0001070081-19-000057 | 10-Q | XBRL Viewer

Intangible assets and goodwill - (Tables)

9 Months Ended

Sep. 30, 2019

Goodwill and Intangible Assets Disclosure [Abstract]

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



	As of September 30, 2019
2019	$	7,034
2020	28,136
2021	28,136
2022	28,136
2023 and thereafter	34,968
Total	$	126,410

Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 523,577	$ 169,498
Marketable securities	185,072	58,088
Trade receivables, net	60,383	67,907
Inventory, net	17,107	16,117
Prepaid expenses and other current assets	20,723	9,247
Total current assets	806,862	320,857
Fixed assets, net	18,484	12,694
Intangible assets, net	702,910	701,031
Goodwill	82,341	82,341
Deposits and other assets	30,889	2,299
Total assets	1,641,486	1,119,222
Current liabilities:
Accounts payable and accrued expenses	128,150	128,199
Current portion of long-term debt	20,000	11,667
Deferred revenue	8,810	3,716
Other current liabilities	6,840	3,814
Deferred consideration payable	19,700	19,400
Total current liabilities	183,500	166,796
Deferred revenue	5,496	9,722
Long-term debt	293,149	141,347
Contingent consideration payable	344,900	310,240
Deferred consideration payable	19,300	18,300
Deferred tax liability	122,032	122,032
Other long-term liabilities	9,455	58
Total liabilities	977,832	768,495
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 61,578,992 shares at September 30, 2019. Authorized 125,000,000 shares; issued and outstanding 50,606,147 shares at December 31, 2018.	61	51
Additional paid-in capital	1,775,799	1,288,137
Accumulated other comprehensive income	616	1,462
Accumulated deficit	(1,112,822)	(938,923)
Total stockholders’ equity	663,654	350,727
Total liabilities and stockholders’ equity	$ 1,641,486	$ 1,119,222

Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Statement of Comprehensive Income [Abstract]
Net loss	$ (59,997)	$ (50,969)	$ (173,899)	$ (79,751)
Other comprehensive (loss) income:
Unrealized (loss) gain on marketable securities	(463)	33	435	(50)
Foreign currency translation loss	(843)	(260)	(1,281)	(2,291)
Comprehensive loss	$ (61,303)	$ (51,196)	$ (174,745)	$ (82,092)

- Definition

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

+ References + Details

Fair value of financial instruments and marketable securities - Unrealized Loss Positions (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Unrealized losses
Securities in an unrealized loss position less than 12 months	$ (4)	$ (8)
Securities in an unrealized loss position greater than 12 months	0	(3)
Total	(4)	(11)
Fair Value
Securities in an unrealized loss position less than 12 months	3,017	16,223
Securities in an unrealized loss position greater than 12 months	0	10,087
Total	3,017	26,310
Commercial paper
Unrealized losses
Securities in an unrealized loss position less than 12 months		(1)
Securities in an unrealized loss position greater than 12 months		0
Total		(1)
Fair Value
Securities in an unrealized loss position less than 12 months		1,993
Securities in an unrealized loss position greater than 12 months		0
Total		1,993
Corporate debt securities
Unrealized losses
Securities in an unrealized loss position less than 12 months	(4)	(7)
Securities in an unrealized loss position greater than 12 months	0	(3)
Total	(4)	(10)
Fair Value
Securities in an unrealized loss position less than 12 months	3,017	14,230
Securities in an unrealized loss position greater than 12 months	0	10,087
Total	$ 3,017	$ 24,317

Intangible assets and goodwill - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018	Apr. 20, 2017
Finite-Lived Intangible Assets [Line Items]
Useful life			7 years
Amortization of acquired intangible assets	$ 7,025	$ 5,793	$ 19,677	$ 16,815
Total allocation of IPR&D assets			576,500
Goodwill	82,341		82,341		$ 82,341
Research and development	63,076	54,368	175,621	118,337
Akcea
Finite-Lived Intangible Assets [Line Items]
Milestone payments	4,000		4,000
Upfront licensing fee			12,000
Non-collaborative Arrangement Transactions \| Akcea
Finite-Lived Intangible Assets [Line Items]
Milestone payments	6,000		$ 6,000
Useful life			10 years
Emflaza asset acquisition
Finite-Lived Intangible Assets [Line Items]
Finite-Lived Intangibles						$ 148,400
Milestone payments	$ 7,400	$ 4,500	$ 7,400	$ 4,500

Summary of significant accounting policies

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

Summary of significant accounting policies

The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2018 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 1, 2019 (the "2018 Form 10-K"). Additional significant accounting policies adopted during the nine month period ended September 30, 2019 are discussed in further detail below.

Basis of presentation

The accompanying financial information as of September 30, 2019 and for the three and nine months ended September 30, 2019 and 2018 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, 2018 and notes thereto included in the 2018 Form 10-K.

In the opinion of management, the unaudited financial information as of September 30, 2019 and for the three and nine months ended September 30, 2019 and 2018 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders' equity, and cash flows. The results of operations for the three and nine month period ended September 30, 2019 are not necessarily indicative of the results to be expected for the year ended December 31, 2019 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, stock-based compensation, valuation procedures for the convertible notes, allowance for doubtful accounts, inventory, acquired intangible assets, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Restricted cash

Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the three-month period ended September 30, 2019 in connection with obligations under a facility lease for our leased biologics facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows:



	Beginning of period- December 31, 2018		End of period- September 30, 2019
Cash and cash equivalents	$	169,498	$	523,577
Restricted cash included in deposits and other assets	—		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	169,498	$	531,077

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. Translarna and Emflaza product 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.

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



	September 30, 2019		December 31, 2018
Raw materials	$	1,853	$	1,431
Work in progress	10,870		9,324
Finished goods	4,384		5,362
Total inventory	$	17,107	$	16,117

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. No write downs were recorded for the three and nine month periods ended September 30, 2019. The Company recorded a $1.6 million inventory write down for the three month period ended September 30, 2018, primarily related to inventory labeling changes. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2019 and 2018, these amounts were immaterial.

Cost of product sales

Costs of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, including personnel costs, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales.

Revenue recognition

In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products (Topic 605) and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services.

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 Translarna or Emflaza 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 either Translarna or Emflaza, 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 either product sales of Translarna or Emflaza. 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 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.

In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred.

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


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


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


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


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

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

Collaboration revenue

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 $0.3 million as of September 30, 2019 and $0.7 million as of December 31, 2018. Bad debt expense was immaterial for the three and nine month periods ended September 30, 2019 and 2018.

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 acquired in business combinations are capitalized. Several

methods may be used to determine the estimated fair value of the IPR&D 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. IPR&D intangible assets that are determined to have had a drop in their fair value are adjusted downward and an impairment is recognized in the statement of operations. These assets are tested at least annually or sooner when a triggering event occurs that could indicate a potential impairment.

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 on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired.

Income Taxes

On December 22, 2017, the U.S. government enacted the 2017 Tax Cuts and Jobs Act ("the 2017 Tax Act"), which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2019.

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

In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)” along with other amendments issued in 2017 and 2018. Topic 842 supersedes the lease accounting requirements in Accounting Standards Codification Topic 840, Leases (Topic 840). Topic 842 requires organizations to recognize leased assets and liabilities on the balance sheet. The standard also requires disclosures to help investors and other financial statement users better understand the amount, timing and uncertainty of cash flows arising from 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.

Under the standard, 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.

Topic 842 requires a lessee 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 the "Impact of recently adopted accounting pronouncements" section within this Note below and Note 3 Leases for additional information. The information presented for periods prior to January 1, 2019 has not been adjusted and is reported under Topic 840.

Recently issued accounting standards

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. The Company expects to adopt this guidance when effective and is assessing what effect the adoption of ASU 2016-13 will have on its consolidated financial statements and accompanying notes with a focus on the potential impact on its accounts receivables and its available for sale debt securities.

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 expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes.

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 expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its 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 expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-18 will have on its consolidated financial statements and accompanying notes.

Impact of recently adopted accounting pronouncements

In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)”. This standard requires organizations that lease assets with lease terms of more than 12 months to recognize assets and liabilities for the rights and obligations created by those leases on their balance sheets. The ASU also requires new qualitative and quantitative disclosures to help investors and other financial

statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for public companies for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018, with early adoption permitted. Additionally, in March 2019, the FASB issued ASU 2019-01,"Leases (Topic 842): Codification Improvements”. ASU 2019-01 clarifies the transition guidance related to interim disclosures provided in the year of adoption. The Company adopted the new guidance on January 1, 2019 using the modified retrospective method. Prior period results were not adjusted and continue to be presented under Topic 840 based on the accounting standards originally in effect for such periods. As part of the adoption, the Company has elected to utilize practical expedients including the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed the Company to: 1) carry forward the historical determination of contracts as leases, lease classification and not reassess initial direct costs for historical lease arrangements, 2) not separate non-lease components from lease components and instead to account for each separate lease component and the non-lease components associated with that lease component as a single lease component (the Company elected to apply this practical expedient to all underlying asset classes), 3) not apply the recognition requirements in ASC 842 to short-term leases, and 4) not record an ROU asset or ROU liability for leases with an asset or liability balance that would be considered immaterial. Upon adoption, the Company recorded an operating lease liability with a corresponding operating lease ROU asset of $11.3 million. The adoption did not have a material impact on the consolidated results of operations, stockholder's equity, and cash flows for the three and nine month periods ended September 30, 2019. As the Company is not a lessor, the aspects of the new guidance pertaining to lessors was not applicable for the Company.

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

In June 2018, the FASB issued ASU 2018-07, "Compensation — Stock Compensation (Topic 718), Improvements to Nonemployee Share-Based Payment Accounting". This standard expands the scope of ASC 718 to include share-based payments granted to nonemployees in exchange for goods or services used or consumed in the entity’s own operations and supersedes the guidance in ASC 505-50. The ASU retains the existing cost attribution guidance, which requires entities to recognize compensation cost for nonemployee awards in the same period and in the same manner they would if they paid cash for the goods or services, but it moves the guidance to ASC 718. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company adopted this guidance on January 1, 2019. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

In May 2014, the FASB issued ASU No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million, which was recorded on January 1, 2018 to deferred revenue and accumulated deficit, related to the product sales of Emflaza.

In January 2016, the FASB issued ASU No. 2016-01, “Financial Instruments — Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities”. This standard enhances the reporting model for financial instruments, which includes amendments to address aspects of recognition, measurement, presentation and disclosure. The new guidance affects all reporting organizations (whether public or private) that hold financial assets or owe financial liabilities. The Company adopted the guidance on January 1, 2018. In March 2018, the FASB issued ASU 2018-04, "Investments - Debt Securities (Topic 320) and Regulated Operations (Topic 980): Amendments to SEC Paragraphs Pursuant to the SEC Staff Accounting Bulletin ("SAB") No. 117 and SEC Release No. 33-9273 (SEC Update)". This standard supersedes SEC paragraphs in ASC 320, Investments- Debt Securities, as a result of the issuance of SAB 117 and also updates the Codification for a 2011 SEC release and is effective when a registrant adopts ASU 2016-01, which in the case of the Company was on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

In August 2016, the FASB issued ASU No. 2016-15, “Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments”. This standard clarifies the presentation of certain specific cash flow issues in the Statement of Cash Flows. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

In November 2016, the FASB issued ASU 2016-16, “Intra-Entity Transfers of Assets Other Than Inventory”. ASU 2016-16 requires companies to account for the income tax effects of intercompany transfers of assets other than inventory (e.g., intangible assets) when the transfer occurs. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

In November 2016, the FASB issued ASU No. 2016-18, “Statement of Cash Flows (Topic 230): Restricted Cash”. This standard requires entities to show the changes in the total of cash, cash equivalents, restricted cash and restricted cash equivalents in the statement of cash flows and no longer present transfers between cash and cash equivalents and restricted cash and restricted cash equivalents in the statement of cash flows. The Company adopted the guidance on January 1, 2018. Upon adoption, the guidance did not have a material impact on the consolidated financial statements and accompanying notes. During the three-month period ended September 30, 2019, the Company entered into an unconditional, irrevocable and transferable letter of credit in connection with obligations under a facility lease for our leased biologics facility. Accordingly, the Company updated its disclosures around restricted cash above within this footnote, including the nature and amount of restricted cash, its classification on the consolidated balance sheet, and a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet to the statement of cash flows.

