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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2016	Aug. 01, 2016
Document and Entity Information
Entity Registrant Name	PTC THERAPEUTICS, INC.
Entity Central Index Key	0001070081
Document Type	10-Q
Document Period End Date	Jun. 30, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		34,247,719
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q2

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 35,658	$ 58,022
Marketable securities	237,235	280,903
Prepaid expenses and other current assets	4,776	5,930
Trade receivables, net	19,765	11,094
Total current assets	297,434	355,949
Fixed assets, net	7,601	8,974
Deposits and other assets	528	358
Total assets	305,563	365,281
Current liabilities:
Accounts payable and accrued expenses	42,183	45,247
Deferred revenue	726	139
Total current liabilities	42,909	45,386
Long-term debt	94,936	91,848
Other long-term liabilities	2,094	2,046
Total liabilities	139,939	139,280
Stockholders' equity:
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 34,083,319 shares at June 30, 2016. Authorized 125,000,000 shares; issued and outstanding 33,916,559 shares at December 31, 2015	34	34
Additional paid-in capital	837,850	820,165
Accumulated other comprehensive income (loss)	885	(1,200)
Accumulated deficit	(673,145)	(592,998)
Total stockholders' equity	165,624	226,001
Total liabilities and stockholders' equity	$ 305,563	$ 365,281

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Revenues:
Net product revenue	$ 15,437	$ 6,161	$ 34,314	$ 11,230
Collaboration and grant revenue	196	613	214	3,026
Total revenues	15,633	6,774	34,528	14,256
Operating expenses:
Research and development	28,827	28,190	60,226	56,128
Selling, general and administrative	23,366	17,210	49,304	34,825
Total operating expenses	52,193	45,400	109,530	90,953
Loss from operations	(36,560)	(38,626)	(75,002)	(76,697)
Interest (expense) income, net	(2,060)	498	(4,016)	1,022
Other expense, net	(387)	(88)	(1,107)	(456)
Loss before income tax expense	(39,007)	(38,216)	(80,125)	(76,131)
Income tax benefit (expense)	93	(145)	(22)	(145)
Net loss attributable to common stockholders	$ (38,914)	$ (38,361)	$ (80,147)	$ (76,276)
Weighted-average shares outstanding:
Basic and diluted (in shares)	34,000,333	33,600,653	33,959,751	33,335,674
Net loss per share-basic and diluted (in dollars per share)
Net loss per share-basic and diluted (in dollars per share)	$ (1.14)	$ (1.14)	$ (2.36)	$ (2.29)

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Consolidated Statements of Comprehensive Loss
Net loss	$ (38,914)	$ (38,361)	$ (80,147)	$ (76,276)
Other comprehensive loss:
Unrealized (loss) gain on marketable securities, net of tax	(40)	(224)	618	(99)
Foreign currency translation (loss) gain	(159)	465	1,467	341
Comprehensive loss	$ (39,113)	$ (38,120)	$ (78,062)	$ (76,034)

- Definition

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

+ References + Details

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Cash flows from operating activities
Net loss	$ (80,147)	$ (76,276)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	1,664	1,319
Change in valuation of warrant liability	47	(72)
Non-cash interest expense	2,941
Amortization of premiums on investments	1,140	915
Amortization of debt issuance costs	147
Share-based compensation expense	17,651	18,076
Benefit for deferred income taxes	(244)
Unrealized foreign currency transaction losses, net	963
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	1,163	(356)
Trade receivables, net	(8,480)	(669)
Deposits and other assets	(170)	258
Accounts payable and accrued expenses	(3,435)	(6,039)
Other long-term liabilities	1	(46)
Deferred revenue	587	(3,354)
Net cash used in operating activities	(66,172)	(66,244)
Cash flows from investing activities
Purchases of fixed assets	(275)	(1,177)
Purchases of marketable securities	(46,256)	(44,988)
Sale and redemption of marketable securities	89,645	83,468
Net cash provided by investing activities	43,114	37,303
Cash flows from financing activities
Proceeds from exercise of options	34	8,072
Net cash provided by financing activities	34	8,072
Effect of exchange rate changes on cash	660	341
Net decrease in cash and cash equivalents	(22,364)	(20,528)
Cash and cash equivalents, beginning of period	58,022	49,748
Cash and cash equivalents, end of period	35,658	29,220
Supplemental disclosure of cash information
Cash paid for interest	2,263
Cash paid for income taxes	264
Supplemental disclosures of non-cash information related to investing and financing activities
Change in unrealized gain (loss) on marketable securities, net of tax	$ 618	$ (99)

