Subsequent events	6 Months Ended
Jun. 30, 2018
Subsequent Events [Abstract]
Subsequent events	Subsequent events Merger Agreement On July 19, 2018, the Company entered into an Agreement and Plan of Merger (the "Merger Agreement" by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and a wholly owned, indirect subsidiary of the Company ("Transitory Subsidiary"), Agilis Biotherapeutics, Inc., a Delaware corporation ("Agilis") and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, a Colorado limited liability company. The Merger Agreement provides for the acquisition of Agilis by the Company through the merger of Transitory Subsidiary into Agilis, with Agilis surviving as a wholly owned, indirect subsidiary of the Company (the "Merger"). Agilis is a privately-held biotechnology company advancing an innovative gene therapy platform for rare monogenic diseases that affect the central nervous system. At the effective time of the Merger, by virtue of the Merger and without any action on the part of the holders of capital stock of Agilis, all issued and outstanding shares of the capital stock and outstanding vested options and warrants of Agilis will be converted into the right to receive, subject to customary adjustments, an aggregate, of (i) $50.0 million in cash and (ii) a number of shares of the Company’s common stock (the "Closing Stock Consideration"), equal to $150.0 million divided by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the ten consecutive trading day period ending on the second trading day immediately preceding the closing of the Merger and will be subject to reduction such that the number of shares issuable will not equal or exceed 20% of the issued and outstanding shares of the Company’s common stock immediately prior to the closing date, which is expected to be a maximum of approximately 9.34 million shares of the Company's common stock. Agilis equityholders would receive additional cash consideration in lieu of any such reduction in Closing Stock Consideration. In addition, pursuant to the Merger Agreement, Agilis equityholders will be entitled to receive contingent payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich ataxia and Angelman Syndrome during specified terms, ranging from 2-6%. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. Pursuant to the Merger Agreement, the Company has agreed (i) in the event that Agilis provides certain required information at least 10 business days prior to the closing of the Merger, on the closing date of the Merger or, (ii) alternatively, following the closing of the Merger, to use commercially reasonable efforts to file a registration statement on Form S-3 with respect to the resale of the shares of the Closing Stock Consideration to be issued to Agilis equityholders as Merger consideration and to maintain the effectiveness of such registration statement until the six month anniversary date of the closing of the Merger or such earlier time as all shares of Company common stock covered by the registration statement have been sold, subject to certain exceptions and the provision of certain information by Agilis. Bridge Loan and Security Agreement In connection with the Merger Agreement, on July 19, 2018, the Company entered into a Bridge Loan and Security Agreement (the "Bridge Loan Agreement"), by and among the Company, Agilis and certain of Agilis’s domestic subsidiaries, as guarantors. Under the Bridge Loan Agreement, the Company made a term loan advance to Agilis on July 23, 2018 in an original principal amount of $10.0 million and, in the event that the Merger does not close prior to September 2, 2018, the Company is obligated to make an additional term loan advance of $10.0 million, in each case, subject to the satisfaction of certain conditions. Each domestic subsidiary of Agilis has agreed to jointly and severally guarantee Agilis’s payment obligations under the Bridge Loan Agreement. The term loans will accrue interest at a fixed rate per annum equal to 3.0%, subject to increase to 8.0% in the event of a default. Upon closing of the Merger or an event of default, Agilis must repay all outstanding term loans plus accrued and unpaid interest thereon, plus any other sums that have then become due and payable under the Bridge Loan Agreement; provided, however, that only the second term loan advance (if any) would be accelerated for payment in an event of default arising due to Agilis's failure to obtain stockholder approval for the Merger or a material breach of the Merger Agreement by Agilis. To the extent not previously repaid, all outstanding credit extensions plus accrued and unpaid interest thereon, plus any other sums that have then become due and payable under the Bridge Loan Agreement, must be repaid by July 19, 2020. Agilis may elect to prepay any or all of the term loan advances at any time without penalty or premium. Under the Bridge Loan Agreement, Agilis granted the Company a continuing, first priority perfected security interest (subject to certain permitted liens) to all right, title and interest in, to and under all present and future real and personal property of Agilis and any guarantor, whether tangible or intangible, subject to certain exceptions in the Bridge Loan Agreement, but not including Agilis’s intellectual property. The Bridge Loan Agreement contains certain customary representations and warranties, affirmative covenants and conditions. The Bridge Loan Agreement also contains a number of negative covenants that, among other things and subject to certain exceptions, restrict Agilis’s and its subsidiaries’ ability to engage in certain actions or undergo certain changes from and after the termination of the Merger Agreement. The Bridge Loan Agreement also contains customary events of default (subject to grace periods in specified circumstances). In an event of default occurring as a result of termination of the Merger Agreement by the Company for Agilis’s material breach or failure to perform or failure to timely obtain the required stockholder approval, the Company has a limited remedy to declare the second term loan advance (if any) immediately due and payable, but