In May 2017, the FASB issued ASU No. 2017-09, "Stock Compensation (Topic 718): Scope of Modification Accounting". This standard clarifies when changes to the terms or conditions of a share-based payment award must be accounted for as a modification, with entities applying the modification accounting guidance if the value, vesting conditions or classification of the award changes. In addition to all disclosures about modifications that are required under the current guidance, entities will also be required to disclose that compensation expense has not changed if applicable. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

Debt - Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Debt - Interest Expense (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Long-term debt
Amortization of debt issuance costs			$ 434	$ 390
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense	$ 1,134	$ 1,134	3,375	3,375
Amortization of debt issuance costs	106	95	308	277
Amortization of debt discount	2,137	1,919	6,192	5,563
Total	$ 3,377	$ 3,148	$ 9,875	$ 9,215
Effective interest rate of the liability component	11.00%	11.00%	11.00%	11.00%
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 130		$ 130
Amortization of debt issuance costs	15		15
Amortization of debt discount	391		391
Total	$ 536		$ 536
Effective interest rate of the liability component	10.20%		10.20%

Fair value of financial instruments and marketable securities - Hierarchy (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018	Aug. 23, 2018
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 185,072	$ 58,088
Deferred consideration payable	19,300	18,300
Contingent consideration payable	344,900	310,240
Recurring basis \| Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	185,072	58,088
Equity Securities, FV-NI	6,529
Stock appreciation rights liability	2,235	3,814
Deferred consideration payable	39,000	37,700
Contingent consideration payable	285,300	257,040
Contingent consideration payable- net sales milestones and royalties	59,600	53,200
Recurring basis \| Quoted prices in active markets for identical assets (level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	0	0
Equity Securities, FV-NI	6,529
Stock appreciation rights liability	0	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	185,072	58,088
Stock appreciation rights liability	0	0
Deferred consideration payable	39,000	37,700
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	0
Stock appreciation rights liability	2,235	3,814
Deferred consideration payable	0	0
Contingent consideration payable	285,300	257,040
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Deferred consideration payable			$ 38,100
Agilis \| Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable- net sales milestones and royalties	$ 59,600	$ 53,200

Capitalization

9 Months Ended

Sep. 30, 2019

Stockholders' Equity Note [Abstract]

Capitalization

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

In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. During the three month period ending September 30, 2019, the Company issued and sold an aggregate of 63,926 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $46.60 per share. The Company received net proceeds of $2.6 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

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

Warrants

During the three month period ended September 30, 2019, all of the Company’s outstanding warrants expired, and the Company wrote off the remaining liability, which was immaterial.

As of December 31, 2018, all of the Company's outstanding warrants were classified as liabilities because they contained non-standard antidilution provisions. The fair value of the warrants as of December 31, 2018 was immaterial.

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



	Warrant shares	Exercise price		Expiration
Common stock	7,030	$	128.00	September 2019
Common stock	130	$	2,520.00	August 2019

Debt - Narrative (Details)		1 Months Ended			3 Months Ended	9 Months Ended
Debt - Narrative (Details)	May 05, 2017 USD ($)	Sep. 30, 2019 USD ($) day $ / shares	May 31, 2017 USD ($)	Aug. 31, 2015 USD ($) day $ / shares	Sep. 30, 2019 USD ($) $ / shares	Sep. 30, 2019 USD ($) $ / shares	Dec. 31, 2018 USD ($)
Long-term debt
Debt Instrument Additional Amount Available For Repurchase						$ 37,500,000
Adjustments to additional paid in capital, equity component of convertible debt					$ 119,489,000	119,489,000
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Debt principal amount		$ 150,000,000		$ 150,000,000.0	$ 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%			98.00%	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		$ 156,400,000			$ 156,400,000	$ 156,400,000	$ 146,600,000
Remaining contractual life of the convertible notes						2 years 10 months 24 days
Convertible debt \| 3.00% Convertible senior notes due 2022 \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| day		19
Consecutive trading days, period \| day		30
Stock price trigger		130.00%
Redemption price		100.00%
Sinking fund		$ 0			0	$ 0
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Debt principal amount		$ 287,500,000			$ 287,500,000	$ 287,500,000
Interest rate ( as a percent )		1.50%			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			$ 52.52	$ 52.52
Term of the convertible notes		7 years		7 years
Adjustments to additional paid in capital, equity component of convertible debt		$ 123,000,000.0
Net deferred tax liability in connection with convertible notes		25,300,000			$ 25,300,000	$ 25,300,000
Fair value of convertible notes		$ 273,800,000			$ 273,800,000	273,800,000
MidCap Financial Trust
Long-term debt
Line of credit facility, maximum borrowing capacity			$ 60,000,000.0
Proceeds from lines of credit	$ 40,000,000.0
Line of credit facility, additional capacity available, net product revenue threshold			20,000,000.0
Debt issuance costs			$ 400,000
Repayments of Debt						$ 6,700,000
Debt instrument, floor interest rate			1.00%
Debt instrument, basis spread on variable rate			6.15%
Debt instrument, interest payment period			24 months

Fair value of financial instruments and marketable securities - Marketable securities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 127,888	$ 58,088
Total Marketable securities, More Than 12 Months	57,184	0
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	47,978	31,699
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	58,533	26,389
Total Marketable securities, More Than 12 Months	57,184	$ 0
Asset-backed securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	21,377
Total Marketable securities, More Than 12 Months	$ 0

Revenue recognition - Narrative (Details)	1 Months Ended					3 Months Ended		9 Months Ended		12 Months Ended
Revenue recognition - Narrative (Details)	Oct. 31, 2017 USD ($)	Nov. 30, 2014 USD ($)	Jan. 31, 2014 USD ($)	Aug. 31, 2013 USD ($)	Nov. 30, 2011 USD ($) compound	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($) deliverable segment	Sep. 30, 2018 USD ($)	Dec. 31, 2017 USD ($) deliverable	Dec. 31, 2018 USD ($)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Contract with Customer, Liability						$ 14,306,000	$ 12,660,000	$ 14,306,000	$ 12,660,000	$ 11,891,000	$ 12,938,000
Number of operating segments \| segment								1
Net product revenue						71,369,000	53,021,000	$ 209,899,000	177,172,000
Upfront cash payment								3,801,000	4,706,000
Revenue						71,416,000	53,591,000	210,521,000	178,396,000
Performance obligations satisfied in current period						69,100,000	53,021,000	207,630,000	177,172,000
Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Upfront cash payment					$ 30,000,000.0
Performance obligations satisfied in current period	$ 20,000,000.0	$ 10,000,000	$ 7,500,000	$ 10,000,000.0
Licensing And Collaboration Agreement \| Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements					135,000,000.0			87,500,000
Licensing And Collaboration Agreement \| Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements					$ 325,000,000.0			325,000,000.0
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
Early Stage Collaborations \| Research And Development Event Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements								143,000,000.0
Early Stage Collaborations \| Sales Milestones
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenue recognition, milestone, potential achievements								252,000,000.0
United States
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue						22,900,000	22,600,000	68,300,000	62,200,000
Non-US
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Net product revenue						48,500,000	30,400,000	$ 141,600,000	115,000,000.0
Collaborative Arrangement \| Roche And Sma Foundation
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of compounds in preclinical development \| compound					3
Number of significant deliverables \| deliverable										2
Collaboration And Discovery Agreements
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Number of significant deliverables \| deliverable								2
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
Roche \| Licensing And Collaboration Agreement
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Revenues						$ 100,000	$ 100,000	$ 100,000	$ 200,000

Summary of significant accounting policies - (Tables)

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

Reconciliation of cash



	Beginning of period- December 31, 2018		End of period- September 30, 2019
Cash and cash equivalents	$	169,498	$	523,577
Restricted cash included in deposits and other assets	—		7,500
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	169,498	$	531,077

Schedule of Inventory

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



	September 30, 2019		December 31, 2018
Raw materials	$	1,853	$	1,431
Work in progress	10,870		9,324
Finished goods	4,384		5,362
Total inventory	$	17,107	$	16,117

Acquisitions - Schedule of Business Acquisitions (Details) - USD ($) $ in Thousands	Aug. 23, 2018	Sep. 30, 2019	Dec. 31, 2018
Business Acquisition [Line Items]
Deferred consideration payable		$ 19,300	$ 18,300
Agilis
Business Acquisition [Line Items]
Cash consideration	$ 49,221
Fair value of PTC common stock issued	155,860
Deferred consideration payable	38,100
Estimated fair value of contingent consideration payable	290,500
Consideration Transferred	$ 533,681

Debt - Convertible Notes (Details) - Convertible debt - USD ($)	Sep. 30, 2019	Dec. 31, 2018	Aug. 31, 2015
3.00% Convertible senior notes due 2022
Long-term debt
Principal	$ 150,000,000	$ 150,000,000	$ 150,000,000.0
Less: Debt issuance costs	(1,438,000)	(1,746,000)
Less: Debt discount, net	(28,862,000)	(35,054,000)
Net carrying amount	119,700,000	$ 113,200,000
1.50% Convertible senior notes due 2026
Long-term debt
Principal	287,500,000
Less: Debt issuance costs	(4,692,000)
Less: Debt discount, net	(122,618,000)
Net carrying amount	$ 160,190,000

Summary of significant accounting policies - (Policies)

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Inventory and cost of product sales

Inventory

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



	September 30, 2019		December 31, 2018
Raw materials	$	1,853	$	1,431
Work in progress	10,870		9,324
Finished goods	4,384		5,362
Total inventory	$	17,107	$	16,117

Cost of product sales

Revenue recognition

Net product revenue

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


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


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


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


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

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

Collaboration revenue

Allowance for doubtful accounts

Indefinite-lived intangible assets

Goodwill

Income Taxes

Leases

Recently issued accounting standards

Impact of recently adopted accounting pronouncements

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 184,317	$ 58,056
Gross Unrealized, Gain	759	43
Gross Unrealized, Loss	(4)	(11)
Fair Value	185,072	58,088
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	47,898	31,657
Gross Unrealized, Gain	80	43
Gross Unrealized, Loss	0	(1)
Fair Value	47,978	31,699
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	115,109	26,399
Gross Unrealized, Gain	612	0
Gross Unrealized, Loss	(4)	(10)
Fair Value	115,717	$ 26,389
Asset-backed securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	21,310
Gross Unrealized, Gain	67
Gross Unrealized, Loss	0
Fair Value	$ 21,377

Other comprehensive income (loss) and accumulated other comprehensive items - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	$ 488,685	$ 350,727
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(1,306)	(846)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(1,306)	(846)
Balance at the end of the period	663,654	663,654
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	929	31
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(463)	435
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(463)	435
Balance at the end of the period	466	466
Foreign Currency Translation
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	993	1,431
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Other comprehensive income before reclassifications	(843)	(1,281)
Amounts reclassified from other comprehensive items	0	0
Other comprehensive income (loss)	(843)	(1,281)
Balance at the end of the period	150	150
AOCI Attributable to Parent
Other comprehensive income (loss) and accumulated other comprehensive items
Balance at the beginning of the period	1,922	1,462
AOCI Including Portion Attributable to Noncontrolling Interest, Net of Tax [Roll Forward]
Balance at the end of the period	$ 616	$ 616

