,500 square feet. The term of occupancy has not yet commenced as of March 31, 2020. The rental term of the Lease is estimated to commence on July 1, 2020 (the “Commencement Date”). Upon the Commencement Date, the Lease has an initial term of fifteen years (the “Initial Term”), with two consecutive five 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.

Fair value of financial instrum

Fair value of financial instruments and marketable securities	3 Months Ended
	Mar. 31, 2020
Fair Value Disclosures [Abstract]
Fair value of financial instruments and marketable securities	Fair value of financial instruments and marketable securities The Company follows the fair value measurement rules, which provide guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority). · Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date. · Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs). · Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available. 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. The carrying amounts for borrowings under the credit and security agreement with MidCap Financial approximate fair value based on market activity for other debt instruments with similar characteristics and comparable risk. In May 2019, the Company purchased $4.0 million of shares of ClearPoint Neuro, Inc.'s ("ClearPoint"), formerly known as MRI Interventions, Inc., common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with ClearPoint, a publicly traded medical device company. The Company determined that the equity investment represents a financial instrument and therefore, recorded it at fair value, which is readily determinable. The equity investment is a component of deposits and other assets on the consolidated balance sheet. During the three month period ended March 31, 2020 , the Company recorded an unrealized loss of $1.6 million , which is a component of other expense, net within the consolidated statement of operations. The fair value of the equity investment was $4.6 million as of March 31, 2020 . The Company classifies its equity investment in ClearPoint as a Level 1 asset within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted. In January 2020, the Company purchased a $10.0 million convertible note from Clearpoint that the Company can convert into Clearpoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its Clearpoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the Clearpoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three month period ended March 31, 2020 , the Company recorded an unrealized loss of $2.8 million , which is a component of other expense, net within the consolidated statement of operations. The fair value of the convertible debt security was $7.2 million as of March 31, 2020 . The convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the equity investment and the convertible debt security, no other items included in deposits and other assets on the consolidated balance sheets are fair valued. Fair value of certain marketable securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices. The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2020 and December 31, 2019 : March 31, 2020 Total Quoted prices Significant Significant Marketable securities $ 472,572 $ — $ 472,572 $ — Equity investment in ClearPoint $ 4,619 $ 4,619 $ — $ — ClearPoint convertible debt security $ 7,201 $ — $ 7,201 $ — Deferred consideration payable $ 40,000 $ — $ 40,000 $ — Contingent consideration payable- development and regulatory milestones $ 273,900 $ — $ — $ 273,900 Contingent consideration payable- net sales milestones and royalties $ 83,300 $ — $ — $ 83,300 December 31, 2019 Total Quoted prices in active markets for identical assets (level 1) Significant other observable inputs (level 2) Significant unobservable inputs (level 3) Marketable securities $ 398,535 $ — $ 398,535 $ — Equity investment in ClearPoint $ 6,194 $ 6,194 $ — $ — Stock appreciation rights liability $ 3,186 $ — $ — $ 3,186 Deferred consideration payable $ 40,000 $ — $ 40,000 $ — Contingent consideration payable- development and regulatory milestones $ 290,500 $ — $ — $ 290,500 Contingent consideration payable- net sales milestones and royalties $ 65,800 $ — $ — $ 65,800 No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended March 31, 2020 and December 31, 2019 . The following is a summary of marketable securities accounted for as available-for-sale securities at March 31, 2020 and December 31, 2019 : March 31, 2020 Amortized Gross Unrealized Fair Gains Losses Commercial paper $ 76,324 $ 149 $ — $ 76,473 Corporate debt securities 259,525 1,086 (649 ) 259,962 Asset-backed securities 45,702 111 (114 ) 45,699 Government obligations 90,412 28 (2 ) 90,438 Total $ 471,963 $ 1,374 $ (765 ) $ 472,572 December 31, 2019 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 157,936 $ 162 $ — $ 158,098 Corporate debt securities 188,778 576 (20 ) 189,334 Asset-backed securities 51,062 49 (8 ) 51,103 Total $ 397,776 $ 787 $ (28 ) $ 398,535 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, 2020 , no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three-month period ended March 31, 2020 , no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. As of March 31, 2020 and December 31, 2019 , the Company had no realized gains/losses from the sale of marketable securities. The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of March 31, 2020 are as follows: March 31, 2020 Securities in an unrealized loss position less than 12 months Securities in an unrealized loss position greater than 12 months Total Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Commercial paper $ — $ — $ — $ — $ — $ — Corporate debt securities (649 ) 168,871 — — (649 ) 168,871 Asset-backed securities (114 ) 28,750 — — (114 ) 28,750 Government obligations (2 ) 9,998 — — (2 ) 9,998 Total $ (765 ) $ 207,619 $ — $ — $ (765 ) $ 207,619 The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2019 are as follows: December 31, 2019 Securities in an unrealized loss position less than 12 months Securities in an unrealized loss position greater than 12 months Total Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Corporate debt securities $ (20 ) $ 71,779 $ — $ — $ (20 ) $ 71,779 Asset-backed securities (8 ) 24,211 — — (8 ) 24,211 Total $ (28 ) $ 95,990 $ — $ — $ (28 ) $ 95,990 Marketable securities on the balance sheet at March 31, 2020 and December 31, 2019 mature as follows: March 31, 2020 Less Than 12 Months More Than 12 Months Commercial paper $ 76,473 $ — Corporate debt securities 196,826 63,136 Asset-backed securities 36,574 9,125 Government obligations 70,439 19,999 Total Marketable securities $ 380,312 $ 92,260 December 31, 2019 Less Than 12 Months More Than 12 Months Commercial paper $ 158,098 $ — Corporate debt securities 139,596 49,738 Asset-backed securities 44,724 6,379 Total Marketable securities $ 342,418 $ 56,117 The Company classifies all of its marketable securities as current as they are all available for sale and are available for current operations. Convertible senior notes In August 2015, the Company issued $150.0 million of 3.00% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.50% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,” together with the “2022 Convertible Notes,” the “Convertible Notes”). The Company separately accounted for the liability and equity components of the Convertible Notes by allocating the proceeds between the liability component and equity component, as further discussed in Note 10. 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, 2020 and December 31, 2019 was $161.6 million and $171.2 million , respectively. The estimated fair value of the 2026 Convertible Notes at March 31, 2020 and December 31, 2019 was $305.3 million and $335.0 million , respectively. Deferred consideration payable Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million and the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million . The Company is required to pay $40.0 million of development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payable at March 31, 2020 was estimated to be $40.0 million . The Company did not apply a discount, as the milestones will be paid within one calendar year. Accordingly, as of March 31, 2020 , the $40.0 million of the deferred consideration payable was classified as current on the balance sheet. Level 3 valuation The stock appreciation rights ("SARs") liability is classified in other liabilities on the Company’s consolidated balance sheets. The SARs liability is marked-to-market each reporting period with the change in fair value recorded as compensation expense on the Company’s consolidated statements of operations until the SARs vest. The fair value of the SARs liability is determined at each reporting period by utilizing the Black-Scholes option pricing model. The last payment of the SARs liability was made in the three-month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of March 31, 2020 was $0 . The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of deferred and contingent consideration on the consolidated statements of operations. The fair value of the development and regulatory milestones is estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. At March 31, 2020 , the weighted average discount rate for the development and regulatory milestones was 6.0% and the weighted average probability of success was 57% . 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, 2020 , the weighted average discount rate for the net sales milestones and royalties was 11.5% and the weighted average probability of success for the net sales milestones was 50% . The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the SARs liability, and the contingent consideration payable for the period ended March 31, 2020 and March 31, 2019 . Level 3 liabilities SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2019 $ 3,186 $ 290,500 $ 65,800 Additions — — — Change in fair value — (16,600 ) 17,500 Payments (3,186 ) — — Ending balance as of March 31, 2020 $ — $ 273,900 $ 83,300 Level 3 liabilities SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2018 $ 3,814 $ 257,040 $ 53,200 Additions — — — Change in fair value 1,035 13,760 6,900 Payments (3,815 ) — — Ending balance as of March 31, 2019 $ 1,034 $ 270,800 $ 60,100 The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended March 31, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019: March 31, 2020 Fair Value Valuation Technique Unobservable Input Range Contingent consideration payable- development and regulatory milestones $273,900 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 5.2% - 7.1% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $83,300 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 94% Potential percentage of net sales for royalties 2% - 6% Discount rate 11.5% Projected years of payments 2022 - 2038 December 31, 2019 Fair Value Valuation Technique Unobservable Input Range SARs $3,186 Option-pricing model Volatility 28.93% Risk free interest rate 0.19% Strike price $6.76 - $30.86 Fair value of common stock $48.03 Expected life 0.01 years Contingent consideration payable- development and regulatory milestones $290,500 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 2.2% - 4.7% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $65,800 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 89% Potential percentage of net sales for royalties 2% - 6% Discount rate 14.5% Projected years of payments 2021 - 2038 The contingent consideration payables are classified Level 3 liabilities as their valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approaches, including but not limited to, assumptions involving probability adjusted sales estimates for the gene therapy platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

Other comprehensive income (los

Other comprehensive income (loss) and accumulated other comprehensive items	3 Months Ended
	Mar. 31, 2020
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Other comprehensive income (loss) and accumulated other comprehensive items	Other comprehensive income (loss) and accumulated other comprehensive items Other comprehensive income (loss) includes changes in equity that are excluded from net income (loss), such as unrealized gains and losses on marketable securities. The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three months ended March 31, 2020 : Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2019 $ 755 $ (11,339 ) $ (10,584 ) Other comprehensive (loss) income before reclassifications (63 ) 8,662 8,599 Amounts reclassified from other comprehensive items — — — Other comprehensive (loss) income (63 ) 8,662 8,599 Balance at March 31, 2020 $ 692 $ (2,677 ) $ (1,985 )

Accounts payable and accrued ex

Accounts payable and accrued expenses	3 Months Ended
	Mar. 31, 2020
Payables and Accruals [Abstract]
Accounts payable and accrued expenses	Accounts payable and accrued expenses Accounts payable and accrued expenses at March 31, 2020 and December 31, 2019 consist of the following: March 31, December 31, Employee compensation, benefits, and related accruals $ 21,770 $ 38,889 Consulting and contracted research 15,227 12,969 Professional fees 5,026 3,562 Sales allowance and other costs 43,229 41,155 Sales rebates and royalties 37,511 42,997 Accounts payable 16,074 10,324 Other 6,549 9,380 Total $ 145,386 $ 159,276

Capitalization

Capitalization	3 Months Ended
	Mar. 31, 2020
Stockholders' Equity Note [Abstract]
Capitalization	Capitalization In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. During the three month period ending March 31, 2020, the Company issued and sold an aggregate of 262,205 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $52.81 per share. The Company received net proceeds of $13.5 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

