uniQure (QURE) 10-Q 1 Nov 17 2017 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2017	Oct. 31, 2017
Document and Entity Information
Entity Registrant Name	uniQure N.V.
Entity Central Index Key	1,590,560
Document Type	10-Q
Document Period End Date	Sep. 30, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		30,800,080
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	Q3

CONSOLIDATED BALANCE SHEETS

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Current assets
Cash and cash equivalents	$ 88,934	$ 132,496
Accounts receivable and accrued income		3,680
Accounts receivable and accrued income from related party	1,945	5,500
Prepaid expenses	689	996
Other current assets	747	1,274
Total current assets	92,315	143,946
Non-current assets
Property, plant and equipment, net	34,653	35,702
Intangible assets, net	9,027	8,324
Goodwill	522	465
Other non-current assets	2,469	1,828
Total non-current assets	46,671	46,319
Total assets	138,986	190,265
Current liabilities
Accounts payable	2,987	5,524
Accrued expenses and other current liabilities	10,165	9,766
Current portion of long-term debt	6,232	605
Current portion of deferred rent	724	684
Current portion of deferred revenue	4,249	6,142
Current portion of contingent consideration	1,017
Total current liabilities	25,374	22,721
Non-current liabilities
Long-term debt, net of current portion	14,353	19,631
Deferred rent, net of current portion	8,829	6,781
Deferred revenue, net of current portion	67,863	75,612
Contingent consideration, net of current portion	2,593	1,838
Other non-current liabilities	367	51
Total non-current liabilities	94,005	103,913
Total liabilities	119,379	126,634
Commitments and contingencies (see note 14)
Shareholders' equity
Ordinary shares, €0.05 par value: 60,000,000 shares authorized at September 30, 2017 and December 31, 2016 and 25,635,849 and 25,257,420 shares issued and outstanding at September 30, 2017 and December 31, 2016, respectively.	1,612	1,593
Additional paid-in-capital	471,648	464,653
Accumulated other comprehensive loss	(5,809)	(6,557)
Accumulated deficit	(447,844)	(396,058)
Total shareholders' equity	19,607	63,631
Total liabilities and shareholders' equity	$ 138,986	$ 190,265

CONSOLIDATED BALANCE SHEETS (Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) - € / shares	Sep. 30, 2017	Dec. 31, 2016
CONSOLIDATED BALANCE SHEETS
Common shares, par value (in euros per share)	€ 0.05	€ 0.05
Common shares, authorized shares	60,000,000	60,000,000
Common shares, issued shares	25,635,849	25,257,420
Common shares, outstanding shares	25,635,849	25,257,420

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
License revenues		$ 246	$ 8	$ 736
License revenues from related party	$ 1,124	993	3,060	2,977
Collaboration revenues		1,850	4,638	4,835
Collaboration revenues from related party	1,136	4,132	2,817	7,419
Total revenues	2,260	7,221	10,523	15,967
Operating expenses:
Research and development expenses	(20,103)	(16,604)	(53,963)	(52,531)
Selling, general and administrative expenses	(5,584)	(5,113)	(17,352)	(20,245)
Total operating expenses	(25,687)	(21,717)	(71,315)	(72,776)
Other income	14,413	336	14,995	1,256
Other expense	(261)		(2,901)
Loss from operations	(9,275)	(14,160)	(48,698)	(55,553)
Interest income	10	14	33	51
Interest expense	(577)	(507)	(1,583)	(1,685)
Foreign currency gains / (losses), net	(681)	(496)	(1,845)	(1,764)
Other non-operating income, net		54	29	701
Loss before income tax expense	(10,523)	(15,095)	(52,064)	(58,250)
Income tax expense	278	(177)	278	(401)
Net loss	(10,245)	(15,272)	(51,786)	(58,651)
Other comprehensive loss, net of income tax:
Foreign currency translation adjustments net of tax impact of $0.3 million and $(0.2) million for the three months ended September 30, 2017 and 2016, respectively, and $0.3 million and $(0.4) million for the nine months ended September 30, 2017 and 2016, respectively.	22	2,801	748	3,380
Total comprehensive loss	$ (10,223)	$ (12,471)	$ (51,038)	$ (55,271)
Basic and diluted net loss per ordinary share	$ (0.40)	$ (0.61)	$ (2.03)	$ (2.35)
Weighted average shares used in computing basic and diluted net loss per ordinary share	25,632,642	25,142,660	25,546,225	24,972,839

CONSOLIDATED STATEMENTS OF OPE5

CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS (Parenthetical) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
Foreign currency translation adjustments, tax	$ 0.3	$ (0.2)	$ 0.3	$ (0.4)

CONSOLIDATED STATEMENTS OF SHAR

CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY - 9 months ended Sep. 30, 2017 - USD ($) $ in Thousands	Ordinary shares	Additional paid-in capital	Accumulated other comprehensive income/(loss)	Accumulated deficit	Total
Beginning balance at Dec. 31, 2016	$ 1,593	$ 464,653	$ (6,557)	$ (396,058)	$ 63,631
Beginning balance (in shares) at Dec. 31, 2016	25,257,420				25,257,420
Increase (decrease) in shareholders' equity
Loss for the period				(51,786)	$ (51,786)
Other comprehensive income			748		748
Exercise of share options	$ 15	1,021			1,036
Exercise of share options (in shares)	294,929
Shares distributed during the period	$ 4	(4)
Shares distributed during the period (in shares)	83,500
Share-based compensation expense		5,978			5,978
Ending balance at Sep. 30, 2017	$ 1,612	$ 471,648	$ (5,809)	$ (447,844)	$ 19,607
Ending balance (in shares) at Sep. 30, 2017	25,635,849				25,635,849

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Cash flows from operating activities
Net loss	$ (51,786)	$ (58,651)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization and impairments	6,036	4,543
Share-based compensation expense	5,978	5,020
Change in fair value of derivative financial instruments and contingent consideration	2,704	(2,270)
Unrealized foreign exchange results	1,821	1,779
Change in deferred taxes		401
Change in lease incentive	1,938	(468)
Changes in operating assets and liabilities:
Accounts receivable, prepaid expenses and other current assets	9,477	(4,685)
Inventories		406
Accounts payable	(1,440)	32
Accrued expenses and other liabilities	(1,331)	2,029
Deferred revenue	(19,620)	(4,651)
Net cash used in operating activities	(46,223)	(56,515)
Cash flows from investing activities
Restricted cash	(567)	(617)
Purchase of intangible assets	(1,124)	(1,897)
Purchase of property, plant and equipment	(3,244)	(11,034)
Net cash used in investing activities	(4,935)	(13,548)
Cash flows from financing activities
Proceeds from issuance of shares	1,036	2,218
Repayment of capital lease obligations		(149)
Net cash generated from financing activities	1,036	2,069
Currency effect cash and cash equivalents	6,560	3,919
Net decrease in cash and cash equivalents	(43,562)	(64,075)
Cash and cash equivalents at beginning of period	132,496	221,626
Cash and cash equivalents at the end of period	88,934	157,551
Supplemental cash flow disclosures:
Cash paid for interest	1,130	1,594
Non-cash increases/(decreases) in accounts payables related to purchases of intangible assets and property, plant and equipment	$ (1,635)	$ 828

General business Information

General business Information	9 Months Ended
	Sep. 30, 2017
General business Information
General business Information	1 uniQure (the “Company”) was incorporated on January 9, 2012 as a private company with limited liability (besloten vennootschap met beperkte aansprakelijkheid) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics (AMT) Holding N.V (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability (naamloze vennootschap) and changed its legal name from uniQure B.V. to uniQure N.V. The Company is registered in the trade register of the Chamber of Commerce (Kamer van Koophandel) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25a, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. The Company’s website address is www.uniqure.com. Effective January 1, 2017, the Company ceased to qualify as a foreign private issuer under the rules and regulations of the Securities Act of 1933, as amended (the “Securities Act”). As a result, as of January 1, 2017, the Company began filing electronically with the Securities and Exchange Commission (the “SEC”) its annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K, and any amendments to those reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). Prior to this time, the Company filed its annual report on Form 20-F and furnished quarterly financial reports as an exhibit on Form 6-K with the SEC. The Company’s ordinary shares are listed on the NASDAQ Global Select Market and trades under the symbol “QURE”.

Summary of significant accounti

Summary of significant accounting policies	9 Months Ended
	Sep. 30, 2017
Summary of significant accounting policies
Summary of significant accounting policies	2 2.1 The Company prepared these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). The unaudited consolidated financial statements are presented in U.S. dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. 2.2 The accompanying interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the periods presented. Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the nine months ended September 30, 2017, are not necessarily indicative of the results to be expected for the full year ending December 31, 2017, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 15, 2017. 2.3 The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates. 2.4 The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2016, and the notes thereto, which are included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 15, 2017. There have been no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2017. 2.5 There have been no new accounting pronouncements or changes to accounting pronouncements during the nine months ended September 30, 2017, compared to the recent accounting pronouncements described in Note 2.3.22 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, which could be expected to materially impact the Company’s unaudited condensed consolidated financial statements except the ones discussed below: In May 2017, the FASB issued ASU 2017-09, Compensation-stock compensation (topic 718)- scope of modification accounting (“ASU 2017-09”), which provides clarity regarding the applicability of modification accounting in relation to share-based payment awards. Under the new guidance, modification accounting is required only if the fair value, the vesting conditions, or the classification of the award (as equity or liability) changes because of the change in terms or conditions. The effective date for the standard is for fiscal years beginning after December 15, 2017, which for the Company is January 1, 2018. Early adoption is permitted. The new standard is to be applied prospectively. The Company does not expect ASU 2017-09 to have a material impact on its consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842). Under the new guidance, lessees will be required to recognize the assets and liabilities that arise from operating leases. A lessee should recognize in the statement of financial position a liability to make lease payments (the lease liability) and a right-of-use asset representing its right to use the underlying asset for the lease term. For leases with a term of 12 months or less, a lessee is permitted to make an accounting policy election by class of underlying asset not to recognize lease assets and lease liabilities. Lessees and lessors are required to recognize and measure leases at the beginning of the earliest period presented using a modified retrospective approach. ASU 2016-02 will be effective for the Company beginning in the first quarter of 2019 and early application is permitted. The Company does expect ASU 2016-02 to have a material impact on its consolidated financial statements, primarily from recognition of a right-of-use asset and lease liability in the balance sheet and a shift of cash outflows from operating activities to financing activities. In July 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers: Deferral of the Effective Date (“ASU 2015-14”), which deferred the effective date for ASU 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”), by one year. ASU 2014-09 will supersede the revenue recognition requirements in ASC 605, Revenue Recognition, and requires entities to recognize revenue in a way that depicts the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. In 2016, the FASB issued ASU 2016-08, 2016-10 and 2016-12, which provided further clarification on ASU 2014-09. ASU 2014-09 is effective for annual reporting periods beginning after December 15, 2017, including interim periods within that reporting period, which for the Company is January 1, 2018. The Company has one active product development collaboration with Bristol Myers Squibb (“BMS”). ASU 2014-09 provides for two possible implementation methods, (i) full retrospective application to all periods from January 1, 2015 onwards for revenue recognized in relation to collaborations; or (ii) application of the standard from January 1, 2018, onwards to the BMS collaboration with an adjustment to retained earnings as of December 31, 2017, to include the cumulative adjustment to revenue recognized in prior periods in relation to the BMS collaboration. The Company currently accounts for the BMS collaboration agreement as a revenue arrangement with multiple elements. The Company’s substantive deliverables under the BMS collaboration agreement include an exclusive license to its technology in the field of cardiovascular disease, research and development services for specific targets chosen by BMS and general development of the Company’s proprietary vector technology, participation in the Joint Steering Committee, and clinical and commercial manufacturing. The Company is continuing to assess the method of adoption as well as its financial statement disclosures.