Accounts payable and accrued expenses - Narrative (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 25,800	$ 27,629
Consulting and contracted research	2,356	11,267
Professional fees	10,300	5,574
Sales allowance and other costs	37,129	29,417
Sales rebates and royalties	33,645	31,874
Accounts payable	8,959	6,001
Other	9,961	16,437
Accounts payable and accrued expenses	$ 128,150	$ 128,199

Acquisitions - Business Acquisition, Pro Forma Information (Details) - Agilis - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018
Business Acquisition [Line Items]
Revenues	$ 53,591	$ 178,396
Net loss attributable to common stockholders	$ (52,458)	$ (89,976)

Stock award plan - Share Base Compensation (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2019
Number of options
Outstanding at the beginning of the period (in shares)	8,534,358
Granted (in shares)	3,265,220
Exercised (in shares)	(645,435)
Forfeited/Cancelled (in shares)	(410,962)
Outstanding at the end of the period (in shares)	10,743,181
Vested or Expected to vest at the end of the period (in shares)	5,138,949
Exercisable at the end of the period (in shares)	5,220,799
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 28.58
Granted (in dollars per share)	34.68
Exercised (in dollars per share)	18.91
Forfeited/Cancelled (in dollars per share)	32.54
Outstanding at the end of the period (in dollars per share)	30.85
Vested or Expected to vest at the end of the period (in dollars per share)	30.27
Exercisable at the end of the period (in dollars per share)	$ 31.32
Weighted- average remaining contractual term
Outstanding at the end of the period	7 years 4 months 20 days
Vested or Expected to vest at the end of the period	8 years 10 months 20 days
Exercisable at the end of the period	5 years 9 months 18 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars)	$ 75,022
Vested or Expected to vest at the end of the period (in dollars)	27,358
Exercisable at the end of the period (in dollars)	$ 46,228
Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	1.71%
Expected volatility (as a percent)	61.90%
Expected term (in years)	5 years 9 months
Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	2.63%
Expected volatility (as a percent)	91.75%
Expected term (in years)	6 years 1 month 9 days

Revenue recognition - Performance Obligations (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018	Sep. 30, 2018	Dec. 31, 2017	Nov. 30, 2011
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Contract with Customer, Liability	$ 14,306	$ 12,938	$ 12,660	$ 11,891
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-10-01 \| 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]: 2018-10-01 \| 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]: 2018-10-01 \| Licensing And Collaboration Agreement
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Deferred consideration payable					$ 30,000
Revenue, performance obligation, period					2 years

Debt

9 Months Ended

Sep. 30, 2019

Debt Disclosure [Abstract]

Debt

2017 Credit Facility

In May 2017, the Company entered into a credit and security agreement (the "Credit Facility") with MidCap Financial, 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 September 30, 2019, the Company had made loan repayments of $6.7 million on the Credit Facility.

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 September 30, 2019, the Company was in compliance with all required covenants.

2026 Convertible Notes

In September 2019, the Company issued, at par value, $287.5 million aggregate principal amount of 1.5% 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 1.5% 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 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 is $123.0 million and was recorded in additional paid-in capital.

In accounting for the transaction costs related to the issuance of the 2026 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2026 Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year term of the 2026 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $25.3 million in connection with the 2026 Convertible Notes.

The 2026 Convertible Notes consist of the following:



Liability component	September 30, 2019
Principal	$	287,500
Less: Debt issuance costs	(4,692		)
Less: Debt discount, net(1)	(122,618		)
Net carrying amount	$	160,190

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

As of September 30, 2019, the remaining contractual life of the 2026 Convertible Notes is approximately 7.0 years.

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



	Three Months Ended September 30,			Nine Months Ended September 30,
	2019			2019
Contractual interest expense	$	130		$	130
Amortization of debt issuance costs	15			15
Amortization of debt discount	391			391
Total	$	536		$	536
Effective interest rate of the liability component	10.2		%	10.2		%

2022 Convertible Notes

In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.0% convertible senior notes due 2022. The 2022 Convertible Notes bear cash interest at a rate of 3.0% 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 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 is $57.5 million and was recorded in additional paid-in capital.

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

The 2022 Convertible Notes consist of the following:



Liability component	September 30, 2019			December 31, 2018
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(1,438		)	(1,746		)
Less: Debt discount, net(1)	(28,862		)	(35,054		)
Net carrying amount	$	119,700		$	113,200

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

As of September 30, 2019, the remaining contractual life of the 2022 Convertible Notes is approximately 2.9 years.

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



	Three Months Ended September 30,						Nine Months Ended September 30,
	2019			2018			2019			2018
Contractual interest expense	$	1,134		$	1,134		$	3,375		$	3,375
Amortization of debt issuance costs	106			95			308			277
Amortization of debt discount	2,137			1,919			6,192			5,563
Total	$	3,377		$	3,148		$	9,875		$	9,215
Effective interest rate of the liability component	11.0		%	11.0		%	11.0		%	11.0		%

Label	Element	Value
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000
Additional Paid-in Capital [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	0
Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 3,266,000

Fair value of financial instruments and marketable securities - Narrative (Details) - USD ($)	3 Months Ended	9 Months Ended		12 Months Ended
	Sep. 30, 2019	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018	May 31, 2019	Aug. 23, 2018	Aug. 31, 2015
Financial assets and liabilities measured at fair value on recurring basis
Realized gain (loss)		$ 0
Estimated fair value of deferred consideration payable	$ 19,300,000	19,300,000		$ 18,300,000
Deferred consideration payable	19,700,000	19,700,000		19,400,000
Unrealized Gain (Loss) on Investments		2,529,000	$ 0
Investment In MRI	6,500,000	6,500,000
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			$ 150,000,000.0
Interest rate ( as a percent )							3.00%
Fair value of convertible notes	156,400,000	156,400,000		146,600,000
1.50% Convertible senior notes due 2026 \| Convertible debt
Financial assets and liabilities measured at fair value on recurring basis
Principal	$ 287,500,000	$ 287,500,000
Interest rate ( as a percent )	1.50%	1.50%
Fair value of convertible notes	$ 273,800,000	$ 273,800,000
Agilis
Financial assets and liabilities measured at fair value on recurring basis
Development milestone payments which the entity is obligated to pay				$ 40,000,000.0		$ 40,000,000.0
Estimated fair value of deferred consideration payable						$ 38,100,000
Agilis \| Minimum
Financial assets and liabilities measured at fair value on recurring basis
Product sales	2.00%	2.00%		2.00%
Agilis \| Maximum
Financial assets and liabilities measured at fair value on recurring basis
Product sales	6.00%	6.00%		6.00%
Development milestone payments which the entity is obligated to pay	$ 60,000,000.0	$ 60,000,000.0		$ 60,000,000.0
Priority review voucher amount		535,000,000.0		535,000,000.0
Net sales amount	150,000,000.0	150,000,000.0		150,000,000.0
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	40,000,000.0	40,000,000.0
Recurring basis \| Total
Financial assets and liabilities measured at fair value on recurring basis
Estimated fair value of deferred consideration payable	39,000,000	39,000,000		$ 37,700,000
Common stock
Financial assets and liabilities measured at fair value on recurring basis
Shares owned					$ 4,000,000.0
Fair value of shares (in dollars per share)					$ 3.10
Unrealized Gain (Loss) on Investments	$ 2,400,000	$ 2,500,000

Other comprehensive income (loss) and accumulated other comprehensive items

9 Months Ended

Sep. 30, 2019

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

Other comprehensive income (loss) and accumulated other comprehensive items

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

The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine months ended September 30, 2019:



	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at June 30, 2019	$	929		$	993		$	1,922
Other comprehensive loss before reclassifications	(463		)	(843		)	(1,306		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(463		)	(843		)	(1,306		)
Balance at September 30, 2019	$	466		$	150		$	616



	Unrealized Gains/(Losses) On Marketable Securities, net of tax		Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2018	$	31	$	1,431		$	1,462
Other comprehensive income (loss) before reclassifications	435		(1,281		)	(846		)
Amounts reclassified from other comprehensive items	—		—			—
Other comprehensive income (loss)	435		(1,281		)	(846		)
Balance at September 30, 2019	$	466	$	150		$	616

Intangible assets and goodwill

9 Months Ended

Sep. 30, 2019

Goodwill and Intangible Assets Disclosure [Abstract]

Intangible assets and goodwill

Definite-lived intangibles

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

and certain contractual rights related to Emflaza. In accordance with ASU No. 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.

The Emflaza rights intangible asset 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 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 periods ended September 30, 2019 and 2018, milestone payments of $7.4 million and $4.5 million were recorded, respectively.

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. 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 September 30, 2019 and 2018, the Company recognized amortization expense of $7.0 million and $5.8 million, respectively, related to the Emflaza rights and Waylivra intangible assets. For the nine month periods ended September 30, 2019 and 2018, the Company recognized amortization expense of $19.7 million and $16.8 million, respectively, related to the Emflaza rights and Waylivra intangible assets.

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



	As of September 30, 2019
2019	$	7,034
2020	28,136
2021	28,136
2022	28,136
2023 and thereafter	34,968
Total	$	126,410

Indefinite-lived intangibles

In connection with the acquisition of 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 Agilis platform also includes a gene therapy 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. An investigational new drug ("IND") submission with the FDA for this program is expected mid-year 2020. Additionally, the Agilis platform includes two other gene therapy 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.

Goodwill

As a result of the Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. There were no changes to the recorded value of goodwill for the three and nine month periods ended September 30, 2019.

Accounts payable and accrued expenses

9 Months Ended

Sep. 30, 2019

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2019 and December 31, 2018 consist of the following:



	September 30, 2019		December 31, 2018
Employee compensation, benefits, and related accruals	$	25,800	$	27,629
Consulting and contracted research	2,356		11,267
Professional fees	10,300		5,574
Sales allowance and other costs	37,129		29,417
Sales rebates and royalties	33,645		31,874
Accounts payable	8,959		6,001
Other	9,961		16,437
Balance at September 30, 2019	$	128,150	$	128,199

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2019 USD ($) $ / shares	Dec. 31, 2018 USD ($) $ / shares
Changes in the fair value of warrant liability and SARs liability
Additions	$ 0
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	3,814
Change in fair value	2,236
Payments	(3,815)
September 30, 2019	2,235	$ 3,814
Commitments
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	257,040
Additions	0
Change in fair value	28,260
Payments	0
September 30, 2019	285,300	257,040
SARs
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	3,814
September 30, 2019	$ 2,235	$ 3,814
Measurement Input, Risk Free Interest Rate \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input	0.0188
Measurement Input, Expected Term \| SARs
Fair value of warrant liability
Expected term (in years)	3 months 3 days
Minimum \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input \| $ / shares	6.76	6.76
Minimum \| Measurement Input, Option Volatility \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input	0.4323	0.4653
Minimum \| Measurement Input, Risk Free Interest Rate \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input		0.0244
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	30.86
Maximum \| Measurement Input, Option Volatility \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input		0.5959
Maximum \| Measurement Input, Risk Free Interest Rate \| SARs
Fair value of warrant liability
Alternative Investment, Measurement Input		0.0263
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	33.82	34.32
Milestones and Royalties \| Minimum \| Probability of Success [Member] \| Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.25	0.25
Milestones and Royalties \| Maximum \| Probability of Success [Member] \| Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.89	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 \| Milestones and Royalties
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	$ 53,200
September 30, 2019	$ 59,600	$ 53,200
Agilis \| Milestones and Royalties \| Measurement Input, Discount Rate \| Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.140	0.140
Agilis \| Milestones and Royalties \| Minimum \| Sales Milestones \| Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 0	$ 0
Agilis \| Milestones and Royalties \| Minimum \| Percentage of Sales for Royalties \| Commitments
Fair value of warrant liability
Alternative Investment, Measurement Input	0.02	0.02
Agilis \| Milestones and Royalties \| Maximum \| Sales Milestones \| Commitments
Fair value of warrant liability
Alternative Investment, Milestone	$ 150,000	$ 150,000
Agilis \| Milestones and Royalties \| 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, 2018	$ 257,040
September 30, 2019	285,300	$ 257,040
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	0.027	0.058
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	0.051	0.08
Significant unobservable inputs (level 3) \| Agilis
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	$ 53,200
September 30, 2019	59,600	$ 53,200
Significant unobservable inputs (level 3) \| Agilis \| Milestones and Royalties
Changes in the fair value of warrant liability and SARs liability
December 31, 2018	53,200
Additions	0
Change in fair value	6,400
Payments	0
September 30, 2019	$ 59,600	$ 53,200