Net loss per share

Net loss per share	3 Months Ended
	Mar. 31, 2020
Earnings Per Share [Abstract]
Net loss per share	Net loss per share Basic earnings per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss by the weighted-average number of common shares plus the effect of any dilutive potential common shares outstanding during the period. The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended March 31, 2020 2019 Numerator Net loss $ (112,687 ) $ (72,113 ) Denominator Denominator for basic and diluted net loss per share 62,389,158 55,855,111 Net loss per share: Basic and diluted $ (1.81 ) * $ (1.29 ) * *In the three months ended March 31, 2020 and 2019 , the Company experienced a net loss and therefore did not report any dilutive share impact. The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. As of March 31, 2020 2019 Stock Options 12,670,068 10,811,383 Unvested restricted stock awards and units 927,151 695,339 Total 13,597,219 11,506,722

Stock award plan

Stock award plan	3 Months Ended
	Mar. 31, 2020
Share-based Payment Arrangement [Abstract]
Stock award plan	Stock award plan On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Company's Board of Directors approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan. In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases. In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan. In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of March 31, 2020 , awards for 677,561 shares of common stock are available for issuance under the 2013 Long Term Incentive Plan. In January 2020, the Company's Board of Directors approved the 2020 Inducement Stock Incentive Plan. The 2020 Inducement Stock Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards for up to an aggregate of 1,000,000 shares of common stock. Any grants made under the 2020 Inducement Stock Incentive Plan must be made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company's new hires’ employment compensation. As of March 31, 2020, awards for 714,100 shares of common stock are available for issuance under the 2020 Inducement Stock Incentive Plan. From January 1, 2020 through March 31, 2020 , the Company issued a total of 2,152,400 stock options to various employees. Of those, 285,900 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: Number of Weighted- Weighted- Aggregate Outstanding at December 31, 2019 11,043,939 $ 31.67 Granted 2,152,400 $ 51.35 Exercised (379,684 ) $ 26.47 Forfeited/Cancelled (146,587 ) $ 50.45 Outstanding at March 31, 2020 12,670,068 $ 34.95 7.56 years $ 150,312 Vested or Expected to vest at March 31, 2020 6,097,752 $ 37.81 9.00 years $ 54,437 Exercisable at March 31, 2020 5,716,856 $ 30.96 5.78 years $ 90,702 The fair value of grants made in the three months ended March 31, 2020 was contemporaneously estimated on the date of grant using the following assumptions: Three months ended Risk-free interest rate 0.62 - 1.45% Expected volatility 87.50 - 89.31% Expected term 5.75 years The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the three -month period ended March 31, 2020 was $37.31 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. The following table summarizes information on the Company’s restricted stock awards and units: Restricted Stock Awards and Units Number of Weighted January 1, 2020 642,419 $ 24.50 Granted 535,450 $ 51.16 Vested (220,361 ) $ 22.67 Forfeited (30,357 ) $ 32.07 Unvested at March 31, 2020 927,151 $ 40.23 Stock Appreciation Rights —SARs entitle the holder to receive, upon exercise, an amount of the Company's common stock or cash (or a combination thereof) determined by reference to appreciation, from and after the date of grant, in the fair market value of a share of the Company's common stock over the measurement price based on the exercise date. In May 2016, a total of 897,290 SARs were granted to non-executive employees (the "2016 SARs"). The 2016 SARs vested annually in equal installments over four years and were settled in cash on each vest date, which required the Company to remeasure the SARs at each reporting period until vesting occurs. For the three month period ended March 31, 2020 , a total of 132,136 SARs vested. The last payment of the SARs liability was made in the three-month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of March 31, 2020 was $0 . Employee Stock Purchase Plan —In June 2016, the Company established an Employee Stock Purchase Plan (“ESPP” or the "Plan”) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Company's Board of Directors. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six -month period through payroll withholdings and may purchase, at the end of the six -month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the three month period ended March 31, 2020 , the Company recorded $0.4 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, 2020 2019 Research and development $ 8,179 $ 4,686 Selling, general and administrative 7,041 4,577 Total $ 15,220 $ 9,263 As of March 31, 2020 , there was approximately $200.7 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 3.23 years.

Debt

Debt	3 Months Ended
	Mar. 31, 2020
Debt Disclosure [Abstract]
Debt	Debt 2017 Credit Facility In May 2017, the Company entered into a credit and security agreement (the "Credit Facility") with MidCap Financial, a Delaware statutory trust, as administrative agent and MidCap Financial and certain other financial institutions as lenders thereunder (the “Credit Agreement”) that provides for a senior secured term loan facility of $60.0 million , of which $40.0 million was drawn by the Company on May 5, 2017. The Company's ability to draw on the remaining $20.0 million under the senior secured term loan facility expired on December 31, 2018. The Company capitalized approximately $0.4 million of debt issuance costs, which were netted against the carrying value of the Credit Facility and will be amortized over the term of the Credit Facility. As of March 31, 2020 , the Company had made loan repayments of $ 16.7 million on the Credit Facility. The remaining balance of the Credit Facility as of March 31, 2020 was $23.3 million , $20.0 million of which was classified as current portion of long term debt and $3.3 million was included within long term debt on the consolidated balance sheet. Borrowings under the Credit Agreement bear interest at a rate per annum equal to the London Interbank Offered Rate, or LIBOR, (with a LIBOR floor rate of 1.00% ) plus 6.15% . The Company was obligated to make interest only payments (payable monthly in arrears) through April 30, 2019. Commencing on May 1, 2019 and continuing for the remaining twenty-four months of the facility, the Company is required to make monthly interest payments and monthly principal payments. The principal payments are to be made based on straight-line amortization of the principal over the twenty-four month period. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier. The Credit Facility is subject to certain financial covenants. As of March 31, 2020 , the Company was in compliance with all required covenants. 2026 Convertible Notes In September 2019, the Company issued, at par value, $287.5 million aggregate principal amount of 1.50% convertible senior notes due 2026, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company. The 2026 Convertible Notes are governed by an indenture (the "2026 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2026 Convertible Notes Trustee"). Holders may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances: · during any calendar quarter commencing on or after December 31, 2019 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day; · during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day; · during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or · upon the occurrence of specified corporate events. On or after March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company's common stock or any combination thereof at the Company's election. The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest. The Company is not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically. If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The 2026 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2026 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately. The Company accounts for the 2026 Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the 2026 Convertible Notes, the Company separated the 2026 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the 2026 Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven -year term of the 2026 Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the 2026 Convertible Notes was $123.0 million and was recorded in additional paid-in capital. In accounting for the transaction costs related to the issuance of the 2026 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2026 Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven -year term of the 2026 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $25.3 million in connection with the 2026 Convertible Notes. The 2026 Convertible Notes consist of the following: Liability component March 31, 2020 December 31, 2019 Principal $ 287,500 $ 287,500 Less: Debt issuance costs (4,443 ) (4,567 ) Less: Debt discount, net(1) (116,116 ) (119,350 ) Net carrying amount $ 166,941 $ 163,583 (1) Included in the consolidated balance sheets within convertible senior notes (due 2026) and amortized to interest expense over the remaining life of the 2026 Convertible Notes using the effective interest rate method. As of March 31, 2020 , the remaining contractual life of the 2026 Convertible Notes is approximately 6.5 years. The following table sets forth total interest expense recognized related to the 2026 Convertible Notes: Three Months Ended March 31, 2020 Contractual interest expense $ 1,076 Amortization of debt issuance costs 124 Amortization of debt discount 3,234 Total $ 4,434 Effective interest rate of the liability component 10.2 % 2022 Convertible Notes In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.00% convertible senior notes due 2022. The 2022 Convertible Notes bear cash interest at a rate of 3.00% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The 2022 Convertible Notes will mature on August 15, 2022, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $145.4 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company. The 2022 Convertible Notes are governed by an indenture (the "2022 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2022 Convertible Notes Trustee"). Holders may convert their 2022 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding February 15, 2022 only under the following circumstances: · during any calendar quarter commencing on or after September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day; · during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2022 Convertible Notes Indenture) per $1,000 principal amount of 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day; · during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or · upon the occurrence of specified corporate events. On or after February 15, 2022, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2022 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay cash up to the aggregate principal amount of the 2022 Convertible Notes to be converted and deliver shares of its common stock in respect of the remainder, if any, of its conversion obligation in excess of the aggregate principal amount of 2022 Convertible Notes being converted. The conversion rate for the 2022 Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest. The Company was not permitted to redeem the 2022 Convertible Notes prior to August 20, 2018. As of August 20, 2018, the Company may redeem for cash all or any portion of the 2022 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2022 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2022 Convertible Notes, which means that the Company is not required to redeem or retire the 2022 Convertible Notes periodically. There have been no redemptions to date. If the Company undergoes a “fundamental change” (as defined in the 2022 Convertible Notes Indenture), subject to certain conditions, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The 2022 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2022 Convertible Notes Indenture contains customary events of default with respect to the 2022 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2022 Convertible Notes when due and payable) occurring and continuing, the 2022 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2022 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2022 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2022 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2022 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2022 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately. The Company accounts for the 2022 Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the 2022 Convertible Notes, the Company separated the 2022 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the 2022 Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven -year term of the 2022 Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the 2022 Convertible Notes 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 are amortized to interest expense over the seven -year term of the 2022 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the 2022 Convertible Notes. The 2022 Convertible Notes consist of the following: Liability component March 31, 2020 December 31, 2019 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,219 ) (1,329 ) Less: Debt discount, net(1) (24,461 ) (26,686 ) Net carrying amount $ 124,320 $ 121,985 (1) Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the 2022 Convertible Notes using the effective interest rate method. As of March 31, 2020 , the remaining contractual life of the 2022 Convertible Notes is approximately 2.4 years. The following table sets forth total interest expense recognized related to the 2022 Convertible Notes: Three Months Ended March 31, 2020 2019 Contractual interest expense $ 1,119 $ 1,110 Amortization of debt issuance costs 111 99 Amortization of debt discount 2,225 1,982 Total $ 3,455 $ 3,191 Effective interest rate of the liability component 11.0 % 11.0 %

Commitments and contingencies

Commitments and contingencies	3 Months Ended
	Mar. 31, 2020
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and contingencies Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company's oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement. The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single-digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon the Company's payment to the SMA Foundation of a specified amount. Pursuant to the Asset Purchase Agreement with Marathon, Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon has the opportunity to receive a single $50.0 million sales-based milestone. Pursuant to the Merger Agreement with Agilis, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million , (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million , (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million , and (iv) a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% - 6% . The Company is required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the Asset Acquisition Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products. The Company also has a Collaboration and License Agreement with Akcea Therapeutics, Inc. ("Akcea") for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean (the "Akcea Collaboration and License Agreement"). Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million . In 2019, a $6.0 million milestone was paid upon receipt of regulatory approval of Waylivra from the EMA and a $4.0 million milestone was paid upon regulatory approval of Tegsedi from ANVISA, the Brazilian health regulatory authority, upon receipt of regulatory approval for Waylivra from ANVISA. In addition, Akcea is eligible to receive an additional milestone payment of $4.0 million upon receipt of regulatory approval for Waylivra from ANVISA. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement. The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur. Additionally, the Company has royalty payments associated with Translarna and Emflaza product net sales, payable quarterly or annually in accordance with the terms of the related agreements. From time to time in the ordinary course of its business, the Company is subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in the Company's clinical trials or otherwise gain access to its product candidates. The Company is not currently aware of any material legal proceedings against it.