Summary of significant accounting policies	6 Months Ended
Summary of significant accounting policies	Jun. 30, 2016
Summary of significant accounting policies
Summary of significant accounting policies	2.Summary of significant accounting policies The Company’s complete listing of significant accounting policies are described in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2015 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (SEC) on February 29, 2016 (2015 Form 10-K). Basis of Presentation The accompanying financial information as of June 30, 2016 and for the three and six months ended June 30, 2016 and 2015 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, 2015 and notes thereto included in the 2015 Form 10-K. In the opinion of management, the unaudited financial information as of June 30, 2016 and for the three and six months ended June 30, 2016 and 2015 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three and six month periods ended June 30, 2016 are not necessarily indicative of the results to be expected for the year ended December 31, 2016 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 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. Inventories and cost of product revenue In 2014, the Company was notified that the European Commission, or EC, granted marketing authorization for Translarna for the treatment of nmDMD in ambulatory patients aged five years and older. The conditional marketing authorization allows the Company to market Translarna for the treatment of nmDMD in the 31 member states of European Economic Area. The launch in these countries is on a country by country basis. This marketing authorization is subject to annual review and renewal by the EC following reassessment by the European Medicines Agency, or EMA, of the risk benefit balance of the authorization, which the Company refers to as the annual EMA reassessment. In the third quarter of 2015, the EMA approved the annual renewal of the marketing authorization for Translarna for the treatment of nmDMD. The authorization was further conditioned on the Company’s submission of the final report, including additional efficacy and safety data, from ACT DMD and the Company’s ability to implement measures, including pharmacovigilance plans that are detailed in the risk management plan for Translarna that was submitted to EMA. In January 2016, the Company submitted the final ACT DMD report to the EMA. The Company made this submission as a type II variation request that sought to have this initial condition to its marketing authorization removed and a full marketing authorization granted. In February 2016, the Company also submitted a marketing authorization renewal request with the EMA. While the Company has been informed that the renewal assessment procedure cannot be completed by mid-year 2016, it expects that, pursuant to applicable regulations, its current marketing authorization status will remain valid while the annual EMA reassessment is ongoing and until it is concluded with an opinion from the European Commission with respect to renewal of its marketing authorization. Based on its interpretation of applicable regulatory timeframes, the Company believes the annual EMA reassessment could be completed, at the earliest, by the end of 2016. The Company plans to seek to renew the marketing authorization on an annual basis until the Company’s obligations have been fulfilled and the approval is converted from a conditional approval into a full approval. If the Company fails to satisfy such requirements, or if it is determined that the balance of risks and benefits of using Translarna changes materially, the EC could, at the EMA’s recommendation, vary, suspend, withdraw or refuse to renew the marketing authorization for Translarna or require additional clinical trials. There continues to be substantial risk that regulators could suspend or not renew the Company’s marketing authorization in the future. As such, as of the date of this filing, the Company has not capitalized inventory given the near term uncertainty with respect to the long term utilization of Translarna finished product for commercial use. Had the Company capitalized as inventory all of the its Translarna product that is available for commercial sale on hand as of June 30, 2016, the value of that inventory would have been approximately $1.2 million. In addition, had the Company expensed the cost of Translarna product sold as a cost of sales, the gross profit margin would have been greater than 90%, which the Company believes is consistent with the cost of producing small molecule therapeutics for orphan drug diseases in the pharmaceutical industry. The Company will continue to assess the appropriateness of inventory capitalization based on the outcome of applicable regulatory approvals which are expected later this year. Revenue Recognition The Company recognizes revenue when amounts are realized or realizable and earned. Revenue is considered realizable and earned when the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the price is fixed or determinable; and (4) collection of the amounts due are reasonably assured. Net Product Sales The Company’s net product sales have consisted solely of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company began recognizing revenue for payments received under the reimbursed EAPs for Translarna in nmDMD patients in select countries in the third quarter of 2014. The Company has now established a pattern of collectability and, since January 2015, the Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition—Products. The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and, in some cases, one of the Company’s third-party partner distributors. The Company’s third-party distributors act as intermediaries between the Company and end users and do not typically stock significant quantities of Translarna. The ultimate payor for Translarna is typically a government authority or institution or a third-party health insurer. The Company records revenue net of estimated third party discounts and rebates. Allowances are recorded as a reduction of revenue at the time revenues from product sales are recognized. These allowances are adjusted to reflect known changes in factors and may impact such allowances in the quarter those changes are known. Collaboration and Grant Revenue The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events. The Company evaluates all contingent consideration earned, such as a milestone payment, using the criteria as provided by the Financial Accounting Standards Board (FASB), guidance on the milestone method of revenue recognition. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from our activities to achieve the milestone; (2) the milestone be related to past performance; and (3) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement. If these criteria are met then the contingent milestones can be considered a substantive milestone and will be recognized as revenue in the period that the milestone is achieved. The Company recognizes royalties as earned in accordance with the terms of various research and collaboration agreements. If not substantive, the contingent consideration is allocated to the existing units of accounting based on relative selling price and recognized following the same basis previously established for the associated unit of accounting. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities. Recently issued accounting standards In May 2014, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 will eliminate transaction- and industry-specific revenue recognition guidance under current GAAP and replace it with a principle-based approach for determining revenue recognition. ASU No. 2014-09 includes the required steps to achieve the core principle that an entity should 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. The ASU will also require additional disclosure about the nature, amount, timing and uncertainty of revenue and cash flows arising from customer contracts, including significant judgments and changes in judgments and assets recognized from costs incurred to obtain or fulfill a contract. With the issuance of ASU No. 2015-14 in August 2015, the FASB deferred the effective date of the revenue recognition guidance to reporting periods beginning after December 15, 2017. Early adoption of the standard is permitted but not before the original effective date, which was for reporting periods beginning after December 15, 2016. With the issuance of ASU No. 2016-08 in March 2016 and ASU No. 2016-10 in April 2016, the FASB further amended guidance on recording revenue on a gross versus a net basis and on identifying performance obligations and licensing, respectively. The Company expects to adopt this guidance when effective and continues to evaluate the effect that the updated standard, as well as additional amendments, may have on its consolidated financial statements and accompanying notes. In August 2014, the FASB issued ASU 2014-15, “Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern”, which defines management’s responsibility to assess an entity’s ability to continue as a going concern, and to provide related footnote disclosures if there is substantial doubt about its ability to continue as a going concern. The pronouncement is effective for annual reporting periods ending after December 15, 2016 with early adoption permitted. The adoption of this guidance is not expected to have a significant impact on the Company’s financial statements. In April 2015, the FASB issued ASU No. 2015-03, “Interest—Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs topic of the Codification”. This standard provides a simplified presentation of debt issuance costs and requires that debt issuance costs related to a recognized debt liability to be presented on the balance sheet as a direct deduction from the carrying amount of that debt liability, consistent with debt discounts. The standard is effective for public companies for annual periods beginning after December 15, 2015. The Company adopted the guidance on January 1, 2016 on a retrospective basis and reclassed $2.8 million from “Deposits and other assets” to “Long-term debt” on the balance sheet as of December 31, 2015. The Company’s unamortized debt issuance cost at June 30, 2016 was $2.6 million which is included within “Long-term debt” on the consolidated balance sheet. In November 2015, the FASB issued ASU No. 2015-17, “Income Taxes (Topic 740): Balance Sheet Classification of Deferred Taxes”. This standard requires all deferred tax assets and liabilities to be classified as non-current on the balance sheet instead of separating deferred taxes into current and non-current amounts. In addition, valuation allowance allocations between current and non-current deferred tax assets are no longer required because those allowances also will be classified as non-current. This standard is effective for public companies for annual periods beginning after December 15, 2016. Earlier application is permitted as of the beginning of an interim or annual reporting period. The Company’s deferred tax assets is provided with full valuation allowance as of June 30, 2016. As such, the Company does not expect that this standard will have a significant impact upon adoption. 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. ASU 2016-01 is effective for years beginning after December 15, 2017, including interim periods within those fiscal years. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-01 will have on its consolidated financial statements and accompanying notes. In February 2016, the FASB issued ASU No. 2016-02, “Leases (Topic 842)”. This standard will require 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 will also require 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. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-02 will have on its consolidated financial statements and accompanying notes. In March 2016, the FASB issued ASU No. 2016-09, “Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting”. This standard requires the recognition of all income tax effects of awards in the income statement when the awards vest or are settled, with Additional Paid in Capital (APIC) pools to be eliminated. In addition, the standard will increase the amount an employer can withhold to cover income taxes on awards and still qualify for the exception to liability classification for shares used to satisfy the employer’s statutory income tax withholding obligation as well as allowing companies to elect whether to account for forfeitures of share-based payments by recognizing forfeitures of awards as they occur or estimating the number of awards expected to be forfeited and adjusting the estimate when it is likely to change, as is currently required. This standard is effective for public companies for fiscal years beginning after December 15, 2016 and interim periods within those years, with early adoption permitted but only if all of the guidance is adopted in the same period. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-09 will have on its consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. 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.

Fair value of financial instruments and marketable securities

6 Months Ended

Jun. 30, 2016

Fair value of financial instruments and marketable securities

Fair value of financial instruments and marketable securities

3.Fair value of financial instruments and marketable securities

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

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

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

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

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

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.

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 June 30, 2016 and December 31, 2015:

	June 30, 2016
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	237,235	$	—	$	237,235	$	—
Warrant liability	$	1	$	—	$	—	$	1
Stock appreciation rights liability	$	140	$	—	$	—	$	140

	December 31, 2015
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	280,903	$	—	$	280,903	$	—
Warrant Liability	$	48	$	—	$	—	$	48
Stock appreciation rights liability	$	—	$	—	$	—	$	—

No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the periods ended June 30, 2016 and December 31, 2015.