Fair value measurement

Fair value measurement	9 Months Ended
	Sep. 30, 2017
Fair value measurement
Fair value measurement	3 Fair value measurement The Company measures certain assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. U.S. GAAP, requires disclosure of methodologies used in determining the reported fair values, and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: · Level 1 - Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. · Level 2 - Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. · Level 3 - Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. Items measured at fair value on a recurring basis include financial instruments and contingent consideration. The carrying amount of cash and cash equivalents, accounts receivable from collaborators, prepaid expenses, other assets, accounts payable, accrued expenses and other current liabilities reflected in the consolidated balance sheets approximate their fair values due to their short-term maturities. The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2017, and December 31, 2016: Quoted prices Significant Significant Total Classification in consolidated in thousands At December 31, 2016 Assets: Cash and cash equivalents $ 132,496 $ — $ — $ 132,496 Total assets 132,496 — — 132,496 Liabilities: Derivative financial instruments - debt — — 11 11 Accrued expenses and other current liabilities Derivative financial instruments - related party — — 51 51 Other non-current liabilities Contingent consideration — — 1,838 1,838 Total liabilities $ — $ — $ 1,900 $ 1,900 At September 30, 2017 Assets: Cash and cash equivalents $ 88,934 $ — $ — $ 88,934 Total assets 88,934 — — 88,934 Liabilities: Derivative financial instruments - debt — — 3 3 Accrued expenses and other current liabilities Derivative financial instruments - related party — — 35 35 Other non-current liabilities Contingent consideration — — 3,610 3,610 Total liabilities $ — $ — $ 3,648 $ 3,648 Changes in Level 3 items during the nine months ended September 30, 2017, and 2016, are as follows: Derivative Contingent financial consideration instruments Total in thousands Balance at December 31, 2016 $ 1,838 $ 62 $ 1,900 (Gains) / losses recognized in profit or loss 2,704 (29) 2,675 Amounts due (presented in Accrued expenses and other current liabilities) (1,181) — (1,181) Currency translation effects 249 5 254 Balance at September 30, 2017 $ 3,610 $ 38 $ 3,648 Derivative Contingent financial consideration instruments Total in thousands Balance at December 31, 2015 $ 2,926 $ 837 $ 3,763 (Gains) / losses recognized in profit or loss (1,569) (701) (2,270) Currency translation effects 87 20 107 Balance at September 30, 2016 $ 1,444 $ 156 $ 1,600 Contingent consideration In connection with the Company’s acquisition of InoCard GmbH (“InoCard”) in 2014, the Company recorded contingent consideration related to amounts potentially payable to InoCard’s former shareholders. In August 2017, the Company and the former shareholders amended the 2014 sale and purchase agreement to waive certain of the Company’s obligations regarding the development of the acquired program pursuant to a plan to be agreed to between the Company and the InoCard former shareholders. The parties also modified the conditions of the agreed milestone payments, including a reduction of the percentage of any future milestone that can be settled in the form of Company ordinary shares from 100% to 50%. The Company recorded $2.3 million in research and development cost in the three and nine months ended September 30, 2017, related to the increase of fair value of the contingent consideration resulting from these modifications. The amounts payable in accordance with the amended sale and purchase agreement are contingent upon realization of the following milestones: · Early candidate nomination of product by third party; · Acceptance of investigational new drug application by the United States Food and Drug Administration or an equivalent filing in defined Western European countries; · Completion of dosing of all patients in the first clinical study; and · Full proof of concept of the product in humans after finalization of the first clinical study. The valuation of the contingent liability is based on significant inputs not observable in the market such as the probability of success (“POS”) of achieving certain research milestones (estimated as probable for the first three milestones as of the balance sheet date), the time at which the research milestones are expected to be achieved (ranging from 2018 to 2021), as well as the discount rate applied, which represents a Level 3 measurement. The POS as well as the discount rate both reflect the probability of achieving a milestone as of a specific date. In June 2017, the Company replaced the risk-adjusted discount rate of 30.0% with the Company’s weighted average rate of capital of 14.5% to reflect the full integration of the acquired business into the Company’s operation. This resulted in a $0.3 million increase of the liability. Varying the timing of the milestones, the discount rate and the POS of unobservable inputs results in the following fair value changes: September 30, 2017 in thousands Change in fair value Moving out of all milestones by 6 months $ (231) Increasing the POS for the first milestone by 20% 1,103 Decreasing the POS for the first milestone by 20% (1,103) Reducing the discount rate from 14.5% to 4.5% 1,004 Increasing the discount rate from 14.5% to 24.5% (590) December 31, 2016 in thousands Change in fair value Moving out of all milestones by 6 months $ (209) Increasing the POS for the first milestone by 20% 367 Decreasing the POS for the first milestone by 20% (367) Reducing the discount rate from 30% to 20% 638 Increasing the discount rate from 30% to 40% (309) Derivative financial instruments The Company issued derivative financial instruments related to its collaboration with Bristol-Meyers Squibb Company (“BMS”) and in relation to the issuance of the Hercules Technology Growth Corp. (“Hercules”) loan facility. The fair value of these derivative financial instruments as of September 30, 2017, was $0.0 million (December 31, 2016: $0.1 million), and these derivative financial instruments are described in more detail below. There were no significant changes in the sensitivity of the fair value from (un)observable inputs as of September 30, 2017, compared to December 31, 2016. BMS collaboration On April 6, 2015, the Company entered into several agreements with BMS (the “BMS Agreements”). Pursuant to the terms of the BMS Agreements the Company granted BMS two warrants: · A warrant allowing BMS to purchase a specific number of uniQure ordinary shares such that its ownership will equal 14.9% immediately after such purchase. The warrant can be exercised on the later of (i) the date on which the Company receives from BMS the Target Designation Fees (as defined in the collaboration agreements) associated with the first six New Targets (as defined in the collaboration agreements); and (ii) the date on which BMS designates the sixth New Target. · A warrant allowing BMS to purchase a specific number of uniQure ordinary shares such that its ownership will equal 19.9% immediately after such purchase. The warrant can be exercised on the later of (i) the date on which uniQure receives from BMS the Target Designation Fees associated with the first nine New Targets; and (ii) the date on which BMS designates the ninth New Target. Pursuant to the terms of the BMS Agreements the exercise price, in respect of each warrant, is equal to the greater of (i) the product of (A) $33.84, multiplied by (B) a compounded annual growth rate of 10% and (ii) the product of (A) 1.10 multiplied by (B) the VWAP for the 20 trading days ending on the date that is five trading days prior to the date of a notice of exercise delivered by BMS. Hercules loan facility On June 14, 2013, the Company entered into a venture debt loan facility with (the “Original Facility”) with Hercules Technology Growth Capital, Inc. (“Hercules”) pursuant to a Loan and Security Agreement (the “Loan Agreement”) which included a warrant. The warrant was not closely related to the host contract and was accounted for separately as a derivative financial liability measured at fair value though profit or loss. The warrant included in the Original Facility remained in place following the 2014 and 2016 amendments of the loan.