Revenue recognition

Revenue recognition	3 Months Ended
	Mar. 31, 2020
Revenue from Contract with Customer [Abstract]
Revenue recognition	Revenue recognition Net product sales The Company views its operations and manages its business in one operating segment. During the three months ended March 31, 2020 and 2019 , net product sales in the United States were $27.5 million and $17.8 million , respectively, consisting solely of Emflaza, and net product sales not in the United States were $40.7 million and $35.3 million , respectively, consisting of Translarna and Tegsedi. For the three months ended March 31, 2020 , two of the Company’s distributors each accounted for over 10% of the Company's net product sales. For the three months ended March 31, 2019 , three of the Company’s distributors each accounted for over 10% of the Company’s net product sales. The Company’s contract liabilities balances as of March 31, 2020 and as of December 31, 2019 were $10.4 million and $11.7 million , respectively. The Company did not have any contract assets as of March 31, 2020 and as of December 31, 2019. During the three months ended March 31, 2020 , the Company recognized $2.0 million of revenue related to the amounts included in the contract liability balance at the beginning of the period. For the three months ended March 31, 2019 , the Company did not recognize any revenues relating to the contract liability balance at the beginning of the period. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three months ended March 31, 2020 and 2019 . Remaining performance obligations Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of March 31, 2020 and December 31, 2019 , the aggregate amount of the transaction price allocated to the remaining performance obligations relating to Translarna net product revenue was $10.4 million and $11.7 million , respectively. The Company expects to recognize revenue over the next one to two years as the specific timing for satisfying the performance obligations is contingent upon a number of factors, including customers’ needs and schedules. Collaboration revenue In November 2011, the Company and the Spinal Muscular Atrophy Foundation (SMA Foundation) entered into a licensing and collaboration agreement with F. Hoffman-La Roche Ltd and Hoffman- La Roche Inc. (collectively, Roche) for a spinal muscular atrophy program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s spinal muscular atrophy program. 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. As of March 31, 2020 , the remaining potential research and development event milestones that can be received is $72.5 million . The remaining potential sales milestones as of March 31, 2020 is $325.0 million upon achievement of certain sales events. In addition, the Company is eligible to receive up to double digit royalties on worldwide annual net sales of a commercial product. For the three months ended March 31, 2020 and 2019 , the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.1 million and $0.1 million , respectively.

Intangible assets and goodwill

Intangible assets and goodwill	3 Months Ended
	Mar. 31, 2020
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible assets and goodwill	Intangible assets and goodwill Definite-lived intangibles On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to the Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. In accordance with ASU 2017-01, the Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and as such accounted for the transaction as an asset acquisition under ASC 805-50 and recorded an intangible asset of $148.4 million , which is being amortized to cost of product sales over its expected useful life of approximately seven years on a straight line basis. Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In accordance with the guidance for an asset acquisition, the Company will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset. For the three month period ended March 31, 2020 , a milestone payment of $2.8 million was recorded and is included on the balance sheet within accounts payable and accrued expenses. For the three months ended March 31, 2019 , no milestone payment was recorded. These payments are being amortized over the remaining useful life of the Emflaza rights asset on a straight line basis. Pursuant to the Akcea Collaboration and License Agreement, in May 2019 the Company made a $6.0 million milestone payment to Akcea upon regulatory approval of Waylivra from the EMA. The payment was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life of approximately ten years on a straight line basis. Additionally, in December 2019, the Company made a $4.0 million milestone payment to Akcea upon regulatory approval of Tegsedi from ANVISA. The payment was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life of approximately ten years on a straight line basis. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement related to sales of Waylivra. In accordance with the guidance for an asset acquisition, the Company will record royalty payments when they become payable to Akcea and increase the cost basis for the Waylivra intangible asset. For the three month periods ended March 31, 2020 and 2019 , the Company recognized amortization expense of $7.9 million and $6.1 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, 2020 2020 $ 23,851 2021 31,801 2022 31,801 2023 31,801 2024 and thereafter 9,540 Total $ 128,794 The weighted average remaining amortization period of the definite-lived intangibles as of March 31, 2020 is 4.2 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 Merger to the underlying assets acquired and liabilities assumed, based upon the estimated fair values of those assets and liabilities at the date of acquisition. The Company classified the fair value of the acquired IPR&D as indefinite lived intangible assets until the successful completion or abandonment of the associated research and development efforts. The value allocated to the indefinite lived intangible assets was $576.5 million . There have been no changes to the balance of the indefinite-lived intangibles since the Merger. Goodwill As a result of the Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. There were no changes to the recorded value of goodwill for the three month periods ended March 31, 2020 .

Subsequent events

Subsequent events	3 Months Ended
	Mar. 31, 2020
Subsequent Events [Abstract]
Subsequent events	Subsequent events On April 29, 2020, the Company, certain of the former equityholders of Agilis, and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC, entered into a Rights Exchange Agreement (the “Rights Exchange Agreement”), pursuant to which the Company agreed to issue 2,821,176 shares of its common stock (the “Common Stock Consideration”) and paid $36.9 million (the “Cash Consideration”), in the aggregate, to such former equityholders of Agilis (the “Participating Rightholders”) in exchange for the cancellation and forfeiture by the Participating Rightholders of their rights to receive certain milestone-based contingent payments under the Merger Agreement, pursuant to which the Company completed the Merger. Also on April 29, 2020, the Company issued 2,723,826 shares of the Common Stock Consideration to certain of the Participating Rightholders pursuant to the Rights Exchange Agreement, with the issuance of the remaining 97,350 shares of the Common Stock Consideration to certain of the Participating Rightholders who are former employees of Agilis or current or former employees of the Company to be deferred until the earlier of (i) December 15, 2020 or (ii) the date on which the Company files a registration statement on Form S-3 with respect to the resale of the shares of the Common Stock Consideration pursuant to the terms of the Rights Exchange Agreement. Pursuant to the terms of the Rights Exchange Agreement, the Participating Rightholders have canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million , in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million , in the aggregate, of $40.0 million in development milestone payments due upon the passing of the second anniversary of the closing of the Merger, regardless of whether the milestones are achieved. The Rights Exchange Agreement has no effect on the Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightholders’ rights to receive $211.6 million , in the aggregate, of the milestone payments described above. As a result, all other rights and obligations under the Merger Agreement remain in effect pursuant to their terms, including the Company’s obligation to pay up to an aggregate maximum amount of $22.4 million upon the achievement of certain development milestones (representing the remaining portion of potential development milestone payments after deducting the $37.6 million for which rights were canceled and forfeited pursuant to the Rights Exchange Agreement from the $40.0 million in development milestone payments that are due upon the passing of the second anniversary of the closing of the Acquisition), up to an aggregate maximum amount of $361.0 million upon the achievement of certain regulatory milestones (representing the remaining portion of potential regulatory milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement), up to a maximum aggregate amount of $150.0 million upon the achievement of certain net sales milestones and a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% to 6% , pursuant to the terms of the Merger Agreement.

Summary of significant accoun_2

Summary of significant accounting policies - (Policies)	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Basis of presentation	Basis of presentation The accompanying financial information as of March 31, 2020 and for the three months ended March 31, 2020 and 2019 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2019 and notes thereto included in the 2019 Form 10-K. In the opinion of management, the unaudited financial information as of March 31, 2020 and for the three months ended March 31, 2020 and 2019 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders' equity, and cash flows. The results of operations for the three month period ended March 31, 2020 are not necessarily indicative of the results to be expected for the year ended December 31, 2020 or for any other interim period or for any other future year.
Use of estimates	Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, 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.
Marketable securities	Marketable securities
Inventory and cost of product sales	Inventory and cost of product sales Inventory Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. Amounts related to clinical development programs and marketing efforts are immaterial. The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2020 December 31, 2019 Raw materials $ 871 $ 874 Work in progress 9,482 9,652 Finished goods 8,780 8,759 Total inventory $ 19,133 $ 19,285 The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. For the three month period ended March 31, 2020 , the Company recorded a $0.2 million inventory write-down, primarily related to product approaching expiration. No write downs were recorded for the three month period ended March 31, 2019 . Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three month periods ended March 31, 2020 and 2019 , these amounts were immaterial. Cost of product sales Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales. Production costs are expensed as cost of product sales when the related products are sold.
Revenue recognition	Revenue recognition Net product revenue The Company's net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of the product, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to product sales. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month. The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained. For the three months ended March 31, 2020 and 2019 , net product sales outside of the United States were $40.7 million and $35.3 million respectively, and net product sales in the United States were $27.5 million and $17.8 million respectively. In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. The Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense. Collaboration revenue The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events. At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations. For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance. For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company's control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.
Allowance for doubtful accounts	Allowance for doubtful accounts
Indefinite-lived intangible assets	Indefinite-lived intangible assets Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset acquired in a business combination. The Company utilizes the "income method”, and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company's outlook and market performance of the Company's industry and recent and forecasted financial performance.
Goodwill	Goodwill Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassess its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount.
Income Taxes	Income Taxes O n 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"), referred to herein as the U.S. Tax Act, for qualified improvement property. As of March 31, 2020, the Company expects that these provisions will not have a material impact. Tax provisions of the Act also include the deferral of certain payroll taxes, relief for retaining employees, and other provisions. The Company is evaluating the impact of the Act and currently expects to benefit from the deferral of certain payroll taxes and retention credit through the end of calendar year 2020. The ultimate impact of the CARES Act may differ from this estimate due to changes in interpretations and guidance that may be issued and actions the Company may take in response to the CARES Act. The Company will continue to assess the impact that various provisions will have on its business. On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended March 31, 2020 . Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized. The Company recorded a deferred tax liability in conjunction with the Merger of $ 122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful.
Leases	Leases The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating 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.
Recently issued accounting standards	Impact of recently adopted accounting pronouncements In December 2019, the FASB issued ASU 2019-12,"Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes”. ASU 2019-12 simplifies the accounting for income taxes by removing certain exceptions to the general principals in Topic 740. The amendments also improve consistent application of and simplify GAAP for other areas of Topic 740 by clarifying and amending the existing guidance. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2020. For all other entities, it is effective for annual periods beginning after December 15, 2021 and interim periods in annual periods beginning after December 15, 2022. Early adoption is permitted, including adoption in any interim period. The Company early adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. In November 2019, the FASB issued ASU 2019-11, Codification Improvements to Topic 326, Financial Instruments - Credit Losses, which expands the scope of the practical expedient that allows entities to exclude the accrued interest component of amortized cost from various disclosures required by ASC 326 to also include certain disclosures required by ASC 320. Entities that elect to apply the practical expedient must disclose the total amount of accrued interest that they exclude from their disclosures of amortized cost. The amendments have the same effective dates as ASU 2016-13 (Topic 326) for entities that have not yet adopted that standard. The Company adopted ASU 2016-13 and ASU 2019-11 effective January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its accounting policy for marketable securities within this footnote as well as its fair value footnote (Note 4) with additional disclosures as required by the standard upon adoption. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820), Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". This standard eliminates certain disclosure requirements for fair value measurements for all entities, requires public entities to disclose certain new information and modifies some disclosure requirements. The new guidance is effective for all entities for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years. An entity is permitted to early adopt either the entire standard or only the provisions that eliminate or modify requirements. Entities can elect to early adopt in interim periods, including periods for which they have not yet issued financial statements or made their financial statements available for issuance. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements. The Company has updated its fair value footnote (Note 4) with additional and modified disclosures as required by the standard upon adoption. In August 2018, the FASB issued ASU 2018-15,"Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract". ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes. In November 2018, the FASB issued ASU 2018-18,"Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606”. ASU 2018-18 provides guidance on whether certain transactions between collaborative arrangement participants should be accounted for with revenue under Topic 606. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company adopted this guidance January 1, 2020. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

