uniQure N.V. 10-K

Item 9A. Controls and Procedures ​ Evaluation of Disclosure Controls and Procedures ​ Our management, with the participation of our chief executive officer (“CEO”), who also serves as our chief financial officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of December 31, 2020. Based on such evaluation, our CEO has concluded that as of December 31, 2020, our disclosure controls and procedures were effective. ​ Management’s Annual Report on Internal Control Over Financial Reporting ​ Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act. This rule defines internal control over financial reporting as a process designed by, or under the supervision of, a company’s chief executive officer and chief financial officer and effected by our board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of our assets that could have a material effect on the financial statements. ​ We assessed the effectiveness of our internal control over financial reporting as of December 31, 2020. This assessment was performed under the direction and supervision of our CEO and based on criteria established in Internal Control—Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). Our management’s assessment of the effectiveness of our internal control over financial reporting included testing and evaluating the design and operating effectiveness of our internal controls. In our management’s opinion, we have maintained effective internal control over financial reporting as of December 31, 2020, based on criteria established in the COSO 2013 framework. ​ Our independent registered public accounting firm, which has audited the consolidated financial statements included in this Annual Report on Form 10-K, has also issued an audit report on the effectiveness of our internal control over financial reporting as of December 31, 2020. Their report is filed within this Annual Report on Form 10-K. ​ Inherent Limitations of Internal Controls Our management, including our CEO, does not expect that our disclosure controls and procedures or our internal controls will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the control. The design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or the degree of compliance with the policies or procedures may deteriorate. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements due to error or fraud. ​ 108 ​ Table of Contents Changes in internal control over financial reporting During the fourth quarter of 2020, there were no changes in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. We have not experienced any material impact to our internal controls over financial reporting even though a large group of our employees are working remotely due to the COVID-19 pandemic. We are continually monitoring and assessing the impact COVID-19 has on the operating effectiveness of our internal controls. ​ Item 9B. Other Information ​ None. ​ ​ 109 ​ Table of Contents Part III ​ Item 10. Directors, Executive Officers and Corporate Governance ​ The information required by this Item regarding our directors, executive directors and corporate governance is incorporated into this section by reference to our Proxy Statement for our 2021 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 11. Executive Compensation ​ The information required by this Item regarding executive compensation is incorporated into this section by reference to our Proxy Statement for our 2021 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters ​ The information required by this Item regarding security ownership of certain beneficial owners, management and related stockholder matters, our equity compensation plans and securities under our equity compensation plans, is incorporated into this section by reference to our Proxy Statement for our 2021 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 13. Certain Relationships and Related Transactions, and Director Independence ​ The information required by this Item regarding certain relationships and related transactions and director independence is incorporated into this section by reference to our Proxy Statement for our 2021 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 14. Principal Accounting Fees and Services ​ The information required by this Item regarding our principal accountant fees and services is incorporated into this section by reference to our Proxy Statement for our 2021 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 110 ​ Table of Contents Part IV ​ Item 15. Exhibits, Financial Statements Schedules ​ Exhibits, Financial Statements Schedules ​ (a) Financial Statements . The following consolidated financial statements of uniQure N.V. are filed as part of this report: ​ ​ Page Report of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 113 Report of Independent Registered Public Accounting Firm – PricewaterhouseCoopers Accountants N.V. 116 Consolidated Balance Sheets as of December 31, 2020 and 2019 117 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2020, 2019 and 2018 118 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2020, 2019 and 2018 119 Consolidated Statements of Cash Flows for the Years Ended December 31, 2020, 2019 and 2018 120 Notes to Consolidated Financial Statements for the Years Ended December 31, 2020, 2019 and 2018 121 ​ (b) Financial Statements Schedules . Financial Statement Schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements or notes. ​ (c) Other Exhibits . The Exhibit Index immediately preceding the signature page of this Annual Report on Form 10-K is incorporated herein by reference. ​ Item 16. Form 10-K Summary ​ Not applicable. ​ ​ 111 ​ Table of Contents ​ ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS FOR THE YEARS ENDED DECEMBER 31, 2020, 2019 AND 2018 ​ ​ ​ Page Report of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 113 Report of Independent Registered Public Accounting Firm – PricewaterhouseCoopers Accountants N.V. 116 Consolidated Balance Sheets as of December 31, 2020 and 2019 117 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2020, 2019 and 2018 118 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2020, 2019 and 2018 119 Consolidated Statements of Cash Flows for the Years Ended December 31, 2020, 2019 and 2018 120 Notes to Consolidated Financial Statements 121 ​ ​ ​ 112 ​ Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Shareholders and Board of Directors uniQure N.V.: ​ Opinions on the Consolidated Financial Statements and Internal Control Over Financial Reporting We have audited the accompanying consolidated balance sheets of uniQure N.V. and subsidiaries (the Company) as of December 31, 2020 and 2019, the related consolidated statements of operations and comprehensive loss, shareholders’ equity, and cash flows for the years then ended, and the related notes (collectively, the consolidated financial statements). We also have audited the Company’s internal control over financial reporting as of December 31, 2020, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of the Company as of December 31, 2020 and 2019, and the results of its operations and its cash flows for the years then ended, in conformity with U.S. generally accepted accounting principles. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2020 based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Change in Accounting Principle As discussed in Note 6, to the consolidated financial statements, the Company changed its method of accounting for leases as of January 1, 2019 due to the adoption of ASC 842, Leases . Basis for Opinions The Company’s management is responsible for these consolidated financial statements, for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s consolidated financial statements and an opinion on the Company’s internal control over financial reporting based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud, and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the consolidated financial statements included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions. ​ 113 ​ Table of Contents Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Critical Audit Matters The critical audit matter communicated below is a matter arising from the current period audit of the consolidated financial statements that was communicated or required to be communicated to the audit committee and that: (1) relates to accounts or disclosures that are material to the consolidated financial statements and (2) involved our especially challenging, subjective, or complex judgments. The communication of a critical audit matter does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing a separate opinion on the critical audit matter or on the accounts or disclosures to which it relates. Assessment of the satisfaction of the license revenue performance obligation within the BMS collaboration and license agreement As discussed in Notes 2.3.18 and 3 to the consolidated financial statements, uniQure biopharma B.V., a subsidiary of uniQure N.V. (the Company) entered into an amended collaboration and license agreement (CLA) with Bristol-Myers Squibb Company (BMS) on December 1, 2020. Based on the terms of the amended agreement, the Company determined that it materially satisfied its performance obligation in relation to the license revenue as of December 1, 2020, and as such recorded the residual balance of unrecognized license revenue of $27.8 million in profit and loss as license revenues from related party. We identified the assessment of the satisfaction of the license revenue performance obligation as a critical audit matter. A high degree of subjective, complex auditor judgement was required in assessing if the remaining rights of the license revenue performance obligation were materially satisfied as of December 1, 2020. 114 ​ Table of Contents The following are the primary procedures we performed to address this critical audit matter: - We evaluated the design and tested the operating effectiveness of an internal control related to the evaluation of the performance obligation and when it was materially satisfied. - In order to assess that the remaining rights of the license revenue performance obligation were materially satisfied, we examined the amended collaboration and license agreement between the Company and BMS. - In order to assess the satisfaction of the performance obligation, we examined minutes of joint steering committee meetings between the Company and BMS, evaluated the services delivered and performed interviews with the Company’s finance and business operations department. ​ /s/ KPMG Accountants N.V. ​ We have served as the Company’s auditor since 2019. Amstelveen, The Netherlands March 1, 2021 ​ ​ 115 ​ Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Management Board and Shareholders of uniQure N.V.: ​ Opinion on the Financial Statements ​ We have audited the consolidated statements of operations and comprehensive loss, of shareholders’ equity and of cash flows of uniQure N.V. and its subsidiaries (the “Company”) for the year ended December 31, 2018, including the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the results of operations and cash flows of the Company for the year ended December 31, 2018 in conformity with accounting principles generally accepted in the United States of America. ​ Basis for Opinion ​ These consolidated financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s consolidated financial statements based on our audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. ​ We conducted our audit of these consolidated financial statements in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud. ​ Our audit included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. We believe that our audit provides a reasonable basis for our opinion. ​ /s/ R.M.N. Admiraal RA ​ PricewaterhouseCoopers Accountants N.V. Amsterdam, the Netherlands ​ February 28, 2019 We served as the Company's auditor from 2006 to 2019. ​ ​ ​ 116 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED BALANCE SHEET S ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2020 2019 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 244,932 ​ $ 377,793 Accounts receivables ​ ​ 6,618 ​ ​ — Accounts receivable from related party ​ ​ — ​ ​ 947 Prepaid expenses ​ ​ 4,337 ​ ​ 4,718 Other current assets ​ ​ 3,024 ​ ​ 748 Total current assets ​ ​ 258,911 ​ ​ 384,206 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 32,328 ​ ​ 28,771 Operating lease right-of-use assets ​ ​ 26,086 ​ ​ 26,797 Intangible assets, net ​ ​ 3,361 ​ ​ 5,427 Goodwill ​ ​ 542 ​ ​ 496 Restricted cash ​ ​ 2,748 ​ ​ 2,933 Deferred tax asset ​ ​ 16,419 ​ ​ — Total non-current assets ​ ​ 81,484 ​ ​ 64,424 Total assets ​ $ 340,395 ​ $ 448,630 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 3,772 ​ $ 5,681 Accrued expenses and other current liabilities ​ ​ 18,038 ​ ​ 12,457 Current portion of operating lease liabilities ​ ​ 5,524 ​ ​ 5,865 Current portion of deferred revenue ​ ​ — ​ ​ 7,627 Total current liabilities ​ ​ 27,334 ​ ​ 31,630 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 35,617 ​ ​ 36,062 Operating lease liabilities, net of current portion ​ ​ 30,403 ​ ​ 31,133 Deferred revenue, net of current portion ​ ​ — ​ ​ 23,138 Derivative financial instruments related party ​ ​ — ​ ​ 3,075 Other non-current liabilities ​ ​ 3,136 ​ ​ 534 Total non-current liabilities ​ ​ 69,156 ​ ​ 93,942 Total liabilities ​ ​ 96,490 ​ ​ 125,572 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 60,000,000 shares authorized at December 31, 2020 and December 31, 2019 and 44,777,799 and 43,711,954 ordinary shares issued and outstanding at December 31, 2020 and December 31, 2019, respectively ​ ​ 2,711 ​ ​ 2,651 Additional paid-in-capital ​ ​ 1,016,018 ​ ​ 986,803 Accumulated other comprehensive income / (loss) ​ ​ 9,907 ​ ​ ( 6,689 ) Accumulated deficit ​ ​ ( 784,731 ) ​ ​ ( 659,707 ) Total shareholders' equity ​ ​ 243,905 ​ ​ 323,058 Total liabilities and shareholders' equity ​ $ 340,395 ​ $ 448,630 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 117 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2020 2019 ​ 2018 ​ ​ (in thousands, except share and per share amounts) License revenues ​ ​ 4,352 ​ ​ — ​ ​ — License revenues from related party ​ ​ 32,967 ​ ​ 4,988 ​ ​ 7,528 Collaboration revenues ​ ​ 59 ​ ​ — ​ ​ — Collaboration revenues from related party ​ ​ 136 ​ ​ 2,293 ​ ​ 3,756 Total revenues ​ ​ 37,514 ​ ​ 7,281 ​ ​ 11,284 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development expenses ​ ​ ( 122,400 ) ​ ​ ( 94,737 ) ​ ​ ( 74,809 ) Selling, general and administrative