Collaboration arrangements and

Collaboration arrangements and concentration of credit risk	9 Months Ended
	Sep. 30, 2017
Collaboration arrangements and concentration of credit risk
Collaboration arrangements and concentration of credit risk	4 Collaboration arrangements and concentration of credit risk In the three and nine months ended September 30, 2017, the Company generated all collaboration and license revenues from its Collaboration and License Agreement with BMS, and its Co-Development Agreement for hemophilia B with Chiesi Farmaceutici S.p.A. (“Chiesi”). On April 19, 2017, the Company and Chiesi entered into an agreement to terminate the Glybera Commercialization Agreement following the Company’s decision to not seek renewal with the European Medicines Agency of the marketing authorization for Glybera by October 2017 (“Glybera Termination Agreement”). In July 2017, the Company and Chiesi terminated their co-development agreement in respect of the hemophilia B program (“hemophilia B Termination Agreement”). As a result, the Company holds the global rights to the development of the hemophilia B program and is not required to provide any further services in relation to the co-development and active contribution to the collaboration by providing technology access in the field of gene therapy to Chiesi. Since June 2015, BMS has been considered a related party given the significance of its equity investment in the Company. Services to the Company’s collaboration partners are rendered by the Dutch operating entity. Total collaboration and license revenue generated from these partners are as follows: Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Bristol Myers Squibb $ 2,260 $ 5,125 $ 5,877 $ 10,396 Chiesi Farmaceutici S.p.A — 2,096 4,646 5,571 Total $ 2,260 $ 7,221 $ 10,523 $ 15,967 Amounts owed by these partners in relation to the collaboration are as follows: September 30, December 31, 2017 2016 in thousands Bristol Myers Squibb $ 1,945 $ 5,500 Chiesi Farmaceutici S.p.A — 3,680 Total $ 1,945 $ 9,180 BMS collaboration In May 2015, the Company closed a Collaboration and License Agreement with BMS (the “BMS Collaboration Agreement”) that provides exclusive access to the Company’s gene therapy technology platform for multiple targets in cardiovascular (and other target specific) diseases. The collaboration included the Company’s proprietary gene therapy program for congestive heart failure which aims to restore the heart's ability to synthesize S100A1, a calcium sensor and master regulator of heart function, and thereby improve clinical outcomes for patients with reduced ejection fraction. Beyond cardiovascular diseases, the agreement also included the potential for a target exclusive collaboration in other disease areas. In total, the companies may collaborate on ten targets, including S100A1. The Company is conducting the discovery, non-clinical, analytical and process development activities and is responsible for manufacturing of clinical and commercial supplies using the Company’s vector technologies and industrial, proprietary insect-cell based manufacturing platform. BMS reimburses the Company for all its research and development efforts in support of the Collaboration, and will lead the clinical development and regulatory activities across all programs. BMS will also be solely responsible for commercialization of all products from the collaboration. The Company evaluated the BMS Collaboration Agreement and determined that it is a revenue arrangement with multiple elements. The Company’s substantive deliverables under the BMS Collaboration Agreement include an exclusive license to its technology in the field of cardiovascular disease, research and development services for specific targets chosen by BMS and general development of the Company’s proprietary vector technology, participation in the Joint Steering Committee, and clinical and commercial manufacturing. The Company concluded that the BMS Collaboration Agreement consists of three units of accounting, including (i) technology (license and target selections), know-how and manufacturing in the field of gene therapy and development and active contribution to the development through the Joint Steering Committee participations, (ii) provision of employees, goods and services for research activities for specific targets and (iii) clinical and commercial manufacturing. The Company determined that the license does not have stand-alone value to BMS without the Company’s know-how and manufacturing technology through the participation of the Joint Steering Committee and accordingly, they were combined into one unit of accounting. License revenue – BMS As of May 21, 2015, the effective date of the BMS Collaboration Agreement, the Company recorded deferred revenue of $60.1 million. On July 31, 2015, BMS selected the second, third and fourth collaboration targets, triggering a $15.0 million target designation payment to the Company. The Company is entitled to an aggregate of $16.5 million in target designation payments upon the selection of the fifth through tenth collaboration targets. The Company will also be eligible to receive research, development and regulatory milestone payments of up to $254.0 million for S100A1 and up to $217.0 million for each of the other selected targets, if milestones are achieved. The Company determined that the contingent payments under the BMS Collaboration Agreement relating to research, development and regulatory milestones do not constitute substantive milestones and will not be accounted for under the milestone method of revenue recognition. The events leading to these payments solely depend on BMS’ performance. Accordingly, any revenue from these contingent payments would be allocated to the first unit of accounting noted above and recognized over the expected performance period. License revenue is recognized over an expected performance period of 19 years on a straight-line basis commencing on May 21, 2015. The expected performance period is reviewed quarterly and adjusted to account for changes, if any, in the Company´s estimated performance period. The estimated performance period did not change in the nine months ended September 30, 2017. The Company recognized $1.1 million and $3.1 million of license revenue for the three and nine months ended September 30, 2017, respectively, and compared to $1.0 million and $3.0 million during the same periods in 2016. Additionally, the Company is eligible to receive net sales-based milestone payments and tiered high single to low double-digit royalties on product sales. These revenues will be recognized when earned. The royalty term is determined on a licensed-product-by-licensed-product and country-by-country basis and begins on the first commercial sale of a licensed product in a country and ends on the expiration of the last to expire of specified patents or regulatory exclusivity covering such licensed product in such country or, with a customary royalty reduction, ten years after such first commercial sale if there is no such exclusivity. Collaboration revenue – BMS The Company provides target-specific research and development services to BMS. Collaboration revenue related to these contracted services is recognized when earned. The Company generated $1.1 million and $2.8 million of collaboration revenue during the three and nine months ended September 30, 2017, respectively, compared to $4.1 million and $7.4 million during the same periods in 2016. Manufacturing revenue – BMS BMS and the Company also entered into a binding term sheet for the Company to supply gene therapy products during the clinical and commercial phase to BMS. Revenues from product sales will be recognized when earned. To date the Company has not supplied any clinical and commercial product to BMS. Chiesi collaboration In 2013, the Company entered into two agreements with Chiesi, one for the co-development and commercialization of the hemophilia B program (the “Hemophilia Collaboration Agreement”) and one for the commercialization of Glybera (the “Glybera Agreement”, and together with the Collaboration Agreement, the “Chiesi Agreements”) in Europe and selected territories. In April 2017, the parties agreed to terminate the Glybera Agreement. Accordingly, the Company will not be required to supply Glybera to Chiesi beyond October 2017. In July 2017, the parties terminated the Hemophilia Collaboration Agreement and the Company reacquired rights associated with its hemophilia B program in Europe and selected territories. License revenue – Chiesi Upon the closing of the Chiesi Agreements on September 30, 2013, the Company received €17.0 million ($22.1 million) in non-refundable up-front payments. The Company determined that the up-front payments constituted a single unit of accounting that should be amortized as license revenue on a straight-line basis over the performance period of July 2013 through September 2032. In July 2017, the Company fully released the outstanding deferred revenue and recorded $13.8 million other income during the three and nine months ended September 30, 2017. The Company recognized $0.0 million and $0.0 million of license revenue during the three and nine months ended September 30, 2017, respectively, compared to $0.2 million and $0.7 million during the same periods in 2016. The Company recognized the license revenue for the nine months ended September 30, 2017, net of a $0.5 million reduction for amounts previously amortized and repaid by the Company in accordance with the Glybera Termination Agreement in 2017. Collaboration revenue – Chiesi Prior to the termination of the Hemophilia Collaboration Agreement up to June 30,2017, Chiesi reimbursed the Company for 50% of the agreed research and development efforts related to hemophilia B. These reimbursable amounts have been presented as collaboration revenue. The Company generated $0.0 million and $4.6 million of collaboration revenue from the co-development of hemophilia B during the three and nine months ended September 30, 2017, respectively, compared to $1.9 million and $4.8 million during the same periods in 2016.

Property, plant and equipment

Property, plant and equipment	9 Months Ended
	Sep. 30, 2017
Property, plant and equipment
Property, plant and equipment	5 Property, plant and equipment The following table presents the Company’s property, plant and equipment as of September 30, 2017, and December 31, 2016: September 30, December 31, 2017 2016 in thousands Leasehold improvements $ 33,054 $ 30,582 Laboratory equipment 15,952 14,166 Office equipment 2,926 2,710 Construction-in-progress 365 313 Total property, plant, and equipment 52,297 47,771 Less accumulated depreciation (17,644) (12,069) Property, plant and equipment, net $ 34,653 $ 35,702 Total depreciation expense was $1.7 million and $5.1 million during the three and nine months ended September 30, 2017, respectively, compared to $1.4 million and $4.1 million during the same periods in 2016. Depreciation expense is allocated to research and development to the extent it relates to the Company’s manufacturing facility and equipment. All other depreciation expenses are allocated to selling, general and administrative expense.

Intangible assets

Intangible assets	9 Months Ended
	Sep. 30, 2017
Intangible assets
Intangible assets	6 Intangible assets The Company’s intangible assets include acquired licenses and acquired research and development (“Acquired R&D”) and are presented in the following table: September 30, December 31, 2017 2016 in thousands Licenses $ 9,417 $ 7,799 Acquired research & development 5,512 4,908 Total intangible assets 14,929 12,707 Less accumulated amortization and impairment (5,902) (4,383) Intangible assets, net $ 9,027 $ 8,324 Amortization expense was $0.1 million and $0.9 million for the three and nine months ended September 30, 2017, respectively, compared to $0.1 million and $0.4 million during the same periods in 2016. All amortization was included in research and development expenses, except for $0.6 million related to the termination of the Chiesi collaboration, which was presented in other expense in the nine months ended September 30, 2017.

Accrued expenses and other curr

Accrued expenses and other current liabilities	9 Months Ended
	Sep. 30, 2017
Accrued expenses and other current liabilities
Accrued expenses and other current liabilities	7 Accrued expenses and other current liabilities Accrued expenses and other current liabilities include the following items: September 30, December 31, 2017 2016 in thousands Accruals for services provided by vendors-not yet billed $ 3,236 $ 3,824 Personnel related accruals and liabilities 4,481 5,559 Other current liabilities 2,448 383 Total $ 10,165 $ 9,766 According to the Glybera Termination Agreement the Company is responsible for terminating the Phase IV post-approval study. The Company accrued $0.9 million (presented as other expenses) during the three months ended June 30, 2017, related to such costs. As of September 30, 2017, the accrual for these amounts was $0.9 million of which $0.6 million is included in other current liabilities. In addition, as of September 30, 2017 the Company owed $1.2 million to the former shareholders of InoCard (included in other current liabilities on the accompanying balance sheet). Restructuring plan In November 2016, the Company announced a plan to restructure its activities resulting from a company-wide strategic review with the aim of refocusing its pipeline, consolidating its manufacturing capabilities into its Lexington, Massachusetts site, reducing operating costs and enhancing overall execution. At various dates between December 2016 and September 2017, the Company entered into termination agreements with certain employees. Depending on the individual fact pattern the Company accrues the related termination costs over the service period or at the date of communication to the employees. Changes in accrued termination benefits (included in research and development expenses) for the nine months ended September 30, 2017, are detailed in the table below. Accrued termination benefits in thousands Balance at December 31, 2016 $ 1,148 Accrued through profit and loss 1,677 Payments (1,812) Currency translation effects 88 Balance at September 30, 2017 $ 1,101

Long-term debt

Long-term debt	9 Months Ended
	Sep. 30, 2017
Long-term debt
Long-term debt	8 Long-term debt On June 14, 2013, the Company entered into a venture debt loan facility with Hercules, which was amended and restated on June 26, 2014, and again on May 6, 2016 (“2016 Amended Facility”). The 2016 Amended Facility extended the maturity date from September 30, 2018, to May 1, 2020. As at September 30, 2017, and December 31, 2016, $20.0 million was outstanding. The interest rate is adjustable and is the greater of (i) 8.25% or (ii) 8.25% plus the prime rate less 5.25%. Under the 2016 Amended Facility, the interest rate will initially be 8.25% per annum with a back-end fee of 4.85% and a facility fee of 0.75% of the outstanding loan amounts. The interest-only payment period expires on November 2017, but can be extended to May 2018 upon the Company raising a cumulative $30.0 million in up-front corporate payments and/or proceeds from equity financings (“Raisings”), and further extended to November 2018 upon the Company raising a cumulative $50.0 million from such Raisings. The amortized cost of the 2016 Amended Facility, was $20.6 million as of September 30, 2017, compared to $20.2 million as of December 31, 2016, and is recorded net of discount and debt issuance costs. The foreign currency gain on the loan in the three and nine months ended September 30, 2017, was $0.7 million and $2.3 million, respectively, compared to a foreign currency loss of $0.2 million and $0.4 million during the same periods in 2016. The fair value of the loan approximates its carrying amount, as the loan is amortized at a market conforming interest rate and the impact of discounting is insignificant. Interest expense associated with the 2016 Amended Facility during the three and nine months ended September 30, 2017, was $0.6 million and $1.6 million, respectively, compared to $0.5 million and $1.7 million during the same periods in 2016. As a covenant in the 2016 Amended Facility, the Company has periodic reporting requirements and is required to keep a minimum cash balance deposited in bank accounts in the United States, equivalent to the lesser of the outstanding balance of principal due and 50% of worldwide cash reserves. This restriction on the cash reserves only relates to the location of the cash reserves, and such cash reserves can be used at the discretion of the Company. In combination with other covenants, the 2016 Amended Facility restricts the Company’s ability to, among other things, incur future indebtedness and obtain additional debt financing, to make investments in securities or in other companies, to transfer assets, to perform certain corporate changes, to make loans to employees, officers and directors, and to make dividend payments and other distributions. The Company secured the facilities by pledging the shares in its subsidiaries, substantially all its receivables, moveable assets as well as the equipment, fixtures, inventory and cash of uniQure Inc.