Summary of significant accoun_3

Summary of significant accounting policies - (Tables)	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Reconciliation of cash	The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows: Beginning of period- December 31, 2019 End of period- March 31, 2020 Cash and cash equivalents $ 288,028 $ 123,287 Restricted cash included in deposits and other assets 7,500 7,500 Total Cash, cash equivalents and restricted cash per statement of cash flows $ 295,528 $ 130,787
Schedule of Inventory	The following table summarizes the components of the Company’s inventory for the periods indicated: March 31, 2020 December 31, 2019 Raw materials $ 871 $ 874 Work in progress 9,482 9,652 Finished goods 8,780 8,759 Total inventory $ 19,133 $ 19,285

Leases - (Tables)

Leases - (Tables)	3 Months Ended
	Mar. 31, 2020
Leases [Abstract]
Lease costs	Supplemental lease term and discount rate information related to leases was as follows as of March 31, 2020 and 2019: March 31, 2020 March 31, 2019 Weighted-average remaining lease terms - operating leases (years) 5.35 4.71 Weighted-average discount rate - operating leases 7.34 % 7.02 % Supplemental cash flow information related to leases was as follows as of March 31, 2020 and 2019: Three Months Ended March 31, 2020 Three Months Ended March 31, 2019 Cash paid for amounts included in the measurement of lease liabilities: Operating cash flows from operating leases $ 1,971 $ 732 Right-of-use assets obtained in exchange for lease obligations: Operating leases $ 22,642 $ 11,314 The components of lease expense were as follows: Three Months Ended March 31, 2020 Three Months Ended March 31, 2019 Operating Lease Cost Fixed lease cost $ 2,118 $ 812 Variable lease cost 228 143 Short-term lease cost 77 53 Total operating lease cost $ 2,423 $ 1,008 Total operating lease cost is a component of operating expenses on the consolidated statements of operations. Supplemental balance sheet information related to leases was as follows: March 31, 2020 December 31, 2019 Operating lease ROU asset $ 17,671 $ 13,693 Operating lease liabilities- current $ 3,589 $ 5,153 Operating lease liabilities- noncurrent 14,645 9,018 Total operating lease liability $ 18,234 $ 14,171
Lease payments	Future minimum lease payments under non-cancelable leases as of March 31, 2020 were as follows: Operating Leases 2020 (excludes the three-months ended March 31, 2020) $ 3,543 2021 4,372 2022 3,846 2023 3,435 2024 and thereafter 6,900 Total lease payments 22,096 Less: Imputed Interest 3,862 Total $ 18,234

Fair value of financial instr_2

Fair value of financial instruments and marketable securities - (Tables)	3 Months Ended
	Mar. 31, 2020
Fair Value Disclosures [Abstract]
Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis	The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2020 and December 31, 2019 : March 31, 2020 Total Quoted prices Significant Significant Marketable securities $ 472,572 $ — $ 472,572 $ — Equity investment in ClearPoint $ 4,619 $ 4,619 $ — $ — ClearPoint convertible debt security $ 7,201 $ — $ 7,201 $ — Deferred consideration payable $ 40,000 $ — $ 40,000 $ — Contingent consideration payable- development and regulatory milestones $ 273,900 $ — $ — $ 273,900 Contingent consideration payable- net sales milestones and royalties $ 83,300 $ — $ — $ 83,300 December 31, 2019 Total Quoted prices in active markets for identical assets (level 1) Significant other observable inputs (level 2) Significant unobservable inputs (level 3) Marketable securities $ 398,535 $ — $ 398,535 $ — Equity investment in ClearPoint $ 6,194 $ 6,194 $ — $ — Stock appreciation rights liability $ 3,186 $ — $ — $ 3,186 Deferred consideration payable $ 40,000 $ — $ 40,000 $ — Contingent consideration payable- development and regulatory milestones $ 290,500 $ — $ — $ 290,500 Contingent consideration payable- net sales milestones and royalties $ 65,800 $ — $ — $ 65,800
Summary of marketable securities accounted for as available-for-sale securities	The following is a summary of marketable securities accounted for as available-for-sale securities at March 31, 2020 and December 31, 2019 : March 31, 2020 Amortized Gross Unrealized Fair Gains Losses Commercial paper $ 76,324 $ 149 $ — $ 76,473 Corporate debt securities 259,525 1,086 (649 ) 259,962 Asset-backed securities 45,702 111 (114 ) 45,699 Government obligations 90,412 28 (2 ) 90,438 Total $ 471,963 $ 1,374 $ (765 ) $ 472,572 December 31, 2019 Amortized Cost Gross Unrealized Fair Value Gains Losses Commercial paper $ 157,936 $ 162 $ — $ 158,098 Corporate debt securities 188,778 576 (20 ) 189,334 Asset-backed securities 51,062 49 (8 ) 51,103 Total $ 397,776 $ 787 $ (28 ) $ 398,535
Summary of unrealized losses and fair values of available-for-sale securities in a continuous unrealized loss position	The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of March 31, 2020 are as follows: March 31, 2020 Securities in an unrealized loss position less than 12 months Securities in an unrealized loss position greater than 12 months Total Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Commercial paper $ — $ — $ — $ — $ — $ — Corporate debt securities (649 ) 168,871 — — (649 ) 168,871 Asset-backed securities (114 ) 28,750 — — (114 ) 28,750 Government obligations (2 ) 9,998 — — (2 ) 9,998 Total $ (765 ) $ 207,619 $ — $ — $ (765 ) $ 207,619 The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2019 are as follows: December 31, 2019 Securities in an unrealized loss position less than 12 months Securities in an unrealized loss position greater than 12 months Total Unrealized losses Fair Value Unrealized losses Fair Value Unrealized losses Fair Value Corporate debt securities $ (20 ) $ 71,779 $ — $ — $ (20 ) $ 71,779 Asset-backed securities (8 ) 24,211 — — (8 ) 24,211 Total $ (28 ) $ 95,990 $ — $ — $ (28 ) $ 95,990
Schedule of marketable securities on the balance sheet	Marketable securities on the balance sheet at March 31, 2020 and December 31, 2019 mature as follows: March 31, 2020 Less Than 12 Months More Than 12 Months Commercial paper $ 76,473 $ — Corporate debt securities 196,826 63,136 Asset-backed securities 36,574 9,125 Government obligations 70,439 19,999 Total Marketable securities $ 380,312 $ 92,260 December 31, 2019 Less Than 12 Months More Than 12 Months Commercial paper $ 158,098 $ — Corporate debt securities 139,596 49,738 Asset-backed securities 44,724 6,379 Total Marketable securities $ 342,418 $ 56,117
Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability and SARs liability	The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended March 31, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019: March 31, 2020 Fair Value Valuation Technique Unobservable Input Range Contingent consideration payable- development and regulatory milestones $273,900 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 5.2% - 7.1% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $83,300 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 94% Potential percentage of net sales for royalties 2% - 6% Discount rate 11.5% Projected years of payments 2022 - 2038 December 31, 2019 Fair Value Valuation Technique Unobservable Input Range SARs $3,186 Option-pricing model Volatility 28.93% Risk free interest rate 0.19% Strike price $6.76 - $30.86 Fair value of common stock $48.03 Expected life 0.01 years Contingent consideration payable- development and regulatory milestones $290,500 Probability-adjusted discounted cash flow Potential development and regulatory milestones $0 - $555 million Probabilities of success 25% - 94% Discount rates 2.2% - 4.7% Projected years of payments 2020 - 2026 Contingent considerable payable- net sales milestones and royalties $65,800 Option-pricing model with Monte Carlo simulation Potential net sales milestones $0 - $150 million Probabilities of success 25% - 89% Potential percentage of net sales for royalties 2% - 6% Discount rate 14.5% Projected years of payments 2021 - 2038
Fair Value Measurement Inputs and Valuation Techniques	The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the SARs liability, and the contingent consideration payable for the period ended March 31, 2020 and March 31, 2019 . Level 3 liabilities SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2019 $ 3,186 $ 290,500 $ 65,800 Additions — — — Change in fair value — (16,600 ) 17,500 Payments (3,186 ) — — Ending balance as of March 31, 2020 $ — $ 273,900 $ 83,300 Level 3 liabilities SARs Contingent consideration payable- development and regulatory milestones Contingent consideration payable- net sales milestones and royalties Beginning balance as of December 31, 2018 $ 3,814 $ 257,040 $ 53,200 Additions — — — Change in fair value 1,035 13,760 6,900 Payments (3,815 ) — — Ending balance as of March 31, 2019 $ 1,034 $ 270,800 $ 60,100