expenses ​ ​ ( 42,580 ) ​ ​ ( 33,544 ) ​ ​ ( 25,305 ) Total operating expenses ​ ​ ( 164,980 ) ​ ​ ( 128,281 ) ​ ​ ( 100,114 ) Other income ​ ​ 3,342 ​ ​ 1,888 ​ ​ 2,146 Other expense ​ ​ ( 1,302 ) ​ ​ ( 2,028 ) ​ ​ ( 1,548 ) Loss from operations ​ ​ ( 125,426 ) ​ ​ ( 121,140 ) ​ ​ ( 88,232 ) Interest income ​ ​ 938 ​ ​ 3,547 ​ ​ 2,729 Interest expense ​ ​ ( 3,825 ) ​ ​ ( 3,810 ) ​ ​ ( 2,160 ) Foreign currency (losses) / gains, net ​ ​ ( 13,613 ) ​ ​ ( 268 ) ​ ​ 4,382 Other non-operating gains / (losses), net ​ ​ 483 ​ ​ ( 2,530 ) ​ ​ 208 Loss before income tax income / (expense) ​ $ ( 141,443 ) ​ $ ( 124,201 ) ​ $ ( 83,073 ) Income tax income / (expense) ​ ​ 16,419 ​ ​ — ​ ​ ( 231 ) Net loss ​ $ ( 125,024 ) ​ $ ( 124,201 ) ​ $ ( 83,304 ) Other comprehensive income / (loss): ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation adjustments net of tax impact of nil for the year ended December 31, 2020 (2019: nil and 2018: $( 0.2 ) million) ​ ​ 16,596 ​ ​ 570 ​ ​ ( 5,261 ) Total comprehensive loss ​ $ ( 108,428 ) ​ $ ( 123,631 ) ​ $ ( 88,565 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 2.81 ) ​ $ ( 3.11 ) ​ $ ( 2.34 ) Weighted average shares used in computing basic and diluted net loss per ordinary share ​ ​ 44,466,365 ​ ​ 39,999,450 ​ ​ 35,639,745 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 118 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital (loss)/income deficit equity ​ (in thousands, except share data) Balance at December 31, 2017 31,339,040 ​ $ 1,947 ​ $ 566,530 ​ $ ( 3,800 ) ​ $ ( 475,318 ) ​ $ 89,359 Cumulative effect of retroactive implementation of ASC 606 Revenue recognition — ​ ​ — ​ ​ — ​ ​ 1,802 ​ ​ 23,116 ​ ​ 24,918 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 83,304 ) ​ ​ ( 83,304 ) Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 5,261 ) ​ ​ — ​ ​ ( 5,261 ) Follow-on public offering 5,175,000 ​ ​ 309 ​ ​ 138,052 ​ ​ — ​ ​ — ​ ​ 138,361 Exercises of share options 425,074 ​ ​ 19 ​ ​ 4,741 ​ ​ — ​ ​ — ​ ​ 4,760 Restricted and performance share units distributed during the period 409,948 ​ ​ 24 ​ ​ ( 24 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 10,708 ​ ​ — ​ ​ — ​ ​ 10,708 Issuance of ordinary shares relating to employee stock purchase plan 2,591 ​ ​ — ​ ​ 65 ​ ​ — ​ ​ — ​ ​ 65 Balance at December 31, 2018 37,351,653 ​ $ 2,299 ​ $ 720,072 ​ $ ( 7,259 ) ​ $ ( 535,506 ) ​ $ 179,606 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 124,201 ) ​ ​ ( 124,201 ) Other comprehensive income — ​ ​ — ​ ​ — ​ ​ 570 ​ ​ — ​ ​ 570 Follow-on public offering 5,625,000 ​ ​ 311 ​ ​ 242,363 ​ ​ — ​ ​ — ​ ​ 242,674 Hercules warrants exercise 37,175 ​ ​ 2 ​ ​ 1,271 ​ ​ — ​ ​ — ​ ​ 1,273 Exercise of share options 453,232 ​ ​ 25 ​ ​ 5,210 ​ ​ — ​ ​ — ​ ​ 5,235 Restricted and performance share units distributed during the period 235,692 ​ ​ 14 ​ ​ ( 14 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 17,533 ​ ​ — ​ ​ — ​ ​ 17,533 Issuance of ordinary shares relating to employee stock purchase plan 9,202 ​ ​ — ​ ​ 368 ​ ​ — ​ ​ — ​ ​ 368 Balance at December 31, 2019 43,711,954 ​ $ 2,651 ​ $ 986,803 ​ $ ( 6,689 ) ​ $ ( 659,707 ) ​ $ 323,058 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 125,024 ) ​ ​ ( 125,024 ) Other comprehensive income — ​ ​ — ​ ​ — ​ ​ 16,596 ​ ​ — ​ ​ 16,596 Exercise of share options 498,678 ​ ​ 29 ​ ​ 7,169 ​ ​ — ​ ​ — ​ ​ 7,198 Restricted and performance share units distributed during the period 560,986 ​ ​ 31 ​ ​ ( 31 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 21,831 ​ ​ — ​ ​ — ​ ​ 21,831 Issuance of ordinary shares relating to employee stock purchase plan 6,181 ​ ​ — ​ ​ 246 ​ ​ — ​ ​ — ​ ​ 246 Balance at December 31, 2020 44,777,799 ​ $ 2,711 ​ $ 1,016,018 ​ $ 9,907 ​ $ ( 784,731 ) ​ $ 243,905 ​ The accompanying notes are an integral part of these consolidated financial statements ​ 119 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2020 2019 2018 ​ ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 125,024 ) ​ $ ( 124,201 ) ​ $ ( 83,304 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation, amortization, and impairment losses ​ ​ 10,648 ​ ​ 6,669 ​ ​ 12,415 Share-based compensation expense ​ ​ 21,831 ​ ​ 17,533 ​ ​ 10,708 Change in fair value of derivative financial instruments and contingent consideration ​ ​ ( 483 ) ​ ​ 2,530 ​ ​ ( 4,054 ) Unrealized foreign exchange losses / (gains) ​ ​ 14,730 ​ ​ 891 ​ ​ ( 5,502 ) Deferred tax (income) / expense ​ ​ ( 16,419 ) ​ ​ - ​ ​ 231 Change in lease incentives ​ ​ - ​ ​ - ​ ​ ( 330 ) Change in deferred revenue ​ ​ ( 33,642 ) ​ ​ ( 4,999 ) ​ ​ ( 8,462 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts receivable and accrued income, prepaid expenses, and other current assets ​ ​ ( 6,967 ) ​ ​ ( 4,769 ) ​ ​ 1,578 Accounts payable ​ ​ ( 2,701 ) ​ ​ 1,652 ​ ​ 1,065 Accrued expenses, other liabilities, and operating leases ​ ​ 3,199 ​ ​ 6,010 ​ ​ ( 382 ) Net cash used in operating activities ​ ​ ( 134,828 ) ​ ​ ( 98,684 ) ​ ​ ( 76,037 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Purchases of intangible assets ​ ​ ( 2,213 ) ​ ​ ( 996 ) ​ ​ ( 1,861 ) Purchases of property, plant, and equipment ​ ​ ( 7,271 ) ​ ​ ( 5,651 ) ​ ​ ( 2,384 ) Net cash used in investing activities ​ ​ ( 9,484 ) ​ ​ ( 6,647 ) ​ ​ ( 4,245 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds from issuance of shares related to employee stock option and purchase plans ​ ​ 7,444 ​ ​ 5,603 ​ ​ 4,825 Proceeds from public offering of shares, net of issuance costs ​ ​ - ​ ​ 242,718 ​ ​ 138,361 Proceeds from loan increment ​ ​ - ​ ​ - ​ ​ 14,775 Proceeds from exercise of warrants ​ ​ - ​ ​ 500 ​ ​ - Net cash generated from financing activities ​ ​ 7,444 ​ ​ 248,821 ​ ​ 157,961 Currency effect on cash, cash equivalents and restricted cash ​ ​ 3,822 ​ ​ ( 106 ) ​ ​ ( 2,187 ) Net (decrease) / increase in cash, cash equivalents and restricted cash ​ ​ ( 133,046 ) ​ ​ 143,384 ​ ​ 75,491 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 380,726 ​ ​ 237,342 ​ ​ 161,851 Cash, cash equivalents and restricted cash at the end of period ​ $ 247,680 ​ $ 380,726 ​ $ 237,342 Cash and cash equivalents ​ $ 244,932 ​ $ 377,793 ​ $ 234,898 Restricted cash related to leasehold and other deposits ​ ​ 2,748 ​ ​ 2,933 ​ ​ 2,444 Total cash, cash equivalents and restricted cash ​ $ 247,680 ​ $ 380,726 ​ $ 237,342 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 4,131 ) ​ $ ( 3,117 ) ​ $ ( 2,141 ) Non-cash increase / (decrease) in accounts payables and accrued expenses and other current liabilities related to purchases of intangible assets and property, plant, and equipment ​ $ 630 ​ $ 313 ​ $ ( 48 ) ​ ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 120 ​ Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS ​ 1. General business information ​ 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 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 Dutch Chamber of Commerce (Kamer van Koophandel) 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. ​ The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trades under the symbol “QURE”. ​ 2. Summary of significant accounting policies ​ 2.1 Basis of preparation ​ The Company prepared its consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”). 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 consolidated financial statements have been prepared under the historical cost convention, except for derivative financial instruments and contingent consideration, which are recorded at fair value through profit or loss. ​ The 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. ​ The consolidated financial statements presented have been prepared on a going concern basis based on the Company’s cash and cash equivalents as of December 31, 2020 and the Company’s budgeted cash flows for the twelve months following the issuance date. ​ 2.2 Use of estimates ​ The preparation of consolidated financial statements, in conformity with U.S. GAAP and Securities and Exchange Commission (“SEC”) rules and regulations, 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 consolidated financial statements and reported amounts of revenues and expenses during the reporting period. Estimates and assumptions are primarily made in relation to the treatment of the commercialization and license agreement entered into between the Company and CSL Behring LLC (“CSL Behring Agreement”), the December 1, 2020, amendment (“amended BMS CLA”) of the 2015 collaboration and license agreement (“BMS CLA”) between the Company and Bristol-Myers Squibb (“BMS”), share-based payments, valuation allowances for deferred tax assets, and accounting for operating leases under ASC 842. If actual results differ from the Company’s estimates, or to the extent these estimates are adjusted in future periods, the Company’s results of operations could either benefit from, or be adversely affected by, any such change in estimate. 121 ​ Table of Contents 2.3 Accounting policies ​ The principal accounting policies applied in the preparation of these consolidated financial statements are set out below. These policies have been consistently applied to all the years presented, unless otherwise stated. ​ 2.3.1 Consolidation ​ The consolidated financial statements comprise the financial statements of the Company and its subsidiaries. Subsidiaries are all entities over which the Company has a controlling financial interest either through variable interest or through voting interest. Currently, the Company has no involvement with variable interest entities. ​ Inter-company transactions, balances, income, and expenses on transactions between uniQure entities are eliminated in consolidation. Profits and losses resulting from inter-company transactions that are recognized in assets are also eliminated. Accounting policies of subsidiaries have been changed where necessary to ensure consistency with the policies adopted by the Company. ​ 2.3.2 Current versus non-current classification ​ The Company presents assets and liabilities in the consolidated balance sheets based on current and non-current classification. ​ The term current assets is used to designate cash and other assets, or resources commonly identified as those that are reasonably expected to be realized in cash or sold or consumed during the normal operating cycle of the business. The Company’s normal operating cycle is twelve months . All other assets are classified as non-current. ​ The term current liabilities is used principally to designate obligations whose liquidation is reasonably expected to require the use of existing resources properly classifiable as current assets, or the creation of other current liabilities. Current liabilities are expected to be settled in the normal operating cycle. The Company classifies all other liabilities as non-current. ​ Deferred tax assets and liabilities are classified as non-current assets and liabilities, if any. ​ 2.3.3 Foreign currency translation ​ The functional currency of the Company and each of its entities (except for uniQure Inc.) is the euro (€). This represents the currency of the primary economic environment in which the entities operate. The functional currency of uniQure Inc. is the U.S. dollar ($). The consolidated financial statements are presented in U.S. dollars. ​ Foreign currency transactions are measured and recorded in the functional currency using the exchange rates prevailing at the dates of the transactions. Foreign exchange gains and losses resulting from the settlement of such transactions and from the re-measurement of monetary assets and liabilities denominated in foreign currencies at exchange rates prevailing at balance sheet date are recognized in profit and loss. ​ Upon consolidation, the assets and liabilities of foreign operations are translated into the functional currency of the shareholding entity at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. The consolidated assets and liabilities are translated from uniQure N.V.’s functional currency, euro, into the reporting currency U.S. dollar at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. Issued capital and additional paid-in capital are translated at historical rates with differences to the balance sheet date rate recorded as translation adjustments in other comprehensive income / loss. The exchange differences arising on translation for consolidation are recognized in “accumulated other comprehensive income / loss”. On disposal of a foreign operation, the component of other comprehensive income / loss relating to that foreign operation is recognized in profit or loss. ​ 122 ​ Table of Contents 2.3.4 Fair value measurement ​ The Company measures certain assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820, Fair Value Measurements and Disclosures 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 (Note 4, “Fair value measurement”). 