Shareholders_ equity

Shareholders’ equity	9 Months Ended
	Sep. 30, 2017
Shareholders’ equity
Shareholders' equity	9 Shareholders’ Equity On September 15, 2017, the Company filed a prospectus supplement to the prospectus dated May 15, 2017, and entered into a sales agreement (the "Sales Agreement") with Leerink Partners LLC (“Leerink”) to establish an “at the market” (“ATM”) equity offering program pursuant to which Leerink can sell, with the Company’s authorization, up to 5 million ordinary shares at prevailing market prices from time to time. The Company will pay Leerink a commission equal to 3% of the gross proceeds of the sales price of all shares sold through it as sales agent under the Sales Agreement. The Company has not yet sold any ordinary shares under the Sales Agreement and has not received any gross proceeds. The Company capitalized $0.4 million of expenses related to this offering (included in other current assets in the accompanying balance sheet).

Share-based compensation

Share-based compensation	9 Months Ended
	Sep. 30, 2017
Share-based compensation
Share-based compensation	10 Share-based compensation Share-based compensation expense recognized by classification included in the consolidated statements of operations and comprehensive loss was as follows: Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Research and development - employees $ 1,131 $ 893 $ 2,612 $ 2,670 Selling, general and administrative - employees 1,316 30 3,366 1,680 Research and development - non-employees — — — 670 Total $ 2,447 $ 923 $ 5,978 $ 5,020 Share-based compensation expense recognized by award type was as follows: Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 Award type in thousands Share options $ 638 $ 718 $ 2,347 $ 4,408 Restricted share units (“RSUs”) 728 88 1,960 323 Performance share units (“PSUs”) 1,081 117 1,671 289 Total $ 2,447 $ 923 $ 5,978 $ 5,020 As of September 30, 2017, the unrecognized compensation costs related to unvested awards under the various share-based compensation plans were: Weighted-average Unrecognized remaining compensation period for costs recognition Award type in thousands in years Share options $ 7,041 2.52 Restricted share units 4,003 1.64 Performance share units 3,747 1.84 Total $ 14,791 2.11 The Company satisfies the exercise of share options and vesting of RSUs and PSUs through newly issued shares. The Company’s share-based compensation plans include the 2014 Amended and Restated Share Option Plan (the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of the NASDAQ Global Select Market with characteristics similar to the 2014 Plan (classified as “Other Plans”). The Company previously had a 2012 Equity Incentive Plan (the “2012 Plan”) and issued options to purchase ordinary shares to the shareholders of 4D in connection with a collaboration and license agreement between the Company and 4D dated as of January 2014 (classified as “Other Plans”). 2014 Plan Share options The following table summarizes option activity under the Company’s 2014 Plan for the nine months ended September 30, 2017: 2014 plan Weighted average Options exercise price Outstanding at December 31, 2016 1,812,766 $ 12.47 Granted 949,350 $ 6.17 Forfeited (348,697) $ 7.95 Expired (164,106) $ 14.46 Exercised (8,125) $ 7.49 Outstanding at September 30, 2017 2,241,188 $ 10.38 Fully vested and exercisable 820,522 $ 12.58 Outstanding and expected to vest 1,420,666 $ 9.10 Total weighted average grant date fair value of options issued during the period (in $ million) $ 3.5 Grants during the period to directors and officers 641,250 $ 6.43 Proceeds from option sales (in $ million) — Options to purchase ordinary shares granted to the Company’s non-executive directors, other than those granted upon appointment will vest one year from the date of grant. The fair value of each option issued was estimated at the date of grant using the Hull & White option pricing model with the following weighted-average assumptions: Three months ended September 30, Nine months ended September 30, Assumptions 2017 2016 2017 2016 Expected volatility 80% 75% 75% - 80% 75% Expected terms (in years) 10 years 10 years 10 years 10 years Risk free interest rate 2.40% - 2.48% 1.52% - 1.89% 2.40% - 2.81% 0.16% - 1.96% Expected dividends 0% 0% 0% 0% Restricted Share Units (RSUs) The following table summarizes the RSUs activity for the nine months ended September 30, 2017: RSU Weighted average grant-date fair Number of shares value Non-vested at December 31, 2016 307,063 $ 9.11 Granted 428,350 $ 6.00 Vested (25,000) $ 18.21 Forfeited (38,550) $ 7.15 Non-vested at September 30, 2017 671,863 $ 6.90 Total weighted average grant date fair value of RSUs issued during the period (in $ million) $ 2.6 Grants during the period to directors and officers 255,000 $ 5.95 RSUs vest over one to three years. RSUs granted in March 2017 to the Company’s Chief Executive Officer will vest equally over two years from the date of grant and RSUs granted to non-executive directors will vest one year from the date of grant. RSUs granted during the period include 255,000 RSUs granted to directors and officers Performance Share Units (PSUs) The following table summarizes the PSUs activity for the nine months ended September 30, 2017: PSU Weighted average grant-date fair Number of shares value Non-vested at December 31, 2016 111,564 $ 5.76 Granted 13,000 $ 4.99 Retired (12,000) $ 5.76 Vested (58,500) $ 5.76 Non-vested at September 30, 2017 54,064 $ 5.57 PSUs awarded but not yet earned 437,060 Total non-vested and discretionary PSUs 491,124 Total weighted average grant date fair value of PSUs awarded during the period (in $ million) $ 2.0 In January 2017, the Company awarded PSUs to its executives and other members of senior management. These PSUs are earned based on the Board’s assessment of the level of achievement of agreed performance targets through December 31, 2017. In September 2016, the Company awarded PSUs to its Chief Executive Officer, subject to the successful implementation of the strategic plan. The earning of these PSUs is based on the Board’s assessment of the Chief Executive Officer’s performance through December 31, 2017. Other Plans Under Rule 5653(c)(4) of the NASDAQ Global Select Market, the Company grants share options and RSUs to officers as a material inducement to enter into employment with the Company. In 2017, the Company granted 175,000 inducement RSUs with a grant date fair value of $1.0 million. The following table summarizes option activity under Other Plans for the nine months ended September 30, 2017: Other plans Weighted average Options exercise price Outstanding at December 31, 2016 187,500 $ 17.93 Granted 300,000 $ 6.90 Expired (62,500) $ 27.82 Outstanding at September 30, 2017 425,000 $ 8.69 Fully vested and exercisable 39,062 $ 12.98 Outstanding and expected to vest 385,938 $ 8.25 Total weighted average grant date fair value of options issued during the period (in $ million) $ 1.2 The fair value of the inducement grant options was estimated at the date of grant using the Hull & White option pricing model with the same assumptions as used in determining the fair value of options issued under the 2014 Plan. 2012 Plan The following table summarizes option activity under the Company’s 2012 Plan for the nine months ended September 30, 2017: 2012 plan Weighted average Options exercise price Outstanding at December 31, 2016 483,006 € 5.13 Exercised (286,804) € 3.07 Forfeited (5,000) € 3.07 Expired (9,000) € 3.07 Outstanding, fully vested and exercisable at September 30, 2017 182,202 € 8.52 Options exercised under the 2012 plan during the nine months ended September 30, 2017, resulted in total proceeds to the Company of $1.0 million.

Income taxes

Income taxes	9 Months Ended
	Sep. 30, 2017
Income taxes
Income taxes	11 Income taxes Deferred tax assets and deferred tax liabilities are recognized based on the expected future tax consequences temporary differences between the financial statement carrying amounts and the income tax basis of assets and liabilities, using current statutory rates. A valuation allowance is recorded against deferred tax assets if it is more likely than not that some or all the deferred tax assets will not be realized. Due to the uncertainty surrounding the realization of the favorable tax attributes in future tax returns, the Company has recorded a full valuation allowance against the Company’s otherwise recognizable net deferred tax assets.

Basic and diluted earnings per

Basic and diluted earnings per share	9 Months Ended
	Sep. 30, 2017
Basic and diluted earnings per share
Basic and diluted earnings per share	12 Basic and diluted earnings per share Diluted earnings per share is calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company has incurred a loss, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share. The potentially dilutive ordinary shares are summarized below: September 30, September 30, 2017 2016 ordinary shares BMS warrants 5,286,254 3,442,655 Warrants 37,175 37,175 Stock options under 2012 Plan 182,202 681,057 Stock options under 2014 Plan 2,241,188 2,036,372 Stock options (other) 425,000 325,000 Non-vested and earned RSUs and PSUs 900,927 297,198 Total potential dilutive ordinary shares 9,072,746 6,819,457

Leases

Leases	9 Months Ended
	Sep. 30, 2017
Leases
Leases	13 Leases The Company leases various office space and laboratory space under the following operating lease agreements: Lexington, Massachusetts / United States In July 2013, uniQure entered into a lease for a facility in Lexington, Massachusetts, United States. The term of the lease commenced in November 2013 and was set for 10 years and is non-cancellable. The lease for this facility terminates in 2024, and subject to the provisions of the lease, may be renewed for two subsequent five-year terms. The lease provides for annual minimum increases in rent, based on a consumer price index. Amsterdam / The Netherlands In March 2016, the Company entered into a 16-year lease for a facility in Amsterdam, the Netherlands, and amended this agreement in June 2016. The Company consolidated its three Amsterdam sites into the new site at the end of May 2017. The lease for this facility terminates in 2032, with an option to extend in increments of five year periods. The lease contract provides for annual minimum increases in rent, based on a consumer price index. As of September 30, 2017, aggregate minimum lease payments for the calendar years and lease incentives received were as follows: Lexington Amsterdam Total in thousands 2017 (three months remaining) $ 453 $ — $ 453 2018 1,849 1,963 3,812 2019 1,903 1,963 3,866 2020 1,956 1,963 3,919 2021 and beyond 6,899 21,595 28,494 Total minimum lease payments $ 13,060 $ 27,484 $ 40,544 Deferred rent related to lease incentives $ 5,739 $ 3,814 $ 9,553 Current portion 724 — 724 Rent expense is calculated on a straight-line basis over the term of the leases and considers the lease incentives received. Aggregate rent expense was as follows: Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Rent expense-Lexington $ 276 $ 276 $ 828 $ 828 Rent expense-Amsterdam 555 782 2,080 2,089 Total rent expense $ 831 $ 1,058 $ 2,908 $ 2,917

Other commitments

Other commitments	9 Months Ended
	Sep. 30, 2017
Other commitments
Other commitments	14 Other commitments The Company’s predecessor entity received a technical development loan from the Dutch government in relation to the development of Glybera. The Company is required to repay the grant through a percentage of revenue derived from product sales of Glybera up to December 31, 2019. Any grant balance remaining at this date will be forgiven. The Company decided not to renew its marketing authorization for Glybera in the European Union, which expires in October 2017. The Company does not expect to derive any revenue from Glybera.