Other comprehensive income (l_2

Other comprehensive income (loss) and accumulated other comprehensive items - (Tables)	3 Months Ended
	Mar. 31, 2020
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Summary of other comprehensive income (loss) and the changes in accumulated other comprehensive items	The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three months ended March 31, 2020 : Unrealized Gains/(Losses) On Marketable Securities, net of tax Foreign Currency Translation Total Accumulated Other Comprehensive Items Balance at December 31, 2019 $ 755 $ (11,339 ) $ (10,584 ) Other comprehensive (loss) income before reclassifications (63 ) 8,662 8,599 Amounts reclassified from other comprehensive items — — — Other comprehensive (loss) income (63 ) 8,662 8,599 Balance at March 31, 2020 $ 692 $ (2,677 ) $ (1,985 )

Accounts payable and accrued _2

Accounts payable and accrued expenses - (Tables)	3 Months Ended
	Mar. 31, 2020
Payables and Accruals [Abstract]
Schedule of components of accounts payable and accrued expenses	Accounts payable and accrued expenses at March 31, 2020 and December 31, 2019 consist of the following: March 31, December 31, Employee compensation, benefits, and related accruals $ 21,770 $ 38,889 Consulting and contracted research 15,227 12,969 Professional fees 5,026 3,562 Sales allowance and other costs 43,229 41,155 Sales rebates and royalties 37,511 42,997 Accounts payable 16,074 10,324 Other 6,549 9,380 Total $ 145,386 $ 159,276

Net loss per share - (Tables)

Net loss per share - (Tables)	3 Months Ended
	Mar. 31, 2020
Earnings Per Share [Abstract]
Schedule of computation of basic and diluted net loss available to common stockholders	The following tables set forth the computation of basic and diluted net loss per share: Three Months Ended March 31, 2020 2019 Numerator Net loss $ (112,687 ) $ (72,113 ) Denominator Denominator for basic and diluted net loss per share 62,389,158 55,855,111 Net loss per share: Basic and diluted $ (1.81 ) * $ (1.29 ) * *In the three months ended March 31, 2020 and 2019 , the Company experienced a net loss and therefore did not report any dilutive share impact.
Schedule of historical dilutive common share equivalents outstanding	The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period. As of March 31, 2020 2019 Stock Options 12,670,068 10,811,383 Unvested restricted stock awards and units 927,151 695,339 Total 13,597,219 11,506,722

Stock award plan - (Tables)

Stock award plan - (Tables)	3 Months Ended
	Mar. 31, 2020
Share-based Payment Arrangement [Abstract]
Summary of stock option activity	A summary of stock option activity is as follows: Number of Weighted- Weighted- Aggregate Outstanding at December 31, 2019 11,043,939 $ 31.67 Granted 2,152,400 $ 51.35 Exercised (379,684 ) $ 26.47 Forfeited/Cancelled (146,587 ) $ 50.45 Outstanding at March 31, 2020 12,670,068 $ 34.95 7.56 years $ 150,312 Vested or Expected to vest at March 31, 2020 6,097,752 $ 37.81 9.00 years $ 54,437 Exercisable at March 31, 2020 5,716,856 $ 30.96 5.78 years $ 90,702
Schedule of assumptions used to estimate fair values of grants made on the date of grant	The fair value of grants made in the three months ended March 31, 2020 was contemporaneously estimated on the date of grant using the following assumptions: Three months ended Risk-free interest rate 0.62 - 1.45% Expected volatility 87.50 - 89.31% Expected term 5.75 years
Summary of information on the Company's restricted stock	The following table summarizes information on the Company’s restricted stock awards and units: Restricted Stock Awards and Units Number of Weighted January 1, 2020 642,419 $ 24.50 Granted 535,450 $ 51.16 Vested (220,361 ) $ 22.67 Forfeited (30,357 ) $ 32.07 Unvested at March 31, 2020 927,151 $ 40.23
Schedule of share-based compensation expense recorded in the statement of operations	The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows: Three Months Ended March 31, 2020 2019 Research and development $ 8,179 $ 4,686 Selling, general and administrative 7,041 4,577 Total $ 15,220 $ 9,263

Debt - (Tables)

Debt - (Tables)	3 Months Ended
	Mar. 31, 2020
1.50% Convertible senior notes due 2026
Debt Instrument, Redemption [Line Items]
Summary of convertible notes	The 2026 Convertible Notes consist of the following: Liability component March 31, 2020 December 31, 2019 Principal $ 287,500 $ 287,500 Less: Debt issuance costs (4,443 ) (4,567 ) Less: Debt discount, net(1) (116,116 ) (119,350 ) Net carrying amount $ 166,941 $ 163,583 (1) Included in the consolidated balance sheets within convertible senior notes (due 2026) and amortized to interest expense over the remaining life of the 2026 Convertible Notes using the effective interest rate method.
Summary of interest expense recognized related to the Convertible Notes	The following table sets forth total interest expense recognized related to the 2026 Convertible Notes: Three Months Ended March 31, 2020 Contractual interest expense $ 1,076 Amortization of debt issuance costs 124 Amortization of debt discount 3,234 Total $ 4,434 Effective interest rate of the liability component 10.2 %
3.00% Convertible senior notes due 2022
Debt Instrument, Redemption [Line Items]
Summary of convertible notes	The 2022 Convertible Notes consist of the following: Liability component March 31, 2020 December 31, 2019 Principal $ 150,000 $ 150,000 Less: Debt issuance costs (1,219 ) (1,329 ) Less: Debt discount, net(1) (24,461 ) (26,686 ) Net carrying amount $ 124,320 $ 121,985 (1) Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the 2022 Convertible Notes using the effective interest rate method.
Summary of interest expense recognized related to the Convertible Notes	The following table sets forth total interest expense recognized related to the 2022 Convertible Notes: Three Months Ended March 31, 2020 2019 Contractual interest expense $ 1,119 $ 1,110 Amortization of debt issuance costs 111 99 Amortization of debt discount 2,225 1,982 Total $ 3,455 $ 3,191 Effective interest rate of the liability component 11.0 % 11.0 %

Intangible assets and goodwill

Intangible assets and goodwill - (Tables)	3 Months Ended
	Mar. 31, 2020
Goodwill and Intangible Assets Disclosure [Abstract]
Future amortization expense	As of March 31, 2020 2020 $ 23,851 2021 31,801 2022 31,801 2023 31,801 2024 and thereafter 9,540 Total $ 128,794

The Company - Narrative (Detail

The Company - Narrative (Details) - USD ($) $ in Thousands	Oct. 25, 2019	Aug. 23, 2018	Apr. 20, 2017	Mar. 31, 2020	Dec. 31, 2019	Sep. 30, 2019	Aug. 31, 2015
Long-term debt
Retained earnings (accumulated deficit)				$ (1,303,404)	$ (1,190,499)
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%
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Long-term debt
Cash consideration			$ 75,000
Equity Interest Issued, number of shares (in shares)			6,683,598
Numerator for calculation of number of shares of equity interests issued to acquire entity			$ 65,000
Trading day period			15 days
Development milestone payments which the entity is obligated to pay			$ 50,000
Agilis
Long-term debt
Cash consideration		$ 49,200
Equity Interest Issued, number of shares (in shares)		3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity		$ 150,000
Trading day period		10 days
Development milestone payments which the entity is obligated to pay		$ 40,000
Agilis | Non-collaborative Arrangement Transactions
Long-term debt
Development milestone payments which the entity is obligated to pay				$ 40,000
BioElectron
Long-term debt
Development milestone payments which the entity is obligated to pay				$ 200,000
Payments for asset acquisitions	$ 10,000
Loan advance	4,000
Escrow	$ 1,500

Summary of significant accoun_4

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Accounting Policies [Abstract]
Raw materials	$ 871	$ 874
Work in progress	9,482	9,652
Finished goods	8,780	8,759
Total inventory	$ 19,133	$ 19,285

Summary of significant accoun_5

Summary of significant accounting policies - Narrative (Details) - USD ($)	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Allowance for credit loss	$ 0
Inventory write-down	200,000	$ 0
Letters of Credit	$ 7,500,000
Term for letter of credit (in years)	5 years
Operating lease ROU asset	$ 17,671,000		$ 13,693,000
Allowance for doubtful accounts receivable	200,000		300,000
Deferred tax liability			$ 122,000,000
Accounts receivable, allowance for credit loss,	0
Fifth Anniversary
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Letters of Credit	$ 3,800,000

Summary of significant accoun_6

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019	Mar. 31, 2019	Dec. 31, 2018
Accounting Policies [Abstract]
Cash and cash equivalents	$ 123,287	$ 288,028
Restricted cash included in deposits and other assets	7,500	7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 130,787	$ 295,528	$ 201,144	$ 169,498

Leases - Narrative (Details)

Leases - Narrative (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2020USD ($)ft²Termoperating_lease	Mar. 31, 2019USD ($)	Dec. 31, 2019ft²
Lessee, Lease, Description [Line Items]
Number Of Operating Leases | operating_lease	3
Term of Contract ( in years )	15 years
Operating lease, expense	$ 2,400	$ 1,000
Area of Real Estate Property | ft²	220,500		185,000
Renewal Term ( in years )	10 years
Aggregate rent, Initial term	$ 22,096
Percent of market rate	95.00%
2020 (excludes the three-months ended March 31, 2020)	$ 3,543
2021	4,372
2022	$ 3,846
Number Of Operating Lease, Lease Not yet Commenced | operating_lease	2
Minimum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	1 month 6 days
Maximum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	7 years 2 months 12 days
NEW JERSEY
Lessee, Lease, Description [Line Items]
Area of Real Estate Property | ft²	59,000
New Building
Lessee, Lease, Description [Line Items]
Area of Real Estate Property | ft²	75,000
Renewal Term ( in years )	5 years
Number of terms | Term	2
The Campus
Lessee, Lease, Description [Line Items]
Aggregate rent, Initial term	$ 111,500
BioElectron
Lessee, Lease, Description [Line Items]
2020 (excludes the three-months ended March 31, 2020)	1,300
2021	1,800
2022	$ 1,400

Leases - Lease costs (Details)

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019
Leases [Abstract]
Fixed lease cost	$ 2,118	$ 812
Variable lease cost	228	143
Short-term lease cost	77	53
Total operating lease cost	2,423	$ 1,008
Assets and Liabilities, Lessee [Abstract]
Operating lease ROU asset	17,671		$ 13,693
Operating lease liabilities- current	3,589		5,153
Operating lease liabilities- noncurrent	14,645		9,018
Total operating lease liability	$ 18,234		$ 14,171
Weighted-average remaining lease terms - operating leases (years)	5 years 4 months 6 days	4 years 8 months 15 days
Weighted-average discount rate - operating leases ( as a percent)	7.34%	7.02%
Operating cash flows from operating leases	$ 1,971	$ 732
Right-of-use assets obtained in exchange for lease obligations	$ 22,642	$ 11,314

Leases - Lease payments (Detail

Leases - Lease payments (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Leases [Abstract]
2020 (excludes the three-months ended March 31, 2020)	$ 3,543
2021	4,372
2022	3,846
2023	3,435
2024 and thereafter	6,900
Total lease payments	22,096
Less: Imputed Interest	3,862
Total	$ 18,234	$ 14,171