The following is a summary of marketable securities accounted for as available-for-sale securities at June 30, 2016 and December 31, 2015:

	June 30, 2016
	Amortized		Gross Unrealized					Fair
	Cost		Gains		Losses			Value
Commercial paper	$	11,969	$	21	$	—		$	11,990
Corporate debt securities	210,640		274		(26		)	210,888
Government obligations	14,353		4		—			14,357

	$	236,962	$	299	$	(26	)	$	237,235

	December 31, 2015
	Amortized		Gross Unrealized					Fair
	Cost		Gains		Losses			Value
Commercial paper	$	26,877	$	80	$	—		$	26,957
Corporate debt securities	226,959		—		(640		)	226,319
Government obligations	27,656		3		(32		)	27,627

	$	281,492	$	83	$	(672	)	$	280,903

At June 30, 2016 and December 31, 2015, 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 June 30, 2016 and December 31, 2015, the Company did not have any realized gains/losses from the sale of marketable securities.

Marketable securities on the balance sheet at June 30, 2016 and December 31, 2015 mature as follows:

	June 30, 2016
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	11,990	$	—
Corporate debt securities	159,714		51,174
Government obligations	14,357		—

Total Marketable securities	$	186,061	$	51,174

	December 31, 2015
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	26,957	$	—
Corporate debt securities	140,831		85,488
Government obligations	18,994		8,633

Total Marketable securities	$	186,782	$	94,121

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

Level 3 valuation

The warrant liability is classified in Other long-term liabilities on the Company’s consolidated balance sheets. The warrant liability is marked-to-market each reporting period with the change in fair value recorded as a gain or loss within Other expense, net, on the Company’s consolidated statements of operations until the warrants are exercised, expire or other facts and circumstances lead the warrant liability to be reclassified as an equity instrument. The fair value of the warrant liability is determined at each reporting period by utilizing the Black-Scholes option pricing model.

The stock appreciation rights (SARs) liability is classified in Other long-term 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 table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the warrant liability and SARs liability for the period ended June 30, 2016:

	Level 3 liabilities
	Warrants			SARs
Beginning balance as of December 31, 2015	$	48		$	—
Change in fair value	(47		)	140

Ending balance as of June 30, 2016	$	1		$	140

Fair value of the warrant liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the stock fair value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of June 30, 2016 include (i) volatility (75%—77%), (ii) risk free interest rate (0.45%—0.71%), (iii) strike price ($128.00-$2,520.00), (iv) fair value of common stock ($7.02), and (v) expected life (0.96—3.23 years). The significant assumptions used in preparing the option pricing model for valuing the Company’s warrants as of December 31, 2015 include (i) volatility (62%-70%), (ii) risk free interest rate (0.86%—1.54%), (iii) strike price ($128.00—$2,520.00), (iv) fair value of common stock ($32.40), and (v) expected life (1.50—3.70 years).

Fair value of the SARs liability is estimated using an option-pricing model, which includes variables such as the expected volatility based on guideline public companies, the stock fair value, and the estimated time to a liquidity event. The significant assumptions used in preparing the option pricing model for valuing the Company’s SARs as of June 30, 2016 include (i) volatility (70%), (ii) risk free interest rate (0.36%—0.86%), (iii) strike price ($6.76-$30.86), (iv) fair value of common stock ($7.02), and (v) expected life (0.52—3.52 years).

- 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

Other comprehensive income (loss) and accumulated other comprehensive items

6 Months Ended

Jun. 30, 2016

Other comprehensive income (loss) and accumulated other comprehensive items

Other comprehensive income (loss) and accumulated other comprehensive items

4.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 six months ended June 30, 2016:

	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at March 31, 2016	$	69		$	1,015		$	1,084
Other comprehensive loss before reclassifications	(40		)	(159		)	(199		)
Amounts reclassified from other comprehensive items	—			—			—

Other comprehensive loss	(40		)	(159		)	(199		)

Balance at June 30, 2016	$	29		$	856		$	885

	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income before reclassifications	618			1,467			2,085
Amounts reclassified from other comprehensive items	—			—			—

Other comprehensive income	618			1,467			2,085

Balance at June 30, 2016	$	29		$	856		$	885

- Definition

The entire disclosure for comprehensive income, which includes, but is not limited to, 1) the amount of income tax expense or benefit allocated to each component of other comprehensive income, including reclassification adjustments, 2) the reclassification adjustments for each classification of other comprehensive income and 3) the ending accumulated balances for each component of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e689-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=36458714&loc=SL7669619-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 12
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e640-108580

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 17
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e716-108580

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e709-108580

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e637-108580

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 14
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e681-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Reclassification Adjustments
-URI http://asc.fasb.org/extlink&oid=6522872

+ Details

Net loss per share

6 Months Ended

Jun. 30, 2016

Net loss per share

Net loss per share

7.Net loss per share

Basic earnings per share is computed by dividing net income (loss) by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net income (loss) by the weighted-average number of common shares plus the effect of 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 June 30,						Six Months Ended June 30,
	2016			2015			2016			2015
Numerator
Net loss	$	(38,914	)	$	(38,361	)	$	(80,147	)	$	(76,276	)
Denominator
Denominator for basic and diluted net loss per share	34,000,333			33,600,653			33,959,751			33,335,674

Net loss per share:
Basic and diluted	$	(1.14	)*	$	(1.14	)*	$	(2.36	)*	$	(2.29	)*

*In the three and six months ended June 30, 2016 and 2015, the Company experienced a net loss and therefore did not report any dilutive share impact.

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

	As of June 30,
	2016	2015
Stock Options	5,969,382	4,663,852
Unvested restricted stock awards and units	274,490	353,135

Total	6,243,872	5,016,987

Stock award plan

6 Months Ended

Jun. 30, 2016

Stock award plan

Stock award plan

8.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 Board approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan.

In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards.

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s IPO. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of June 30, 2016, awards for 326,101 shares of common stock are available for issuance.

From January 1, 2016 through June 30, 2016, the Company issued a total of 1,403,045 stock options to various employees. Of those, 93,100 were inducement grants for non-statutory stock options. The inducement grant awards were made pursuant to the NASDAQ inducement grant exception as a material component of our 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, 2015	4,826,477		$	37.20
Granted	1,403,045		$	29.06
Exercised	(3,125	)	$	10.85
Forfeited/Cancelled	(257,015	)	$	47.36
Outstanding at June 30, 2016	5,969,382		$	35.02	8.21 years	$	6
Vested or Expected to vest at June 30, 2016	3,361,980		$	35.89	8.66 years	$	5
Exercisable at June 30, 2016	2,357,502		$	33.60	7.50 years	$	—

The fair value of grants made in the six months ended June 30, 2016 was contemporaneously estimated on the date of grant using the following assumptions:

		Six months ended June 30, 2016
Risk-free interest rate		1.31% —2.24%
Expected volatility		67%—71%
Expected term		5.05– 10.00 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the six month period ended June 30, 2016 was $17.98 per share.