Related party transaction

Related party transaction	9 Months Ended
	Sep. 30, 2017
Related party transaction
Related party transaction	15 Related party transaction On August 7, 2017, the Company appointed Dr. Sander van Deventer as its Chief Scientific Officer and General Manager of its Amsterdam site. Dr. van Deventer served on the Company’s Board until September 14, 2017. Dr. van Deventer currently is Managing Director at the Company’s largest shareholder Forbion Capital Partners. Dr. van Deventer has agreed to resign as Managing Partner of Forbion Capital Partners by June 30, 2018, it being understood that he will thereafter continue as a venture partner or similar function with Forbion Capital Partners or its affiliated funds for up to 50% of his time. Dr. van Deventer is entitled to EUR 200,000 gross annual salary (“Base Salary”), including an 8% holiday allowance to be paid annually in May based upon the previous year’s gross annual salary. Dr. van Deventer will also be eligible for a bonus amounting to a maximum of 40% of his annual gross salary, such amount to be determined by the Board. On September 20, 2017, Dr. van Deventer was granted an option to purchase 150,000 shares at a price of $8.49, in accordance with the Company’s Amended and Restated 2014 Share Incentive Plan. On October 26, 2017, the Company and our Chief Executive Officer and Executive Director, Matthew Kapusta, entered into an amendment (the “Amendment”) to Mr. Kapusta’s employment agreement dated December 9, 2014, as previously amended (the “Agreement”). The Amendment changes Mr. Kapusta’s severance entitlement in the event of a termination of his employment that occurs within the period that starts ninety days preceding a Change of Control (as defined in the Agreement) and ends one year following a Change of Control. Mr. Kapusta will be entitled in such circumstances to a lump sum payment equal to two times Mr. Kapusta’s then-current base salary (as defined in the Agreement) to be paid no later than sixty days after the termination date, his bonus (as defined in the Agreement) for the year of termination pro-rated based upon Mr. Kapusta’s termination date, and a lump sum representing and additional two times Mr. Kapusta’s bonus , to be paid no later than sixty days following the termination date. Mr. Kapusta’s employment agreement previously provided for severance payments of one times his then- current base salary, his pro-rated bonus for the year of termination and a lump-sum payment representing one times his bonus. Mr. Kapusta’s other severance entitlements with respect to a termination connected with a Change of Control have not changed.

Subsequent event

Subsequent event	9 Months Ended
	Sep. 30, 2017
Subsequent event
Subsequent event	16 Subsequent event On October 27, 2017, the Company completed its public offering which was announced on October 23, 2017. The Company issued and sold 5,000,000 ordinary shares at $18.25 per ordinary share, resulting in gross proceeds to the Company of approximately $91.3 million. The net proceeds to the Company from this offering were approximately $85.4 million, after deducting underwriting discounts and commissions and other estimated offering expenses payable by the Company. The Company has granted the underwriters an option to purchase up to 750,000 ordinary shares at the public offering price of $18.25 for within thirty days of the date of the underwriting agreement. The Company intends to use the net proceeds from this offering to fund the continued clinical development of AMT-061 in hemophilia B and other programs, including AMT-130 in Huntington’s disease and other preclinical product candidates focused on rare and orphan diseases and to fund general corporate and working capital purposes. The above equity financing entitles the Company to extend the interest interest-only payment period of its 2016 Amended Facility by 12 months from November 2017 to November 2018 as described in footnote 8.

Summary of significant accoun24

Summary of significant accounting policies (Policies)	9 Months Ended
	Sep. 30, 2017
Summary of significant accounting policies
Basis of preparation	2.1 The Company prepared these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). The unaudited consolidated financial statements are presented in U.S. dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date.
Unaudited interim financial information	2.2 The accompanying interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the periods presented. Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the nine months ended September 30, 2017, are not necessarily indicative of the results to be expected for the full year ending December 31, 2017, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 15, 2017.
Use of estimates	2.3 The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.
Accounting policies	2.4 The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2016, and the notes thereto, which are included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the SEC on March 15, 2017. There have been no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2017.
Recent accounting pronouncements	2.5 There have been no new accounting pronouncements or changes to accounting pronouncements during the nine months ended September 30, 2017, compared to the recent accounting pronouncements described in Note 2.3.22 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, which could be expected to materially impact the Company’s unaudited condensed consolidated financial statements except the ones discussed below: In May 2017, the FASB issued ASU 2017-09, Compensation-stock compensation (topic 718)- scope of modification accounting (“ASU 2017-09”), which provides clarity regarding the applicability of modification accounting in relation to share-based payment awards. Under the new guidance, modification accounting is required only if the fair value, the vesting conditions, or the classification of the award (as equity or liability) changes because of the change in terms or conditions. The effective date for the standard is for fiscal years beginning after December 15, 2017, which for the Company is January 1, 2018. Early adoption is permitted. The new standard is to be applied prospectively. The Company does not expect ASU 2017-09 to have a material impact on its consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842). Under the new guidance, lessees will be required to recognize the assets and liabilities that arise from operating leases. A lessee should recognize in the statement of financial position a liability to make lease payments (the lease liability) and a right-of-use asset representing its right to use the underlying asset for the lease term. For leases with a term of 12 months or less, a lessee is permitted to make an accounting policy election by class of underlying asset not to recognize lease assets and lease liabilities. Lessees and lessors are required to recognize and measure leases at the beginning of the earliest period presented using a modified retrospective approach. ASU 2016-02 will be effective for the Company beginning in the first quarter of 2019 and early application is permitted. The Company does expect ASU 2016-02 to have a material impact on its consolidated financial statements, primarily from recognition of a right-of-use asset and lease liability in the balance sheet and a shift of cash outflows from operating activities to financing activities. In July 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers: Deferral of the Effective Date (“ASU 2015-14”), which deferred the effective date for ASU 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”), by one year. ASU 2014-09 will supersede the revenue recognition requirements in ASC 605, Revenue Recognition, and requires entities to recognize revenue in a way that depicts the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. In 2016, the FASB issued ASU 2016-08, 2016-10 and 2016-12, which provided further clarification on ASU 2014-09. ASU 2014-09 is effective for annual reporting periods beginning after December 15, 2017, including interim periods within that reporting period, which for the Company is January 1, 2018. The Company has one active product development collaboration with Bristol Myers Squibb (“BMS”). ASU 2014-09 provides for two possible implementation methods, (i) full retrospective application to all periods from January 1, 2015 onwards for revenue recognized in relation to collaborations; or (ii) application of the standard from January 1, 2018, onwards to the BMS collaboration with an adjustment to retained earnings as of December 31, 2017, to include the cumulative adjustment to revenue recognized in prior periods in relation to the BMS collaboration. The Company currently accounts for the BMS collaboration agreement as a revenue arrangement with multiple elements. The Company’s substantive deliverables under the BMS collaboration agreement include an exclusive license to its technology in the field of cardiovascular disease, research and development services for specific targets chosen by BMS and general development of the Company’s proprietary vector technology, participation in the Joint Steering Committee, and clinical and commercial manufacturing. The Company is continuing to assess the method of adoption as well as its financial statement disclosures

Fair value measurement (Tables)

Fair value measurement (Tables)	9 Months Ended
	Sep. 30, 2017
Fair value measurement
Schedule of assets and liabilities measured at fair value on recurring basis	Quoted prices Significant Significant Total Classification in consolidated in thousands At December 31, 2016 Assets: Cash and cash equivalents $ 132,496 $ — $ — $ 132,496 Total assets 132,496 — — 132,496 Liabilities: Derivative financial instruments - debt — — 11 11 Accrued expenses and other current liabilities Derivative financial instruments - related party — — 51 51 Other non-current liabilities Contingent consideration — — 1,838 1,838 Total liabilities $ — $ — $ 1,900 $ 1,900 At September 30, 2017 Assets: Cash and cash equivalents $ 88,934 $ — $ — $ 88,934 Total assets 88,934 — — 88,934 Liabilities: Derivative financial instruments - debt — — 3 3 Accrued expenses and other current liabilities Derivative financial instruments - related party — — 35 35 Other non-current liabilities Contingent consideration — — 3,610 3,610 Total liabilities $ — $ — $ 3,648 $ 3,648
Schedule of changes in Level 3 items	Derivative Contingent financial consideration instruments Total in thousands Balance at December 31, 2016 $ 1,838 $ 62 $ 1,900 (Gains) / losses recognized in profit or loss 2,704 (29) 2,675 Amounts due (presented in Accrued expenses and other current liabilities) (1,181) — (1,181) Currency translation effects 249 5 254 Balance at September 30, 2017 $ 3,610 $ 38 $ 3,648 Derivative Contingent financial consideration instruments Total in thousands Balance at December 31, 2015 $ 2,926 $ 837 $ 3,763 (Gains) / losses recognized in profit or loss (1,569) (701) (2,270) Currency translation effects 87 20 107 Balance at September 30, 2016 $ 1,444 $ 156 $ 1,600
Schedule of changes in fair value of unobservable inputs	September 30, 2017 in thousands Change in fair value Moving out of all milestones by 6 months $ (231) Increasing the POS for the first milestone by 20% 1,103 Decreasing the POS for the first milestone by 20% (1,103) Reducing the discount rate from 14.5% to 4.5% 1,004 Increasing the discount rate from 14.5% to 24.5% (590) December 31, 2016 in thousands Change in fair value Moving out of all milestones by 6 months $ (209) Increasing the POS for the first milestone by 20% 367 Decreasing the POS for the first milestone by 20% (367) Reducing the discount rate from 30% to 20% 638 Increasing the discount rate from 30% to 40% (309)