Fair value of financial instr_3

Fair value of financial instruments and marketable securities - Narrative (Details)	1 Months Ended	3 Months Ended
	Jan. 31, 2020USD ($)	Mar. 31, 2020USD ($)$ / shares	Mar. 31, 2019USD ($)	Dec. 31, 2019USD ($)	Sep. 30, 2019	May 31, 2019USD ($)$ / shares	Dec. 31, 2018USD ($)	Aug. 23, 2018USD ($)	Aug. 31, 2015USD ($)$ / shares
Financial assets and liabilities measured at fair value on recurring basis
Debt Securities, Available-for-sale, Allowance for Credit Loss, Writeoff		$ 0
Marketable Securities, Realized Gain (Loss)		0
Deferred consideration payable		40,000,000		$ 40,000,000
Unrealized gain (loss) on equity investment		(1,574,000)	$ 0
Investment In MRI		4,600,000
Purchase of convertible debt investment	$ 10,000,000	$ 10,000,000	0
Conversion price per share (in dollars per share) | $ / shares		$ 6
Debt instrument, convertible, period		5 years
Unrealized loss		$ 2,800,000
Marketable securities		472,572,000		398,535,000
Debt Securities, Available-for-sale, Allowance for Credit Loss, Period Increase (Decrease)		0
Commitments
Financial assets and liabilities measured at fair value on recurring basis
Liability value		273,900,000	270,800,000	290,500,000			$ 257,040,000
SARs
Financial assets and liabilities measured at fair value on recurring basis
Liability value		0	$ 1,034,000	3,186,000			$ 3,814,000
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
Interest rate ( as a percent )									3.00%
Fair value of convertible notes		161,600,000		171,200,000
Conversion price per share (in dollars per share) | $ / shares									$ 56.34
1.50% Convertible senior notes due 2026 | Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal		$ 287,500,000		287,500,000
Interest rate ( as a percent )		1.50%			1.50%
Fair value of convertible notes		$ 305,300,000		335,000,000
Conversion price per share (in dollars per share) | $ / shares		$ 52.52
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay								$ 40,000,000
Agilis | Minimum
Financial assets and liabilities measured at fair value on recurring basis
Product sales		2.00%
Agilis | Maximum
Financial assets and liabilities measured at fair value on recurring basis
Product sales		6.00%
Development milestone payments which the entity is obligated to pay		$ 60,000,000
Priority review voucher amount		535,000,000
Net sales amount		150,000,000
Non-collaborative Arrangement Transactions | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay		40,000,000
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Estimated fair value of deferred consideration payable		40,000,000		40,000,000
Liability value		83,300,000		65,800,000
Marketable securities				$ 398,535,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Marketable Securities, Realized Gain (Loss)		0
Shares owned						$ 4,000,000
Fair value of shares (in dollars per share) | $ / shares						$ 3.10
Unrealized gain (loss) on equity investment		1,600,000
Deferred consideration payable | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		$ 7,201,000
Development and Regulatory Milestone | Probability of Success [Member] | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.25		0.25
Development and Regulatory Milestone | Probability of Success [Member] | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.94		0.94
Development and Regulatory Milestone | Probability of Success [Member] | Weighted Average [Member] | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.57
Development and Regulatory Milestone | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Liability value		$ 273,900,000		$ 290,500,000
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.052		0.022
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.071		0.047
Development and Regulatory Milestone | Agilis | Measurement Input, Discount Rate | Weighted Average [Member] | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.060
Liability, Net Sales Milestones and Royalties [Member] | Probability of Success [Member] | Minimum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.25		0.25
Liability, Net Sales Milestones and Royalties [Member] | Probability of Success [Member] | Maximum | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.94		0.89
Liability, Net Sales Milestones and Royalties [Member] | Probability of Success [Member] | Weighted Average [Member] | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.50
Liability, Net Sales Milestones and Royalties [Member] | Agilis
Financial assets and liabilities measured at fair value on recurring basis
Liability value		$ 83,300,000		$ 65,800,000
Liability, Net Sales Milestones and Royalties [Member] | Agilis | Measurement Input, Discount Rate | Commitments
Financial assets and liabilities measured at fair value on recurring basis
Alternative Investment, Measurement Input		0.115		0.145

Fair value of financial instr_4

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 472,572	$ 398,535
Contingent consideration payable	357,200	356,300
Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable- net sales milestones and royalties	83,300
Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		398,535
Equity investment in ClearPoint	4,619	6,194
Stock appreciation rights liability		3,186
Deferred consideration payable	40,000	40,000
Contingent consideration payable	273,900	290,500
Contingent consideration payable- net sales milestones and royalties	83,300	65,800
Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		0
Equity investment in ClearPoint	4,619	6,194
Stock appreciation rights liability		0
Deferred consideration payable	0	0
Contingent consideration payable	0	0
Contingent consideration payable- net sales milestones and royalties	0	0
Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		398,535
Equity investment in ClearPoint	0	0
Stock appreciation rights liability		0
Deferred consideration payable	40,000	40,000
Contingent consideration payable	0	0
Contingent consideration payable- net sales milestones and royalties	0	0
Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities		0
Equity investment in ClearPoint	0	0
Stock appreciation rights liability		3,186
Deferred consideration payable	0	0
Contingent consideration payable	273,900	$ 290,500
Marketable securities | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	472,572
Marketable securities | Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0
Marketable securities | Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	472,572
Marketable securities | Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0
Deferred consideration payable | Recurring basis | Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	7,201
Deferred consideration payable | Recurring basis | Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0
Deferred consideration payable | Recurring basis | Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	7,201
Deferred consideration payable | Recurring basis | Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 0

Fair value of financial instr_5

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($)	3 Months Ended
	Mar. 31, 2020	Dec. 31, 2019
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Allowance for Credit Loss, Securities Sold	$ 0
Debt Securities, Available-for-sale, Allowance for Credit Loss, Writeoff	0
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	765,000	$ 28,000
Amortized Cost	471,963,000	397,776,000
Gross Unrealized, Gain	1,374,000	787,000
Gross Unrealized, Loss	(765,000)	(28,000)
Fair Value	472,572,000	398,535,000
Securities in an unrealized loss position less than 12 months	207,619,000	95,990,000
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0
Securities in an unrealized loss position greater than 12 months	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	765,000	28,000
Debt Securities, Held-to-maturity, Unrealized Loss Position, Fair Value	207,619,000	95,990,000
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	0
Amortized Cost	76,324,000	157,936,000
Gross Unrealized, Gain	149,000	162,000
Gross Unrealized, Loss	0	0
Fair Value	76,473,000	158,098,000
Securities in an unrealized loss position less than 12 months	0
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0
Securities in an unrealized loss position greater than 12 months	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	0
Debt Securities, Held-to-maturity, Unrealized Loss Position, Fair Value	0
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	649,000	20,000
Amortized Cost	259,525,000	188,778,000
Gross Unrealized, Gain	1,086,000	576,000
Gross Unrealized, Loss	(649,000)	(20,000)
Fair Value	259,962,000	189,334,000
Securities in an unrealized loss position less than 12 months	168,871,000	71,779,000
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0
Securities in an unrealized loss position greater than 12 months	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	649,000	20,000
Debt Securities, Held-to-maturity, Unrealized Loss Position, Fair Value	168,871,000	71,779,000
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	114,000	8,000
Amortized Cost	45,702,000	51,062,000
Gross Unrealized, Gain	111,000	49,000
Gross Unrealized, Loss	(114,000)	(8,000)
Fair Value	45,699,000	51,103,000
Securities in an unrealized loss position less than 12 months	28,750,000	24,211,000
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0	0
Securities in an unrealized loss position greater than 12 months	0	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	114,000	8,000
Debt Securities, Held-to-maturity, Unrealized Loss Position, Fair Value	28,750,000	$ 24,211,000
Government obligations
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, Less than 12 Months, Accumulated Loss	2,000
Amortized Cost	90,412,000
Gross Unrealized, Gain	28,000
Gross Unrealized, Loss	(2,000)
Fair Value	90,438,000
Securities in an unrealized loss position less than 12 months	9,998,000
Debt Securities, Available-for-sale, Continuous Unrealized Loss Position, 12 Months or Longer, Accumulated Loss	0
Securities in an unrealized loss position greater than 12 months	0
Debt Securities, Available-for-sale, Unrealized Loss Position, Accumulated Loss	2,000
Debt Securities, Held-to-maturity, Unrealized Loss Position, Fair Value	$ 9,998,000

Fair value of financial instr_6

Fair value of financial instruments and marketable securities - Fair Value Measurement Inputs and Valuation Techniques (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019	Dec. 31, 2018
Level 3 roll forward
Additions	$ 0	$ 0
Significant unobservable inputs (level 3)
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	83,300
SARs
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	0	1,034	$ 3,186	$ 3,814
Change in fair value	0	1,035
Payments	(3,186)	(3,815)
Commitments
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	273,900	270,800	290,500	257,040
Additions	0	0
Change in fair value	(16,600)	13,760
Payments	0	0
Agilis | Significant unobservable inputs (level 3)
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties			65,800
Liability, Net Sales Milestones and Royalties [Member] | Agilis
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	83,300		65,800
Liability, Net Sales Milestones and Royalties [Member] | Agilis | Significant unobservable inputs (level 3)
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	83,300	60,100	$ 65,800	$ 53,200
Additions	0	0
Change in fair value	17,500	6,900
Payments	$ 0	$ 0

Fair value of financial instr_7

Fair value of financial instruments and marketable securities - Unrealized Loss Positions (Details) - USD ($)	3 Months Ended
	Mar. 31, 2020	Dec. 31, 2019
Debt Securities, Available-for-sale [Line Items]
Debt Securities, Available-for-sale, Allowance for Credit Loss, Securities Sold	$ 0
Unrealized losses
Securities in an unrealized loss position less than 12 months	(765,000)	$ (28,000)
Securities in an unrealized loss position greater than 12 months	0	0
Total	(765,000)	(28,000)
Fair Value
Securities in an unrealized loss position less than 12 months	207,619,000	95,990,000
Securities in an unrealized loss position greater than 12 months	0	0
Total	207,619,000	95,990,000
Debt Securities, Available-for-sale, Allowance for Credit Loss, Writeoff	0
Commercial paper
Unrealized losses
Securities in an unrealized loss position less than 12 months	0
Securities in an unrealized loss position greater than 12 months	0
Total	0
Fair Value
Securities in an unrealized loss position less than 12 months	0
Securities in an unrealized loss position greater than 12 months	0
Total	0
Corporate debt securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(649,000)	(20,000)
Securities in an unrealized loss position greater than 12 months	0	0
Total	(649,000)	(20,000)
Fair Value
Securities in an unrealized loss position less than 12 months	168,871,000	71,779,000
Securities in an unrealized loss position greater than 12 months	0	0
Total	168,871,000	71,779,000
Asset-backed securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(114,000)	(8,000)
Securities in an unrealized loss position greater than 12 months	0	0
Total	(114,000)	(8,000)
Fair Value
Securities in an unrealized loss position less than 12 months	28,750,000	24,211,000
Securities in an unrealized loss position greater than 12 months	0	0
Total	28,750,000	$ 24,211,000
Government obligations
Unrealized losses
Securities in an unrealized loss position less than 12 months	(2,000)
Securities in an unrealized loss position greater than 12 months	0
Total	(2,000)
Fair Value
Securities in an unrealized loss position less than 12 months	9,998,000
Securities in an unrealized loss position greater than 12 months	0
Total	$ 9,998,000