the first term loan advance would remain outstanding and accrue interest at 8.0% per annum. Consent under Credit Agreement In connection with the execution of the Merger Agreement and Bridge Loan Agreement, on July 19, 2018, the Company entered into an amendment and consent agreement (the “Credit Agreement Amendment”) to the Credit Agreement with MidCap. Pursuant to the Credit Agreement Amendment, MidCap and the requisite lenders agreed to, among other things, amend and modify certain covenants and other provisions in the Credit Agreement to permit the entering into of the Merger Agreement and the Bridge Loan Agreement, and the consummation and performance of the transactions contemplated thereby, in each case, subject to certain terms and conditions. Collaboration and Licensing Agreement On August 1, 2018 ("the Effective Date") PTC Therapeutics International Limited ("PTC International"), a subsidiary of the Company, entered into a Collaboration and License Agreement (the "Akcea Agreement") with Akcea Therapeutics, Inc. ("Akcea") for the commercialization by PTC International of Tegsedi^TM (inotersen), Waylivra^TM (volanesorsen) and products containing those compounds (collectively the "Products"), in countries in Latin America and the Caribbean (the "PTC Territory”). Tegsedi is an antisense oligonucleotide inhibitor of human transthyretin production ("TTR protein") for the treatment of patients with hereditary transthyretin amyloidosis (hATTR amyloidosis), a severe, rare and fatal genetic disease. Waylivra is an antisense drug candidate in development for two rare metabolic disorders: familial chylomicronemia syndrome (FCS) and familial partial lipodystrophy (FPL). Neither Tegsedi nor Waylivra is currently approved for marketing in the PTC Territory. In addition, Akcea has granted to PTC International a right of first negotiation (a "ROFN") to commercialize AKCEA-TTR-Lrx, a follow-on product candidate to inotersen, on an exclusive basis in the PTC Territory. Under the terms of the Akcea Agreement, Akcea has granted to PTC International an exclusive right and license, with the right to grant certain sublicenses, under Akcea’s product-specific intellectual property to develop, manufacture and commercialize the Products in the PTC Territory. In addition, Akcea has granted to PTC International a non-exclusive right and license, with the right to grant certain sublicenses, under Akcea’s core intellectual property and manufacturing intellectual property to develop, manufacture and commercialize the Products in the PTC Territory and to manufacture the Products worldwide in accordance with a supply agreement with Akcea. Akcea has in-licensed certain of the Akcea intellectual property from its affiliate, Ionis Pharmaceuticals, Inc. ("Ionis"). Each party has agreed not to, independently or with any third party, commercialize any competing oligonucleotide product in the PTC Territory for the same gene target as inotersen. Within 30 days after the effective date, Akcea has agreed to assign and transfer to PTC International the ownership and sponsorship of applicable regulatory approvals in countries in the PTC Territory, after which PTC International has agreed to prepare, file and maintain regulatory filings and approvals for the applicable Products in such countries. After the Effective Date, PTC International is responsible for all meetings, communications and other interactions with regulatory authorities in the PTC Territory. PTC International has agreed to pay to Akcea an upfront licensing fee of $18.0 million, consisting of a payment of $12.0 million within ten business days after the Effective Date, and $6.0 million within 30 days after receipt of regulatory approval of Waylivra from the United States Food and Drug Administration or the European Medicines Agency, whichever occurs earlier. In addition, Akcea is eligible to receive milestone payments, on a Product-by-Product basis, of $4.0 million upon receipt of regulatory approval for a Product from ANVISA, the Brazilian Health Regulatory Authority, subject to a maximum aggregate amount of $8.0 million for all such Products. Akcea is also entitled to receive royalty payments in the mid-twenty percent range of net sales on a country-by-country and Product-by-Product basis, commencing on the earlier to occur of (1) 12 months after the first commercial sale of such product in Brazil or (2) the date when PTC International, its affiliates or sublicensees have recognized revenue of $10.0 million or more in cumulative net sales for such product in the PTC Territory. The royalty payments are subject to reduction in certain circumstances as set forth in the Agreement. Akcea has granted to PTC International a ROFN to commercialize AKCEA-TTR-Lrx, a follow-on product candidate to inotersen, on an exclusive basis in the PTC Territory, subject to negotiation of the terms of a definitive agreement and certain other terms and conditions. Such a definitive agreement would provide for a royalty rate to be paid by PTC International for AKCEA-TTR-Lrx equal to the royalty rate PTC International has agreed to pay for Tegsedi under the Akcea Agreement, or in the mid-twenty percent range of net sales, and the term of such royalty payments would be the same as the term of the Tegsedi royalty payments. During a specified period in the Akcea Agreement, neither Akcea nor Ionis may enter into an agreement or grant any license to AKCEA-TTR-Lrx that is inconsistent with PTC International’s ROFN. The activities of the parties pursuant to the Akcea Agreement will be overseen by a Joint Steering Committee, to be composed of an equal number of representatives appointed by each of PTC International and Akcea. The Akcea Agreement continues until the expiration of the last to expire royalty term with respect to all Products in all countries in the PTC Territory. Either party may terminate the Akcea Agreement on written notice to the other party if such other party is in material breach of its obligations thereunder and has not cured such breach within 30 days after notice in the case of a payment breach or 60 days after notice in the case of any other breach.