Collaboration arrangements an26

Collaboration arrangements and concentration of credit risk (Tables)	9 Months Ended
	Sep. 30, 2017
Collaboration arrangements and concentration of credit risk
Schedule of collaboration and license revenue	Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Bristol Myers Squibb $ 2,260 $ 5,125 $ 5,877 $ 10,396 Chiesi Farmaceutici S.p.A — 2,096 4,646 5,571 Total $ 2,260 $ 7,221 $ 10,523 $ 15,967
Schedule of amounts owed in relation to collaboration	September 30, December 31, 2017 2016 in thousands Bristol Myers Squibb $ 1,945 $ 5,500 Chiesi Farmaceutici S.p.A — 3,680 Total $ 1,945 $ 9,180

Property, plant and equipment (

Property, plant and equipment (Tables)	9 Months Ended
	Sep. 30, 2017
Property, plant and equipment
Schedule of property, plant and equipment	September 30, December 31, 2017 2016 in thousands Leasehold improvements $ 33,054 $ 30,582 Laboratory equipment 15,952 14,166 Office equipment 2,926 2,710 Construction-in-progress 365 313 Total property, plant, and equipment 52,297 47,771 Less accumulated depreciation (17,644) (12,069) Property, plant and equipment, net $ 34,653 $ 35,702

Intangible assets (Tables)

Intangible assets (Tables)	9 Months Ended
	Sep. 30, 2017
Intangible assets
Schedule of finite-lived intangible assets	September 30, December 31, 2017 2016 in thousands Licenses $ 9,417 $ 7,799 Acquired research & development 5,512 4,908 Total intangible assets 14,929 12,707 Less accumulated amortization and impairment (5,902) (4,383) Intangible assets, net $ 9,027 $ 8,324

Accrued expenses and other cu29

Accrued expenses and other current liabilities (Tables)	9 Months Ended
	Sep. 30, 2017
Accrued expenses and other current liabilities
Schedule of accrued expenses and other current liabilities	September 30, December 31, 2017 2016 in thousands Accruals for services provided by vendors-not yet billed $ 3,236 $ 3,824 Personnel related accruals and liabilities 4,481 5,559 Other current liabilities 2,448 383 Total $ 10,165 $ 9,766
Schedule of change in accrual of termination benefits	Accrued termination benefits in thousands Balance at December 31, 2016 $ 1,148 Accrued through profit and loss 1,677 Payments (1,812) Currency translation effects 88 Balance at September 30, 2017 $ 1,101

Share-based compensation (Table

Share-based compensation (Tables)	9 Months Ended
	Sep. 30, 2017
Share-based compensation
Schedule of share-based compensation expense by classification included in consolidated statements of operations and comprehensive loss	Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Research and development - employees $ 1,131 $ 893 $ 2,612 $ 2,670 Selling, general and administrative - employees 1,316 30 3,366 1,680 Research and development - non-employees — — — 670 Total $ 2,447 $ 923 $ 5,978 $ 5,020
Schedule of share-based compensation expense	Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 Award type in thousands Share options $ 638 $ 718 $ 2,347 $ 4,408 Restricted share units (“RSUs”) 728 88 1,960 323 Performance share units (“PSUs”) 1,081 117 1,671 289 Total $ 2,447 $ 923 $ 5,978 $ 5,020
Schedule of unrecognized compensation cost related to unvested awards	Weighted-average Unrecognized remaining compensation period for costs recognition Award type in thousands in years Share options $ 7,041 2.52 Restricted share units 4,003 1.64 Performance share units 3,747 1.84 Total $ 14,791 2.11
Schedule of weighted-average assumptions for fair value of option issued	Three months ended September 30, Nine months ended September 30, Assumptions 2017 2016 2017 2016 Expected volatility 80% 75% 75% - 80% 75% Expected terms (in years) 10 years 10 years 10 years 10 years Risk free interest rate 2.40% - 2.48% 1.52% - 1.89% 2.40% - 2.81% 0.16% - 1.96% Expected dividends 0% 0% 0% 0%
Summary of RSUs activity	RSU Weighted average grant-date fair Number of shares value Non-vested at December 31, 2016 307,063 $ 9.11 Granted 428,350 $ 6.00 Vested (25,000) $ 18.21 Forfeited (38,550) $ 7.15 Non-vested at September 30, 2017 671,863 $ 6.90 Total weighted average grant date fair value of RSUs issued during the period (in $ million) $ 2.6 Grants during the period to directors and officers 255,000 $ 5.95
Summary of PSUs activity	PSU Weighted average grant-date fair Number of shares value Non-vested at December 31, 2016 111,564 $ 5.76 Granted 13,000 $ 4.99 Retired (12,000) $ 5.76 Vested (58,500) $ 5.76 Non-vested at September 30, 2017 54,064 $ 5.57 PSUs awarded but not yet earned 437,060 Total non-vested and discretionary PSUs 491,124 Total weighted average grant date fair value of PSUs awarded during the period (in $ million) $ 2.0
2014 Plan
Share-based compensation
Summary of option activity	2014 plan Weighted average Options exercise price Outstanding at December 31, 2016 1,812,766 $ 12.47 Granted 949,350 $ 6.17 Forfeited (348,697) $ 7.95 Expired (164,106) $ 14.46 Exercised (8,125) $ 7.49 Outstanding at September 30, 2017 2,241,188 $ 10.38 Fully vested and exercisable 820,522 $ 12.58 Outstanding and expected to vest 1,420,666 $ 9.10 Total weighted average grant date fair value of options issued during the period (in $ million) $ 3.5 Grants during the period to directors and officers 641,250 $ 6.43 Proceeds from option sales (in $ million) —
2012 Plan
Share-based compensation
Summary of option activity	2012 plan Weighted average Options exercise price Outstanding at December 31, 2016 483,006 € 5.13 Exercised (286,804) € 3.07 Forfeited (5,000) € 3.07 Expired (9,000) € 3.07 Outstanding, fully vested and exercisable at September 30, 2017 182,202 € 8.52
Other Plans
Share-based compensation
Summary of option activity	Other plans Weighted average Options exercise price Outstanding at December 31, 2016 187,500 $ 17.93 Granted 300,000 $ 6.90 Expired (62,500) $ 27.82 Outstanding at September 30, 2017 425,000 $ 8.69 Fully vested and exercisable 39,062 $ 12.98 Outstanding and expected to vest 385,938 $ 8.25 Total weighted average grant date fair value of options issued during the period (in $ million) $ 1.2

Basic and diluted earnings pe31

Basic and diluted earnings per share (Tables)	9 Months Ended
	Sep. 30, 2017
Basic and diluted earnings per share
Schedule of potential dilutive common shares	September 30, September 30, 2017 2016 ordinary shares BMS warrants 5,286,254 3,442,655 Warrants 37,175 37,175 Stock options under 2012 Plan 182,202 681,057 Stock options under 2014 Plan 2,241,188 2,036,372 Stock options (other) 425,000 325,000 Non-vested and earned RSUs and PSUs 900,927 297,198 Total potential dilutive ordinary shares 9,072,746 6,819,457

Leases (Tables)

Leases (Tables)	9 Months Ended
	Sep. 30, 2017
Leases
Schedule of minimum lease payments	Lexington Amsterdam Total in thousands 2017 (three months remaining) $ 453 $ — $ 453 2018 1,849 1,963 3,812 2019 1,903 1,963 3,866 2020 1,956 1,963 3,919 2021 and beyond 6,899 21,595 28,494 Total minimum lease payments $ 13,060 $ 27,484 $ 40,544 Deferred rent related to lease incentives $ 5,739 $ 3,814 $ 9,553 Current portion 724 — 724
Summary of aggregate rent expense	Three months ended September 30, Nine months ended September 30, 2017 2016 2017 2016 in thousands Rent expense-Lexington $ 276 $ 276 $ 828 $ 828 Rent expense-Amsterdam 555 782 2,080 2,089 Total rent expense $ 831 $ 1,058 $ 2,908 $ 2,917

Fair value measurement - Assets

Fair value measurement - Assets and Liabilities (Details) - Recurring - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	$ 88,934	$ 132,496
Total assets	88,934	132,496
Liabilities, Fair Value Disclosure [Abstract]
Contingent consideration	3,610	1,838
Total liabilities	3,648	1,900
Related party
Liabilities, Fair Value Disclosure [Abstract]
Derivative financial instruments	35	51
Debt
Liabilities, Fair Value Disclosure [Abstract]
Derivative financial instruments	3	11
Fair value hierarchy Level 1
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	88,934	132,496
Total assets	88,934	132,496
Fair value hierarchy Level 3
Liabilities, Fair Value Disclosure [Abstract]
Contingent consideration	3,610	1,838
Total liabilities	3,648	1,900
Fair value hierarchy Level 3 | Related party
Liabilities, Fair Value Disclosure [Abstract]
Derivative financial instruments	35	51
Fair value hierarchy Level 3 | Debt
Liabilities, Fair Value Disclosure [Abstract]
Derivative financial instruments	$ 3	$ 11

Fair value measurement - Change

Fair value measurement - Changes in Level 3 Liabilities and Contingent Consideration (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended	9 Months Ended		12 Months Ended
	Aug. 31, 2017	Jun. 30, 2017	Sep. 30, 2017	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016	Dec. 31, 2014
Changes in Level 3 liabilities
Beginning Balance				$ 1,900	$ 3,763	$ 3,763
(Gains) / losses recognized in profit or loss				2,675	(2,270)
Amounts due (presented in Accrued expenses and other current liabilities)				(1,181)
Currency translation effects				254	107
Ending Balance			$ 3,648	3,648	1,600	1,900
Contingent consideration
Risk-free adjusted discount rate (as a percent)		30.00%
Company's weighted average rate of capital		14.50%
Percentage of future milestones that can be settled with ordinary shares							100.00%
Percentage of future milestones that can be settled with ordinary shares, reduced rate	50.00%
Increase in fair value of the contingent consideration		$ 300	2,300	2,300
Contingent consideration
Changes in Level 3 liabilities
Beginning Balance				1,838	2,926	2,926
(Gains) / losses recognized in profit or loss				2,704	(1,569)
Amounts due (presented in Accrued expenses and other current liabilities)				(1,181)
Currency translation effects				249	87
Ending Balance			3,610	$ 3,610	1,444	$ 1,838
Contingent consideration | InoCard
Contingent consideration
Moving out of all milestones, in months				6 months		6 months
Increasing the POS for the first milestone				20.00%		20.00%
Decreasing the POS for the first milestone				20.00%		20.00%
Reducing the discount rate				4.50%		20.00%
Increasing the discount rate				24.50%		40.00%
Level 3 Derivative financial instruments
Changes in Level 3 liabilities
Beginning Balance				$ 62	837	$ 837
(Gains) / losses recognized in profit or loss				(29)	(701)
Currency translation effects				5	20
Ending Balance			$ 38	38	$ 156	62
Delay in milestones by 6 months | Contingent consideration | InoCard
Contingent consideration
Change in fair value				(231)		(209)
Increasing the POS for the first milestone by 20% | Contingent consideration | InoCard
Contingent consideration
Change in fair value				1,103		367
Decreasing the POS for the first milestone by 20% | Contingent consideration | InoCard
Contingent consideration
Change in fair value				(1,103)		(367)
Reducing the discount rate from 30% to 20% | Contingent consideration | InoCard
Contingent consideration
Change in fair value				1,004		638
Increasing the discount rate from 30% to 40% | Contingent consideration | InoCard
Contingent consideration
Change in fair value				$ (590)		$ (309)