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018	Sep. 30, 2018	Dec. 31, 2017
Accounting Policies [Abstract]
Cash and cash equivalents	$ 523,577	$ 169,498
Restricted cash included in deposits and other assets	7,500	0
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 531,077	$ 169,498	$ 206,913	$ 111,792

Revenue recognition - (Tables)

9 Months Ended

Sep. 30, 2019

Revenue from Contract with Customer [Abstract]

Contract liabilities, rollforward and revenue recognition

During the three and nine month periods ended September 30, 2019 and 2018, the Company recognized revenue in the period from:



	Three Months Ended September 30, 2019		Three Months Ended September 30, 2018		Nine Months Ended September 30, 2019		Nine Months Ended September 30, 2018
Amounts included in contract liabilities at the beginning of the period	$	2,269	$	—	$	2,269	$	—
Performance obligations satisfied in current period	69,100		53,021		207,630		177,172
Total product revenue	$	71,369	$	53,021	$	209,899	$	177,172

The following table presents changes in the Company’s contract liabilities from December 31, 2018 to September 30, 2019 and December 31, 2017 to September 30, 2018:



	Balance as of December 31, 2018		Additions		Deductions			ASC 606 Adjustment		Balance as of September 30, 2019
Deferred Revenue	$	12,938	$	3,801	$	(2,433	)	$	—	$	14,306



	Balance as of December 31, 2017		Additions		Deductions		ASC 606 Adjustment			Balance as of September 30, 2018
Deferred Revenue	$	11,891	$	4,706	$	—	$	(3,937	)	$	12,660

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
Leases - Lease costs (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2019	Sep. 30, 2018	Jan. 01, 2019
Leases [Abstract]
Fixed lease cost	$ 1,431	$ 3,078
Variable lease cost	184	488
Short-term lease cost	94	235
Total operating lease cost	1,709	3,801
Assets and Liabilities, Lessee [Abstract]
Operating lease ROU asset	13,708	13,708		$ 11,300
Operating lease liabilities- current	4,605	4,605
Operating lease liabilities- noncurrent	9,455	9,455
Total operating lease liability	$ 14,060	$ 14,060
Weighted-average remaining lease terms - operating leases (years)	3 years 6 months 29 days	3 years 6 months 29 days
Weighted-average discount rate - operating leases ( as a percent)	7.05%	7.05%
Operating cash flows from operating leases		$ 2,751
Right-of-use assets obtained in exchange for lease obligations		$ 16,120	$ 0

Cover - shares	9 Months Ended
Cover - shares	Sep. 30, 2019	Oct. 25, 2019
cover page [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2019
Document Transition Report	false
Entity File Number	001-35969
Entity Registrant Name	PTC Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3416587
Entity Address, Address Line One	100 Corporate Court
Entity Address, City or Town	South Plainfield,
Entity Address, State or Province	NJ
Entity Address, Postal Zip Code	07080
City Area Code	908
Local Phone Number	222-7000
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		61,630,979
Entity Central Index Key	0001070081
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3

Net loss per share - (Tables)

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

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

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



	Three Months Ended September 30,								Nine Months Ended September 30,
	2019				2018				2019				2018
Numerator
Net loss	$	(59,997	)		$	(50,969	)		$	(173,899	)		$	(79,751	)
Denominator
Denominator for basic and diluted net loss per share	56,463,528				48,096,521				57,798,968				45,310,690
Net loss per share:
Basic and diluted	$	(1.06	)	*	$	(1.06	)	*	$	(3.01	)	*	$	(1.76	)	*

*In the three and nine months ended September 30, 2019 and 2018, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding

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



	As of September 30,
	2019	2018
Stock Options	10,743,181	9,545,522
Unvested restricted stock awards and units	650,103	580,347
Total	11,393,284	10,125,869

Revenue recognition

9 Months Ended

Sep. 30, 2019

Revenue from Contract with Customer [Abstract]

Revenue recognition

Net product sales

The Company views its operations and manages its business in one operating segment. During the three months ended September 30, 2019 and 2018, net product sales in the United States were $22.9 million and $22.6 million respectively, consisting solely of Emflaza, and net product sales not in the United States were $48.5 million and $30.4 million, respectively, consisting of Translarna and Tegsedi. During the nine months ended September 30, 2019 and 2018, net product sales in the United States were $68.3 million and $62.2 million respectively, consisting solely of Emflaza, and net product sales not in the United States were $141.6 million and $115.0 million, respectively, consisting of Translarna and Tegsedi.

The following table presents changes in the Company’s contract liabilities from December 31, 2018 to September 30, 2019 and December 31, 2017 to September 30, 2018:



	Balance as of December 31, 2018		Additions		Deductions			ASC 606 Adjustment		Balance as of September 30, 2019
Deferred Revenue	$	12,938	$	3,801	$	(2,433	)	$	—	$	14,306



	Balance as of December 31, 2017		Additions		Deductions		ASC 606 Adjustment			Balance as of September 30, 2018
Deferred Revenue	$	11,891	$	4,706	$	—	$	(3,937	)	$	12,660

The Company did not have any contract assets for the three and nine month periods ended September 30, 2019 and 2018.

During the three and nine month periods ended September 30, 2019 and 2018, the Company recognized revenue in the period from:



	Three Months Ended September 30, 2019		Three Months Ended September 30, 2018		Nine Months Ended September 30, 2019		Nine Months Ended September 30, 2018
Amounts included in contract liabilities at the beginning of the period	$	2,269	$	—	$	2,269	$	—
Performance obligations satisfied in current period	69,100		53,021		207,630		177,172
Total product revenue	$	71,369	$	53,021	$	209,899	$	177,172

The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine month periods ended September 30, 2019 and 2018.

Remaining performance obligations

Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of September 30, 2019 and 2018, the aggregate amount of transaction price allocated to remaining performance obligations relating to Translarna net product revenue was $14.3 million and $12.7 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

The Company has ongoing collaborations with the SMA Foundation and Roche and early stage discovery arrangements with other institutions. The following are the key terms to the Company’s (i) ongoing collaborations and (ii) early stage discovery and development arrangements.

Roche and SMA Foundation

In November 2011, the Company and the SMA Foundation entered into a licensing and collaboration agreement with Roche for an SMA program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program, which includes three compounds currently in preclinical development, as well as potential back-up compounds. The Company received a nonrefundable upfront cash payment of $30.0 million during the research term, which was terminated effective December 31, 2014, after which Roche provided the Company with funding, based on an agreed- upon full-time equivalent rate, for an agreed-upon number of full-time equivalent employees that the Company contributed to the research program.

The Company identified two material promises in the collaboration agreement, the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises were bundled into one distinct performance obligation. As a result, the Company deferred the $30.0 million upfront payment which was recognized over the estimated performance period of two years, which was the contracted research period. As of adoption of ASC Topic 606 on January 1, 2018, all performance obligations had been satisfied and the balance of the remaining deferred upfront payment was fully recognized.

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

In August 2013, a lead development compound, RG7800, was selected to move into IND-enabling studies, which triggered a milestone payment to the Company from Roche of $10.0 million. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2013.

In January 2014, the Company announced the initiation of a Phase 1 clinical program in its SMA collaboration with Roche and the SMA Foundation which triggered a $7.5 million milestone payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014.

In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its SMA collaboration with Roche and the SMA Foundation which triggered a $10 million payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014.

In October 2017, the Company announced that the Sunfish, a two-part clinical trial in pediatric and adult type 2 and type 3 SMA initiated in the fourth quarter of 2016 with Roche and SMA Foundation, had transitioned into the pivotal second part of its study. The achievement of this milestone triggered a $20.0 million payment to the Company from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2017.

The remaining potential research and development event milestones that can be received as of September 30, 2019 is $87.5 million. The remaining potential sales milestones as of September 30, 2019 is $325.0 million upon achievement of certain sales events. In addition, the Company is eligible to receive up to double digit royalties on worldwide annual net sales of a commercial product.

For the three months ended September 30, 2019 and 2018, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.1 million and $0.1 million, respectively. For the nine months ended September 30, 2019 and 2018, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.1 million and $0.2 million, respectively.

Early stage collaboration and discovery agreements

From time to time, the Company has arrangements with several organizations pursuant to which the Company uses its discovery technologies to help identify potential drug candidates. The Company does not take ownership of the potential compounds, but rather provides research services to the collaborator using its specialized technology platform.

Generally, these arrangements are structured such that the collaborator and the Company work together to jointly select targets from which to apply its discovery technologies. The research period for the Company to apply its technology is generally three to four years. The Company will typically receive a nonrefundable, upfront cash payment and the collaborator agrees to provide funding for research activities performed on its behalf.

Generally, the two material promises in these arrangements are the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises are bundled into one distinct performance obligation. As of adoption of ASC Topic 606 on January 1, 2018, all deferred revenue related to these arrangements had been recognized. For the three and nine months ended September 30, 2019 and 2018, the Company did not recognize any revenue related to discovery agreements.

The Company is eligible to receive additional payments from its early stage discovery research arrangements if the discovery compounds are ultimately developed and commercialized. The aggregate potential payments the Company is eligible for if all products are developed is $143.0 million and up to $252.0 million in sales milestones upon achievement of specified sales events and up to double digit royalties on worldwide annual net sales of the licensed product. The Company will recognize revenue when it is probable the milestones will be achieved (see Note 2). For the three and nine months ended September 30, 2019 and 2018, the Company did not recognize any revenue related to early stage collaborations.