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. ​ 2.3.5 Notes to the consolidated statements of cash flows ​ The consolidated statements of cash flows have been prepared using the indirect method. The cash disclosed in the consolidated statements of cash flows is comprised of cash and cash equivalents. Cash and cash equivalents include bank balances, demand deposits and other short-term highly liquid investments (with maturities of less than three months at the time of purchase) that are readily convertible into a known amount of cash and are subject to an insignificant risk of fluctuation in value. ​ Cash flows denominated in foreign currencies have been translated at the average exchange rates. Exchange differences, if any, affecting cash and cash equivalents are shown separately in the consolidated statements of cash flows. Interest paid and received, and income taxes are included in net cash (used in) provided by operating activities. ​ 2.3.6 Segment information ​ Operating segments are identified as a component of an enterprise for which separate discrete financial information is available for evaluation by the chief operating decision maker, or decision-making group, in making decisions on how to allocate resources and assess performance. The Company views its operations and manages its business as one operating segment, which comprises the discovery, development, and commercialization of innovative gene therapies. ​ 2.3.7 Net loss per share ​ The Company follows the provisions of ASC 260, Earnings Per Share . In accordance with these provisions, loss per share is calculated by dividing net loss by the weighted average number of ordinary shares outstanding during the period. ​ Diluted net loss per share reflects the dilution that would occur if share options or warrants to issue ordinary shares were exercised, or performance or restricted share units were distributed. However, potential ordinary shares are excluded if their effect is anti-dilutive. The Company currently has no dilutive securities due to the net loss position and as such, basic and diluted net loss per share are the same for the periods presented. ​ 123 ​ Table of Contents 2.3.8 Impairment of long-lived assets ​ Long-lived assets, which include property, plant, and equipment and finite-lived intangible assets, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying value of an asset or asset group may not be recoverable. Right-of-use assets are also reviewed for impairment in accordance with ASC 360. The recoverability of the carrying value of an asset or asset group depends on the successful execution of the Company’s business initiatives and its ability to earn sufficient returns on approved products and product candidates. When such events or changes in circumstances occur, the Company assesses recoverability by determining whether the carrying value of such assets will be recovered through the undiscounted expected future cash flows. If the future undiscounted cash flows are less than the carrying amount of these assets, the Company recognizes an impairment loss based on the excess of the carrying value over the fair value of the assets. Fair value is determined through various valuation techniques, including discounted cash flow models, quoted market values, and third-party independent appraisals, as considered necessary. ​ Goodwill is not amortized but is evaluated for impairment within the Company’s single reporting unit on an annual basis, during the fourth quarter, or more frequently if an event occurs or circumstances change that would more-likely-than-not reduce the fair value of the Company’s reporting unit below its carrying amount. The Company performs the same quantitative analysis discussed above for long-lived assets and finite-lived intangible assets. ​ 2.3.9 Property, plant, and equipment ​ Property, plant, and equipment is comprised mainly of laboratory equipment, leasehold improvements, construction-in-progress (“CIP”) and office equipment. All property, plant and equipment is stated at cost less accumulated depreciation. CIP consists of capitalized expenses associated with construction of assets not yet placed into service. Depreciation commences on CIP once the asset is placed into service based on its useful life determined at that time. ​ Maintenance and repairs that do not improve or extend the lives of the respective assets are expensed as incurred. Upon disposal, the related cost and accumulated depreciation is removed from the accounts and any resulting gain or loss on the transaction is recognized in the consolidated statements of operations and comprehensive loss. ​ Depreciation is calculated using the straight-line method over the estimated useful lives of the assets (or in the case of leasehold improvements a shorter lease term), which are as follows: ​ ​ ​ ​ · Leasehold improvements Between 10 – 15 years · Laboratory equipment ​ 5 years · Office equipment ​ Between 3 – 5 years ​ 2.3.10 Leases ​ The Company adopted ASC 842 using the modified retrospective approach with an effective date as of the beginning of the Company’s fiscal year, January 1, 2019, to operating leases that existed on that date. Comparative financial information related to profit and loss and cash flows for the twelve-month period ended December 31, 2018, was not recast under the new standard, and continues to be presented under ASC 840. ​ The Company measured lease liabilities at the present value of the future lease payments as of January 1, 2019. The Company used an incremental borrowing rate to discount the lease payments. The Company derived the discount rate, adjusted for differences such as in the term and payment patterns, from the Company’s loan from Hercules Technology Growth Capital, Inc (“Hercules Capital”), which was refinanced immediately prior to the January 1, 2019 adoption date in December 2018. The right-of-use asset is valued at the amount of the lease liability reduced by the remaining December 31, 2018 balance of lease incentives received. The lease liability is subsequently measured at the present value of the future lease payments as of the reporting date with a corresponding adjustment to the right-to-use asset. Absent a lease modification, the Company will continue to utilize the January 1, 2019, incremental borrowing rate. ​ The Company recognizes lease cost on a straight-line basis and presents these costs as operating expenses within the Consolidated statements of operations and comprehensive loss. The Company presents lease payments and landlord incentive payments within cash flows from operations within the Consolidated statements of cash flows. ​ 124 ​ Table of Contents The financial results for the years ended December 31, 2020 and 2019 are presented in accordance with ASC 842, while the financial results for the year ended December 31, 2018 are presented in accordance with the Company’s historical accounting policy based on ASC 840. ​ 2.3.11 Other (non) current assets ​ Deposits paid are either presented as other current assets or as other non-current assets based on duration of the underlying contractual arrangement. Deposits are classified as restricted cash and primarily relate to facility leases. ​ Contract assets are presented in other current assets or as other non-current assets based on the timing of the right to consideration. ​ 2.3.12 Prepaid expenses ​ Prepaid expenses are amounts paid in the period, for which the benefit has not been realized, and include payments made for insurance and research and clinical contracts. The related expense will be recognized in the subsequent period as incurred. ​ 2.3.13 Accounts receivable ​ Accounts receivables include amounts due from services provided to the Company’s collaboration partner as well as unconditional rights to consideration from its collaboration partners. ​ 2.3.14 Accounts payable and accrued expenses ​ Accounts payables are invoiced amounts related to obligations to pay for goods or services that have been acquired in the ordinary course of business from suppliers. Accounts payables are recognized at the amounts invoiced by suppliers. ​ Accrued expenses are recognized for goods or services that have been acquired in the ordinary course of business. ​ Contract liabilities are presented in accounts payable and accrued expenses. ​ 2.3.15 Long-term debt ​ Long-term debt is initially recognized at cost and presented net of original issue discount or premium and debt issuance costs on the consolidated balance sheets. Amortization of debt discount and debt issuance costs is recognized as interest expense in profit and loss over the period of the debt, using the effective interest rate method. ​ 2.3.16 Pensions and other post-retirement benefit plans ​ The Company has a defined contribution pension plan for all employees at its Amsterdam facility in the Netherlands, which is funded by the Company through payments to an insurance company, with individual accounts for each participants’ assets. The Company has no legal or constructive obligation to pay further contributions if the plan does not hold sufficient assets to pay all employees the benefits relating to services rendered in the current and prior periods. The contributions are expensed as incurred. Prepaid contributions are recognized as an asset to the extent that a cash refund or a reduction in the future payments is available. ​ Starting in 2016, the Company adopted a qualified 401(k) Plan for all employees at its Lexington facility in the USA, which offers both a pre-tax and post-tax (Roth) component. Employees may contribute up to 50 % of their pre-tax compensation, which is subject to IRS statutory limits for each calendar year. The Company matches $ 0.50 for every $ 1.00 contributed to the plan by participants up to 6 % of base compensation. Employer contributions are recognized as they are contributed, as long as the employee is rendering services in that period. If employer contributions are made in periods after an individual retires or terminates, the estimated cost is accrued during the employee’s service period. ​ 125 ​ Table of Contents 2.3.17 Share-based compensation ​ The Company accounts for its share-based compensation awards in accordance with ASC 718, Compensation-Stock Compensation. ​ All the Company’s share-based compensation plans for employees are equity-classified. ​ ASC 718 requires all share-based compensation to employees, including grants of employee options, restricted share units, performance share units and modifications to existing instruments, to be recognized in the consolidated statements of operations and comprehensive loss based on their grant-date fair values, net of an estimated forfeiture rate, over the requisite service period. Forfeitures of employee options are recognized as they occur. The requirements of ASC 718 are also applied to nonemployee share-based payment transactions except for specific guidance on certain inputs to an option-pricing model and the attribution of cost. ​ The Company uses a Hull & White option model to determine the fair value of option awards. The model captures early exercises by assuming that the likelihood of exercises will increase when the share-price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ 2.3.18 Revenue recognition ​ The Company primarily generates revenue from its collaboration, research, and license agreements with its collaboration partner BMS for the development and commercialization of product candidates. The Company initially entered into these agreements in 2015 and amended them in 2020. ​ On January 1, 2018, the Company adopted new revenue recognition policies in accordance with ASC 606 using the modified retrospective approach. The Company evaluated the initial BMS CLA and determined that its performance obligations were as follows: ​ ● Providing pre-clinical research activities (“Collaboration Revenue”); ● Providing clinical and commercial manufacturing services for products (“Manufacturing Revenue”); and ● Providing access to its technology and know-how in the field of gene therapy as well as actively contributing to the target selection, the collaboration as a whole, the development during the target selection, the pre-clinical and the clinical phase through participating in joint steering committee and other governing bodies (“License Revenue”). As further discussed in Note 3, “Collaboration arrangements and concentration of credit risk”, as a result of the December 2020 amended BMS CLA, the Company’s performance obligation related to License Revenues was materially completed as of the date of the amendment effective date of December 1, 2020. The Company may still be required to provide pre-clinical research activities or clinical and commercial manufacturing services when BMS exercises its options for those services. ​ License Revenue ​ Until the December 2020 amendment of the BMS CLA the Company recognized License Revenue over the expected performance period based on its measure of progress towards the completion of certain activities related to its services. Following the December 2020 amendment of the BMS CLA the Company’s performance was materially completed and it had satisfied its performance obligation (see Note 3, “Collaboration arrangements and concentration of credit risk”, for a detailed discussion). ​ Collaboration and Manufacturing Revenue ​ The Company recognizes Collaboration Revenues associated to optional work orders it receives from BMS to provide analytical development and process development activities that are reimbursable by BMS in accordance with the BMS CLA as well as the amended BMS CLA. ​ 126 ​ Table of Contents BMS and the Company entered into a Master Clinical Supply Agreement in April 2017 for the Company to supply gene therapy products during the clinical phase as well as into a binding term sheet to supply gene therapy products during the commercial phase to BMS. In December 2020, BMS and the Company also entered into a Research Supply Agreement. Revenues from product sales will be recognized when earned. The Company will provide these services as it receives optional work orders from BMS in relation to such services. ​ 2.3.19 Other income, other expense ​ The Company receives certain government and regional grants, which support its research efforts in defined projects, and include contributions towards the cost of research and development. These grants generally provide for reimbursement of approved costs incurred as defined in the respective grants and are deferred and recognized in the statements of operations and comprehensive loss over the period necessary to match them with the costs they are intended to compensate, when it is probable that the Company has complied with any conditions attached to the grant and will receive the reimbursement. ​ The Company’s other income also consists of income from the subleasing of the Amsterdam facility while other expense consists of expenses incurred in relation to the subleasing income. ​ 2.3.20 Research and development expenses ​ Research and development costs are expensed as incurred. Research and development expenses generally consist of laboratory research, clinical trials, statistical analysis, and report writing, regulatory compliance costs incurred with clinical research organizations and other third-party vendors (including post-approval commitments to conduct consistency and comparability studies). In addition, research and development expenses consist of start-up and validation costs related to the Company’s Lexington facility and the development and improvement of the Company’s manufacturing processes and methods. Furthermore, research and development costs include costs of materials and costs of intangible assets purchased from others for use in research and development activities. The costs of intangibles that are purchased from others for a particular research and development project and that have no alternative future uses (in other research and development projects or otherwise) are expensed as research and development costs at the time the costs are incurred or at the time when no alternative future use is identified. ​ 2.3.21 Income taxes ​ Income taxes are recorded in accordance with ASC 740, Income Taxes , which provides for deferred taxes using an asset and liability approach. The Company recognizes deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying amount and the tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. Valuation allowances are provided, if based upon the weight of available evidence, it is more-likely-than-not that some or all the deferred tax assets will not be realized. ​ The benefits of tax positions are recognized only if those positions are more likely than not, based on the technical merits, to be sustained upon examination. Recognized tax positions are measured at the largest amount of tax benefit that is greater than 50 percent likely of being realized upon settlement. The determination as to whether the tax benefit will more-likely-than-not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. As of December 31, 2020, and 2019, the Company did not have any significant unrecognized tax benefits. ​ 127 ​ Table of Contents 2.3.22 Recently Adopted Accounting Pronouncements ​ ASU 2018-13: Fair Value Measurement ​ In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820) which modifies the disclosure requirements on fair value measurements. ASU 2018-13 is effective for fiscal years beginning after December 15, 2019, which for the Company was January 1, 2020. The new disclosure requirements for changes in unrealized gains and losses in other comprehensive income for recurring Level 3 measurements, the range and weighted average of significant unobservable inputs and the amended requirements for the narrative description of measurement uncertainty should be applied prospectively for only the most recent interim or annual period presented in the initial fiscal year of adoption. All other amendments should be applied retrospectively. ASU 2018-13 did not have a material impact on the Company’s consolidated financial statements. ​ Recent Accounting Pronouncements Not Yet Effective ​ None. ​ ​ ​ 128 ​ Table of Contents 3. Collaboration arrangements and concentration of credit risk ​ CSL Behring collaboration ​ On June 24, 2020, uniQure biopharma B.V., a wholly-owned subsidiary of uniQure N.V., entered into the CSL Behring Agreement with CSL Behring LLC, (“CSL Behring”), pursuant to which CSL Behring will receive exclusive global rights to etranacogene dezaparvovec, the Company’s investigational gene therapy for patients with hemophilia B, (the “Product”). ​ Under the terms of the CSL Behring Agreement, the Company will receive a $ 450.0 million upfront cash payment upon the closing of the CSL Behring Agreement and be eligible to receive up to $ 1.6 billion in additional payments based on regulatory and commercial milestones. The CSL Behring Agreement also provides that the Company will be eligible to receive tiered double-digit royalties in a range of up to a low-twenties percent of net sales of the Product based on sales thresholds. Pursuant to the CSL Behring Agreement, the Company will be responsible for the completion of the HOPE-B clinical trial, manufacturing process validation, and the manufacturing supply of the Product until such time that these capabilities may be transferred to CSL Behring or its designated contract manufacturing organization. Concurrently with the execution of the CSL Behring Agreement, the Company and CSL Behring entered into a development and commercial supply agreement, pursuant to which, among other things, the Company will supply the Product to CSL Behring at an agreed-upon price. Clinical development and regulatory activities performed by the Company pursuant to the CSL Behring Agreement will be reimbursed by CSL Behring. CSL Behring will be responsible for global regulatory submissions and commercialization requirements for the Product. The effectiveness of the transactions contemplated by the CSL Behring Agreement is contingent on completion of review under antitrust laws in the United States, Australia, and the United Kingdom, and certain provisions of the CSL Behring Agreement will not become effective until after we receive all such regulatory approvals. As of December 31, 2020, such regulatory approvals had not been received in all jurisdictions. As of December 31, 2020, the Company concluded it has no enforceable right to the upfront payment, the regulatory and sale milestone payments, or the royalties (together “CSL Behring License Revenue”) that the Company may receive in accordance with the CSL Behring Agreement, as all payments are contingent upon the successful completion of reviews under the Hart-Scott-Rodino Antitrust Improvements Act of 1976. Therefore, the Company determined it will not recognize any revenue in relation to the CSL Behring License Revenue, in accordance with ASC 606 during the year ended December 31, 2020. In accordance with its existing license and other agreements, the Company is contractually required to pay in total a low to high single digit percentage of any upfront payment to its licensors and financial advisor (“License Fees”). The Company did not record any License Fees in the year ended December 31, 2020, as the Company had not recognized the upfront payment as this date. The Company incurred $ 2.1 million of expenses related to the obligations related to the CSL Behring Agreement that had not been satisfied as of December 31, 2020. The Company capitalized these expenses as contract fulfillment costs (presented within Other current assets). As of December 31, 2020, the Company also recognized a $ 2.1 million receivable (presented within Accounts receivable) from CSL Behring for expenses for which it has a right of reimbursement as well as a contract liability (presented within Accrued expenses and other current liabilities) for the same amount. In accordance with ASC 606 it cannot recognize any CSL Behring License Revenue as of this date. 129 ​ Table of Contents Bristol-Myers Squibb collaboration ​ 2015 Agreement ​ In May 2015, the Company entered into the BMS CLA and various related agreements with BMS, which the Company collectively refers to as the BMS CLA, which provided BMS with exclusive access to the Company’s gene therapy technology platform for the research, development and commercialization of therapeutics aimed at multiple Collaboration Targets. The initial four-year research term under the collaboration terminated on May 21, 2019. During the initial research term of the BMS CLA, the Company supported BMS in discovery, non-clinical, analytical and process development efforts in respect of the Collaboration Targets. For any Collaboration Targets that may be advanced, the Company will be responsible for manufacturing of clinical and commercial supplies. BMS reimbursed the Company for all its research and development costs in support of the collaboration, and will lead development, regulatory and commercial activities for any Collaboration Targets that may be advanced. The BMS CLA initially provided that the Company and BMS could potentially have collaborated on up to ten Collaboration Targets in total. ​ BMS initially designated four Collaboration Targets, including S100A1 for congestive heart failure (“AMT-126”). In October 2018, the Company and BMS completed a heart function proof-of-concept study of AMT-126 in a pre-clinical, diseased animal model. The data did not show a benefit on heart function at six months and, consequently, work on S100A1 was discontinued. The Company impaired a $ 5.4 million acquired research and development asset associated with the program and released a contingent liability of $ 3.8 million related to the acquisition of the asset to income in the year ended December 31, 2018. In April 2019, BMS designated a new cardiovascular Collaboration Target to replace S100A1. As a result, BMS had designated a total of four Collaboration Targets as of December 31, 2019. ​ 2020 Amendment ​ In February 2019, BMS requested a one-year extension of the initial research term. In April 2019, following an assessment of the progress of the collaboration and the Company’s expanding proprietary programs, the Company notified BMS that the Company did not intend to agree to an extension of the initial research term but rather preferred to restructure or amend the collaboration to reduce or eliminate certain of the Company’s obligations under it. ​ On December 1, 2020, the Company and BMS entered into the amended BMS CLA. Under the amended BMS CLA, BMS is limited to four Collaboration Targets. For a period of one-year from the effective date of the amended BMS CLA, BMS may replace up to two of these four Collaboration Targets with up to two new targets in the field of cardiovascular disease. The Company continues to be eligible to receive research, development, and regulatory milestone payments of up to $ 217.0 million for each Collaboration Target, if defined milestones are achieved. ​ BMS is no longer entitled to designate the fifth to tenth Collaboration Targets and as such the Company’s remaining obligations under the amended BMS CLA are substantially reduced. The Company is no longer entitled to receive up to an aggregate $ 16.5 million in target designation payments for the research, development and regulatory milestone payments associated with the fifth to tenth Collaboration Targets. ​ For as long as any of the four Collaboration Targets are being advanced, BMS may place a purchase order to be supplied with research, clinical and commercial supplies. Subject to the terms of the amended BMS CLA, BMS has the right to terminate the research, clinical and commercial supply relationships, and has certain remedies for failures of supply, up to and including technology transfer for any such failure that otherwise cannot be reasonably resolved. Both BMS and the Company may agree to a technology transfer of manufacturing capabilities pursuant to the terms of the amended BMS CLA. ​ The amended BMS CLA does not extend the initial research term. BMS may place purchase orders to provide limited services primarily related to analytical and development efforts in respect of the four Collaboration Targets. BMS may request such services for a period not to exceed the earlier of (i) the completion of all activities under a Research Plan and (ii) either (A) three years after the last replacement target has been designated by BMS during the one year replacement period following the amended BMS CLA effective date or (B) three years if no replacement targets are designated during this one year period and BMS continues to reimburse the Company for these services. ​ 130 ​ Table of Contents The Company evaluated the impact of the amendment of the BMS CLA in relation to its performance obligation related to: ​ – Providing access to its technology and know-how in the field of gene therapy and participating in joint steering committee and other governing bodies (materially satisfied as of December 1, 2020) (“License Revenue”). The Company did not identify any new distinct performance obligations and determined the amended BMS CLA did not represent a separate contract in accordance with ASC 606. The Company evaluated the effect the modification has on its measure of progress towards the completion of its performance obligation related to License Revenue and recorded an adjustment to License Revenue as of December 1, 2020. ​ Services to BMS are rendered by the Dutch operating entity. Total collaboration and license revenue generated with BMS are as follows (presented as revenue from a related party until November 30, 2020, and as revenue from December 1, 2020 onwards): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 ​ ​ 2019 ​ ​ 2018 ​ ​ (in thousands) Bristol Myers Squibb $ 37,514 ​ $ 7,281 ​ $ 11,284 Total $ 37,514 ​ $ 7,281 ​ $ 11,284 ​ Amounts owed by BMS in relation to the Collaboration and License Revenue are as follows (presented as “Accounts receivables” as of December 31, 2020 and as “Accounts receivable from related party” as of December 31, 2019): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2020 2019 ​ ​ (in thousands) Bristol Myers Squibb ​ $ 4,536 ​ $ 947 Total ​ $ 4,536 ​ $ 947 ​ Collaboration Revenue ​ The Company recognizes collaboration revenues associated with Collaboration Target-specific pre-clinical analytical development and process development activities that are reimbursable by BMS under the BMS CLA and the amended BMS CLA as well as other related agreements. Collaboration Revenue related to these contracted services is recognized when performance obligations are satisfied. ​ The Company generated $ 0.2 million collaboration revenue for the year ended December 31, 2020 (December 31, 2019: $ 2.3 million; December 31, 2018: $ 3.8 million). 131 ​ Table of Contents License Revenue ​ The Company recognized $ 33.0 million of License Revenue for the year ended December 31, 2020 (December 31, 2019: $ 5.0 million, December 31, 2018: $ 7.5 million). On May 21, 2015, the Company recorded a $ 60.1 million upfront payment and in August 2015 it recorded a $ 15.0 million payment it received from BMS in relation to the designation of the second, third and fourth Collaboration Targets. The Company recognizes License Revenue over the expected performance period based on its measure of progress towards the completion of certain activities related to its services. The Company determines such progress by comparing activities performed at the end of each reporting period with total activities expected to be performed. The Company estimates total expected activities using several unobservable inputs, such as the probability of BMS designating additional targets, the probability of successfully completing each phase and estimated time required to provide services during the various development stages. The estimation of total services at the end of each reporting period involves considerable judgement. The amount of services the Company expects to provide is significantly impacted by the number of Collaboration Targets that it estimates BMS would pursue. As a result of the December 1, 2020 amendment of the BMS CLA the Company no longer is required to potentially provide any services in relation to six additional targets that BMS might have designated. The Company determined its remaining performance obligation is immaterial. The Company adjusted its measure of progress towards the completion of its activities related to its services as of the December 1, 2020 modification date accordingly. The Company recognized the remaining balance of unrecognized License Revenue as of November 30, 2020 of $ 27.8 million in profit and loss during the year ended December 31, 2020 as License Revenue from a related party. The Company includes variable consideration related to any research, development, and regulatory milestone payments, in the transaction price once it is considered probable that including these payments in the transaction price would not result in the reversal of cumulative revenue recognized. Due to the significant uncertainty surrounding the development of gene-therapy product candidates and the dependence on BMS’s performance and decisions, the Company does not currently (with below exception) consider this probable. ​ On December 17, 2020 BMS designated one of the four Collaboration Targets as a candidate to advance into IND-enabling studies entitling the Company to receive a $ 4.4 million research milestone payment. The Company recorded the $ 4.4 million as License Revenue in the twelve-month period ended December 31, 2020. The Company recognizes License Revenue related to product sales by BMS from any of the Collaboration Targets when the sales occur. The Company is eligible to receive net sales-based milestone payments and tiered mid-single to low double-digit royalties on product sales. 