The Company uses 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. 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. 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, 2016	344,335		$	10.85
Granted	141,185		$	30.86
Vested	(163,635	)	$	10.85
Forfeited	(47,395	)	$	18.19

Unvested at June 30, 2016	274,490		$	19.86

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

	Three Months Ended June 30,				Six Months Ended June 30,
	2016		2015		2016		2015

Research and development	$	4,087	$	3,957	$	8,415	$	8,624
Selling, general and administrative	4,649		4,371		9,236		9,452

Total	$	8,736	$	8,328	$	17,651	$	18,076

Stock Appreciation Rights—Stock appreciation rights (SARs) entitle the holder to receive, upon exercise, an amount of 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 Common Stock over the measurement price based on the exercise date.

In May 2016, a total of 897,290 SARs were granted to non-executive employees (the 2016 SARs). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the period ending June 30, 2016, the Company recorded $0.1 million in compensation expense related to the 2016 SARs.

As of June 30, 2016 there was approximately $78.2 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 inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 2.56 years.

Convertible Senior Notes

6 Months Ended

Jun. 30, 2016

Convertible Senior Notes

Convertible Senior Notes

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

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

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

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

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

upon the occurrence of specified corporate events

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

The conversion rate for the Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock.

The Company may not redeem the Convertible Notes prior to August 20, 2018. The Company may redeem for cash all or any portion of the Convertible Notes, at its option, on or after August 20, 2018 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 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the Convertible Notes, which means that the Company is not required to redeem or retire the Convertible Notes periodically.

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

The Convertible Notes Indenture contains customary events of default with respect to the Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the Convertible Notes when due and payable) occurring and continuing, the Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the Convertible Notes Trustee at the request of such holders (subject to the provisions of the Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 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 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 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 Convertible Notes, the Company separated the 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 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 Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification.

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

The Convertible Notes consist of the following:

Liability component	June 30, 2016			December 31, 2015
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,613		)	(2,760		)
Less: Debt discount, net(1)	(52,451		)	(55,392		)

Net carrying amount	$	94,936		$	91,848

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

The fair value of the Convertible Notes was approximately $71.3 million as of June 30, 2016. The Company estimates the fair value of its Convertible Notes utilizing market quotations for debt that have quoted prices in active markets. As of June 30, 2016, the remaining contractual life of the Convertible Notes is approximately 6.1 years.

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

	Three Months Ended June 30,					Six Months Ended June 30,
	2016			2015		2016			2015
Contractual interest expense	$	1,125		$	—	$	2,241		$	—
Amortization of debt issuance costs	75			—		147			—
Amortization of debt discount	1,495			—		2,941			—

Total	$	2,695		$	—	$	5,329		$	—

Effective interest rate of the liability component	11		%	—		11		%	—

Summary of significant accounting policies (Policies)	6 Months Ended
Summary of significant accounting policies (Policies)	Jun. 30, 2016
Summary of significant accounting policies
Basis of Presentation	Basis of Presentation The accompanying financial information as of June 30, 2016 and for the three and six months ended June 30, 2016 and 2015 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, 2015 and notes thereto included in the 2015 Form 10-K. In the opinion of management, the unaudited financial information as of June 30, 2016 and for the three and six months ended June 30, 2016 and 2015 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations and cash flows. The results of operations for the three and six month periods ended June 30, 2016 are not necessarily indicative of the results to be expected for the year ended December 31, 2016 or for any other interim period or for any other future year.
Use of estimates	Use of estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes 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.
Inventories and cost of product revenue	Inventories and cost of product revenue In 2014, the Company was notified that the European Commission, or EC, granted marketing authorization for Translarna for the treatment of nmDMD in ambulatory patients aged five years and older. The conditional marketing authorization allows the Company to market Translarna for the treatment of nmDMD in the 31 member states of European Economic Area. The launch in these countries is on a country by country basis. This marketing authorization is subject to annual review and renewal by the EC following reassessment by the European Medicines Agency, or EMA, of the risk benefit balance of the authorization, which the Company refers to as the annual EMA reassessment. In the third quarter of 2015, the EMA approved the annual renewal of the marketing authorization for Translarna for the treatment of nmDMD. The authorization was further conditioned on the Company’s submission of the final report, including additional efficacy and safety data, from ACT DMD and the Company’s ability to implement measures, including pharmacovigilance plans that are detailed in the risk management plan for Translarna that was submitted to EMA. In January 2016, the Company submitted the final ACT DMD report to the EMA. The Company made this submission as a type II variation request that sought to have this initial condition to its marketing authorization removed and a full marketing authorization granted. In February 2016, the Company also submitted a marketing authorization renewal request with the EMA. While the Company has been informed that the renewal assessment procedure cannot be completed by mid-year 2016, it expects that, pursuant to applicable regulations, its current marketing authorization status will remain valid while the annual EMA reassessment is ongoing and until it is concluded with an opinion from the European Commission with respect to renewal of its marketing authorization. Based on its interpretation of applicable regulatory timeframes, the Company believes the annual EMA reassessment could be completed, at the earliest, by the end of 2016. The Company plans to seek to renew the marketing authorization on an annual basis until the Company’s obligations have been fulfilled and the approval is converted from a conditional approval into a full approval. If the Company fails to satisfy such requirements, or if it is determined that the balance of risks and benefits of using Translarna changes materially, the EC could, at the EMA’s recommendation, vary, suspend, withdraw or refuse to renew the marketing authorization for Translarna or require additional clinical trials. There continues to be substantial risk that regulators could suspend or not renew the Company’s marketing authorization in the future. As such, as of the date of this filing, the Company has not capitalized inventory given the near term uncertainty with respect to the long term utilization of Translarna finished product for commercial use. Had the Company capitalized as inventory all of the its Translarna product that is available for commercial sale on hand as of June 30, 2016, the value of that inventory would have been approximately $1.2 million. In addition, had the Company expensed the cost of Translarna product sold as a cost of sales, the gross profit margin would have been greater than 90%, which the Company believes is consistent with the cost of producing small molecule therapeutics for orphan drug diseases in the pharmaceutical industry. The Company will continue to assess the appropriateness of inventory capitalization based on the outcome of applicable regulatory approvals which are expected later this year.
Revenue Recognition	Revenue Recognition The Company recognizes revenue when amounts are realized or realizable and earned. Revenue is considered realizable and earned when the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the price is fixed or determinable; and (4) collection of the amounts due are reasonably assured. Net Product Sales The Company’s net product sales have consisted solely of sales of Translarna for the treatment of nmDMD in territories outside of the U.S. The Company began recognizing revenue for payments received under the reimbursed EAPs for Translarna in nmDMD patients in select countries in the third quarter of 2014. The Company has now established a pattern of collectability and, since January 2015, the Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, title to product and associated risk of loss has passed to the customer, the price is fixed or determinable, collectability is reasonably assured and the Company has no further performance obligations in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition—Products. The Company has recorded revenue on sales where Translarna is available either on a commercial basis or through a reimbursed EAP program. Orders for Translarna are generally received from hospital and retail pharmacies and, in some cases, one of the Company’s third-party partner distributors. The Company’s third-party distributors act as intermediaries between the Company and end users and do not typically stock significant quantities of Translarna. The ultimate payor for Translarna is typically a government authority or institution or a third-party health insurer. The Company records revenue net of estimated third party discounts and rebates. Allowances are recorded as a reduction of revenue at the time revenues from product sales are recognized. These allowances are adjusted to reflect known changes in factors and may impact such allowances in the quarter those changes are known. Collaboration and Grant Revenue The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events. The Company evaluates all contingent consideration earned, such as a milestone payment, using the criteria as provided by the Financial Accounting Standards Board (FASB), guidance on the milestone method of revenue recognition. At the inception of a collaboration arrangement, the Company evaluates if a milestone payment is substantive. The criteria requires that (1) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from our activities to achieve the milestone; (2) the milestone be related to past performance; and (3) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement. If these criteria are met then the contingent milestones can be considered a substantive milestone and will be recognized as revenue in the period that the milestone is achieved. The Company recognizes royalties as earned in accordance with the terms of various research and collaboration agreements. If not substantive, the contingent consideration is allocated to the existing units of accounting based on relative selling price and recognized following the same basis previously established for the associated unit of accounting. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.
Recently issued accounting standards	Recently issued accounting standards In May 2014, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 will eliminate transaction- and industry-specific revenue recognition guidance under current GAAP and replace it with a principle-based approach for determining revenue recognition. ASU No. 2014-09 includes the required steps to achieve the core principle that an entity should 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. The ASU will also require additional disclosure about the nature, amount, timing and uncertainty of revenue and cash flows arising from customer contracts, including significant judgments and changes in judgments and assets recognized from costs incurred to obtain or fulfill a contract. With the issuance of ASU No. 2015-14 in August 2015, the FASB deferred the effective date of the revenue recognition guidance to reporting periods beginning after December 15, 2017. Early adoption of the standard is permitted but not before the original effective date, which was for reporting periods beginning after December 15, 2016. With the issuance of ASU No. 2016-08 in March 2016 and ASU No. 2016-10 in April 2016, the FASB further amended guidance on recording revenue on a gross versus a net basis and on identifying performance obligations and licensing, respectively. The Company expects to adopt this guidance when effective and continues to evaluate the effect that the updated standard, as well as additional amendments, may have on its consolidated financial statements and accompanying notes. In August 2014, the FASB issued ASU 2014-15, “Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern”, which defines management’s responsibility to assess an entity’s ability to continue as a going concern, and to provide related footnote disclosures if there is substantial doubt about its ability to continue as a going concern. The pronouncement is effective for annual reporting periods ending after December 15, 2016 with early adoption permitted. The adoption of this guidance is not expected to have a significant impact on the Company’s financial statements. In April 2015, the FASB issued ASU No. 2015-03, “Interest—Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs topic of the Codification”. This standard provides a simplified presentation of debt issuance costs and requires that debt issuance costs related to a recognized debt liability to be presented on the balance sheet as a direct deduction from the carrying amount of that debt liability, consistent with debt discounts. The standard is effective for public companies for annual periods beginning after December 15, 2015. The Company adopted the guidance on January 1, 2016 on a retrospective basis and reclassed $2.8 million from “Deposits and other assets” to “Long-term debt” on the balance sheet as of December 31, 2015. The Company’s unamortized debt issuance cost at June 30, 2016 was $2.6 million which is included within “Long-term debt” on the consolidated balance sheet. In November 2015, the FASB issued ASU No. 2015-17, “Income Taxes (Topic 740): Balance Sheet Classification of Deferred Taxes”. This standard requires all deferred tax assets and liabilities to be classified as non-current on the balance sheet instead of separating deferred taxes into current and non-current amounts. In addition, valuation allowance allocations between current and non-current deferred tax assets are no longer required because those allowances also will be classified as non-current. This standard is effective for public companies for annual periods beginning after December 15, 2016. Earlier application is permitted as of the beginning of an interim or annual reporting period. The Company’s deferred tax assets is provided with full valuation allowance as of June 30, 2016. As such, the Company does not expect that this standard will have a significant impact upon adoption. 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. ASU 2016-01 is effective for years beginning after December 15, 2017, including interim periods within those fiscal years. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-01 will have on its consolidated financial statements and accompanying notes. In February 2016, the FASB issued ASU No. 2016-02, “Leases (Topic 842)”. This standard will require 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 will also require 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. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-02 will have on its consolidated financial statements and accompanying notes. In March 2016, the FASB issued ASU No. 2016-09, “Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting”. This standard requires the recognition of all income tax effects of awards in the income statement when the awards vest or are settled, with Additional Paid in Capital (APIC) pools to be eliminated. In addition, the standard will increase the amount an employer can withhold to cover income taxes on awards and still qualify for the exception to liability classification for shares used to satisfy the employer’s statutory income tax withholding obligation as well as allowing companies to elect whether to account for forfeitures of share-based payments by recognizing forfeitures of awards as they occur or estimating the number of awards expected to be forfeited and adjusting the estimate when it is likely to change, as is currently required. This standard is effective for public companies for fiscal years beginning after December 15, 2016 and interim periods within those years, with early adoption permitted but only if all of the guidance is adopted in the same period. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2016-09 will have on its consolidated financial statements and accompanying notes. In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. 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.