Consolidated Balance Sheets (unaudited) (Parenthetical) - $ / shares	Sep. 30, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares (in shares)	125,000,000	125,000,000
Common stock, issued shares (in shares)	61,578,992	50,606,147
Common stock, outstanding shares (in shares)	61,578,992	50,606,147

Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Cash flows from operating activities
Net loss	$ (173,899)	$ (79,751)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	22,903	19,316
Change in valuation of warrant liability	0	3
Change in valuation of deferred and contingent consideration	35,960	0
Unrealized gain on MRI investment	(2,529)	0
Non-cash interest expense	6,583	5,563
Loss on disposal of asset	0	2
Amortization of discounts on investments, net	(1,374)	(354)
Amortization of debt issuance costs	434	390
Share-based compensation expense	30,668	24,773
Unrealized foreign currency transaction losses (gains), net	205	(977)
Changes in operating assets and liabilities:
Inventory	(1,574)	(3,252)
Prepaid expenses and other current assets	(11,771)	(1,301)
Trade receivables, net	5,879	(2,681)
Deposits and other assets	(14,747)	(385)
Accounts payable and accrued expenses	695	18,606
Other liabilities	12,553	1,617
Deferred revenue	1,581	5,933
Net cash used in operating activities	(88,433)	(12,498)
Cash flows from investing activities
Purchases of fixed assets	(9,104)	(2,489)
Purchases of equity investment in MRI	(4,000)	0
Purchases of marketable securities	(239,386)	(28,656)
Sale and redemption of marketable securities	114,500	65,923
Acquisition of product rights and licenses	(20,250)	(3,903)
Business acquisition, net of cash acquired	0	(48,892)
Net cash used in investing activities	(158,240)	(18,017)
Cash flows from financing activities
Proceeds from exercise of options	12,195	8,631
Net proceeds from public offerings	324,262	117,915
Proceeds from Convertible Debt	279,571	0
Proceeds from shares issued under employee stock purchase plan	1,564	1,299
Repayments of Secured Debt	(6,667)	0
Net cash provided by financing activities	610,925	127,845
Effect of exchange rate changes on cash	(2,673)	(2,209)
Net increase in cash and cash equivalents	361,579	95,121
Cash and cash equivalents, and restricted cash beginning of period	169,498	111,792
Cash and cash equivalents, and restricted cash end of period	523,577
Supplemental disclosure of cash information
Cash paid for interest	7,042	6,927
Cash paid for income taxes	1,931	919
Supplemental disclosure of non-cash investing and financing activity
Unrealized (loss) gain on marketable securities	435	(50)
Right-of-use assets obtained in exchange for lease obligations	16,120	0
Acquisition of product rights and licenses	7,432	4,530
Accrued transaction costs related to public offerings	506	0
Accrued transaction costs related to issuance of convertible notes	$ 298	$ 0

Summary of significant accounting policies - Narrative (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Jan. 01, 2019	Dec. 31, 2018	Jan. 01, 2018
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Inventory Write-down	$ 1,600
Letters of Credit		$ 7,500
Term for letter of credit (in years)		5 years
Operating lease ROU asset		$ 13,708		$ 11,300
Allowance for doubtful accounts receivable		300			$ 700
Deferred tax liability					122,000
Retained earnings (accumulated deficit)		(1,112,822)			$ (938,923)
ASC 606 Adjustment		0	$ (3,937)
Adjustments
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Retained earnings (accumulated deficit)						$ 3,300
Fifth Anniversary
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Letters of Credit		$ 3,800

Leases - (Tables)

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Lease costs

The components of lease expense were as follows:



	Three Months Ended September 30, 2019		Nine Months Ended September 30, 2019
Operating Lease Cost
Fixed lease cost	$	1,431	$	3,078
Variable lease cost	184		488
Short-term lease cost	94		235
Total operating lease cost	$	1,709	$	3,801

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

Supplemental balance sheet information related to leases was as follows:



	September 30, 2019

Operating lease ROU asset	$	13,708

Operating lease liabilities- current	$	4,605
Operating lease liabilities- noncurrent	9,455
Total operating lease liability	$	14,060

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



	September 30, 2019

Weighted-average remaining lease terms - operating leases (years)	3.58
Weighted-average discount rate - operating leases	7.05	%

Supplemental cash flow information related to leases was as follows:



	Nine Months Ended September 30, 2019
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	2,751
Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	16,120

Lease payments

Future minimum lease payments under non-cancelable leases as of September 30, 2019 were as follows:



	Operating Leases
2019 (Excludes the nine months ended September 30, 2019)	$	1,336
2020	5,463
2021	3,705
2022	2,110
2023 and thereafter	2,124
Total lease payments	14,738
Less: Imputed Interest	678
Total	$	14,060

Debt - (Tables)

9 Months Ended

Sep. 30, 2019

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	September 30, 2019
Principal	$	287,500
Less: Debt issuance costs	(4,692		)
Less: Debt discount, net(1)	(122,618		)
Net carrying amount	$	160,190

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 September 30,			Nine Months Ended September 30,
	2019			2019
Contractual interest expense	$	130		$	130
Amortization of debt issuance costs	15			15
Amortization of debt discount	391			391
Total	$	536		$	536
Effective interest rate of the liability component	10.2		%	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	September 30, 2019			December 31, 2018
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(1,438		)	(1,746		)
Less: Debt discount, net(1)	(28,862		)	(35,054		)
Net carrying amount	$	119,700		$	113,200

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 September 30,						Nine Months Ended September 30,
	2019			2018			2019			2018
Contractual interest expense	$	1,134		$	1,134		$	3,375		$	3,375
Amortization of debt issuance costs	106			95			308			277
Amortization of debt discount	2,137			1,919			6,192			5,563
Total	$	3,377		$	3,148		$	9,875		$	9,215
Effective interest rate of the liability component	11.0		%	11.0		%	11.0		%	11.0		%

Stock award plan

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [Abstract]

Stock award plan

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

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

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of September 30, 2019, awards for 453,992 shares of common stock are available for issuance.

From January 1, 2019 through September 30, 2019, the Company issued a total of 3,265,220 stock options to various employees. Of those, 999,300 were inducement grants for non-statutory stock options. The inducement grant awards were 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 and not under the 2013 Long Term Incentive Plan.

A summary of stock option activity is as follows:



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

Outstanding at December 31, 2018	8,534,358		$	28.58
Granted	3,265,220		$	34.68
Exercised	(645,435	)	$	18.91
Forfeited/Cancelled	(410,962	)	$	32.54
Outstanding at September 30, 2019	10,743,181		$	30.85	7.39 years	$	75,022
Vested or Expected to vest at September 30, 2019	5,138,949		$	30.27	8.89 years	$	27,358
Exercisable at September 30, 2019	5,220,799		$	31.32	5.80 years	$	46,228

The fair value of grants made in the nine months ended September 30, 2019 was contemporaneously estimated on the date of grant using the following assumptions:



		Nine months ended September 30, 2019
Risk-free interest rate		1.71 - 2.63%
Expected volatility		61.90 - 91.75%
Expected term		5.75 - 6.11 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine-month period ended September 30, 2019 was $21.49 per share.

Prior to the three-month period ended September 30, 2019, the Company used the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. During the three-month period ended September 30, 2019, the Company determined that it had sufficient exercise history to be able to estimate the expected term of its options. Accordingly, for the three-month period ended September 30, 2019, the expected term of options was estimated based on the Company's historical exercise data.

Prior to the three-month period ended September 30, 2019, the expected volatility of share options was estimated based on a historical volatility analysis of peers that were similar to the Company with respect to industry, stage of life cycle, size, and financial leverage. During the three-month period ended September 30, 2019, the Company determined that it had sufficient Company stock volatility history to be able to estimate the expected volatility of its options. Accordingly, for the three-month period ended September 30, 2019, the expected volatility of options was estimated based on the Company's historical stock volatility.

The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.

Restricted Stock Awards—Restricted stock awards 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, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.

Restricted Stock Units—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 units, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
January 1, 2019	571,479		$	17.61
Granted	306,549		$	32.97
Vested	(180,827	)	$	17.56
Forfeited	(47,098	)	$	22.34
Unvested at September 30, 2019	650,103		$	24.54

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

In May 2016, a total of 897,290 SARs were granted to non-executive employees (the "2016 SARs"). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the nine month period ended September 30, 2019, a total of 157,930 SARs vested. For the three and nine month periods ended September 30, 2019, the Company recorded $0.4 million and $2.3 million, respectively, in compensation expense related to the 2016 SARs.

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (“ESPP” or the "Plan”) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the 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 and nine month periods ended September 30, 2019, the Company recorded $0.3 million and $0.9 million, respectively, in compensation expense related to the ESPP.

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



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
Research and development	$	4,988	$	4,431	$	15,191	$	12,109
Selling, general and administrative	5,496		4,511		15,477		12,664
Total	$	10,484	$	8,942	$	30,668	$	24,773

As of September 30, 2019, there was approximately $104.0 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 3.03 years.

Acquisitions - (Tables)

9 Months Ended

Sep. 30, 2019

Business Combinations [Abstract]

Schedule of Business Acquisitions

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



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

Preliminary Allocation and Purchase Consideration

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



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

Business Acquisition, Pro Forma Information

The following table summarizes certain supplemental pro forma financial information for the three and nine-month periods ended September 30, 2018 as if the Merger had occurred as of January 1, 2018. The unaudited pro-forma financial information for the three month and nine month periods ended September 30, 2018 reflects adjustments of $0.8 million and $1.5 million , respectively, related to acquisition fees that are non-recurring in nature.



	Three Months Ended September 30,			Nine Months Ended September 30,
	2018			2018
Revenues	$	53,591		$	178,396
Net loss attributable to common stockholders	$	(52,458	)	$	(89,976	)

Net loss per share

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

Net loss per share

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

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



	Three Months Ended September 30,								Nine Months Ended September 30,
	2019				2018				2019				2018
Numerator
Net loss	$	(59,997	)		$	(50,969	)		$	(173,899	)		$	(79,751	)
Denominator
Denominator for basic and diluted net loss per share	56,463,528				48,096,521				57,798,968				45,310,690
Net loss per share:
Basic and diluted	$	(1.06	)	*	$	(1.06	)	*	$	(3.01	)	*	$	(1.76	)	*

*In the three and nine months ended September 30, 2019 and 2018, the Company experienced a net loss and therefore did not report any dilutive share impact.



	As of September 30,
	2019	2018
Stock Options	10,743,181	9,545,522
Unvested restricted stock awards and units	650,103	580,347
Total	11,393,284	10,125,869

Subsequent events	9 Months Ended
Subsequent events	Sep. 30, 2019
Subsequent Events [Abstract]
Subsequent events	Subsequent events Acquisition of BioElectron Technology Corporation On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, (the “Acquisition”) pursuant to an Asset Purchase Agreement by and between the Company and BioElectron, dated October 1, 2019 (the “Acquisition Agreement”). Upon the closing of the 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 to be held in an escrow account to secure potential indemnification obligations owed to the Company. The loan advance was included in prepaid expenses and other current assets on the consolidated balance sheet as of September 30, 2019. Subject to the terms and conditions of the 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 Acquisition Agreement, BioElectron may also become entitled to receive contingent payments of a low single digit percentage of net sales of certain products. Tegsedi Approval in Brazil Tegsedi received marketing authorization from ANVISA in October 2019 for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis in Brazil. Refer to Note 12 for further details regarding our commitments and contingencies related to Tegsedi.