Fair value of financial instr_8

Fair value of financial instruments and marketable securities - Marketable securities (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 380,312	$ 342,418
Total Marketable securities, More Than 12 Months	92,260	56,117
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	76,473	158,098
Total Marketable securities, More Than 12 Months	0	0
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	196,826	139,596
Total Marketable securities, More Than 12 Months	63,136	49,738
Asset-backed securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	36,574	44,724
Total Marketable securities, More Than 12 Months	9,125	$ 6,379
Government obligations
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	70,439
Total Marketable securities, More Than 12 Months	$ 19,999

Fair value of financial instr_9

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) $ in Thousands	3 Months Ended		12 Months Ended
	Mar. 31, 2020USD ($)	Mar. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Dec. 31, 2019USD ($)$ / shares
Changes in the fair value of warrant liability and SARs liability
Additions	$ 0	$ 0
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	3,186	3,814
Change in fair value	0	1,035
Payments	(3,186)	(3,815)
March 31, 2020	0	1,034	$ 3,814
Commitments
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	290,500	257,040
Additions	0	0
Change in fair value	(16,600)	13,760
Payments	0	0
March 31, 2020	273,900	270,800	$ 257,040
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	$ 3,186
Minimum | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares				6.76
Minimum | Measurement Input, Option Volatility | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input				0.2893
Minimum | Measurement Input, Risk Free Interest Rate | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input				0.0019
Minimum | Measurement Input, Expected Term | SARs
Fair value of warrant liability
Expected term (in years)			3 days
Maximum | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares				30.86
Maximum | Measurement Input, Option Volatility | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input				0.2893
Maximum | Measurement Input, Risk Free Interest Rate | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input				0.0019
Maximum | Measurement Input, Expected Term | SARs
Fair value of warrant liability
Expected term (in years)			1 year 3 days
Common stock | Measurement Input, Share Price | SARs
Fair value of warrant liability
Alternative Investment, Measurement Input | $ / shares				48.03
Liability, Net Sales Milestones and Royalties [Member] | Minimum | Probability of Success [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.25			0.25
Liability, Net Sales Milestones and Royalties [Member] | Maximum | Probability of Success [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.94			0.89
Development and Regulatory Milestone | Minimum | Probability of Success [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.25			0.25
Development and Regulatory Milestone | Maximum | Probability of Success [Member] | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.94			0.94
Agilis | Liability, Net Sales Milestones and Royalties [Member]
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	$ 65,800
March 31, 2020	$ 83,300
Agilis | Liability, Net Sales Milestones and Royalties [Member] | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.115			0.145
Agilis | Liability, Net Sales Milestones and Royalties [Member] | Minimum | Sales Milestones | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 0			$ 0
Agilis | Liability, Net Sales Milestones and Royalties [Member] | Minimum | Percentage of Sales for Royalties | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.02			0.02
Agilis | Liability, Net Sales Milestones and Royalties [Member] | Maximum | Sales Milestones | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 150,000			$ 150,000
Agilis | Liability, Net Sales Milestones and Royalties [Member] | Maximum | Percentage of Sales for Royalties | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.06			0.06
Agilis | Development and Regulatory Milestone
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	$ 290,500
March 31, 2020	273,900
Agilis | Development and Regulatory Milestone | Minimum | Development and Regulatory Milestone | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 0			$ 0
Agilis | Development and Regulatory Milestone | Minimum | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.052			0.022
Agilis | Development and Regulatory Milestone | Maximum | Development and Regulatory Milestone | Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 555,000			$ 555,000
Agilis | Development and Regulatory Milestone | Maximum | Measurement Input, Discount Rate | Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.071			0.047
Significant unobservable inputs (level 3)
Changes in the fair value of warrant liability and SARs liability
March 31, 2020	$ 83,300
Significant unobservable inputs (level 3) | Agilis
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	65,800
Significant unobservable inputs (level 3) | Agilis | Liability, Net Sales Milestones and Royalties [Member]
Changes in the fair value of warrant liability and SARs liability
December 31, 2019	65,800	53,200
Additions	0	0
Change in fair value	17,500	6,900
Payments	0	0
March 31, 2020	$ 83,300	$ 60,100	$ 53,200

Other comprehensive income (l_3

Other comprehensive income (loss) and accumulated other comprehensive items - Narrative (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2020USD ($)
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	$ 594,330
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	8,599
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	8,599
Balance at the end of the period	528,734
Unrealized Gains/(Losses) On Marketable Securities, net of tax
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	755
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(63)
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	(63)
Balance at the end of the period	692
Foreign Currency Translation
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	(11,339)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	8,662
Amounts reclassified from other comprehensive items	0
Other comprehensive (loss) income	8,662
Balance at the end of the period	(2,677)
AOCI Attributable to Parent
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	(10,584)
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Balance at the end of the period	$ (1,985)

Accounts payable and accrued _3

Accounts payable and accrued expenses - Narrative (Details) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 21,770	$ 38,889
Consulting and contracted research	15,227	12,969
Professional fees	5,026	3,562
Sales allowance and other costs	43,229	41,155
Sales rebates and royalties	37,511	42,997
Accounts payable	16,074	10,324
Other	6,549	9,380
Accounts payable and accrued expenses	$ 145,386	$ 159,276

Capitalization - Narrative (Det

Capitalization - Narrative (Details) - USD ($) $ / shares in Units, $ in Millions	1 Months Ended	3 Months Ended
	Aug. 31, 2019	Mar. 31, 2020
Warrants
Consideration received on transaction		$ 13.5
Number of shares issued in transaction (in shares)		262,205
Price per share (in USD per share)		$ 52.81
Maximum
Warrants
Consideration received on transaction	$ 125

Net loss per share - Numerator

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Numerator
Net loss	$ (112,687)	$ (72,113)
Denominator
Denominator for basic and diluted net loss per share (in shares)	62,389,158	55,855,111
Net loss per share:
Basic and diluted (in dollars per share)	$ (1.81)	$ (1.29)

Net loss per share - Antidiluti

Net loss per share - Antidilutive (Details) - shares	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Net loss per share
Total shares excluded from calculation (in shares)	13,597,219	11,506,722
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	12,670,068	10,811,383
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	927,151	695,339

Stock award plan - Narrative (D

Stock award plan - Narrative (Details) - USD ($)	Mar. 05, 2013	Jan. 31, 2020	Jun. 30, 2016	May 31, 2016	May 31, 2013	Mar. 31, 2020	Mar. 31, 2019
Stock option plan
Share-based compensation expense						$ 15,220,000	$ 9,263,000
Unrecognized compensation cost						$ 200,700,000
Weighted average remaining service period for recognition of unrecognized compensation cost						3 years 2 months 23 days
Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						677,561
Unvested restricted stock
Stock option plan
Grants in period (in shares)						535,450
Stock option
Stock option plan
Granted (in shares)						2,152,400
Inducement grants for non-statutory stock options (in shares)						285,900
Expected dividend yield (as a percent)						0.00%
Weighted average grant date fair value (in dollars per share)						$ 37.31
SARs
Stock option plan
Granted (in shares)				897,290
Vesting period						4 years
Vested (in shares)						132,136
Stock appreciation rights liability						$ 0
2013 Stock Incentive Plan
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant	0
2013 Stock Incentive Plan | Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan | Unvested restricted stock
Stock option plan
Grants in period (in shares)	735,324
2013 Stock Incentive Plan | Stock option
Stock option plan
Granted (in shares)	4,613
2009 Equity and Long Term Incentive Plan
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						0
Number of additional shares authorized (in shares)					2,500,000
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant					122,296
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan | 1998 Employee, Director and Consultant Stock Option Plan | Common stock | Maximum
Stock option plan
Number of shares subject to outstanding awards (in shares)					3,040,444
2013 Long Term Incentive Plan | Minimum
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number					2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year					4.00%
2020 inducement stock incentive plan [Member] | Minimum
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number		1,000,000
2020 inducement stock incentive plan [Member] | Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant						714,100
Employee Stock [Member]
Stock option plan
Number of shares authorized (in shares)			1,000,000,000,000
Share-based compensation expense						$ 400,000
Award requisite service period			6 months
Purchase price of common stock, percent			85.00%
Employee stock purchase plan, voting percentage limit			5.00%

Stock award plan - Share Base C

Stock award plan - Share Base Compensation (Details) - Stock option $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2020USD ($)$ / sharesshares
Number of options
Outstanding at the beginning of the period (in shares) | shares	11,043,939
Granted (in shares) | shares	2,152,400
Exercised (in shares) | shares	(379,684)
Forfeited/Cancelled (in shares) | shares	(146,587)
Outstanding at the end of the period (in shares) | shares	12,670,068
Vested or Expected to vest at the end of the period (in shares) | shares	6,097,752
Exercisable at the end of the period (in shares) | shares	5,716,856
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share) | $ / shares	$ 31.67
Granted (in dollars per share) | $ / shares	51.35
Exercised (in dollars per share) | $ / shares	26.47
Forfeited/Cancelled (in dollars per share) | $ / shares	50.45
Outstanding at the end of the period (in dollars per share) | $ / shares	34.95
Vested or Expected to vest at the end of the period (in dollars per share) | $ / shares	37.81
Exercisable at the end of the period (in dollars per share) | $ / shares	$ 30.96
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 6 months 21 days
Vested or Expected to vest at the end of the period	9 years
Exercisable at the end of the period	5 years 9 months 10 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars) | $	$ 150,312
Vested or Expected to vest at the end of the period (in dollars) | $	54,437
Exercisable at the end of the period (in dollars) | $	$ 90,702
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	0.62%
Expected volatility (as a percent)	87.50%
Expected term (in years)	5 years 9 months
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	1.45%
Expected volatility (as a percent)	89.31%
Expected term (in years)	5 years 9 months