- Definition

Disclosure of accounting policy for revenue recognition. If the entity has different policies for different types of revenue transactions, the policy for each material type of transaction is generally disclosed. If a sales transaction has multiple element arrangements (for example, delivery of multiple products, services or the rights to use assets) the disclosure may indicate the accounting policy for each unit of accounting as well as how units of accounting are determined and valued. The disclosure may encompass important judgment as to appropriateness of principles related to recognition of revenue. The disclosure also may indicate the entity's treatment of any unearned or deferred revenue that arises from the transaction.

+ References + Details

Fair value of financial instruments and marketable securities (Tables)

6 Months Ended

Jun. 30, 2016

Fair value of financial instruments and marketable securities

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

	June 30, 2016
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	237,235	$	—	$	237,235	$	—
Warrant liability	$	1	$	—	$	—	$	1
Stock appreciation rights liability	$	140	$	—	$	—	$	140

	December 31, 2015
	Total		Quoted prices in active markets for identical assets (level 1)		Significant other observable inputs (level 2)		Significant unobservable inputs (level 3)
Marketable securities	$	280,903	$	—	$	280,903	$	—
Warrant Liability	$	48	$	—	$	—	$	48
Stock appreciation rights liability	$	—	$	—	$	—	$	—

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

	June 30, 2016
	Amortized		Gross Unrealized					Fair
	Cost		Gains		Losses			Value
Commercial paper	$	11,969	$	21	$	—		$	11,990
Corporate debt securities	210,640		274		(26		)	210,888
Government obligations	14,353		4		—			14,357

	$	236,962	$	299	$	(26	)	$	237,235

	December 31, 2015
	Amortized		Gross Unrealized					Fair
	Cost		Gains		Losses			Value
Commercial paper	$	26,877	$	80	$	—		$	26,957
Corporate debt securities	226,959		—		(640		)	226,319
Government obligations	27,656		3		(32		)	27,627

	$	281,492	$	83	$	(672	)	$	280,903

Schedule of marketable securities on the balance sheet

	June 30, 2016
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	11,990	$	—
Corporate debt securities	159,714		51,174
Government obligations	14,357		—

Total Marketable securities	$	186,061	$	51,174

	December 31, 2015
	Less Than 12 Months		More Than 12 Months
Commercial paper	$	26,957	$	—
Corporate debt securities	140,831		85,488
Government obligations	18,994		8,633

Total Marketable securities	$	186,782	$	94,121

Summary of changes in the fair value of the Company's Level 3 valuation for warrant liability and SARs liability