Consolidated Statements of Operations (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Revenue	$ 71,416	$ 53,591	$ 210,521	$ 178,396
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible assets	3,006	3,292	8,593	8,909
Amortization of acquired intangible assets	7,025	5,793	19,677	16,815
Research and development	63,076	54,368	175,621	118,337
Selling, general and administrative	49,284	38,368	139,044	104,882
Change in the fair value of deferred and contingent consideration	9,500	0	35,960	0
Total operating expenses	131,891	101,821	378,895	248,943
Loss from operations	(60,475)	(48,230)	(168,374)	(70,547)
Interest expense, net	(2,666)	(3,118)	(7,028)	(9,306)
Other income, net	2,800	734	2,509	1,066
Loss before income tax expense	(60,341)	(50,614)	(172,893)	(78,787)
Income tax benefit (expense)	344	(355)	(1,006)	(964)
Net loss attributable to common stockholders	$ (59,997)	$ (50,969)	$ (173,899)	$ (79,751)
Weighted-average shares outstanding:
Basic and diluted (in shares)	56,463,528	48,096,521	57,798,968	45,310,690
Net loss per share-basic and diluted (in dollars per share)
Net loss per share—basic and diluted (in dollars per share)	$ (1.06)	$ (1.06)	$ (3.01)	$ (1.76)
Net product revenue
Revenues:
Revenue	$ 71,369	$ 53,021	$ 209,899	$ 177,172
Collaboration and grant revenue
Revenues:
Revenue	$ 47	$ 570	$ 622	$ 1,224

Capitalization - Warrants (Details) - Common stock	Dec. 31, 2018 $ / shares shares
Period One
Warrants
Warrant shares (in shares) \| shares	7,030
Exercise price (in dollars per share) \| $ / shares	$ 128.00
Period Five
Warrants
Warrant shares (in shares) \| shares	130
Exercise price (in dollars per share) \| $ / shares	$ 2,520.00

Subsequent events - Narrative (Details) - BioElectron - Subsequent Event $ in Millions	Oct. 25, 2019 USD ($)
Subsequent Event [Line Items]
Cash consideration	$ 10.0
Loan Advance	4.0
Escrow	1.5
Maximum
Subsequent Event [Line Items]
Net sales amount	$ 200.0

Revenue recognition - Contract Liabilities, Rollforward (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Movement in Deferred Revenue [Roll Forward]
Beginning balance	$ 12,938	$ 11,891
Additions	3,801	4,706
Deductions	(2,433)	0
ASC 606 Adjustment	0	(3,937)
Ending balance	$ 14,306	$ 12,660

- (Notes)	9 Months Ended
- (Notes)	Sep. 30, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and contingencies	Commitments and contingencies Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with 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 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 no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. 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. An additional $6.0 million was paid to Akcea in the three month period ended June 30, 2019 upon regulatory approval of Waylivra from the EMA. In addition, Akcea is eligible to receive milestone payments, on a Product-by-Product basis, of $4.0 million upon receipt of regulatory approval for a product from ANVISA, subject to a maximum aggregate amount of $8.0 million for all such products. 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.

Net loss per share - Antidilutive (Details) - shares	9 Months Ended
Net loss per share - Antidilutive (Details) - shares	Sep. 30, 2019	Sep. 30, 2018
Net loss per share
Total shares excluded from calculation (in shares)	11,393,284	10,125,869
Stock Options
Net loss per share
Total shares excluded from calculation (in shares)	10,743,181	9,545,522
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	650,103	580,347

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

9 Months Ended

Sep. 30, 2019

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

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

The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine months ended September 30, 2019:



	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at June 30, 2019	$	929		$	993		$	1,922
Other comprehensive loss before reclassifications	(463		)	(843		)	(1,306		)
Amounts reclassified from other comprehensive items	—			—			—
Other comprehensive loss	(463		)	(843		)	(1,306		)
Balance at September 30, 2019	$	466		$	150		$	616



	Unrealized Gains/(Losses) On Marketable Securities, net of tax		Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2018	$	31	$	1,431		$	1,462
Other comprehensive income (loss) before reclassifications	435		(1,281		)	(846		)
Amounts reclassified from other comprehensive items	—		—			—
Other comprehensive income (loss)	435		(1,281		)	(846		)
Balance at September 30, 2019	$	466	$	150		$	616

The Company	9 Months Ended
The Company	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
The Company	The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-led 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 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 has two products, Translarna™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged five years and older in the 31 member states of the European Economic Area, or EEA. In July 2018, the European Commission approved a label-extension request to the marketing authorization for Translarna in the EEA to include patients from two to up to five years of age. 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, including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC, deficiency, or AADC deficiency. The Company is preparing a biologics license application, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which it anticipates submitting to the U.S. Food and Drug Administration, or FDA, in late 2019, with anticipated commercial launch in 2020, subject to approval. The Company is also preparing a marketing authorization application, or MAA, for PTC-AADC for the treatment of AADC deficiency in the European Union, or EU, for submission to the European Medicines Agency, or EMA, which will follow its BLA submission to the FDA. 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. Tegsedi has received marketing authorization in the U.S., EU and Canada for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis. Tegsedi also received marketing authorization from ANVISA in October 2019 for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis in Brazil. Waylivra has received conditional marketing authorization in the EU for the treatment of familial chylomicronemia syndrome, or FCS. 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. Currently, its collaboration has two pivotal clinical trials ongoing to evaluate the safety and effectiveness of risdiplam (RG7916, RO7034067), the lead compound in the SMA program. Roche is preparing an NDA and a MAA for risdiplam for the treatment of SMA in the United States and the EU, respectively, which Roche anticipates submitting to the FDA in the second half of 2019 and the EMA in the first half of 2020. 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 June 2014, the Company initiated reimbursed early access programs, or EAP programs, for Translarna for nmDMD patients in selected territories in the EEA and recorded its first sales of Translarna in the third quarter of 2014 pursuant to an EAP program. In December 2014, the Company recorded its first commercial sales in Germany. As of September 30, 2019, Translarna was available in over 40 countries on a commercial basis or pursuant to an EAP program. The Company expects to expand its commercial activities across the EEA pursuant to the marketing authorization granted by the EMA throughout 2019 and future years, subject to continued renewal of its marketing authorization following annual EMA reassessments and successful completion of pricing and reimbursement negotiations. Concurrently, the Company plans to continue to pursue EAP programs in select countries where those mechanisms exist, both within the EEA and in other countries that will reference the marketing authorization in the EEA. Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application, or NDA, over protest with the FDA, for which the FDA granted a standard review. In October 2017, the Office of Drug Evaluation I of the FDA issued a complete response letter for the NDA, stating that it was unable to approve the application in its current form. In response, the Company filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied PTC’s appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company intends to follow the FDA’s recommendation and will collect, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, which the Company initiated in the fourth quarter of 2018. The Company expects that a potential re-submission of an NDA could occur in 2020. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework. Emflaza was initially approved in the United States for the treatment of DMD in patients five years and older. In June 2019, the FDA approved the Company's label expansion request for Emflaza for patients two to five years of age. On April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. 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 no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. As of September 30, 2019, the Company had an accumulated deficit of approximately $1,112.8 million. The Company has financed its operations to date primarily through the private offerings in September 2019 of 1.5% convertible senior notes due 2026 and in August 2015 of 3.0% convertible senior notes due 2022 (see Note 11), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offerings" of its common stock, its initial public offering of common stock in June 2013, 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.

Acquisitions

9 Months Ended

Sep. 30, 2019

Business Combinations [Abstract]

Acquisitions

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

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. The fair value of the stock on the acquisition date was determined to be $155.9 million.

Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2%-6%. The fair value of the contingent consideration payments at the acquisition date was estimated to be $290.5 million. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments mentioned above no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payments at the closing date was estimated to be $38.1 million. Refer to Footnote 5 for further fair value considerations.

The Company evaluated the acquisition of Agilis under ASU No. 2017-01, Business Combinations: Clarifying the Definition of a Business. Because the business contained both inputs and processes necessary to manage products and provide economic benefits directly to its owners and substantially all the value of the acquisition did not relate to a similar group of assets, it was determined that the acquisition represents a business combination. Therefore, the transaction has been accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the total purchase price of the acquisition is allocated to the net tangible and identifiable intangible assets acquired and liabilities assumed based on their fair values as of the date of acquisition.

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



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

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



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

The Company incurred approximately $1.5 million in acquisition related expenses as of September 30, 2018, which were included in selling, general and administrative expenses in the consolidated statement of operations. The results of Agilis’s operations have been included in the consolidated statements of operations beginning on the acquisition date of August 23, 2018.

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

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

The net loss of Agilis included in the consolidated statement of operations for the period August 23, 2018 through September 30, 2018 was $1.9 million.

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



	Three Months Ended September 30,			Nine Months Ended September 30,
	2018			2018
Revenues	$	53,591		$	178,396
Net loss attributable to common stockholders	$	(52,458	)	$	(89,976	)

Bridge Loan

In connection with the Merger Agreement, on July 19, 2018, the Company also entered into a Bridge Loan and Security Agreement, or the Bridge Loan Agreement, by and among the Company, Agilis and certain of Agilis’s domestic subsidiaries, as guarantors. Under the Bridge Loan Agreement, the Company made a term loan advance to Agilis on July 23, 2018 in an original principal amount of $10.0 million. In connection with the closing of the Merger, the original principal amount of $10.0 million plus all accrued and unpaid interest thereon was credited against the cash portion of the upfront consideration paid by the Company pursuant to the terms of the Merger Agreement in satisfaction of Agilis’s outstanding payment obligations under the Bridge Loan Agreement, and the Company has no further obligation to extend any further loan amounts under the Bridge Loan Agreement.

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Numerator
Net loss	$ (59,997)	$ (50,969)	$ (173,899)	$ (79,751)
Denominator
Denominator for basic and diluted net loss per share (in shares)	56,463,528	48,096,521	57,798,968	45,310,690
Net loss per share:
Basic and diluted (in dollars per share)	$ (1.06)	$ (1.06)	$ (3.01)	$ (1.76)

Acquisitions - Preliminary Allocation of purchase price (Details) - USD ($) $ in Thousands	4 Months Ended
	Dec. 31, 2018	Sep. 30, 2019	Aug. 23, 2018
Finite-Lived Intangible Assets [Line Items]
Intangible assets - IPR&D	$ 576,500
Goodwill	82,341	$ 82,341
Agilis
Finite-Lived Intangible Assets [Line Items]
Cash and cash equivalents	328		$ 328
Prepaid expenses and other current assets	181		181
Fixed assets	153		153
Other assets	38		38
Intangible assets - IPR&D			480,000
Intangible assets - in process research and development (“IPRD”) Adjustment	96,500
Accounts payable and accrued expenses	(3,828)		(3,828)
Deferred tax liability	(122,032)		(115,200)
Deferred tax liability adjustment	(6,832)
Fair value of net assets acquired	451,340		361,672
Fair value of net assets acquired adjustment	89,668
Goodwill			100,309
Goodwill Adjustment	(17,968)
Total purchase price	533,681		$ 461,981
Total purchase price adjustment	$ 71,700

Accounts payable and accrued expenses - (Tables)

9 Months Ended

Sep. 30, 2019

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2019 and December 31, 2018 consist of the following:



	September 30, 2019		December 31, 2018
Employee compensation, benefits, and related accruals	$	25,800	$	27,629
Consulting and contracted research	2,356		11,267
Professional fees	10,300		5,574
Sales allowance and other costs	37,129		29,417
Sales rebates and royalties	33,645		31,874
Accounts payable	8,959		6,001
Other	9,961		16,437
Balance at September 30, 2019	$	128,150	$	128,199

Capitalization - Narrative (Details) - USD ($) $ / shares in Units, $ in Millions	1 Months Ended			3 Months Ended
	Sep. 30, 2019	Aug. 31, 2019	Jan. 31, 2019	Sep. 30, 2019
Warrants
Sale of Stock, Number of Shares Issued in Transaction	2,475,248		7,563,725	63,926
Sale of Stock, Price Per Share	$ 46.60		$ 30.20	$ 46.60
Sale of Stock, Consideration Received on Transaction	$ 97.0		$ 224.2	$ 2.6
Over-Allotment Option
Warrants
Sale of Stock, Number of Shares Issued in Transaction	371,287		843,725
Maximum
Warrants
Sale of Stock, Consideration Received on Transaction		$ 125.0
Common stock
Warrants
Sale of Stock, Price Per Share	$ 40.40			$ 40.40

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

9 Months Ended

Sep. 30, 2019

Fair Value Disclosures [Abstract]

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

The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2019 and December 31, 2018:



	September 30, 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	$	185,072	$	—	$	185,072	$	—
Equity investment in MRI	$	6,529	$	6,529	$	—	$	—
Stock appreciation rights liability	$	2,235	$	—	$	—	$	2,235
Deferred consideration payable	$	39,000	$	—	$	39,000	$	—
Contingent consideration payable- development and regulatory milestones	$	285,300	$	—	$	—	$	285,300
Contingent consideration payable- net sales milestones and royalties	$	59,600	$	—	$	—	$	59,600



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

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

The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2019 and December 31, 2018:



	September 30, 2019
	Amortized Cost		Gross Unrealized					Fair Value
	Amortized Cost		Gains		Losses			Fair Value
Commercial paper	$	47,898	$	80	$	—		$	47,978
Corporate debt securities	115,109		612		(4		)	115,717
Asset-backed securities	21,310		67		—			21,377
Total	$	184,317	$	759	$	(4	)	$	185,072



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

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

The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2019 are as follows:



	September 30, 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	(4		)	3,017		—		—		(4		)	3,017
Total	$	(4	)	$	3,017	$	—	$	—	$	(4	)	$	3,017

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, 2018 are as follows:



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

Schedule of marketable securities on the balance sheet

Marketable securities on the balance sheet at September 30, 2019 and December 31, 2018 mature as follows:



	September 30, 2019
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	47,978	$	—
Corporate debt securities	58,533		57,184
Asset-backed securities	21,377		—
Total Marketable securities	$	127,888	$	57,184



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

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 SARs liability, and the contingent consideration payable for the periods ended September 30, 2019 and December 31, 2018:



	September 30, 2019
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$2,235	Option-pricing model	Volatility	43.23%
			Risk free interest rate	1.88%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$33.82
			Expected life	0.26 years
Contingent consideration payable- development and regulatory milestones	$285,300	Probability-adjusted discounted cash flow	Potential development and regulatory milestones	$0 - $555 million
			Probabilities of success	25% - 94%
			Discount rates	2.7% - 5.1%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$59,600	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.0%
			Projected years of payments	2021 - 2038



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

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 September 30, 2019. The changes in the fair value of the Company's Level 3 valuations for the period ended September 30, 2018 were immaterial.