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 the first commercial sale if there is no such exclusivity. ​ ​ ​ 132 ​ Table of Contents 4. Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ​ 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 Company’s only material financial assets measured at fair value using Level 1 inputs is cash and cash equivalents. ​ The liability measured at fair value using Level 3 inputs as of December 31, 2020 was the derivative financial instrument. The Company had recorded derivative financial instruments as of December 31, 2019, that were measured at fair value using Level 3 inputs. Changes in Level 3 items during the years ended December 31, 2020, 2019 and 2018 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative ​ ​ ​ ​ ​ Contingent ​ financial ​ ​ ​ ​ consideration instruments Total ​ ​ (in thousands) Balance at December 31, 2017 ​ $ 3,964 ​ $ 1,635 ​ $ 5,599 Net gains recognized in profit or loss ​ ​ ( 3,846 ) ​ ​ ( 208 ) ​ ​ ( 4,054 ) Currency translation effects ​ ​ ( 118 ) ​ ​ ( 52 ) ​ ​ ( 170 ) Balance at December 31, 2018 ​ $ — ​ $ 1,375 ​ $ 1,375 Net losses recognized in profit or loss ​ ​ — ​ ​ 2,530 ​ ​ 2,530 Exercise of Hercules warrants ​ ​ — ​ ​ ( 770 ) ​ ​ ( 770 ) Currency translation effects ​ ​ — ​ ​ ( 60 ) ​ ​ ( 60 ) Balance at December 31, 2019 ​ $ — ​ $ 3,075 ​ $ 3,075 Net gains recognized in profit or loss ​ ​ — ​ ​ ( 2,300 ) ​ ​ ( 2,300 ) Derecognition of warrants ​ ​ — ​ ​ ( 796 ) ​ ​ ( 796 ) Recognition of derivative financial liability of CoC-payment ​ ​ — ​ ​ 2,613 ​ ​ 2,613 Currency translation effects ​ ​ — ​ ​ 53 ​ ​ 53 Balance at December 31, 2020 ​ $ — ​ $ 2,645 ​ $ 2,645 ​ Derivative financial instruments ​ The Company issued derivative financial instruments related to its collaboration with BMS and in relation to the issuance of the Hercules loan facility. ​ Derivative financial instruments BMS ​ Pursuant to the BMS CLA, the Company in 2015 granted BMS two warrants that were subsequently terminated in connection with the amendment to the BMS CLA on December 1, 2020. The Company granted to BMS: ​ ● A warrant that allowed BMS to purchase a specific number of the Company’s ordinary shares such that its ownership would have equaled 14.9 % immediately after such purchase (“1 st warrant”). The 1 st warrant could have been exercised on the later of (i) the date on which the Company received from BMS the Target Designation Fees (as defined in the BMS CLA) associated with the first six new targets (a total of seven Collaboration Targets); and (ii) the date on which BMS designated the sixth new target (the seventh Collaboration Target); and ● A warrant that allowed BMS to purchase a specific number of the Company’s ordinary shares such that its ownership would have equaled 19.9 % immediately after such purchase (“2 nd warrant” and together with 1 st warrant, the “warrants”). The warrant could have been exercised on the later of (i) the date on which the Company received from BMS the Target Designation Fees associated with the first nine new targets (a total of ten Collaboration Targets); and (ii) the date on which BMS designated the ninth new target (the tenth Collaboration Target). 133 ​ Table of Contents On December 1, 2020, the Company derecognized the warrants when these were terminated in accordance with the amended BMS CLA. ​ Pursuant to the terms of the BMS CLA the exercise price in respect of each warrant was equal to the greater of (i) the product of (A) $ 33.84 , multiplied by (B) a compounded annual growth rate of 10 % (or approximately $ 57.32 as of November 30, 2020) and (ii) the product of (A) 1.10 multiplied by (B) the weighted average volume price (“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. ​ The fair value of the warrants as of December 31, 2019 was $ 3.1 million. During the year ended December 31, 2020, the Company recognized a $ 3.1 million gain in non-operating income / expense (December 31, 2019: $ 2.3 million loss; December 31, 2018: $ 0.5 million gain) related to fair value changes of the BMS warrants. The gain recognized in the year ended December 31, 2020 includes $ 0.8 million from the derecognition of the BMS warrants on December 1, 2020. ​ The Company used Monte-Carlo simulations to determine the fair market value of the BMS warrants. The valuation model incorporated several inputs, the risk-free rate adjusted for the period affected, an expected volatility based on historical Company volatility, the expected yield on any dividends and management’s expectations on the timelines of reaching certain defined trigger events for the exercising of the warrants, as well as management’s expectations regarding the number of ordinary shares that would be issued upon exercise of the warrants. All of these represent Level 3 inputs. Additionally, the model assumed BMS would exercise the warrants only if it was financially rational to do so. ​ The warrants could only have been exercised following the occurrence of events contractually defined in the warrant agreements. The probability of the occurrence of these events represented another significant unobservable input used in the calculation of the fair value of the warrants. ​ On December 1, 2020, the Company and BMS terminated the BMS warrants and agreed that upon the consummation of a change of control transaction of uniQure that occurs prior to December 1, 2026 or BMS’ delivery of a target cessation notice for all four Collaboration Targets, uniQure (or its third party acquirer) shall pay to BMS a one-time, non-refundable, non-creditable cash payment of $ 70.0 million, provided that (x) if $ 70.0 million is greater than five percent ( 5.0 %) of the net proceeds (as contractually defined) from such change of control transaction, the payment shall be an amount equal to five percent of such net proceeds, and (y) if $ 70.0 million is less than one percent of such net proceeds, the change of control payment shall be an amount equal to one percent of such net proceeds (“CoC-payment”). The Company has not consummated any change of control transaction as of December 31, 2020 that would obligate it to make a CoC-payment. The Company determined that the CoC-payment should be recorded as a derivative financial liability as of December 1, 2020 and that subsequent changes in the fair market value of this derivative financial liability should be recorded in profit and loss. The fair market value of the derivative financial liability is materially impacted by probability that market participants assign to the likelihood of the occurrence of a change of control transaction that would give rise to a CoC-payment. This probability represents an unobservable input. The Company determined the fair market value of the derivative financial liability by using a present value model based on expected cash flow. The expected cash flows are materially impacted by the probability that market participants assign to the likelihood of the occurrence of a change of control event within the biotechnology industry. The Company estimated this unobservable input using the best information available as of December 1, 2020 and December 31, 2020. The Company obtained reasonably available market information that it believed market participants would use in determining the likelihood of the occurrence of a change-of control transaction within the biotechnology industry. Selecting and evaluating market information involves considerable judgement and uncertainty. Based on all such information and its judgment the Company estimated that the fair market value of the derivative financial liability (presented within “Other non-current liabilities”) as of December 1, 2020 and December 31, 2020 was $ 2.6 million. The Company recorded a $ 2.6 million loss within “Other non-operating expenses” in the twelve-month period ended December 31, 2020 related to the initial recognition of this derivative financial liability. ​ 134 ​ Table of Contents Hercules loan facility ​ On June 14, 2013, the Company entered into a venture debt loan facility (the “Original Facility”) with Hercules (see Note 8, “Long-term debt”) pursuant to a Loan and Security Agreement (the “Loan Agreement”), which included a warrant maturing on February 5, 2019. 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, 2016 and 2018 amendments of the loan. The Hercules warrants were exercised as of February 1, 2019. The Company issued 37,175 ordinary shares at $ 34.25 following the exercise of all Hercules warrants and receipt of $ 0.5 million from Hercules. During the year ended December 31, 2020, the Company recognized no more gains or losses in other non-operating income / (expense) (December 31, 2019: $ 0.2 million loss; December 31, 2018: $ 0.3 million loss) related to fair value changes of the Hercules warrants. ​ Contingent consideration ​ In connection with the Company’s acquisition of the InoCard business (“InoCard”) in 2014, the Company recorded contingent consideration related to amounts potentially payable to InoCard’s former shareholders. The amounts payable in accordance with the sale and purchase agreement (as amended in August 2017) were contingent upon realization of milestones associated with its S100A1 protein research program. Following the discontinuation of the research program the Company since 2018 no longer expects to realize those milestones and recorded a $ 3.8 million gain within research and development expenses for the year ended December 31, 2018, to release the liability to profit and loss. ​ 5. Property, plant, and equipment, net ​ The following table presents the Company’s property, plant, and equipment as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2020 2019 ​ ​ (in thousands) Leasehold improvements ​ $ 37,849 ​ $ 34,611 Laboratory equipment ​ ​ 22,106 ​ ​ 18,232 Office equipment ​ ​ 5,025 ​ ​ 4,212 Construction-in-progress ​ ​ 2,574 ​ ​ 341 Total property, plant, and equipment ​ ​ 67,554 ​ ​ 57,396 Less accumulated depreciation ​ ​ ( 35,226 ) ​ ​ ( 28,625 ) Property, plant and equipment, net ​ $ 32,328 ​ $ 28,771 ​ Total depreciation expense was $ 5.7 million for the year ended December 31, 2020 (December 31, 2019: $ 6.0 million, December 31, 2018: $ 6.5 million). Depreciation expense is allocated to research and development expenses to the extent it relates to the Company’s manufacturing facility and equipment and laboratory equipment. All other depreciation expenses are allocated to selling, general and administrative expense. ​ The following table summarizes property, plant, and equipment by geographic region. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2020 ​ 2019 ​ ​ (in thousands) Lexington, Massachusetts (United States of America) ​ $ 15,949 ​ $ 15,490 Amsterdam (the Netherlands) ​ 16,379 ​ 13,281 Total ​ $ 32,328 ​ $ 28,771 ​ 135 ​ Table of Contents ​ 6. Right-of-use asset and lease liabilities ​ The Company adopted ASU 2016-02 “Leases (Topic 842)” as well as ASU 2018-10 and ASU 2018-11, which both relate to improvements to ASC 842. The Company adopted the standard using the modified retrospective approach with an effective date as of the beginning of the Company’s fiscal year, January 1, 2019 (“new lease accounting standard”). The standard requires the balance sheet recognition for leases. Prior years were not recast under the new standard and therefore, those amounts are presented in accordance with the requirements of the previously effective lease standard ASC 840 (“historic lease accounting standard”). The Company elected to utilize practical expedients available for expired or existing contracts which allowed the Company to carryforward historical assessments of (1) whether contracts are or contain leases, (2) lease classification, and (3) initial direct costs. ​ The Company’s most significant leases relate to office and laboratory space under the following operating lease agreements: ​ Lexington, Massachusetts / United States ​ In July 2013, the Company entered into a lease for a facility in Lexington, Massachusetts, United States. The term of the lease commenced in November 2013, was set for 10 years starting from the 2014 rent commencement date and is non-cancellable. Originally, the lease for this facility had a termination date of 2024. In November 2018, the term was expanded by five years to June 2029. The lease continues to be renewable for two subsequent five-year terms. Additionally, the lease was expanded to include an additional 30,655 square feet within the same facility and for the same term. The lease of the expansion space commenced on June 1, 2019. ​ The contractually fixed annual increase of lease payments through 2029 for both the extension and expansion lease have been included in the lease payments. ​ 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 the new facility terminates in 2032, with an option to extend in increments of five-year periods. The lease contract includes variable lease payments related to annual increases in payments based on a consumer price index. ​ On December 1, 2017, the Company entered into an agreement to sub-lease three of the seven floors of its Amsterdam facility for a ten-year term ending on December 31, 2027, with an option for the sub-lessee to extend until December 31, 2031. In February 2020, the Company amended the agreement to sub-lease to take back one of the three floors effective March 1, 2020. The fixed lease payments to be received during the remaining term under the agreement to sub-lease amount to $ 6.6 million (EUR 5.4 million) as of December 31, 2020. ​ Operating lease liabilities ​ The components of lease cost in accordance with the new lease accounting standard were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2020 2019 ​ ​ (in thousands) Operating lease cost ​ $ 5,052 ​ $ 4,474 Variable lease cost ​ ​ 607 ​ ​ 507 Sublease income ​ ​ ( 904 ) ​ ​ ( 1,053 ) Total lease cost ​ $ 4,755 ​ $ 3,928 ​ 136 ​ Table of Contents The rent expense in accordance with the historical lease accounting standard for the year ended December 31, 2018, was calculated on a straight-line basis over the term of the lease and considered $ 12.2 million of lease incentives received. Aggregate rent expense was as follows: ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2018 ​ ​ (in thousands) Rent expense - Lexington ​ $ 1,583 Rent expense - Amsterdam ​ ​ 1,667 Total lease cost ​ $ 3,250 ​ The table below presents the lease-related assets and liabilities recorded on the Consolidate balance sheets in accordance with the new lease accounting standard. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2020 ​ 2019 ​ ​ (in thousands) Assets ​ ​ ​ ​ ​ ​ Operating lease right-of-use assets ​ $ 26,086 ​ ​ 26,797 Liabilities ​ ​ ​ ​ ​ ​ Current ​ ​ ​ ​ ​ ​ Current operating lease liabilities ​ ​ 5,524 ​ ​ 5,865 Non-current ​ ​ ​ ​ ​ ​ Non-current operating lease liabilities ​ ​ 30,403 ​ ​ 31,133 Total lease liabilities ​ $ 35,927 ​ ​ 36,998 ​ Other information The weighted-average remaining lease term as of December 31, 2020, is 9.4 years, compared to 10.3 years as of December 31, 2019, and the weighted-average discount rate as of December 31, 2020, is 11.37 % , compared to 11.33 % as of December 31, 2019. The Company derived the weighted-average discount rate, adjusted for differences such as in the term and payment patterns, from the Company’s loan from Hercules capital which was refinanced immediately prior to the January 1, 2019, adoption date in December 2018. The table below presents supplemental cash flow and non-cash information related to leases required in accordance with the new lease accounting standard. ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2020 2019 ​ ​ (in thousands) Operating cash flows for operating leases (1) ​ $ 5,769 ​ $ 4,717 ​ (1) The Company has received $ 1.5 million of landlord incentive payments for the year ended December 31, 2019, which are not included in the cash paid amounts.) The Company did not obtain any right-of-use assets in exchange for the lease obligations during the year ended December 31, 2020. Besides the initial recognition of operating right-of-use assets of $ 19.0 million upon adoption of the new lease standards on January 1, 2019, the Company obtained $ 9.0 million of additional right-of-use assets in exchange for lease obligations during the year ended December 31, 2019. ​ ​ ​ ​ ​ ​ ​ ​ 137 ​ Table of Contents Undiscounted cash flows The table below reconciles the undiscounted cash flows as of December 31, 2020, for each of the first five years and the total of the remaining years to the operating lease liabilities recorded on the Consolidated balance sheet as of December 31, 2020 in accordance with the new lease accounting standard. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Lexington ​ Amsterdam (1) ​ Total ​ (in thousands) 2021 $ 3,455 ​ $ 2,069 ​ $ 5,524 2022 ​ 3,552 ​ ​ 2,069 ​ ​ 5,621 2023 ​ 3,650 ​ ​ 2,069 ​ ​ 5,719 2024 ​ 4,146 ​ ​ 2,069 ​ ​ 6,215 2025 ​ 4,465 ​ ​ 2,069 ​ ​ 6,534 Thereafter ​ 16,279 ​ ​ 12,239 ​ ​ 28,518 Total lease payments $ 35,547 ​ $ 22,584 ​ $ 58,131 ​ ​ ​ ​ ​ ​ ​ ​ ​ Less: amount of lease payments representing interest payments ​ ( 12,576 ) ​ ​ ( 9,628 ) ​ ​ ( 22,204 ) Present value of lease payments ​ 22,971 ​ ​ 12,956 ​ ​ 35,927 Less: current operating lease liabilities ​ ( 3,455 ) ​ ​ ( 2,069 ) ​ ​ ( 5,524 ) Non-current operating lease liabilities $ 19,516 ​ $ 10,887 ​ $ 30,403 (1) Payments are due in EUR and have been translated at the foreign exchange rate as of December 31, 2020, of $ 1.23 / €1.00) ​ 7. Intangible assets ​ a. Acquired licenses ​ The following table presents the Company’s acquired licenses as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2020 ​ 2019 ​ ​ (in thousands) Licenses ​ $ 5,660 ​ $ 8,317 Less accumulated amortization and impairment ​ ​ ( 2,299 ) ​ ​ ( 2,890 ) Licenses, net ​ $ 3,361 ​ $ 5,427 ​ All intangible assets are owned by uniQure biopharma B.V, a subsidiary of the Company. The acquired licenses have a weighted average remaining life of 8.5 years as of December 31, 2020. ​ During the year ended December 31, 2020, the Company capitalized $ 2.2 million of expenditures related to costs incurred in relation to rights to exclusively evaluate certain technologies during a two-year period that commenced on February 1, 2020. During the same period, the Company disposed of a number of licenses determined to have no alternative future use. During the year ended December 31, 2019, the Company capitalized $ 1.0 million of expenditures related to contractual milestone payments under existing license agreements. ​ As of December 31, 2020, the estimated future amortization expense for each of the five succeeding years and the period thereafter is as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2021 ​ $ 1,277 2022 ​ 427 2023 ​ 144 2024 ​ 144 2025 ​ 144 Thereafter ​ 1,225 Total ​ $ 3,361 ​ 138 ​ Table of Contents The amortization expense related to licenses for the year ended December 31, 2020 was $ 4.6 million (December 31, 2019: $ 0.6 million; December 31, 2018: $ 0.4 million). The impairment expense related to licenses for the year ended December 31, 2020 was $ 0.3 million (December 31, 2019: $ 0.0 million; December 31, 2018 $ 0.1 million). ​ b. Acquired research and development ​ The Company acquired research and development assets as part of its acquisition of InoCard in July 2014. Based on the review of pre-clinical data associated with those assets, the Company does not expect that it will pursue further research related to those assets. Accordingly, the Company recorded a $ 5.4 million impairment loss within research and development expenses in the year ended December 31, 2018, to reduce the asset’s carrying amount to its fair value of nil . ​ 8. Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2020 2019 ​ ​ (in thousands) Accruals for services provided by vendors-not yet billed ​ $ 8,269 ​ $ 5,425 Personnel related accruals and liabilities ​ ​ 7,687 ​ ​ 7,032 Contract liability (see Note 3. Collaboration arrangements) ​ ​ 2,082 ​ ​ — Total ​ $ 18,038 ​ $ 12,457 ​ ​ 9. 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”). On December 6, 2018, the Company signed an amendment to the Second Amended and Restated Loan and Security Agreement that both refinanced the then-existing $ 20.0 million 2016 Amended Facility and provided an additional unconditional commitment of $ 15.0 million as well as a conditional commitment of $ 15.0 million that expired on June 30, 2020 (the “2018 Amended Facility”). At signing of the 2018 Amended Facility, the Company drew down an additional $ 15.0 million for a total of $ 35.0 million outstanding. The 2018 Amended Facility extended the loan’s maturity date from May 1, 2020 until June 1, 2023. The interest-only period was initially extended from November 2018 to January 1, 2021, and was further extended to January 1, 2022, as a result of meeting the provision in the 2018 Amended Facility of raising more than $ 90.0 million in equity financing in September 2019. The Company is required to repay the facility in equal monthly installments of principal and interest between the end of the interest-only period and the maturity date. The interest rate continues to be adjustable and is the greater of (i) 8.85 % or (ii) 8.85 % plus the prime rate less 5.50 % per annum. ​ Under the 2018 Amended Facility, the Company paid a facility fee of 0.50 % of the $ 35.0 million outstanding as of signing and owes a back-end fee of 4.95 % of the outstanding debt. In addition, in May 2020 the Company paid a back-end fee of $ 1.0 million in relation to the 2016 Amended Facility. ​ The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2018 Amended Facility was $ 35.9 million as of December 31, 2020, compared to $ 36.3 million as of December 31, 2019, and is recorded net of discount and debt issuance costs. The foreign currency gain on the loan was $ 3.1 million in 2020 (2019: loss of $ 0.7 million; 2018: loss of $ 0.9 million). The fair value of the loan approximates its carrying amount. Inputs to the fair value of the loan are considered Level 3 inputs. ​ 139 ​ Table of Contents Interest expense recorded during the years ended December 31 was as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in millions) 2020 ​ $ 3.7 2019 ​ 3.7 2018 ​ ​ 2.0 ​ As a covenant in the 2018 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 (i) 65 % of the outstanding balance of principal due or (ii) 100% of worldwide cash and cash equivalents. This restriction on cash and cash equivalents only relates to the location of the cash and cash equivalents, and such cash and cash equivalents can be used at the discretion of the Company. In combination with other covenants, the 2018 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 directly or indirectly pledging its total assets of $ 340.4 million with the exception of $ 115.2 million of cash and cash equivalents and other current assets held by uniQure N.V. ​ The 2018 Amended Facility contains provisions that include the occurrence of a material adverse effect, as defined therein, which would entitle Hercules to declare all principal, interest and other amounts owed by the Company immediately due and payable. As of December 31, 2020, the Company was in compliance with all covenants and provisions. ​ The aggregate maturities of the loan, including $ 7.4 million of coupon interest payments and financing fees, for each of the 29 months after December 31, 2020, are as follows (prior to the January 2021 loan amendment – see Note 18, “Subsequent events”): ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2021 ​ $ 3,141 2022 ​ 25,002 2023 ​ ​ 14,269 Total ​ $ 42,412 ​ ​ 10. Shareholders’ equity ​ As of December 31, 2020, the Company’s authorized share capital is € 3.0 million (or $ 3.7 million when translated at an exchange rate as of December 31, 2020, of $ 1.23 / €1.00), divided into 60,000,000 ordinary shares, each with a nominal value of € 0.05 . Under Dutch law, the authorized share capital is the maximum capital that the Company may issue without amending its articles of association. ​ All ordinary shares issued by the Company were fully paid. Besides the minimum amount of share capital to be held under Dutch law, there are no distribution restrictions applicable to the equity of the Company. ​ As of December 31, 2020, and 2019 and 2018 the Company’s reserves were restricted for payment of dividends for an accumulated foreign currency translation gain of $ 9.9 million in 2020 and accumulated foreign currency translation losses of $ 6.7 million and $ 7.3 million in 2019 and 2018, respectively. ​ On September 10, 2019, the Company completed a follow-on public offering of 4,891,305 ordinary shares at a public offering price of $ 46.00 per ordinary share, and on September 13, 2019, the Company completed the sale of an additional 733,695 ordinary shares at a public offering price of $ 46.00 per ordinary share pursuant to the exercise by the underwriters of the option to purchase additional ordinary shares, resulting in total gross proceeds to the Company of $ 258.8 million. The net proceeds to the Company from this offering were $ 242.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company. The Company deducted $ 0.6 million of expenses incurred related to this offering from additional paid-in capital in the accompanying consolidated balance sheets and reflected this within the proceeds from public offering of shares, net of issuance costs within the cash flows from financing activities. ​ 140 ​ Table of Contents On May 7, 2018, the Company completed a follow-on public offering of 5,175,000 ordinary shares at a public offering price of $ 28.50 per ordinary share, resulting in gross proceeds to the Company of $ 147.5 million. The net proceeds to the Company from this offering were $ 138.4 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company. The Company deducted $ 0.2 million of expenses incurred related to this offering from additional paid-in capital in the accompanying consolidated balance sheet and reflected this within the proceeds from public offering of shares, net of issuance costs within the cash flows from financing activities. ​ In February 2019, the Company issued 37,175 ordinary shares to Hercules pursuant to exercised warrants for $ 0.5 million in aggregate cash consideration. The Company deemed the sale and issuance of these shares to be exempt from registration under the Securities Act in reliance on Regulation S of the Securities Act, as an offshore offering of securities and such shares were issued as restricted shares. Hercules represented to us that they were in compliance with the requirements of Regulation S. ​ ​ ​ ​ ​ ​ 141 ​ Table of Contents 11. Share-based compensation ​ Share-based compensation expense recognized by classification included in the consolidated statements of operations and comprehensive loss was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2020 ​ 2019 ​ 2018 ​ ​ (in thousands) Research and development ​ $ 11,965 ​ $ 8,029 ​ $ 3,994 Selling, general and administrative ​ ​ 9,823 ​ ​ 9,439 ​ ​ 6,699 Total ​ $ 21,788 ​ $ 17,468 ​ $ 10,693 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2020 ​ 2019 ​ 2018 ​ ​ (in thousands) Award type ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 11,434 ​ $ 7,896 ​ $ 4,766 Restricted share units ​ ​ 7,364 ​ ​ 4,117 ​ ​ 3,020 Performance share units ​ ​ 2,990 ​ ​ 5,455 ​ ​ 2,907 Total ​ $ 21,788 ​ $ 17,468 ​ $ 10,693 ​ ​ As of December 31, 2020, the unrecognized compensation cost related to unvested awards under the various share-based compensation plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 23,492 ​ 2.78 Restricted share units ​ ​ 14,489 ​ 2.09 Performance share units ​ ​ 1,763 ​ 1.03 Total ​ $ 39,744 ​ 2.45 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“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 terms similar to the 2014 Plan (together the “2014 Plans”). The Company previously had a 2012 Equity Incentive Plan (the “2012 Plan”). As of December 31, 2020, 14,000 fully vested share options are outstanding (December 31, 2019: 14,000 ) under the 2012 Plan. ​ At the general meeting of shareholders on January 9, 2014, the Company’s shareholders approved the adoption of the 2014 Plan. At the annual general meetings of shareholders in June 2015, 2016 and 2018, uniQure shareholders approved amendments of the 2014 Plan, increasing the shares authorized for issuance by 1,070,000 shares in 2015, 3,000,000 in 2016 and 3,000,000 shares in 2018, for a total of 8,601,471 shares. Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. 142 ​ Table of Contents 2014 Plan The following tables summarize option activity under the Company’s 2014 Plans for the year ended December 31, 2019: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ Weighted average ​ Aggregate intrinsic ​ ordinary shares exercise price remaining contractual life value ​ ​ ​ ​ ​ ​ ​ in years ​ ​ (in thousands) Outstanding at December 31, 2019 ​ 2,683,104 ​ $ 21.29 ​ 7.46 ​ $ 135,238 Granted ​ 653,852 ​ $ 49.63 ​ ​ ​ ​ ​ Forfeited ​ ( 172,548 ) ​ $ 42.03 ​ ​ ​ ​ ​ Expired ​ ( 6,451 ) ​ $ 45.76 ​ ​ ​ ​ ​ Exercised ​ ( 498,678 ) ​ $ 14.43 ​ ​ ​ ​ ​ Outstanding at December 31, 2020 ​ 2,659,279 ​ $ 28.13 ​ 7.18 ​ ​ 32,729 Thereof, fully vested and exercisable at December 31, 2020 ​ 1,542,405 ​ $ 18.05 ​ 6.15 ​ ​ 29,161 Thereof, outstanding and expected to vest after December 31, 2020 ​ 1,116,874 ​ $ 42.06 ​ 8.61 ​ ​ 3,568 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Outstanding and expected to vest at December 31, 2019 ​ 1,346,337 ​ $ 28.76 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 18.4 ​ ​ ​ ​ ​ Granted to directors and officers during the period (options, grant date fair value $ in millions) ​ 209,254 ​ $ 5.7 ​ ​ ​ ​ ​ Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 7.2 ​ ​ ​ ​ ​ ​ The following table summarizes information about the weighted average grant-date fair value of options during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Granted, 2020 653,852 ​ $ 28.08 Granted, 2019 647,526 ​ ​ 23.57 Granted, 2018 937,832 ​ ​ 15.90 Vested, 2020 ​ 713,924 ​ ​ 14.04 Forfeited, 2020 ​ ( 172,548 ) ​ ​ 24.63 ​ The following table summarizes information about the weighted average grant-date fair value of options at December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Outstanding and expected to vest, 2020 1,116,874 ​ $ 24.25 Outstanding and expected to vest, 2019 1,346,337 ​ ​ 17.05 ​ The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, Assumptions 2020 2019 ​ 2018 Expected volatility ​ 70 % ​ 70 % - 75 % ​ 75 % - 80 % Expected terms ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 0.76 % - 1.44 % ​ 1.92 % - 2.87 % ​ 2.67 % - 3.20 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ 143 ​ Table of Contents The Hull & White option model captures early exercises by assuming that the likelihood of exercises will increase when the share price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ The following table summarizes information about options exercised during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Exercised ​ ​ ​ ​ during the year ​ Intrinsic value ​ ​ ​ ​ (in thousands) 2020 498,678 ​ $ 11,927 2019 434,665 ​ 17,700 2018 388,203 ​ 7,515 ​ Restricted Share Units ​ The following table summarizes the RSU activity for the year ended December 31, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2019 ​ 370,830 ​ $ 28.62 Granted ​ 376,799 ​ $ 48.18 Vested ​ ( 206,881 ) ​ $ 24.18 Forfeited ​ ( 73,404 ) ​ $ 46.41 Non-vested at December 31, 2020 ​ 467,344 ​ $ 43.56 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 18.2 Granted to directors and officers during the period (shares, $ in millions) ​ 158,623 ​ $ 7.4 ​ The following table summarizes information about the weighted average grant-date fair value of RSUs granted during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2020 376,799 ​ $ 48.18 2019 198,504 ​ ​ 38.63 2018 262,599 ​ ​ 23.61 ​ The following table summarizes information about the total fair value of RSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2020 $ 12,156 2019 10,152 2018 8,546 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors will vest one year from the date of grant. ​ 144 ​ Table of Contents Performance Share Units ​ The following table summarizes the PSU activity for the year ended December 31, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2019 ​ 479,422 ​ $ 21.17 Granted ​ 91,003 ​ $ 57.56 Vested ​ ( 354,105 ) ​ $ 17.44 Forfeited ​ ( 3,706 ) ​ $ 57.56 Non-vested at December 31, 2020 ​ 212,614 ​ $ 42.32 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of PSUs granted during the period (in $ millions) ​ ​ ​ $ 5.2 ​ In January 2019, the Company awarded PSUs to its executives and other members of senior management. These PSUs were earned in January 2020 based on the Board’s assessment of the level of achievement of agreed upon performance targets through December 31, 2019. The PSUs awarded for the year ended December 31, 2019 will vest on the third anniversary of the grant, subject to the grantee’s continued employment. ​ The following table summarizes information about the weighted average grant-date fair value, determined at of the date these were earned, of PSUs granted during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2020 91,003 ​ $ 57.56 2019 132,362 ​ $ 31.71 2018 — ​ $ — ​ The following table summarizes information about the total fair value of PSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2020 $ 21,852 2019 1,056 2018 1,350 ​ Employee Share Purchase Plan (“ESPP”) ​ In June 2018, the Company’s shareholders adopted and approved an ESPP allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the shares on each purchase date is equal to 85 % of the lower of the closing market price on the offering date or the closing market price on the purchase date of each three-month offering period. During the year ended December 31, 2020, 6,181 shares have been issued (December 31, 2019: 9,202 and December 31, 2018: 2,591 ). As of December 31, 2020, a total of 132,026 ordinary shares remains available for issuance under the ESPP plan. ​ ​ 145 ​ Table of Contents 12. Expenses by nature ​ Operating expenses excluding expenses presented in other expenses included the following expenses by nature: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 2018 ​ ​ (in thousands) Employee-related expenses ​ $ 75,926 ​ $ 59,130 ​ $ 46,254 Laboratory and development expenses ​ 35,977 ​ 30,130 ​ 23,596 Office and housing expenses ​ 13,388 ​ 10,588 ​ 7,281 Legal and advisory expenses ​ 17,370 ​ 11,297 ​ 7,748 Depreciation, amortization, and impairment expenses ​ 10,648 ​ 6,669 ​ 12,415 Patent and license expenses ​ 2,899 ​ 1,654 ​ 1,202 Other operating expenses ​ 8,772 ​ 8,813 ​ 1,618 Total ​ $ 164,980 ​ $ 128,281 ​ $ 100,114 ​ Details of employee-related expenses for the years ended December 31 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 2018 ​ ​ (in thousands) Wages and salaries ​ $ 40,919 ​ $ 32,029 ​ $ 26,646 Share-based compensation expenses ​ 21,831 ​ 17,533 ​ 10,708 Consultant expenses ​ 2,423 ​ 2,464 ​ 2,974 Social security costs ​ 4,068 ​ 2,727 ​ 2,231 Health insurance ​ 2,271 ​ 1,933 ​ 1,471 Pension costs - defined contribution plans ​ 1,779 ​ 1,052 ​ 907 Other employee expenses ​ 2,635 ​ 1,392 ​ 1,317 Total ​ $ 75,926 ​ $ 59,130 ​ $ 46,254 ​ ​ 13. Other non-operating income / (expense) ​ Other non-operating income / (expense) consists of changes in the fair value of derivative financial instruments (see Note 4, “Fair value measurement”). ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2020 ​ 2019 ​ 2018 ​ ​ (in thousands) Other non-operating income: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative gains ​ $ 483 ​ $ — ​ $ 208 Total other non-operating income: ​ ​ 483 ​ ​ — ​ ​ 208 Other non-operating expense: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative losses ​ ​ — ​ ​ ( 2,530 ) ​ ​ — Total other non-operating expense: ​ ​ — ​ ​ ( 2,530 ) ​ ​ — Other non-operating income / (expense), net ​ $ 483 ​ $ ( 2,530 ) ​ $ 208 ​ The Company recorded a net gain of $ 0.5 million for the year ended December 31, 2020, compared to a net loss of $ 2.3 million and a net gain of $ 0.5 million for the years ended December 31, 2019 and December 31, 2018, respectively, related to the derivative financial instruments issued as part of its collaboration with BMS. The $ 0.5 million gain for the year ended December 31, 2020 includes a $ 2.3 million gain related to the reduction of the fair market value of the BMS warrants, a $ 0.8 million gain related to the derecognition of the BMS warrants on December 1, 2020 and a $ 2.6 million loss related to the initial recognition of the derivative financial liability related to the CoC-payment. The Company recorded a net loss of $ 0.2 million and $ 0.3 million for the years ended December 31, 2019 and December 31, 2018, respectively, related to warrants issued to Hercules. ​ ​ ​ 146 ​ Table of Contents 14. Income taxes ​ a. Income tax benefit / (expense) ​ No current tax expense or liabilities were recorded in 2020 by the Company’s Dutch and U.S entities. Due to the uncertainty surrounding the realization of favorable tax attributes in future tax returns, the Company has recorded a full valuation allowance against the Company’s net deferred tax assets in the Netherlands. The Company released the full valuation allowance against the Company’s net deferred tax assets in the United States as of December 31, 2020. ​ There are no significant unrecognized tax benefits as of December 31, 2020 and 2019. ​ For the years ended December 31, 2020, 2019 and 2018, loss before income taxes consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 2018 ​ ​ (in thousands) Dutch operations ​ $ ( 130,493 ) ​ $ ( 111,820 ) ​ $ ( 85,721 ) U.S. operations ​ ( 10,950 ) ​ ( 12,381 ) ​ 2,646 Foreign operations ​ — ​ — ​ 3 Total ​ $ ( 141,443 ) ​ $ ( 124,201 ) ​ $ ( 83,073 ) ​ The income tax benefit / (expense) for the years ended December 31, 2020, 2019 and 2018, consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 2018 ​ ​ (in thousands) Current tax expense ​ ​ ​ ​ ​ ​ ​ ​ ​ Dutch operations ​ $ — ​ $ — ​ $ — U.S. operations ​ — ​ — ​ — Foreign operations ​ — ​ ​ — ​ ( 22 ) Total current tax expense ​ $ — ​ $ — ​ $ ( 22 ) Deferred tax benefit / (expense) ​ ​ ​ ​ ​ ​ Dutch operations ​ $ — ​ $ — ​ $ ( 209 ) U.S. operations ​ 16,419 ​ — ​ — Foreign operations ​ — ​ — ​ — Total deferred tax benefit / (expense) ​ $ 16,419 ​ $ — ​ $ ( 209 ) Total income tax benefit / (expense) ​ $ 16,419 ​ $ — ​ $ ( 231 ) ​ b. Tax rate reconciliation ​ The reconciliation of the amount of income tax benefit / (expense) that would result from applying the Dutch statutory income tax rate to the Company’s reported amount of income tax benefit / (expense) for the years ended December 31, 2020, 2019 and 2018, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2020 ​ 2019 ​ 2018 ​ ​ (in thousands) Loss before income tax income / (expense) for the period ​ $ ( 141,443 ) ​ $ ( 124,201 ) ​ $ ( 83,073 ) Expected income tax benefit at the tax rate enacted in the Netherlands (25%) ​ 35,361 ​ 31,050 ​ 20,768 Difference in tax rates between the Netherlands and the U.S. as well as other foreign countries ​ 247 ​ ( 495 ) ​ ( 106 ) Release of valuation allowance related to expected future taxable income of U.S. operations ​ ​ 16,419 ​ ​ — ​ ​ — Other net change in valuation allowance ​ ( 30,568 ) ​ ( 25,583 ) ​ ( 19,207 ) Nondeductible expenses ​ ( 5,041 ) ​ ( 4,972 ) ​ ( 2,648 ) Change in fair value of contingent consideration ​ — ​ — ​ 962 Income tax benefit / (expense) ​ $ 16,419 ​ $ — ​ $ ( 231 ) 147 ​ Table of Contents ​ Nondeductible expenses predominantly relate to share-based compensation expenses and affected the effective tax rate by an amount of $ 5.8 million in 2020 (2019: $ 4.4 million; 2018: $ 2.7 million). Derivative financial instruments affected the effective tax rate by income of $ 0.8 million in 2020 (expense of $ 0.6 million in 2019; $ 0.0 million in 2018), which reduced the nondeductible expenses resulting from share-based compensation expenses. ​ c. Significant components of deferred taxes ​ The tax effects of temporary differences and carryforwards that give rise to significant portions of deferred tax assets and deferred tax liabilities at December 31, 2020 and 2019 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2020 ​ 2019 ​ ​ (in thousands) Deferred tax assets: ​ ​ Net operating loss carryforwards ​ $ 158,614 ​ $ 99,644 Lease liabilities ​ ​ 9,515 ​ ​ 7,861 Intangible assets ​ 1,702 ​ 770 Interest carryforwards ​ ​ 1,597 ​ ​ — Accrued expenses and other current liabilities ​ ​ 1,118 ​ ​ 628 Property, plant and equipment ​ 1,072 ​ 761 Derivative financial instrument ​ ​ 661 ​ ​ - Deferred revenue ​ — ​ 6,676 Gross deferred tax asset ​ $ 174,279 ​ $ 116,340 Less valuation allowance ​ ( 150,113 ) ​ ( 109,856 ) Net deferred tax asset ​ $ 24,166 ​ $ 6,484 Right-of-use asset ​ ​ ( 7,702 ) ​ ​ ( 6,484 ) Prepaid expenses ​ ​ ( 45 ) ​ ​ — Deferred tax liability ​ $ ( 7,747 ) ​ $ ( 6,484 ) Net deferred tax asset ​ $ 16,419 ​ $ — ​ Changes in the valuation allowance were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 2018 ​ ​ (in thousands) January 1, ​ $ 109,856 ​ $ 85,100 ​ $ 93,682 Changes related to reduction of deferred revenue recorded in equity upon implementation of ASC 606 Revenue recognition as of January 1, 2018 ​ ​ — ​ ​ — ​ ​ ( 6,229 ) Changes recorded in profit and loss ​ ​ 30,568 ​ ​ 25,583 ​ ​ 19,207 Increase/(reduction) related to 2020, 2019 and 2018 Dutch tax reforms ​ 18,287 ​ 4,059 ​ ( 15,670 ) Release of valuation allowance related to expected current year and future periods recorded in profit and loss ​ ​ ( 16,419 ) ​ ​ — ​ ​ — Other changes including currency translation effects ​ 7,821 ​ ( 4,886 ) ​ ( 5,890 ) December 31, ​ $ 150,113 ​ $ 109,856 ​ $ 85,100 ​ Included within changes recorded in profit and loss for the year ended December 31, 2020 are benefits of $ 1.2 million from the utilization of U.S. net operating loss carryforwards ($ 0.8 million for the year ended December 31, 2019 and $ 0.9 million for the year ended December 31, 2018). ​ The valuation allowance as of December 31, 2020 is primarily related to net operating loss carryforwards in the Netherlands that, in the judgment of management, are not more-likely than-not to be realized. In addition, the valuation allowance as of December 31, 2019 included deferred tax assets for net operating loss carryforwards and temporary differences in the United States of America. Management considered projected future taxable income and tax-planning strategies in making this assessment. A valuation allowance will be recorded against deferred tax assets if it is more likely than not