Fair value measurement - BMS wa

Fair value measurement - BMS warrants (Details) - USD ($) $ in Millions	Sep. 30, 2017	Dec. 31, 2016
Recurring | Fair value hierarchy Level 3 | BMS Warrants
Fair value measurements
Fair value of derivative asset	$ 0	$ 0.1

Fair value measurement - BMS co

Fair value measurement - BMS collaboration (Details)	9 Months Ended
	Sep. 30, 2017$ / shares
BMS Warrants
Collaboration arrangements
Number of trading days used to calculate Volume Weighted Average Price ("VWAP")	20 days
Number of days prior to purchase or exercise used to calculate Volume Weighted Average Price ("VWAP")	5 days
Exercise price in respect of each warrant	$ 33.84
Compounded annual growth rate used to determine fair value of exercise price	10.00%
uniQure N.V. | First Six New Targets Or Designation Of Sixth Target | BMS
Collaboration arrangements
Ownership percentage required per agreement	14.90%
uniQure N.V. | First Nine New Targets Or Designation Of Ninth Target | BMS
Collaboration arrangements
Ownership percentage required per agreement	19.90%

Collaboration arrangements an37

Collaboration arrangements and concentration of credit risk - Revenues from and amounts owed with collaboration partners (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Collaboration arrangements
Revenues	$ 2,260	$ 7,221	$ 10,523	$ 15,967
Collaboration arrangement
Collaboration arrangements
Revenues	2,260	7,221	10,523	15,967
Amounts owed from partners in relation to the collaboration	1,945		1,945		$ 9,180
Collaboration arrangement | BMS
Collaboration arrangements
Revenues	2,260	5,125	5,877	10,396
Amounts owed from partners in relation to the collaboration	$ 1,945		1,945		5,500
Collaboration arrangement | Chiesi Pharmaceutical
Collaboration arrangements
Revenues		$ 2,096	$ 4,646	$ 5,571
Amounts owed from partners in relation to the collaboration					$ 3,680

Collaboration arrangements an38

Collaboration arrangements and concentration of credit risk - BMS collaboration (Details) $ in Thousands	Jul. 31, 2015USD ($)	Sep. 30, 2017USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2017USD ($)item	Sep. 30, 2016USD ($)	Dec. 31, 2016USD ($)	May 21, 2015USD ($)
Collaboration arrangements
License revenues from related party		$ 1,124	$ 993	$ 3,060	$ 2,977
Collaboration revenues from related party		$ 1,136	$ 4,132	$ 2,817	$ 7,419
Collaboration arrangement | BMS
Collaboration arrangements
Unit of accounting | item				3
License revenue | BMS
Collaboration arrangements
Number of potential targets included in collaborative agreement | item				10
Deferred Revenue							$ 60,100
Expected performance term (in years)				19 years
Royalty term after the first commercial sale						10 years
License revenue | BMS | First Target Selection
Collaboration arrangements
Milestone payments to be received upon achievement						$ 254,000
License revenue | BMS | Second, Third, and Fourth Targets Selection
Collaboration arrangements
Target designation payment received	$ 15,000
License revenue | BMS | Fifth through Tenth Targets Selection
Collaboration arrangements
Maximum target designation payments to which entitled per agreement						16,500
License revenue | BMS | Other Selected Targets
Collaboration arrangements
Milestone payments to be received upon achievement						$ 217,000

Collaboration arrangements an39

Collaboration arrangements and concentration of credit risk - Chiesi collaboration (Details) $ in Thousands, € in Millions	Sep. 30, 2013EUR (€)	Sep. 30, 2013USD ($)	Jul. 31, 2017USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2017USD ($)	Sep. 30, 2016USD ($)	Dec. 31, 2016
Collaboration arrangements
License revenues				$ 246	$ 8	$ 736
Percentage of costs to be paid by counterparty							50.00%
Collaboration Revenue				$ 1,850	4,638	$ 4,835
License revenue | Chiesi Pharmaceutical
Collaboration arrangements
Up-front payment received	€ 17	$ 22,100
Fully released outstanding deferred revenue recorded in other income			$ 13,800
Glybera | License revenue | Chiesi Pharmaceutical
Collaboration arrangements
Reduction to license revenue that was previously amortized and repaid by the Company in accordance with the Termination Agreement					$ 500

Property, plant and equipment,

Property, plant and equipment, net (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Property, plant and equipment, net
Total property, plant, and equipment	$ 52,297		$ 52,297		$ 47,771
Less accumulated depreciation	(17,644)		(17,644)		(12,069)
Property, plant and equipment, net	34,653		34,653		35,702
Depreciation	1,700	$ 1,400	5,100	$ 4,100
Leasehold improvements
Property, plant and equipment, net
Total property, plant, and equipment	33,054		33,054		30,582
Laboratory equipment
Property, plant and equipment, net
Total property, plant, and equipment	15,952		15,952		14,166
Office equipment
Property, plant and equipment, net
Total property, plant, and equipment	2,926		2,926		2,710
Construction-in-progress
Property, plant and equipment, net
Total property, plant, and equipment	$ 365		$ 365		$ 313

Intangible assets (Details)

Intangible assets (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Intangible assets
Total intangible assets	$ 14,929		$ 14,929		$ 12,707
Less accumulated amortization	(5,902)		(5,902)		(4,383)
Intangible assets, net	9,027		9,027		8,324
Amortization expense	100	$ 100	900	$ 400
Licenses
Intangible assets
Total intangible assets	9,417		9,417		7,799
Acquired research & development
Intangible assets
Total intangible assets	$ 5,512		5,512		$ 4,908
Chiesi Pharmaceutical | Other Expense
Intangible assets
Amortization expense			$ 600

Accrued expenses and other cu42

Accrued expenses and other current liabilities (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Jun. 30, 2017	Dec. 31, 2016
Accrued expenses and other current liabilities
Accruals for services provided by vendors-not yet billed	$ 3,236		$ 3,824
Personnel related accruals and liabilities	4,481		5,559
Other current liabilities	2,448		383
Total	10,165		$ 9,766
Amount owed to former shareholders of Inocard	1,200
Restructuring Reserve
Beginning Balance	1,148
Accrued through profit and loss	1,677
Payments	(1,812)
Currency translation effects	88
Ending Balance	1,101
Glybera | Other Current Liabilities
Accrued expenses and other current liabilities
Accrued liability current in relation to Phase IV termination	$ 600
Glybera | Other Expense
Accrued expenses and other current liabilities
Accrued liability in relation to Phase IV termination		$ 900

Long-term debt (Details)

Long-term debt (Details) - USD ($) $ in Millions	May 06, 2016	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Long-term Debt
Foreign currency gain				$ 2.3
Foreign currency loss			$ 0.2		$ 0.4
Interest expense on debt		$ 0.6	$ 0.5	1.6	$ 1.7
Venture debt loan facility with Hercules
Long-term Debt
Outstanding debt		20		20		$ 20
Interest rate (as a percent)	8.25%
Discount rate (as a percent)	5.25%
Back-end fee (as a percent)	4.85%
Facility fee (as a percent)	0.75%
Amount of first cumulative raisings	$ 30
Amount of second cumulative raisings	$ 50
Amortized cost net of discount and debt issuance costs		20.6		$ 20.6		$ 20.2
Foreign currency gain		$ 0.7
Percentage of worldwide cash reserves	50.00%

Shareholders_ equity (Details)

Shareholders’ equity (Details) - USD ($) $ in Millions	Sep. 15, 2017	Sep. 30, 2017	Dec. 31, 2016
Shareholders’ equity
Shares authorized under the sales agreement with Leerink	5,000,000	60,000,000	60,000,000
Commission fee based on gross proceeds of shares sold	3.00%
Expenses capitalized related to offering	$ 0.4

Share-based compensation - Comp

Share-based compensation - Compensation cost (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Share-based compensation
Share-based compensation expense	$ 2,447	$ 923	$ 5,978	$ 5,020
Unrecognized compensation costs	14,791		$ 14,791
Weighted-average remaining period for recognition (in years)			2 years 1 month 10 days
Research and development expenses | Employees
Share-based compensation
Share-based compensation expense	1,131	893	$ 2,612	2,670
Research and development expenses | Non-employees
Share-based compensation
Share-based compensation expense				670
Selling, general and administrative expense | Employees
Share-based compensation
Share-based compensation expense	1,316	30	3,366	1,680
Share options
Share-based compensation
Share-based compensation expense	638	718	2,347	4,408
Unrecognized compensation costs	7,041		$ 7,041
Weighted-average remaining period for recognition (in years)			2 years 6 months 7 days
Restricted share units ("RSUs")
Share-based compensation
Share-based compensation expense	728	88	$ 1,960	323
Unrecognized compensation costs	4,003		$ 4,003
Weighted-average remaining period for recognition (in years)			1 year 7 months 21 days
Performance share units ("PSUs")
Share-based compensation
Share-based compensation expense	1,081	$ 117	$ 1,671	$ 289
Unrecognized compensation costs	$ 3,747		$ 3,747
Weighted-average remaining period for recognition (in years)			1 year 10 months 2 days