Subsequent events

Merger Agreement

On July 19, 2018, the Company entered into an Agreement and Plan of Merger (the "Merger Agreement" by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and a wholly owned, indirect subsidiary of the Company ("Transitory Subsidiary"), Agilis Biotherapeutics, Inc., a Delaware corporation ("Agilis") and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, a Colorado limited liability company. The Merger Agreement provides for the acquisition of Agilis by the Company through the merger of Transitory Subsidiary into Agilis, with Agilis surviving as a wholly owned, indirect subsidiary of the Company (the "Merger"). Agilis is a privately-held biotechnology company advancing an innovative gene therapy platform for rare monogenic diseases that affect the central nervous system.

At the effective time of the Merger, by virtue of the Merger and without any action on the part of the holders of capital stock of Agilis, all issued and outstanding shares of the capital stock and outstanding vested options and warrants of Agilis will be converted into the right to receive, subject to customary adjustments, an aggregate, of (i) $50.0 million in cash and (ii) a number of shares of the Company’s common stock (the "Closing Stock Consideration"), equal to $150.0 million divided by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the ten consecutive trading day period ending on the second trading day immediately preceding the closing of the Merger and will be subject to reduction such that the number of shares issuable will not equal or exceed 20% of the issued and outstanding shares of the Company’s common stock immediately prior to the closing date, which is expected to be a maximum of approximately 9.34 million shares of the Company's common stock. Agilis equityholders would receive additional cash consideration in lieu of any such reduction in Closing Stock Consideration.

In addition, pursuant to the Merger Agreement, Agilis equityholders will be entitled to receive contingent payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich ataxia and Angelman Syndrome during specified terms, ranging from 2-6%. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved.