	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	2,236			28,260		6,400
Payments	(3,815		)	$	—	—
Ending balance as of September 30, 2019	$	2,235		$	285,300	$	59,600

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, 2017		41,612,395
Balance at the beginning of the period at Dec. 31, 2017	$ 156,437	$ 42	$ 966,534	$ 3,969	$ (814,108)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)		4,600,000
Issuance of common stock related to equity offerings	117,915	$ 4	117,911
Issuance of common stock related to acquisition (in shares)		3,500,907
Issuance of common stock related to acquisition	155,861	$ 4	155,857
Exercised (in shares)		512,145
Exercise of options	8,631	$ 1	8,630
Restricted stock vesting and issuance (in shares)		119,691
Restricted stock vesting and issuance	0
Issuance of common stock in connection with an employee stock purchase plan (in shares)		87,517
Issuance of common stock in connection with an employee stock purchase plan	1,299		1,299
Share-based compensation expense	24,773		24,773
Net loss	(79,751)				(79,751)
Comprehensive income	(2,341)			(2,341)
Balance (in shares) at Sep. 30, 2018		50,432,655
Balance at the end of the period at Sep. 30, 2018	386,090	$ 51	1,275,004	1,628	(890,593)
Balance (in shares) at Dec. 31, 2017		41,612,395
Balance at the beginning of the period at Dec. 31, 2017	156,437	$ 42	966,534	3,969	(814,108)
Balance (in shares) at Dec. 31, 2018		50,606,147
Balance at the end of the period at Dec. 31, 2018	350,727	$ 51	1,288,137	1,462	(938,923)
Balance (in shares) at Jun. 30, 2018		46,680,482
Balance at the beginning of the period at Jun. 30, 2018	267,402	$ 47	1,105,124	1,855	(839,624)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offerings	42		42
Issuance of common stock related to acquisition (in shares)		3,500,907
Issuance of common stock related to acquisition	155,861	$ 4	155,857
Exercised (in shares)		251,266
Exercise of options	5,039		5,039
Share-based compensation expense	8,942		8,942
Net loss	(50,969)				(50,969)
Comprehensive income	(227)			(227)
Balance (in shares) at Sep. 30, 2018		50,432,655
Balance at the end of the period at Sep. 30, 2018	386,090	$ 51	1,275,004	1,628	(890,593)
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)		10,102,899
Issuance of common stock related to equity offerings	323,756	$ 10	323,746
Adjustments to additional paid in capital, equity component of convertible debt	119,489		119,489
Exercised (in shares)		645,435
Exercise of options	12,195		12,195
Restricted stock vesting and issuance, net (in shares)		169,792
Restricted stock vesting and issuance, net	0
Issuance of common stock in connection with an employee stock purchase plan (in shares)		54,719
Issuance of common stock in connection with an employee stock purchase plan	1,564		1,564
Share-based compensation expense	30,668		30,668
Net loss	(173,899)				(173,899)
Comprehensive income	(846)			(846)
Balance (in shares) at Sep. 30, 2019		61,578,992
Balance at the end of the period at Sep. 30, 2019	663,654	$ 61	1,775,799	616	(1,112,822)
Balance (in shares) at Jun. 30, 2019		58,707,185
Balance at the beginning of the period at Jun. 30, 2019	488,685	$ 58	1,539,530	1,922	(1,052,825)
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to equity offering (in shares)		2,539,174
Issuance of common stock related to equity offerings	99,211	$ 3	99,208
Adjustments to additional paid in capital, equity component of convertible debt	119,489		119,489
Exercised (in shares)		334,433
Exercise of options	7,088	$ 0	7,088
Restricted stock vesting and issuance, net (in shares)		(1,800)
Restricted stock vesting and issuance, net	0
Share-based compensation expense	10,484		10,484
Net loss	(59,997)
Comprehensive income	(1,306)			(1,306)
Balance (in shares) at Sep. 30, 2019		61,578,992
Balance at the end of the period at Sep. 30, 2019	$ 663,654	$ 61	$ 1,775,799	$ 616	$ (1,112,822)

Leases - Narrative (Details) $ in Thousands	Sep. 30, 2019 USD ($) ft² Term operating_lease
Lessee, Lease, Description [Line Items]
Area of Real Estate Property \| ft²	185,000
Number Of Operating Leases \| operating_lease	3
Term of Contract ( in years )	15 years
Renewal Term ( in years )	10 years
Aggregate rent, Initial term \| $	$ 14,738
Percent Of Market Rate	95.00%
Minimum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	2 months 12 days
Maximum
Lessee, Lease, Description [Line Items]
Term of Contract ( in years )	6 years 8 months 12 days
New Building
Lessee, Lease, Description [Line Items]
Area of Real Estate Property \| ft²	75,000
Renewal Term ( in years )	10 years
Number of terms \| Term	2
The Campus
Lessee, Lease, Description [Line Items]
Aggregate rent, Initial term \| $	$ 88,100

Stock award plan - (Tables)

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [Abstract]

Summary of stock option activity

A summary of stock option activity is as follows:



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

Outstanding at December 31, 2018	8,534,358		$	28.58
Granted	3,265,220		$	34.68
Exercised	(645,435	)	$	18.91
Forfeited/Cancelled	(410,962	)	$	32.54
Outstanding at September 30, 2019	10,743,181		$	30.85	7.39 years	$	75,022
Vested or Expected to vest at September 30, 2019	5,138,949		$	30.27	8.89 years	$	27,358
Exercisable at September 30, 2019	5,220,799		$	31.32	5.80 years	$	46,228

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

The fair value of grants made in the nine months ended September 30, 2019 was contemporaneously estimated on the date of grant using the following assumptions:



		Nine months ended September 30, 2019
Risk-free interest rate		1.71 - 2.63%
Expected volatility		61.90 - 91.75%
Expected term		5.75 - 6.11 years

Summary of information on the Company's restricted stock

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



	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
January 1, 2019	571,479		$	17.61
Granted	306,549		$	32.97
Vested	(180,827	)	$	17.56
Forfeited	(47,098	)	$	22.34
Unvested at September 30, 2019	650,103		$	24.54

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



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
Research and development	$	4,988	$	4,431	$	15,191	$	12,109
Selling, general and administrative	5,496		4,511		15,477		12,664
Total	$	10,484	$	8,942	$	30,668	$	24,773

Leases - Lease payments (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Leases [Abstract]
2019 (Excludes the nine months ended September 30, 2019)	$ 1,336
2020	5,463
2021	3,705
2022	2,110
2023 and thereafter	2,124
Total lease payments	14,738
Less: Imputed Interest	678
Total	$ 14,060

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Stock option plan
Share-based compensation expense	$ 10,484	$ 8,942	$ 30,668	$ 24,773
Research and development
Stock option plan
Share-based compensation expense	4,988	4,431	15,191	12,109
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 5,496	$ 4,511	$ 15,477	$ 12,664

The Company - Narrative (Details) $ in Thousands			1 Months Ended	9 Months Ended
The Company - Narrative (Details) $ in Thousands	Aug. 23, 2018 USD ($) shares	Apr. 20, 2017 USD ($) shares	Aug. 31, 2014 member_state	Sep. 30, 2019 USD ($) country product	Dec. 31, 2018 USD ($)	Aug. 31, 2015
Long-term debt
Number of products \| product				2
Number of member states of the European Economic Area \| member_state			31
Retained earnings (accumulated deficit)				$ (1,112,822)	$ (938,923)
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Interest rate ( as a percent )				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) \| 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
Translarna
Long-term debt
Number of countries ( over ) \| country				40
Agilis
Long-term debt
Cash consideration	$ 49,221
Equity Interest Issued, number of shares (in shares) \| shares	3,500,907
Numerator for calculation of number of shares of equity interests issued to acquire entity	$ 150,000
Trading day period	10 days
Development milestone payments which the entity is obligated to pay	$ 40,000				$ 40,000
Agilis \| Non-collaborative Arrangement Transactions
Long-term debt
Development milestone payments which the entity is obligated to pay				$ 40,000

Fair value of financial instruments and marketable securities - Fair Value Measurement Inputs and Valuation Techniques (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Dec. 31, 2018
Level 3 roll forward
Additions	$ 0
SARs
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	2,235	$ 3,814
Change in fair value	2,236
Payments	(3,815)
Commitments
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	285,300	257,040
Additions	0
Change in fair value	28,260
Payments	0
Agilis \| Significant unobservable inputs (level 3)
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	59,600	53,200
Milestones and Royalties \| Agilis
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	59,600	53,200
Milestones and Royalties \| Agilis \| Significant unobservable inputs (level 3)
Level 3 roll forward
Contingent consideration payable- net sales milestones and royalties	59,600	$ 53,200
Additions	0
Change in fair value	6,400
Payments	$ 0

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended			3 Months Ended		9 Months Ended
	Mar. 05, 2013	Jun. 30, 2016	May 31, 2016	May 31, 2013	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Stock option plan
Share-based compensation expense					$ 10,484	$ 8,942	$ 30,668	$ 24,773
Unrecognized compensation cost					$ 104,000		$ 104,000
Weighted average remaining service period for recognition of unrecognized compensation cost							3 years 10 days
Common stock
Stock option plan
Number of shares available for issuance (in shares)					453,992		453,992
Unvested restricted stock
Stock option plan
Grants in period (in shares)							306,549
Stock option
Stock option plan
Granted (in shares)							3,265,220
Inducement grants for non-statutory stock options (in shares)							999,300
Expected dividend yield (as a percent)							0.00%
Weighted average grant date fair value (in dollars per share)							$ 21.49
SARs
Stock option plan
Granted (in shares)			897,290
Vesting period							4 years
Vested (in shares)							157,930
Share-based compensation expense					$ 400		$ 2,300
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance (in shares)	0
2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares authorized (in shares)	739,937
2013 Stock Incentive Plan \| Unvested restricted stock
Stock option plan
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
Number of shares available for issuance (in shares)					0		0
Number of additional shares authorized (in shares)				2,500,000
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance (in shares)				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
Annual increase in the number of shares (in shares) on the first day of the fiscal year				2,500,000
Annual increase in the number of shares outstanding on the first day of the fiscal year				4.00%
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)		1,000,000,000,000
Share-based compensation expense					$ 300		$ 900
Award requisite service period		6 months
Purchase price of common stock, percent		85.00%
Employee stock purchase plan, voting percentage limit		5.00%

Leases

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Leases

The Company leases office space in South Plainfield, New Jersey for its principal office under three noncancelable operating leases through May 2022 and August 2024, in addition to office space in various countries for international employees primarily through workspace providers. The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s operating leases have remaining lease terms ranging from 0.2 years to 6.7 years and certain of the leases include renewal options to extend the lease for up to 10 years.