	Level 3 liabilities
	Warrants			SARs
Beginning balance as of December 31, 2015	$	48		$	—
Change in fair value	(47		)	140

Ending balance as of June 30, 2016	$	1		$	140

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

6 Months Ended

Jun. 30, 2016

Other comprehensive income (loss) and accumulated other comprehensive items

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

	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at March 31, 2016	$	69		$	1,015		$	1,084
Other comprehensive loss before reclassifications	(40		)	(159		)	(199		)
Amounts reclassified from other comprehensive items	—			—			—

Other comprehensive loss	(40		)	(159		)	(199		)

Balance at June 30, 2016	$	29		$	856		$	885

	Unrealized Gains/(Losses) On Marketable Securities, net of tax			Foreign Currency Translation			Total Accumulated Other Comprehensive Items
Balance at December 31, 2015	$	(589	)	$	(611	)	$	(1,200	)
Other comprehensive income before reclassifications	618			1,467			2,085
Amounts reclassified from other comprehensive items	—			—			—

Other comprehensive income	618			1,467			2,085

Balance at June 30, 2016	$	29		$	856		$	885

Net loss per share (Tables)

6 Months Ended

Jun. 30, 2016

Net loss per share

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

	Three Months Ended June 30,						Six Months Ended June 30,
	2016			2015			2016			2015
Numerator
Net loss	$	(38,914	)	$	(38,361	)	$	(80,147	)	$	(76,276	)
Denominator
Denominator for basic and diluted net loss per share	34,000,333			33,600,653			33,959,751			33,335,674

Net loss per share:
Basic and diluted	$	(1.14	)*	$	(1.14	)*	$	(2.36	)*	$	(2.29	)*

*In the three and six months ended June 30, 2016 and 2015, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding

	As of June 30,
	2016	2015
Stock Options	5,969,382	4,663,852
Unvested restricted stock awards and units	274,490	353,135

Total	6,243,872	5,016,987

Stock award plan (Tables)

6 Months Ended

Jun. 30, 2016

Stock award plan

Summary of stock option activity

	Number of options		Weighted- average exercise price		Weighted- average remaining contractual term	Aggregate intrinsic value
						(in thousands)
Outstanding at December 31, 2015	4,826,477		$	37.20
Granted	1,403,045		$	29.06
Exercised	(3,125	)	$	10.85
Forfeited/Cancelled	(257,015	)	$	47.36
Outstanding at June 30, 2016	5,969,382		$	35.02	8.21 years	$	6
Vested or Expected to vest at June 30, 2016	3,361,980		$	35.89	8.66 years	$	5
Exercisable at June 30, 2016	2,357,502		$	33.60	7.50 years	$	—

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

		Six months ended June 30, 2016
Risk-free interest rate		1.31% —2.24%
Expected volatility		67%—71%
Expected term		5.05– 10.00 years

Summary of information on the Company's restricted stock

	Restricted Stock Awards and Units
	Number of Shares		Weighted Average Grant Date Fair Value
January 1, 2016	344,335		$	10.85
Granted	141,185		$	30.86
Vested	(163,635	)	$	10.85
Forfeited	(47,395	)	$	18.19

Unvested at June 30, 2016	274,490		$	19.86

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

	Three Months Ended June 30,				Six Months Ended June 30,
	2016		2015		2016		2015

Research and development	$	4,087	$	3,957	$	8,415	$	8,624
Selling, general and administrative	4,649		4,371		9,236		9,452

Total	$	8,736	$	8,328	$	17,651	$	18,076

Convertible Senior Notes (Tables)

6 Months Ended

Jun. 30, 2016

Convertible Senior Notes

Summary of convertible notes

Liability component	June 30, 2016			December 31, 2015
Principal	$	150,000		$	150,000
Less: Debt issuance costs	(2,613		)	(2,760		)
Less: Debt discount, net(1)	(52,451		)	(55,392		)

Net carrying amount	$	94,936		$	91,848

Summary of interest expense recognized related to the Convertible Notes

	Three Months Ended June 30,					Six Months Ended June 30,
	2016			2015		2016			2015
Contractual interest expense	$	1,125		$	—	$	2,241		$	—
Amortization of debt issuance costs	75			—		147			—
Amortization of debt discount	1,495			—		2,941			—

Total	$	2,695		$	—	$	5,329		$	—

Effective interest rate of the liability component	11		%	—		11		%	—

Fair value of financial instruments and marketable securities - Warrants and SARs (Details) - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2016	Dec. 31, 2015
Stock Appreciation Rights (SARs)
Changes in the fair value of warrant liability and SARs liability
Change in fair value	$ 140
Ending balance	$ 140
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)	70.00%
Minimum \| Stock Appreciation Rights (SARs)
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)	0.36%
Strike price (in dollars per share)	$ 6.76
Expected life	6 months 7 days
Maximum \| Stock Appreciation Rights (SARs)
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Risk-free interest rate (as a percent)	0.86%
Strike price (in dollars per share)	$ 30.86
Expected life	3 years 6 months 7 days
Common stock \| Stock Appreciation Rights (SARs)
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 7.02
Warrants
Changes in the fair value of warrant liability and SARs liability
Beginning balance	$ 48
Change in fair value	(47)
Ending balance	$ 1	$ 48
Warrants \| Minimum
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)	75.00%	62.00%
Risk-free interest rate (as a percent)	0.45%	0.86%
Strike price (in dollars per share)	$ 128.00	$ 128.00
Expected life	11 months 16 days	1 year 6 months
Warrants \| Maximum
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Volatility (as a percent)	77.00%	70.00%
Risk-free interest rate (as a percent)	0.71%	1.54%
Strike price (in dollars per share)	$ 2,520.00	$ 2,520.00
Expected life	3 years 2 months 23 days	3 years 8 months 12 days
Warrants \| Common stock
Assumption used to estimate the fair value of warrant liability and SARs liability by utilizing the Black-Scholes option-pricing model
Fair value of shares (in dollars per share)	$ 7.02	$ 32.40

Other comprehensive income (loss) and accumulated other comprehensive items (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2016
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance		$ 226,001
Ending balance	$ 165,624	165,624
Unrealized Gains/(Losses) On Marketable Securities, net of tax
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	69	(589)
Other comprehensive income (loss) before reclassifications	(40)	618
Other comprehensive income (loss)	(40)	618
Ending balance	29	29
Foreign Currency Translation
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	1,015	(611)
Other comprehensive income (loss) before reclassifications	(159)	1,467
Other comprehensive income (loss)	(159)	1,467
Ending balance	856	856
Total Accumulated Other Comprehensive Items
Other comprehensive income (loss) and accumulated other comprehensive items
Beginning balance	1,084	(1,200)
Other comprehensive income (loss) before reclassifications	(199)	2,085
Other comprehensive income (loss)	(199)	2,085
Ending balance	$ 885	$ 885

Accounts payable and accrued expenses (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Accounts payable and accrued expenses
Employee compensation, benefits, and related accruals	$ 4,688	$ 11,187
Consulting and contracted research	12,846	13,753
Professional fees	1,638	2,523
Accounts payable	16,800	11,940
Accrued severance	995
Other	5,216	5,844
Accounts payable and accrued expenses	$ 42,183	$ 45,247