Pursuant to the Merger Agreement, the Company has agreed (i) in the event that Agilis provides certain required information at least 10 business days prior to the closing of the Merger, on the closing date of the Merger or, (ii) alternatively, following the closing of the Merger, to use commercially reasonable efforts to file a registration statement on Form S-3 with respect to the resale of the shares of the Closing Stock Consideration to be issued to Agilis equityholders as Merger consideration and to maintain the effectiveness of such registration statement until the six month anniversary date of the closing of the Merger or such earlier time as all shares of Company common stock covered by the registration statement have been sold, subject to certain exceptions and the provision of certain information by Agilis.

Bridge Loan and Security Agreement

In connection with the Merger Agreement, on July 19, 2018, the Company entered into a Bridge Loan and Security Agreement (the "Bridge Loan Agreement"), by and among the Company, Agilis and certain of Agilis’s domestic subsidiaries, as guarantors. Under the Bridge Loan Agreement, the Company made a term loan advance to Agilis on July 23, 2018 in an original principal amount of $10.0 million and, in the event that the Merger does not close prior to September 2, 2018, the Company is obligated to make an additional term loan advance of $10.0 million, in each case, subject to the satisfaction of certain conditions. Each domestic subsidiary of Agilis has agreed to jointly and severally guarantee Agilis’s payment obligations under the Bridge Loan Agreement.

The term loans will accrue interest at a fixed rate per annum equal to 3.0%, subject to increase to 8.0% in the event of a default. Upon closing of the Merger or an event of default, Agilis must repay all outstanding term loans plus accrued and unpaid interest thereon, plus any other sums that have then become due and payable under the Bridge Loan Agreement; provided, however, that only the second term loan advance (if any) would be accelerated for payment in an event of default arising due to Agilis's failure to obtain stockholder approval for the Merger or a material breach of the Merger Agreement by Agilis. To the extent not previously repaid, all outstanding credit extensions plus accrued and unpaid interest thereon, plus any other sums that have then become due and payable under the Bridge Loan Agreement, must be repaid by July 19, 2020. Agilis may elect to prepay any or all of the term loan advances at any time without penalty or premium.

Under the Bridge Loan Agreement, Agilis granted the Company a continuing, first priority perfected security interest (subject to certain permitted liens) to all right, title and interest in, to and under all present and future real and personal property of Agilis and any guarantor, whether tangible or intangible, subject to certain exceptions in the Bridge Loan Agreement, but not including Agilis’s intellectual property.

The Bridge Loan Agreement contains certain customary representations and warranties, affirmative covenants and conditions. The Bridge Loan Agreement also contains a number of negative covenants that, among other things and subject to certain exceptions, restrict Agilis’s and its subsidiaries’ ability to engage in certain actions or undergo certain changes from and after the termination of the Merger Agreement. The Bridge Loan Agreement also contains customary events of default (subject to grace periods in specified circumstances). In an event of default occurring as a result of termination of the Merger Agreement by the Company for Agilis’s material breach or failure to perform or failure to timely obtain the required stockholder approval, the Company has a limited remedy to declare the second term loan advance (if any) immediately due and payable, but the first term loan advance would remain outstanding and accrue interest at 8.0% per annum.

Consent under Credit Agreement

In connection with the execution of the Merger Agreement and Bridge Loan Agreement, on July 19, 2018, the Company entered into an amendment and consent agreement (the “Credit Agreement Amendment”) to the Credit Agreement with MidCap. Pursuant to the Credit Agreement Amendment, MidCap and the requisite lenders agreed to, among other things, amend and modify certain covenants and other provisions in the Credit Agreement to permit the entering into of the Merger Agreement and the Bridge Loan Agreement, and the consummation and performance of the transactions contemplated thereby, in each case, subject to certain terms and conditions.

Collaboration and Licensing Agreement

On August 1, 2018 ("the Effective Date") PTC Therapeutics International Limited ("PTC International"), a subsidiary of the Company, entered into a Collaboration and License Agreement (the "Akcea Agreement") with Akcea Therapeutics, Inc. ("Akcea") for the commercialization by PTC International of Tegsedi^TM (inotersen), Waylivra^TM (volanesorsen) and products containing those compounds (collectively the "Products"), in countries in Latin America and the Caribbean (the "PTC Territory”). Tegsedi is an antisense oligonucleotide inhibitor of human transthyretin production ("TTR protein") for the treatment of patients with hereditary transthyretin amyloidosis (hATTR amyloidosis), a severe, rare and fatal genetic disease. Waylivra is an antisense drug candidate in development for two rare metabolic disorders: familial chylomicronemia syndrome (FCS) and familial partial lipodystrophy (FPL). Neither Tegsedi nor Waylivra is currently approved for marketing in the PTC Territory. In addition, Akcea has granted to PTC International a right of first negotiation (a "ROFN") to commercialize AKCEA-TTR-Lrx, a follow-on product candidate to inotersen, on an exclusive basis in the PTC Territory.