Stock award plan - Restricted S

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	3 Months Ended
	Mar. 31, 2020$ / sharesshares
Number of Shares
Balance at the beginning of the period (in shares) | shares	642,419
Granted (in shares) | shares	535,450
Vested (in shares) | shares	(220,361)
Forfeited (in shares) | shares	(30,357)
Balance at the end of the period (in shares) | shares	927,151
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) | $ / shares	$ 24.50
Granted (in dollars per share) | $ / shares	51.16
Vested (in dollars per share) | $ / shares	22.67
Forfeited (in dollars per share) | $ / shares	32.07
Balance at the end of the period (in dollars per share) | $ / shares	$ 40.23

Stock award plan - Share-based

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended
	Jan. 31, 2020	Mar. 31, 2020	Mar. 31, 2019
Stock option plan
Share-based compensation expense		$ 15,220	$ 9,263
Research and development
Stock option plan
Share-based compensation expense		8,179	4,686
Selling, general and administrative
Stock option plan
Share-based compensation expense		$ 7,041	$ 4,577
2020 inducement stock incentive plan [Member] | Minimum
Stock option plan
Share based Compensation Arrangement by Share based Payment Award Number of Shares Authorized Annual Increase Number	1,000,000
Common stock
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant		677,561
Common stock | 2020 inducement stock incentive plan [Member]
Stock option plan
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant		714,100

Debt - Narrative (Details)

Debt - Narrative (Details)	May 05, 2017USD ($)	Sep. 30, 2019USD ($)day	May 31, 2017USD ($)	Aug. 31, 2015USD ($)day$ / shares	Mar. 31, 2020USD ($)$ / shares	Dec. 31, 2019USD ($)
Long-term debt
Long-term debt					$ 294,574,000	$ 293,859,000
Current portion of long-term debt					20,000,000	20,000,000
Debt instrument additional amount available for repurchase					$ 37,500,000
Conversion price per share (in dollars per share) | $ / shares					$ 6
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Net carrying amount					$ 124,320,000	121,985,000
Debt principal amount				$ 150,000,000	$ 150,000,000	150,000,000
Interest rate ( as a percent )				3.00%
Net proceeds from issuance of convertible notes				$ 145,400,000
Trading days, number | day				20
Consecutive trading days, period | day				30
Stock price trigger		130.00%
Business days, period				5 days
Consecutive trading-day period				5 days
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day					98.00%
Conversion ratio				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%
Adjustments to additional paid in capital, equity component of convertible debt				$ 57,500,000
Net deferred tax liability in connection with convertible notes				$ 22,300,000
Fair value of convertible notes					$ 161,600,000	171,200,000
Remaining contractual life of the convertible notes					2 years 4 months 24 days
Convertible debt | 3.00% Convertible senior notes due 2022 | Redemption on or after August 20, 2018
Long-term debt
Trading days, number | day		19
Consecutive trading days, period | day		30
Stock price trigger		130.00%
Redemption price		100.00%
Sinking fund					$ 0
Convertible debt | 1.50% Convertible senior notes due 2026
Long-term debt
Net carrying amount					166,941,000	163,583,000
Debt principal amount					$ 287,500,000	287,500,000
Interest rate ( as a percent )		1.50%			1.50%
Net proceeds from issuance of convertible notes					$ 279,300,000
Trading days, number | day		20
Business days, period		5 days
Consecutive trading-day period		5 days
Conversion ratio		19.0404
Conversion price per share (in dollars per share) | $ / shares					$ 52.52
Term of the convertible notes		7 years		7 years	6 years 6 months
Adjustments to additional paid in capital, equity component of convertible debt		$ 123,000,000
Net deferred tax liability in connection with convertible notes					$ 25,300,000
Fair value of convertible notes					305,300,000	$ 335,000,000
MidCap Financial Trust
Long-term debt
Line of credit facility, maximum borrowing capacity			$ 60,000,000
Proceeds from lines of credit	$ 40,000,000
Line of credit facility, additional capacity available, net product revenue threshold			20,000,000
Debt issuance costs			$ 400,000
Repayments of debt					16,700,000
Net carrying amount					23,300,000
Long-term debt					20,000,000
Current portion of long-term debt					$ 3,300,000
Debt instrument, floor interest rate			1.00%
Debt instrument, basis spread on variable rate			6.15%
Debt instrument, interest payment period			24 months

Debt - Convertible Notes (Detai

Debt - Convertible Notes (Details) - Convertible debt - USD ($)	Mar. 31, 2020	Dec. 31, 2019	Aug. 31, 2015
3.00% Convertible senior notes due 2022
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000
Less: Debt issuance costs	(1,219,000)	(1,329,000)
Less: Debt discount, net	(24,461,000)	(26,686,000)
Net carrying amount	124,320,000	121,985,000
1.50% Convertible senior notes due 2026
Long-term debt
Principal	287,500,000	287,500,000
Less: Debt issuance costs	(4,443,000)	(4,567,000)
Less: Debt discount, net	(116,116,000)	(119,350,000)
Net carrying amount	$ 166,941,000	$ 163,583,000

Debt - Interest Expense (Detail

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Long-term debt
Amortization of debt issuance costs	$ 256	$ 139
Convertible debt | 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	1,119	1,110
Amortization of debt issuance costs	111	99
Amortization of debt discount	2,225	1,982
Total	$ 3,455	$ 3,191
Effective interest rate of the liability component	11.00%	11.00%
Convertible debt | 1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 1,076
Amortization of debt issuance costs	124
Amortization of debt discount	3,234
Total	$ 4,434
Effective interest rate of the liability component	10.20%

Commitments and contingencies -

Commitments and contingencies - Narrative (Details) - USD ($) $ in Millions	3 Months Ended
	Mar. 31, 2020	Dec. 31, 2019	Jun. 30, 2019	Aug. 23, 2018	Apr. 20, 2017	Jun. 30, 2016
Akcea
Other Commitments [Abstract]
Upfront licensing fee	$ 12
Akcea | Maximum
Other Commitments [Abstract]
Milestone payments		$ 4
Non-collaborative Arrangement Transactions | Marathon Pharmaceuticals, LLC
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay					$ 50
Non-collaborative Arrangement Transactions | Akcea
Other Commitments [Abstract]
Milestone payments	4		$ 6
Agilis
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay				$ 40
Agilis | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	60
Priority review voucher amount	535
Net sales amount	$ 150
Product sales	6.00%
Agilis | Non-collaborative Arrangement Transactions
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 40
BioElectron | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	200
Product | Wellcome trust
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay						$ 0.8
Product | Wellcome trust | Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 22.4

Revenue recognition - Narrative

Revenue recognition - Narrative (Details)	1 Months Ended	3 Months Ended
	Nov. 30, 2011USD ($)	Mar. 31, 2020USD ($)Number_Distributorsegment	Mar. 31, 2019USD ($)Number_Distributor
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of operating segments | segment		1
Percentage of net product sales		10.00%
Number of distributors | Number_Distributor		2	3
Revenue		$ 68,259,000	$ 53,583,000
Performance obligations satisfied in current period		2,000,000
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue		100,000	100,000
Licensing And Collaboration Agreement | Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements	$ 135,000,000	72,500,000
Licensing And Collaboration Agreement | Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements	$ 325,000,000	325,000,000
Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenues		0	0
Early Stage Collaborations
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenues		0	0
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue		27,500,000	17,800,000
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue		$ 40,700,000	$ 35,300,000
Minimum | Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements research period for applying discovery technology		3 years
Maximum | Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Collaborative arrangements research period for applying discovery technology		4 years

Revenue recognition - Performan

Revenue recognition - Performance Obligations (Details) $ in Millions	3 Months Ended
	Mar. 31, 2020USD ($)Number_Distributor	Mar. 31, 2019Number_Distributor	Dec. 31, 2019USD ($)	Nov. 30, 2011USD ($)
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Number of distributors | Number_Distributor	2	3
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-04-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Contract with Customer, Liability			$ 11.7
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01 | Minimum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, performance obligation, period			1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01 | Maximum
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Revenue, performance obligation, period			3 years
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-04-01
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Contract with Customer, Liability	$ 10.4
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-04-01 | Licensing And Collaboration Agreement
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable				$ 30
Revenue, performance obligation, period				2 years

Intangible assets and goodwil_2

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended		12 Months Ended
	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019	Jun. 30, 2019	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life	7 years		7 years
Amortization of acquired intangible assets	$ 7,949	$ 6,077
Total allocation of IPR&D assets	576,500
Goodwill	82,341		$ 82,341
Research and development	$ 90,107	$ 52,566
Remaining amortization period	4 years 2 months 12 days
Akcea
Finite-Lived Intangible Assets [Line Items]
Upfront licensing fee	$ 12,000
Non-collaborative Arrangement Transactions | Akcea
Finite-Lived Intangible Assets [Line Items]
Milestone payments	$ 4,000			$ 6,000
Useful life	10 years
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Finite-Lived intangibles					$ 148,400
Milestone payments	$ 2,800

Intangible assets and goodwil_3

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Mar. 31, 2020USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2020	$ 23,851
2021	31,801
2022	31,801
2023	31,801
2024 and thereafter	9,540
Total	$ 128,794

Subsequent events Narrative (De

Subsequent events Narrative (Details) - USD ($) $ in Millions	Apr. 29, 2020	Mar. 31, 2020	Aug. 23, 2018
Agilis
Subsequent Event [Line Items]
Development milestone payments which the entity is obligated to pay			$ 40
Agilis | Non-collaborative Arrangement Transactions
Subsequent Event [Line Items]
Development milestone payments which the entity is obligated to pay		$ 40
Maximum | Subsequent Event [Member]
Subsequent Event [Line Items]
Development Milestone Payment Obligations, Net of Cancellation and Forfeiture	$ 22.4
Maximum | Agilis
Subsequent Event [Line Items]
Priority review voucher amount		535
Development milestone payments which the entity is obligated to pay		60
Net sales amount		$ 150
Product sales		6.00%
Minimum | Agilis
Subsequent Event [Line Items]
Product sales		2.00%
Rights Exchange Agreement [Member] | Subsequent Event [Member]
Subsequent Event [Line Items]
Deferred Compensation Arrangement with Individual, Shares Issued	2,821,176
Cash consideration payment under Rights Exchange Agreement	$ 36.9
Shares, Issued	2,723,826
Shares remaining to issue under Rights Exchange Agreement	97,350
Priority review voucher amount	$ 174
Development milestone payments which the entity is obligated to pay	37.6
Milestone, Potential Achievements, Regulatory Approval	211.6
Rights Exchange Agreement [Member] | Maximum | Subsequent Event [Member]
Subsequent Event [Line Items]
Contingent Liability, Milestone, Potential Achievements, Priority Review Voucher Amount, Net of Cancellation and Forfeiture	$ 361