Share-based compensation - 2014

Share-based compensation - 2014 Plan Share Options (Details) $ / shares in Units, $ in Millions	Sep. 20, 2017$ / sharesshares	Sep. 30, 2017€ / shares$ / sharesshares	Sep. 30, 2017$ / sharesshares	Sep. 30, 2016	Sep. 30, 2017€ / shares$ / sharesshares	Sep. 30, 2017USD ($)$ / sharesshares	Sep. 30, 2016
Weighted average exercise price
Outstanding at beginning of year (in euros/dollars per share) | € / shares					€ 5.13
Forfeited (in euros/dollars per share) | € / shares					3.07
Expired (in euros/dollars per share) | € / shares					3.07
Exercised (in euros/dollars per share) | € / shares					3.07
Outstanding at end of year (in euros/dollars per share) | € / shares		€ 8.52			€ 8.52
Weighted-average assumptions used to estimate fair value of share options granted during year
Expected volatility (as a percent)		80.00%	80.00%	75.00%			75.00%
Expected terms (in years)		10 years	10 years	10 years		10 years	10 years
Risk free interest rate, minimum (as a percent)		2.40%	2.40%	1.52%		2.40%	0.16%
Risk free interest rate, maximum (as a percent)		2.48%	2.48%	1.89%		2.81%	1.96%
Expected dividend (as a percent)		0.00%	0.00%	0.00%		0.00%	0.00%
Minimum
Weighted-average assumptions used to estimate fair value of share options granted during year
Expected volatility (as a percent)						75.00%
Maximum
Weighted-average assumptions used to estimate fair value of share options granted during year
Expected volatility (as a percent)						80.00%
2014 Plan | Share options
Options
Outstanding at beginning of year (in shares) | shares						1,812,766
Granted (in shares) | shares	150,000					949,350
Forfeited (in shares) | shares						(348,697)
Expired (in shares) | shares						(164,106)
Exercised (in shares) | shares						(8,125)
Outstanding at end of year (in shares) | shares		2,241,188	2,241,188			2,241,188
Fully vested and exercisable at end of year (in shares) | shares		820,522	820,522		820,522	820,522
Outstanding and expected to vest at end of year (in shares) | shares		1,420,666	1,420,666		1,420,666	1,420,666
Weighted average exercise price
Outstanding at beginning of year (in euros/dollars per share) | $ / shares						$ 12.47
Granted (in dollars per share) | $ / shares	$ 8.49					6.17
Forfeited (in euros/dollars per share) | $ / shares						7.95
Expired (in euros/dollars per share) | $ / shares						14.46
Exercised (in euros/dollars per share) | $ / shares						7.49
Outstanding at end of year (in euros/dollars per share) | $ / shares			$ 10.38			10.38
Fully vested and exercisable at end of year (in dollars per share) | $ / shares		€ 12.58	$ 12.58		€ 12.58	12.58
Outstanding and expected to vest at end of year (in dollars per share) | $ / shares						$ 9.10
Total weighted average grant date fair value of options issued during the period (in $ million) | $						$ 3.5
2014 Plan | Non-executive directors | Share options
Weighted average exercise price
Vesting period						1 year
2014 Plan | Directors and Officers | Share options
Options
Granted (in shares) | shares						641,250
Weighted average exercise price
Granted (in dollars per share) | $ / shares						$ 6.43

Share-based compensation - 2047

Share-based compensation - 2014 Plan RSUs (Details) - Restricted share units ("RSUs") - 2014 Plan $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2017USD ($)$ / sharesshares
Number of shares
Non-vested at beginning of year (in shares) | shares	307,063
Granted (in shares) | shares	428,350
Vested (in shares) | shares	(25,000)
Forfeited (in shares) | shares	(38,550)
Non-vested at end of year (in shares) | shares	671,863
Weighted average grant-date fair value
Non-vested at beginning of year (in dollars per share) | $ / shares	$ 9.11
Granted (in dollars per share) | $ / shares	6
Vested (in dollars per share) | $ / shares	18.21
Forfeited (in dollars per share) | $ / shares	7.15
Non-vested at end of year (in dollars per share) | $ / shares	$ 6.90
Other disclosure
Total fair value of shares that vested (in dollars) | $	$ 2.6
Chief Executive Officer
Other disclosure
Vesting period	2 years
Non-executive directors
Other disclosure
Vesting period	1 year
Directors and Officers
Number of shares
Granted (in shares) | shares	255,000
Weighted average grant-date fair value
Granted (in dollars per share) | $ / shares	$ 5.95
Minimum
Other disclosure
Vesting period	1 year
Maximum
Other disclosure
Vesting period	3 years

Share-based compensation - 2048

Share-based compensation - 2014 Plan PSUs (Details) - 2014 Plan $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2017USD ($)$ / sharesshares
Performance share units ("PSUs")
Number of shares
Non-vested at beginning of year (in shares)	111,564
Granted (in shares)	13,000
Retired (in shares)	(12,000)
Vested (in shares)	(58,500)
Non-vested at end of year (in shares)	54,064
Weighted average grant-date fair value
Non-vested at beginning of year (in dollars per share) | $ / shares	$ 5.76
Granted (in dollars per share) | $ / shares	4.99
Retired (in dollars per share) | $ / shares	5.76
Vested (in dollars per share) | $ / shares	5.76
Non-vested at end of year (in dollars per share) | $ / shares	$ 5.57
Other disclosure
Total fair value of shares that vested (in dollars) | $	$ 2
PSUs awarded but not yet earned
Number of shares
Non-vested at end of year (in shares)	437,060
Total non-vested and discretionary PSUs
Number of shares
Non-vested at end of year (in shares)	491,124

Share-based compensation - Othe

Share-based compensation - Other Plans (Details) $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2017€ / shares$ / sharesshares	Sep. 30, 2017USD ($)$ / sharesshares
Weighted average exercise price
Outstanding at beginning of year (in euros/dollars per share) | € / shares	€ 5.13
Expired (in euros/dollars per share) | € / shares	3.07
Outstanding at end of year (in euros/dollars per share) | € / shares	€ 8.52
Other plans
Other disclosures
Total weighted average grant date fair value of options issued during the period (in $ million) | $		$ 1.2
Other plans | Share options
Options
Outstanding at beginning of year (in shares)		187,500
Granted (in shares)		300,000
Expired (in shares)		(62,500)
Outstanding at end of year (in shares)		425,000
Fully vested and exercisable at end of year (in shares)	39,062	39,062
Outstanding and expected to vest at end of year (in shares)	385,938	385,938
Weighted average exercise price
Outstanding at beginning of year (in euros/dollars per share) | $ / shares		$ 17.93
Granted (in dollars per share) | $ / shares		6.90
Expired (in euros/dollars per share) | $ / shares		27.82
Outstanding at end of year (in euros/dollars per share) | $ / shares		8.69
Fully vested and exercisable at end of year (in dollars per share) | $ / shares	€ 12.98	12.98
Outstanding and expected to vest at end of year (in dollars per share) | $ / shares		$ 8.25
Other plans | Restricted share units ("RSUs") | Officers
Other disclosures
Granted (in shares)		175,000
Total weighted average grant date fair value of RSUs granted during the period (in $ million) | $		$ 1

Share-based compensation - 2012

Share-based compensation - 2012 Plan (Details) - 9 months ended Sep. 30, 2017 $ in Millions	€ / shares	USD ($)shares
Weighted average exercise price
Outstanding at beginning of year (in euros/dollars per share) | € / shares	€ 5.13
Exercised (in euros/dollars per share) | € / shares	3.07
Forfeited (in euros/dollars per share) | € / shares	3.07
Expired (in euros/dollars per share) | € / shares	3.07
Outstanding at end of year (in euros/dollars per share) | € / shares	€ 8.52
2012 Plan
Options
Outstanding at beginning of year (in shares) | shares		483,006
Exercised (in shares) | shares		(286,804)
Forfeited (in shares) | shares		(5,000)
Expired (in shares) | shares		(9,000)
Outstanding at end of year (in shares) | shares		182,202
2012 Plan | Share options
Share-based compensation
Proceeds from options exercised | $		$ 1

Basic and diluted earnings pe51

Basic and diluted earnings per share (Details) - shares	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Basic and diluted earnings per share
Total potential dilutive common shares	9,072,746	6,819,457
Warrants
Basic and diluted earnings per share
Total potential dilutive common shares	37,175	37,175
Warrants | BMS
Basic and diluted earnings per share
Total potential dilutive common shares	5,286,254	3,442,655
Stock options | 2012 Plan
Basic and diluted earnings per share
Total potential dilutive common shares	182,202	681,057
Stock options | 2014 Plan
Basic and diluted earnings per share
Total potential dilutive common shares	2,241,188	2,036,372
Stock options | Other Plans
Basic and diluted earnings per share
Total potential dilutive common shares	425,000	325,000
Non-vested and earned RSUs and PSUs
Basic and diluted earnings per share
Total potential dilutive common shares	900,927	297,198

Leases - Minimum Lease Payments

Leases - Minimum Lease Payments and Rent Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Minimum lease payments
2017 (three months remaining)	$ 453		$ 453
2,018	3,812		3,812
2,019	3,866		3,866
2,020	3,919		3,919
2021 and beyond	28,494		28,494
Total minimum lease payments	40,544		40,544
Deferred rent related to lease incentives	9,553		9,553
Current portion	724		724
Aggregate rent expense
Rent expense	831	$ 1,058	2,908	$ 2,917
Lexington
Minimum lease payments
2017 (three months remaining)	453		453
2,018	1,849		1,849
2,019	1,903		1,903
2,020	1,956		1,956
2021 and beyond	6,899		6,899
Total minimum lease payments	13,060		13,060
Deferred rent related to lease incentives	5,739		5,739
Current portion	724		724
Aggregate rent expense
Rent expense	276	276	828	828
Amsterdam
Minimum lease payments
2,018	1,963		1,963
2,019	1,963		1,963
2,020	1,963		1,963
2021 and beyond	21,595		21,595
Total minimum lease payments	27,484		27,484
Deferred rent related to lease incentives	3,814		3,814
Aggregate rent expense
Rent expense	$ 555	$ 782	$ 2,080	$ 2,089

Leases - Narrative (Details)

Leases - Narrative (Details)	1 Months Ended
	May 31, 2017facility	Jun. 30, 2016	Mar. 31, 2016	Nov. 30, 2013item
Lexington
Leases
Lease term (in years)				10 years
Number of subsequent renewals | item				2
Renewal term (in years)				5 years
Amsterdam
Leases
Lease term (in years)			16 years
Renewal term (in years)		5 years
Number of facility sites consolidated into new site | facility	3

Related party transaction (Deta

Related party transaction (Details)	Sep. 20, 2017$ / sharesshares	Aug. 07, 2017EUR (€)	Sep. 30, 2017$ / sharesshares
Related Party Transaction [Line Items]
Base salary | €		€ 200,000
Holiday allowance, as a percent		8.00%
Maximum bonus, as a percent		40.00%
Share options | 2014 Plan
Related Party Transaction [Line Items]
Granted (in shares) | shares	150,000		949,350
Granted (in dollars per share) | $ / shares	$ 8.49		$ 6.17

Subsequent event (Details)

Subsequent event (Details) - USD ($) $ / shares in Units, $ in Thousands	Oct. 27, 2017	Sep. 30, 2017	Sep. 30, 2016
Subsequent event
Gross proceeds received from public offering		$ 1,036	$ 2,218
Subsequent events
Subsequent event
Shares issued in connection with offering	5,000,000
Offering price per share of shares issued	$ 18.25
Gross proceeds received from public offering	$ 91,300
Net proceeds received from public offering	$ 85,400
Options granted to underwriters	750,000