Under the terms of the Akcea Agreement, Akcea has granted to PTC International an exclusive right and license, with the right to grant certain sublicenses, under Akcea’s product-specific intellectual property to develop, manufacture and commercialize the Products in the PTC Territory. In addition, Akcea has granted to PTC International a non-exclusive right and license, with the right to grant certain sublicenses, under Akcea’s core intellectual property and manufacturing intellectual property to develop, manufacture and commercialize the Products in the PTC Territory and to manufacture the Products worldwide in accordance with a supply agreement with Akcea. Akcea has in-licensed certain of the Akcea intellectual property from its affiliate, Ionis Pharmaceuticals, Inc. ("Ionis"). Each party has agreed not to, independently or with any third party, commercialize any competing oligonucleotide product in the PTC Territory for the same gene target as inotersen.

Within 30 days after the effective date, Akcea has agreed to assign and transfer to PTC International the ownership and sponsorship of applicable regulatory approvals in countries in the PTC Territory, after which PTC International has agreed to prepare, file and maintain regulatory filings and approvals for the applicable Products in such countries. After the Effective Date, PTC International is responsible for all meetings, communications and other interactions with regulatory authorities in the PTC Territory.

PTC International has agreed to pay to Akcea an upfront licensing fee of $18.0 million, consisting of a payment of $12.0 million within ten business days after the Effective Date, and $6.0 million within 30 days after receipt of regulatory approval of Waylivra from the United States Food and Drug Administration or the European Medicines Agency, whichever occurs earlier. In addition, Akcea is eligible to receive milestone payments, on a Product-by-Product basis, of $4.0 million upon receipt of regulatory approval for a Product from ANVISA, the Brazilian Health Regulatory Authority, subject to a maximum aggregate amount of $8.0 million for all such Products. Akcea is also entitled to receive royalty payments in the mid-twenty percent range of net sales on a country-by-country and Product-by-Product basis, commencing on the earlier to occur of (1) 12 months after the first commercial sale of such product in Brazil or (2) the date when PTC International, its affiliates or sublicensees have recognized revenue of $10.0 million or more in cumulative net sales for such product in the PTC Territory. The royalty payments are subject to reduction in certain circumstances as set forth in the Agreement.

Akcea has granted to PTC International a ROFN to commercialize AKCEA-TTR-Lrx, a follow-on product candidate to inotersen, on an exclusive basis in the PTC Territory, subject to negotiation of the terms of a definitive agreement and certain other terms and conditions. Such a definitive agreement would provide for a royalty rate to be paid by PTC International for AKCEA-TTR-Lrx equal to the royalty rate PTC International has agreed to pay for Tegsedi under the Akcea Agreement, or in the mid-twenty percent range of net sales, and the term of such royalty payments would be the same as the term of the Tegsedi royalty payments. During a specified period in the Akcea Agreement, neither Akcea nor Ionis may enter into an agreement or grant any license to AKCEA-TTR-Lrx that is inconsistent with PTC International’s ROFN. The activities of the parties pursuant to the Akcea Agreement will be overseen by a Joint Steering Committee, to be composed of an equal number of representatives appointed by each of PTC International and Akcea.

The Akcea Agreement continues until the expiration of the last to expire royalty term with respect to all Products in all countries in the PTC Territory. Either party may terminate the Akcea Agreement on written notice to the other party if such other party is in material breach of its obligations thereunder and has not cured such breach within 30 days after notice in the case of a payment breach or 60 days after notice in the case of any other breach.