The components of lease expense were as follows:



	Three Months Ended September 30, 2019		Nine Months Ended September 30, 2019
Operating Lease Cost
Fixed lease cost	$	1,431	$	3,078
Variable lease cost	184		488
Short-term lease cost	94		235
Total operating lease cost	$	1,709	$	3,801

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

Supplemental balance sheet information related to leases was as follows:



	September 30, 2019

Operating lease ROU asset	$	13,708

Operating lease liabilities- current	$	4,605
Operating lease liabilities- noncurrent	9,455
Total operating lease liability	$	14,060

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

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



	September 30, 2019

Weighted-average remaining lease terms - operating leases (years)	3.58
Weighted-average discount rate - operating leases	7.05	%

Supplemental cash flow information related to leases was as follows:



	Nine Months Ended September 30, 2019
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	2,751
Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	16,120

Future minimum lease payments under non-cancelable leases as of September 30, 2019 were as follows:



	Operating Leases
2019 (Excludes the nine months ended September 30, 2019)	$	1,336
2020	5,463
2021	3,705
2022	2,110
2023 and thereafter	2,124
Total lease payments	14,738
Less: Imputed Interest	678
Total	$	14,060

As of September 30, 2019, the Company had one operating lease that had not yet commenced, and accordingly, is not reflected in the tables above. On August 4, 2019, the Company and Bristol-Myers Squibb Company, (the “Landlord”), entered into a Lease Agreement (the “Lease”), relating to the lease of approximately 185,000 square feet of office, production and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”).

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

The aggregate rent for the Initial Term will be approximately $88.1 million. The rental rate for the renewal periods will be 95% of the Prevailing Market Rate (as defined in the Lease) and determined at the time of the exercise of the renewal. The Company is also responsible for maintaining certain insurance and the payment of proportional taxes, utilities and common area operating expenses. The Lease contains customary events of default, representations, warranties and covenants.

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.

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Accounting Policies [Abstract]
Raw materials	$ 1,853	$ 1,431
Work in progress	10,870	9,324
Finished goods	4,384	5,362
Total inventory	$ 17,107	$ 16,117

Commitments and contingencies - Narrative (Details) - USD ($) $ in Millions	9 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2018	Aug. 23, 2018	Jun. 30, 2016
Akcea
Other Commitments [Abstract]
Upfront licensing fee	$ 12.0
Milestone payments	4.0
Akcea \| Maximum
Other Commitments [Abstract]
Milestone payments	8.0
Non-collaborative Arrangement Transactions \| Akcea
Other Commitments [Abstract]
Milestone payments	6.0
Agilis
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay		$ 40.0	$ 40.0
Agilis \| Maximum
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	60.0	60.0
Priority review voucher amount	535.0	535.0
Net sales amount	$ 150.0	$ 150.0
Product sales	6.00%	6.00%
Agilis \| Non-collaborative Arrangement Transactions
Other Commitments [Abstract]
Development milestone payments which the entity is obligated to pay	$ 40.0
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

Stock award plan - Restricted Stock (Details) - Unvested restricted stock	9 Months Ended
	Sep. 30, 2019 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	571,479
Granted (in shares) \| shares	306,549
Vested (in shares) \| shares	(180,827)
Forfeited (in shares) \| shares	(47,098)
Balance at the end of the period (in shares) \| shares	650,103
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 17.61
Granted (in dollars per share) \| $ / shares	32.97
Vested (in dollars per share) \| $ / shares	17.56
Forfeited (in dollars per share) \| $ / shares	22.34
Balance at the end of the period (in dollars per share) \| $ / shares	$ 24.54

Capitalization - (Tables)

9 Months Ended

Sep. 30, 2019

Stockholders' Equity Note [Abstract]

Summary of the Company's outstanding warrants

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



	Warrant shares	Exercise price		Expiration
Common stock	7,030	$	128.00	September 2019
Common stock	130	$	2,520.00	August 2019

Fair value of financial instruments and marketable securities

9 Months Ended

Sep. 30, 2019

Fair Value Disclosures [Abstract]

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 investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments. 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 MRI Interventions, Inc.'s ("MRI") common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with MRI, a publicly traded medical device company. The Company determined that the equity investment represents a financial instrument and therefore, recorded it at fair value, which is readily determinable. The equity investment is a component of deposits and other assets on the consolidated balance sheet. During the three and nine month periods ended September 30, 2019, the Company recorded an unrealized gain of $2.4 million and $2.5 million, respectively, which are components of other (expense) income, net within the consolidated statement of operations. The fair value of the equity investment was $6.5 million as of September 30, 2019. The Company classifies its equity investment in MRI 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.

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



	September 30, 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	$	185,072	$	—	$	185,072	$	—
Equity investment in MRI	$	6,529	$	6,529	$	—	$	—
Stock appreciation rights liability	$	2,235	$	—	$	—	$	2,235
Deferred consideration payable	$	39,000	$	—	$	39,000	$	—
Contingent consideration payable- development and regulatory milestones	$	285,300	$	—	$	—	$	285,300
Contingent consideration payable- net sales milestones and royalties	$	59,600	$	—	$	—	$	59,600



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

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2019 and December 31, 2018.

The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2019 and December 31, 2018:



	September 30, 2019
	Amortized Cost		Gross Unrealized					Fair Value
	Amortized Cost		Gains		Losses			Fair Value
Commercial paper	$	47,898	$	80	$	—		$	47,978
Corporate debt securities	115,109		612		(4		)	115,717
Asset-backed securities	21,310		67		—			21,377
Total	$	184,317	$	759	$	(4	)	$	185,072



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

At September 30, 2019 and December 31, 2018, the Company held securities with an unrealized loss position that were not considered to be other-than-temporarily impaired as the Company has the ability to hold such investments until recovery of their fair value. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. As of September 30, 2019 and December 31, 2018, the Company did not have any realized gains/losses from the sale of marketable securities.



	September 30, 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	(4		)	3,017		—		—		(4		)	3,017
Total	$	(4	)	$	3,017	$	—	$	—	$	(4	)	$	3,017



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

Marketable securities on the balance sheet at September 30, 2019 and December 31, 2018 mature as follows:



	September 30, 2019
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	47,978	$	—
Corporate debt securities	58,533		57,184
Asset-backed securities	21,377		—
Total Marketable securities	$	127,888	$	57,184



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

The Company classifies all of its securities as current as they are all available for sale and are available for current operations.

Convertible senior notes

In August 2015, the Company issued $150.0 million of 3.0% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.5% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,” together with the “2022 Convertible Notes,” the “Convertible Notes”). The Company separately accounted for the liability and equity components of the Convertible Notes by allocating the proceeds between the liability component and equity component, as further discussed in Note 11. The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the 2022 Convertible Notes at September 30, 2019 and December 31, 2018 was $156.4 million and $146.6 million, respectively. The estimated fair value of the 2026 Convertible Notes at September 30, 2019 was $273.8 million.

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 no later than 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 September 30, 2019 was estimated to be $39.0 million by applying a 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 candidates. As of September 30, 2019, $19.7 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 contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss in the consolidated statements of operations. The fair value of the development and regulatory milestones 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. 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.



	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	2,236			28,260		6,400
Payments	(3,815		)	$	—	—
Ending balance as of September 30, 2019	$	2,235		$	285,300	$	59,600



	September 30, 2019
	Fair Value	Valuation Technique	Unobservable Input	Range
SARs	$2,235	Option-pricing model	Volatility	43.23%
			Risk free interest rate	1.88%
			Strike price	$6.76 - $30.86
			Fair value of common stock	$33.82
			Expected life	0.26 years
Contingent consideration payable- development and regulatory milestones	$285,300	Probability-adjusted discounted cash flow	Potential development and regulatory milestones	$0 - $555 million
			Probabilities of success	25% - 94%
			Discount rates	2.7% - 5.1%
			Projected years of payments	2020 - 2026
Contingent considerable payable- net sales milestones and royalties	$59,600	Option-pricing model with Monte Carlo simulation	Potential net sales milestones	$0 - $150 million
			Probabilities of success	25% - 89%
			Potential percentage of net sales for royalties	2% - 6%
			Discount rate	14.0%
			Projected years of payments	2021 - 2038



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

The contingent consideration is classified as a Level 3 liability as its 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 approach, including but not limited to, assumptions involving probability adjusted sales estimates for the Agilis platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

- Definition

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

+ References + Details

Acquisitions - Narrative (Details) - USD ($) $ in Thousands			1 Months Ended	3 Months Ended	9 Months Ended		12 Months Ended
Acquisitions - Narrative (Details) - USD ($) $ in Thousands	Aug. 23, 2018	Apr. 20, 2017	Sep. 30, 2018	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018	Jul. 23, 2018
Finite-Lived Intangible Assets [Line Items]
Contingent consideration payable					$ 344,900		$ 310,240
Deferred consideration payable					$ 19,300		$ 18,300
Issuance of common stock related to acquisition				$ 155,861		$ 155,861
Useful life					7 years
Loans								$ 10,000
Non-collaborative Arrangement Transactions \| Marathon Pharmaceuticals, LLC
Finite-Lived Intangible Assets [Line Items]
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
Finite-Lived Intangible Assets [Line Items]
Cash consideration	$ 49,221
Equity Interest Issued, number of shares (in shares)	3,500,907
Fair value of PTC common stock issued	$ 155,860
Estimated fair value of contingent consideration payable	290,500
Deferred consideration payable	38,100
Consideration Transferred	533,681
Acquisition Related Costs						1,500
Net loss attributable to common stockholders				(52,458)		(89,976)
Issuance of common stock related to acquisition (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
Earnings (loss) of acquire since acquisition date			$ (1,900)
Development milestone payments which the entity is obligated to pay	$ 40,000						$ 40,000
Agilis \| Non-collaborative Arrangement Transactions
Finite-Lived Intangible Assets [Line Items]
Development milestone payments which the entity is obligated to pay					$ 40,000
Acquisition-related Costs \| Agilis
Finite-Lived Intangible Assets [Line Items]
Net loss attributable to common stockholders				$ 800		$ 1,500
Maximum \| Agilis
Finite-Lived Intangible Assets [Line Items]
Priority review voucher amount					535,000		535,000
Net sales amount					$ 150,000		$ 150,000
Product sales					6.00%		6.00%
Development milestone payments which the entity is obligated to pay					$ 60,000		$ 60,000
Minimum \| Agilis
Finite-Lived Intangible Assets [Line Items]
Product sales					2.00%		2.00%

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2019	$ 7,034
2020	28,136
2021	28,136
2022	28,136
2023 and thereafter	34,968
Total	$ 126,410

Revenue recognition - Recognized revenue in the period (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenue from Contract with Customer [Abstract]
Amounts included in contract liabilities at the beginning of the period	$ 2,269	$ 0	$ 2,269	$ 0
Performance obligations satisfied in current period	69,100	53,021	207,630	177,172
Total product revenue	$ 71,369	$ 53,021	$ 209,899	$ 177,172