Stock award plan - Share Base Compensation (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended	6 Months Ended
	Mar. 05, 2013	May 31, 2013	Jun. 30, 2016
Unvested restricted stock
Number of options
Granted (in shares)			141,185
Stock option
Number of options
Outstanding at the beginning of the period (in shares)			4,826,477
Granted (in shares)			1,403,045
Exercised (in shares)			(3,125)
Forfeited/Cancelled (in shares)			(257,015)
Outstanding at the end of the period (in shares)			5,969,382
Vested or Expected to vest at the end of the period (in shares)			3,361,980
Exercisable at the end of the period (in shares)			2,357,502
Weighted-average exercise price
Outstanding at the beginning of the period (in dollars per share)			$ 37.20
Granted (in dollars per share)			29.06
Exercised (in dollars per share)			10.85
Forfeited/Cancelled (in dollars per share)			47.36
Outstanding at the end of the period (in dollars per share)			35.02
Vested or Expected to vest at the end of the period (in dollars per share)			35.89
Exercisable at the end of the period (in dollars per share)			$ 33.60
Weighted-average remaining contractual term
Outstanding at the end of the period			8 years 2 months 16 days
Vested or Expected to vest at the end of the period			8 years 7 months 28 days
Exercisable at the end of the period			7 years 6 months
Aggregate intrinsic value
Outstanding at the end of the period (in dollars)			$ 6
Vested or Expected to vest at the end of the period (in dollars)			$ 5
Valuation assumptions
Inducement grants for non-statutory stock options			93,100
Expected dividend yield (as a percent)			0.00%
Weighted average grant date fair value (in dollars per share)			$ 17.98
Stock option \| Minimum
Valuation assumptions
Risk-free interest rate (as a percent)			1.31%
Expected volatility (as a percent)			67.00%
Expected term			5 years 18 days
Stock option \| Maximum
Valuation assumptions
Risk-free interest rate (as a percent)			2.24%
Expected volatility (as a percent)			71.00%
Expected term			10 years
Common stock
Stock option plan
Number of shares available for issuance			326,101
2009 Equity and Long Term Incentive Plan
Stock option plan
Number of additional shares authorized		2,500,000
2013 Stock Incentive Plan
Stock option plan
Number of shares available for issuance	0
2013 Stock Incentive Plan \| Unvested restricted stock
Stock option plan
Number of shares of restricted stock granted	735,324
2013 Stock Incentive Plan \| Stock option
Number of options
Granted (in shares)	4,613
2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares authorized	739,937
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance		122,296
2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan \| Common stock \| 1998 Employee, Director and Consultant Stock Option Plan \| Maximum
Stock option plan
Number of shares subject to outstanding awards		3,040,444
2013 Long Term Incentive Plan \| Minimum
Stock option plan
Annual increase in the number of 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 (as a percent)		4.00%

Stock award plan - Restricted Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		6 Months Ended
	May 31, 2016	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Weighted Average Grant Date Fair Value
Share-based compensation expense		$ 8,736	$ 8,328	$ 17,651	$ 18,076
Research and development
Weighted Average Grant Date Fair Value
Share-based compensation expense		4,087	3,957	8,415	8,624
Selling, general and administrative
Weighted Average Grant Date Fair Value
Share-based compensation expense		$ 4,649	$ 4,371	$ 9,236	$ 9,452
Unvested restricted stock
Number of Shares
Balance at the beginning of the period (in shares)				344,335
Granted (in shares)				141,185
Vested (in shares)				(163,635)
Forfeited (in shares)				(47,395)
Balance at the end of the period (in shares)		274,490		274,490
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share)				$ 10.85
Granted (in dollars per share)				30.86
Vested (in dollars per share)				10.85
Forfeited (in dollars per share)				18.19
Balance at the end of the period (in dollars per share)		$ 19.86		$ 19.86
Stock Appreciation Rights (SARs)
Number of Shares
Granted (in shares)	897,290
Weighted Average Grant Date Fair Value
Share-based compensation expense				$ 100
Vesting period				4 years

Convertible Senior Notes (Details)	1 Months Ended	3 Months Ended	6 Months Ended
Convertible Senior Notes (Details)	Aug. 31, 2015 USD ($) item $ / shares	Jun. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Dec. 31, 2015 USD ($)
Long-term debt
Amortization of debt issuance costs			$ 147,000
3.00% Convertible senior notes due 2022 \| Convertible debt
Long-term debt
Principal amount of notes	$ 150,000,000	$ 150,000,000	150,000,000	$ 150,000,000
Less: Debt issuance costs		(2,613,000)	(2,613,000)	(2,760,000)
Less: Debt discount, net		(52,451,000)	(52,451,000)	(55,392,000)
Net carrying amount		94,936,000	94,936,000	$ 91,848,000
Interest rate	3.00%
Net proceeds from issuance of convertible notes	$ 145,400,000
Trading days, number \| item	20
Consecutive trading days, period	30 days
Stock price trigger (as a percent)	130.00%
Business days, period	5 days
Consecutive trading-day period	5 days
Common stock per principal amount	$ 1,000
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day (as a percent)	98.00%
Conversion ratio	17.7487
Conversion price per share \| $ / shares	$ 56.34
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default (as a percent)	25.00%
Convertible Instruments Principal And Unpaid Interest Payable Upon Events Of Default	100.00%
Term of the convertible notes	7 years
Net deferred tax liability in connection with convertible notes	$ 22,300,000
Fair value of convertible notes		71,300,000	$ 71,300,000
Remaining contractual life of the convertible notes			6 years 1 month 6 days
Contractual interest expense		1,125,000	$ 2,241,000
Amortization of debt issuance costs		75,000	147,000
Amortization of debt discount		1,495,000	2,941,000
Total		$ 2,695,000	$ 5,329,000
Effective interest rate of the liability component (as a percent)		11.00%	11.00%
3.00% Convertible senior notes due 2022 \| Convertible debt \| Redemption on or after August 20, 2018
Long-term debt
Trading days, number \| item	19
Consecutive trading days, period	30 days
Stock price trigger (as a percent)	130.00%
Redemption price (as a percent)	100.00%
Sinking fund	$ 0

The Company	6 Months Ended
The Company	Jun. 30, 2016
The Company
The Company	1.The Company PTC Therapeutics, Inc. (the “Company” or “PTC”) was incorporated as a Delaware corporation on March 31, 1998. PTC is a global biopharmaceutical company focused on the discovery, development and commercialization of orally administered, small molecule therapeutics targeting an area of RNA biology referred to as post transcriptional control. Post-transcriptional control processes are the regulatory events that occur in cells during and after a messenger RNA molecule is copied from DNA through the transcription process. PTC has discovered all of its compounds currently under development using its proprietary technologies. PTC plans to continue to develop these compounds both on its own and through selective collaboration arrangements with leading pharmaceutical and biotechnology companies. PTC’s internally discovered pipeline addresses multiple therapeutic areas, including rare disorders and oncology. PTC’s lead product candidate is ataluren, an investigational new drug in the United States, for the treatment of patients with genetic disorders that arise from a type of genetic mutation known as a nonsense mutation. The Company holds worldwide commercialization rights to ataluren for all indications in all territories. The brand name of ataluren is Translarna™. The Company received conditional marketing authorization from the European Commission in August 2014 for Translarna for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients age five years and older in the 31 member states of the European Economic Area, or EEA. The marketing authorization is subject to annual review and renewal by the European Commission following reassessment by the European Medicines Agency, or EMA, of the risk-benefit balance of the authorization, or the annual EMA reassessment, as well as the Company’s satisfaction of any conditions and obligations that have been or may be placed upon the marketing authorization. The Company has been informed that the annual EMA assessment procedure cannot be completed by mid-year 2016. During 2016, the Company’s revenues have been and are expected to be primarily generated from sales of Translarna for the treatment of nmDMD in countries in the EEA where pricing and reimbursement approval is obtained at acceptable levels and in other territories where the Company is permitted to distribute Translarna under reimbursed early access programs, or EAPs. The Company is subject to a number of risks similar to those of other early stage companies, including dependence on key individuals, the difficulties inherent in the development of commercially usable products, the potential need to obtain additional capital necessary to fund the development of its products, and competition from other companies. As of June 30, 2016, the Company had an accumulated deficit of approximately $673.1 million. The Company has financed its operations to date primarily through the private offering in August 2015 of 3.00% convertible senior notes due 2022 (see Note 9), public offerings of common stock in February 2014 and October 2014, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, convertible debt financings, 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.

Commitments and contingencies	6 Months Ended
Commitments and contingencies	Jun. 30, 2016
Commitments and contingencies
Commitments and contingencies	11.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. To the extent that the Company develops and commercializes program intellectual property on a for-profit basis, it may become obligated to pay to Wellcome Trust development and regulatory milestone payments of up to an aggregate of $68.9 million 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. 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 we successfully develop and subsequently commercialize or, if we outlicense rights to a collaboration product, a specified percentage of certain payments we receive from our 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 our payment to the SMA Foundation of a specified amount. 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.

Subsequent events	6 Months Ended
Subsequent events	Jun. 30, 2016
Subsequent events
Subsequent events	12.Subsequent events The Company has evaluated all subsequent events and transactions through the filing date. There were no material events that impacted the unaudited consolidated financial statements or disclosures.

Summary of significant accounting policies (Details) $ in Millions		1 Months Ended
	Jan. 01, 2016 USD ($)	Aug. 31, 2014 state	Jun. 30, 2016 USD ($)
Minimum age of ambulatory patient		5 years
Number of member states of the European Economic Area \| state		31
Capitalized inventory			$ 1.2
Accounting Standards Update 2015-03 \| Deposits and other assets
Debt issuance cost	$ 2.8
Accounting Standards Update 2015-03 \| Long-term debt.
Debt issuance cost	$ 2.8
Unamortized debt issuance cost			$ 2.6
Minimum
Gross profit margin (as a percent)			90.00%

Warrants (Details) - Warrants - Common stock - $ / shares	Jun. 30, 2016	Dec. 31, 2015
2017
Warrants
Warrant shares	6,250	6,250
Exercise price (in dollars per share)	$ 128.00	$ 128.00
2019
Warrants
Warrant shares	7,030	7,030
Exercise price (in dollars per share)	$ 128.00	$ 128.00
2019.
Warrants
Warrant shares	130	130
Exercise price (in dollars per share)	$ 2,520.00	$ 2,520.00

Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2016	Dec. 31, 2015
Consolidated Balance Sheets
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares	125,000,000	125,000,000
Common stock, issued shares	34,083,319	33,916,559
Common stock, outstanding shares	34,083,319	33,916,559

The Company (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015	Aug. 31, 2015
Accumulated deficit	$ (673,145)	$ (592,998)
Convertible debt \| 3.00% Convertible senior notes due 2022
Interest rate			3.00%

Fair value of financial instruments and marketable securities - Hierachy (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	$ 237,235	$ 280,903
Recurring basis \| Total
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	237,235	280,903
Warrant liability	1	48
Stock appreciation rights liability	140
Recurring basis \| Significant other observable inputs (level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities	237,235	280,903
Recurring basis \| Significant unobservable inputs (level 3)
Financial assets and liabilities measured at fair value on recurring basis
Warrant liability	1	$ 48
Stock appreciation rights liability	$ 140

Fair value of financial instruments and marketable securities - Available for sale (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Marketable securities accounted for as available-for-sale securities
Amortized Cost	$ 236,962	$ 281,492
Gross Unrealized Gains	299	83
Gross Unrealized Losses	(26)	(672)
Marketable securities	237,235	280,903
Transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy	0	0
Commercial paper
Marketable securities accounted for as available-for-sale securities
Amortized Cost	11,969	26,877
Gross Unrealized Gains	21	80
Marketable securities	11,990	26,957
Corporate debt securities
Marketable securities accounted for as available-for-sale securities
Amortized Cost	210,640	226,959
Gross Unrealized Gains	274
Gross Unrealized Losses	(26)	(640)
Marketable securities	210,888	226,319
Government obligations
Marketable securities accounted for as available-for-sale securities
Amortized Cost	14,353	27,656
Gross Unrealized Gains	4	3
Gross Unrealized Losses		(32)
Marketable securities	$ 14,357	$ 27,627

Fair value of financial instruments and marketable securities - Balance Sheet (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 186,061	$ 186,782
Total Marketable securities, More Than 12 Months	51,174	94,121
Commercial paper
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	11,990	26,957
Corporate debt securities
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	159,714	140,831
Total Marketable securities, More Than 12 Months	51,174	85,488
Government obligations
Marketable securities on the balance sheet
Total Marketable securities, Less Than 12 Months	$ 14,357	18,994
Total Marketable securities, More Than 12 Months		$ 8,633

Net loss per share - Antidilutive (Details) - shares	6 Months Ended
Net loss per share - Antidilutive (Details) - shares	Jun. 30, 2016	Jun. 30, 2015
Net loss per share
Total shares excluded from calculation	6,243,872	5,016,987
Stock Options
Net loss per share
Total shares excluded from calculation	5,969,382	4,663,852
Unvested restricted stock awards and units
Net loss per share
Total shares excluded from calculation	274,490	353,135

Stock award plan - Share Base Expense (Details) $ in Millions	6 Months Ended
	Jun. 30, 2016 USD ($)
Stock award plan
Unrecognized compensation cost	$ 78.2
Weighted average remaining service period for recognition of unrecognized compensation cost	2 years 6 months 22 days

Restructuring (Details) $ in Thousands	3 Months Ended
Restructuring (Details) $ in Thousands	Jun. 30, 2016 USD ($)
2016 Workforce Reduction
Restructuring Reserve, Beginning Balance	$ 1,903
Expenses, net	548
Cash	(1,456)
Restructuring Reserve, Ending Balance	995
Research and development and selling, general and administrative expenses
Work-force reduction charges	$ 2,500

Commitments and contingencies (Details) - Funding agreement - Wellcome trust $ in Millions	Jun. 30, 2016 USD ($)
Other Commitments [Abstract]
Development and regulatory milestone payments which the entity may be obligated to pay	$ 0.8
Maximum
Other Commitments [Abstract]
Development and regulatory milestone payments which the entity may be obligated to pay	$ 68.9