that some or all the deferred tax assets will not be realized. ​ 148 ​ Table of Contents Netherlands ​ The Company determined that in accordance with Dutch tax law it would recognize the CSL Behring License Revenue as well as the License Fees as taxable results as of the date on which the Company is contractually entitled to receive (or obligated to make) a payment under the CSL Behring Agreement. The Company expects to continue to incur taxable losses in the Netherlands except for the period in which it would receive the $ 450.0 million upfront payment under the CSL Behring Agreement. In the event that the Company recognizes the $ 450.0 million upfront payment in 2021, such payment is expected to be subject to Dutch corporate income tax at a rate of 25.0 %. However, the Company does not expect that it will be required to pay any income taxes in the period in which it recognizes the $ 450.0 million upfront payment as taxable revenue, as such payment is not expected to exceed the net operating losses that it carries forward in the Netherlands. The Company specifically assessed the impact of the CSL Behring agreement with respect to retaining a full valuation allowance as of December 31, 2020. Closing of the CSL Behring Agreement is contingent on the successful completion of reviews under the antitrust laws in the United States, Australia, and the United Kingdom. The transactions have not closed as of December 31, 2020 as the Company received a Second Request from the United States Federal Trade Commission, on January 4, 2021. Closing of the transaction is dependent on the timing, extent, and result of the Second Request. In its assessment of whether or not it was more likely than not that the Company’s deferred tax assets in the Netherlands will be realized, the Company considered all relevant facts and circumstances, including similar regulatory reviews as well as the five-year cumulative losses reported by the Company in the Netherlands. The Company concluded that it should continue to record a full valuation allowance as of December 31, 2020 in relation to its Dutch net operating loss carryforwards. ​ A portion of the valuation allowance for deferred tax assets relates to follow-on offering costs. Any subsequently recognized tax benefits will be credited directly to contributed capital. As of December 31, 2020, that amount was $ 7.7 million ($ 6.9 million as of December 31, 2019). The change is attributable to changes in the foreign currency rate. ​ The Dutch corporate tax rate for fiscal years 2018, 2019 and 2020 was 25 %. During the years 2018 and 2019, the Dutch government enacted various changes to the corporate income tax rate applicable to future fiscal years. In September 2020, further changes were enacted that retain the corporate rate at 25 % from 2021 onwards. ​ A tax reform in December 2018 limited the carryforward of tax losses arising from January 1, 2019, to six years after the end of the respective period. Tax losses incurred prior to this date continue to expire nine years after the end of the respective period. ​ As of December 31, 2020, new loss compensation rules were accepted by the Dutch Senate. However, the bill includes a provision that the new compensation rules will be effective by a separate Governmental Decree, which has not been introduced as of December 31, 2020. Hence, the new loss compensation rules are not enacted as of December 31, 2020. If enacted, the rules allow losses to be carried forward indefinitely, but from fiscal year 2022 onwards would limit offsetting taxable profit in excess of EUR 1.0 million to 50% of the taxable profit. ​ The Dutch fiscal unity as of December 31, 2020 has an estimated $ 588.2 million (2019: $ 414.0 million; 2018: $ 311.7 million) of taxable losses that can be offset in the following six to seven years . The expiration dates of these Dutch losses are summarized in the following table. In the year ended December 31, 2020 unused tax losses of $ 18.5 million (December 31, 2019: $ 20.7 million) expired. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 2021 2022 2023 2024 2025-2027 ​ ​ (in thousands) Loss expiring ​ $ 15,206 ​ $ 25,878 ​ $ 25,202 ​ $ — ​ $ 521,931 ​ The fiscal periods after 2017 are still open for inspection by the Dutch tax authorities. ​ United States of America ​ The federal corporate tax rate in the U.S. is 21 %. In addition, the Company is subject to state taxes resulting in a combined tax rate of 27.32 % for its U.S. operation. As of December 31, 2020, an estimated $ 42.3 million of net operating losses remain to be carried forward. These losses will expire between 2035 and 2037. ​ 149 ​ Table of Contents The Company’s U.S. operations generated taxable income in the fiscal years 2018, 2019 and 2020. Based on the current design of the Company’s worldwide operations, the Company expects to continue to generate taxable income in the U.S. during the foreseeable future. As of December 31, 2020, the Company considers it more likely than not that it will utilize its net deferred tax assets in the U.S. and therefore released the remaining valuation allowance of $ 16.4 million through profit and loss as of this date. ​ Under the provision of the Internal Revenue Code, the U.S. net operating losses may become subject to an annual limitation in the event of certain cumulative exchange in the ownership interest of significant shareholders over a three-year period in excess of 50 percent, as defined under Section 382 and 383 of the Internal Revenue Code. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation. ​ The fiscal periods after 2017 are still open for inspection by the Internal Revenue Service. The Company is currently not under examination by the IRS for any tax years. ​ ​ 15. 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 in the years presented, 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 shares are presented without giving effect to the application of the treasury method or exercise prices that would be above the share price as of December 31, 2020, December 31, 2019, and December 31, 2018, respectively. In addition, the BMS warrants were not exercisable as of December 31, 2019, and December 31, 2018, since this would have required the prior designation of Collaboration Targets by BMS. This would generally have resulted in a lower number of potentially dilutive ordinary shares as some stock option grants as well as the BMS warrants would have been excluded. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2020 2019 ​ 2018 ​ ​ (ordinary shares) BMS warrants (derecognized as of December 1, 2020 - see Note 4, "Fair value measurement") ​ — ​ 8,893,000 ​ 8,575,000 Stock options under 2014 Plans ​ 2,659,279 ​ 2,683,104 ​ 2,673,712 Non-vested RSUs and earned PSUs ​ 679,958 ​ 850,252 ​ 789,490 Stock options under previous option plan ​ 14,000 ​ 14,000 ​ 32,567 Hercules warrants (exercised February 1, 2019) ​ — ​ — ​ 37,175 Employee share purchase plan ​ 560 ​ 485 ​ 1,012 Total potential dilutive ordinary shares ​ 3,353,797 ​ 12,440,841 ​ 12,108,956 ​ ​ ​ 16. Commitments and contingencies ​ In the course of its business, the Company enters as a licensee into contracts with other parties regarding the development and marketing of its pipeline products. Among other payment obligations, the Company is obligated to pay royalties to the licensors based on future sales levels and milestone payments whenever specified development, regulatory and commercial milestones are met. As both future sales levels and the timing and achievement of milestones are uncertain, the financial effect of these agreements cannot be estimated reliably. ​ 150 ​ Table of Contents 17. Related party transaction ​ Between June 2015 and December 2020, BMS was considered a related party due to the combination of its equity investment in the Company (December 31, 2020: 2.4 million ordinary shares or 5.3 % of outstanding ordinary shares), the warrants as well as the potential obligations arising from the expansion of collaboration targets. On December 1, 2020, the Company entered into the amended BMS CLA. All transactions subsequent to the effective date of the amended BMS CLA are considered to no longer be with a related party due to the elimination of the potential obligations related to additional Collaboration Targets (see Note 3 “Collaboration arrangements and concentration of credit risk”) as well as the elimination of the BMS warrants (see Note 4, “Fair value measurement”). ​ On September 14, 2020, the Company appointed Ricardo Dolmetsch, Ph.D. as President, Research and Development. Dr. Dolmetsch succeeded Sander van Deventer, M.D., Ph.D., the former Executive Vice President, Research and Product Development. On August 25, 2020, the Company entered into a separation agreement with Robert Gut, M.D., Ph.D., pursuant to which Dr. Gut transitioned from his role as Chief Medical Officer on October 14, 2020, to be appointed a non-executive director of the Board of Directors. On December 1, 2020, at an extraordinary general meeting, the Company’s shareholders voted to approve the appointment of Dr. Gut as a non-executive director on the Board of Directors. Dr. Gut had previously been appointed as a non-executive director on the Board of Directors on June 13, 2018 by the Company’s shareholders and had resigned as a non-executive director on August 20, 2018, to be appointed as the Company’s Chief Medical Officer. On October 24, 2018, at an extraordinary general meeting, the Company’s shareholders voted to approve the appointment of Dr. Gut as an executive director on the Board of Directors. ​ On June 17, 2020, the Company’s shareholders voted to approve the appointment of Leonard E. Post, Ph.D., as a non-executive director of the Board of Directors. Dr. Post replaced Dr. David Schaffer, whose term as a non-executive director of the Board of Directors ended on the same date. Dr. Post has also assumed the role of chair of the Company’s Research and Development Committee of the Board of Directors. ​ On August 20, 2019, the Company promoted Alex Kuta, Ph.D., to Executive Vice President, Operations. Dr. Kuta, in addition to regulatory affairs, became responsible for global quality as well as GMP manufacturing at the Company’s facility in Lexington, Massachusetts. As of the same date Sander van Deventer, M.D., Ph.D., was promoted to Executive Vice President, Research and Product Development, and Dr. van Deventer, in addition to his responsibilities for research, also became responsible for the Company’s product development. As a result of these changes Scott McMillan, Ph.D. retired from uniQure. The employment of Dr. van Deventer terminated on September 14, 2020. ​ In August 2019, the Company entered into an Amended and Restated Agreement Collaboration and License Agreement (“Amended CLA”) as well as an additional new Collaboration and License Agreement (“New CLA”) with its related party 4DMT Molecular Therapeutics, Inc. (“4DMT”). In the Amended CLA, the Company received from 4DMT an exclusive, sublicensable, worldwide license under certain 4DMT intellectual property rights to research, develop, make, use, and commercialize previously selected Adeno-associated virus (“AAV”) capsid variants and certain associated products using 4DMT proprietary AAV technology for delivery of gene therapy constructs to cells in the central nervous system and the liver (“the Field”). In the New CLA, the parties agreed to research and develop, at 4DMT’s cost, new AAV capsid variants using 4DMT proprietary AAV technology for delivery of up to six additional transgene constructs in the Field that will be selected by the Company. As of June 2020, 4DMT is no longer considered a related party as a result of David Schaffer no longer being a non-executive member of the Company’s Board of Directors. ​ 151 ​ Table of Contents 18. Subsequent events ​ Amendment Loan Facility ​ As of December 31, 2020, a $ 35.0 million term loan was outstanding in accordance with the 2018 Amended Facility between the Company and Hercules. ​ On January 29, 2021, the Company and Hercules amended the Company’s loan facility with Hercules Capital Inc. entered, (“2021 Amended Facility”). Pursuant to the 2021 Amended Facility, Hercules agreed to the 2021 Term Loan, increasing the aggregate principal amount of the term loan facility from $ 35.0 million to $ 135.0 million. On January 29, 2021, the Company drew down $ 35.0 million of the 2021 Term Loan. The Company may draw down the remaining $ 65.0 million under the 2021 Term Loan in a series of one or more advances of not less than $ 20.0 million each until December 15, 2021. Advances under the 2021 Term Loan bear interest at a rate equal to the greater of (i) 8.25 % or (ii) 8.25 % plus the prime rate, less 3.25 % per annum. The principal balance and all accrued but unpaid interest on advances under 2021 Term Loan is due on June 1, 2023, which date may be extended by the Company by up to two twelve-month periods. Advances under the 2021 Term Loan may not be prepaid until six months after the Closing Date, following which the Company may prepay all such advances without charge. ​ In addition to the 2021 Term Loan, the amendment also extends the interest-only payment period of the previously funded $ 35.0 million term loan from January 1, 2022 to June 1, 2023. ​ The Company paid a $ 0.4 million facility charge on January 29, 2021. End of term charges in respect of advances under the 2021 Term Loan range from 1.65 % to 6.85 % depending on the maturity date. ​ 152 ​ Table of Contents EXHIBIT INDEX ​ Exhibit No. Description 3.1 ​ Amended Articles of Association of the Company (incorporated by reference to Exhibit 3.1 of the Company’s annual report on Form 10-K for the year ended December 31, 2018 (file no. 0001-36294) filed with the Securities and Exchange Commission). 4.1* ​ Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934. 10.1 t ​ 2014 Share Incentive Plan (incorporated by reference to Exhibit 4.3 of the Company's registration statement on Form S-8 (file no. 333-225629) filed with the Securities and Exchange Commission). 10.2 t ​ Form of Inducement Share Option Agreement under 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.2 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 10.3 t ​ Form of Share Option Agreement under 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.3 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 10.4 t ​ Form of Restricted Stock Unit Award under the 2014 Share Incentive (incorporated by reference to Exhibit 10.4 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2017 filed with the Securities and Exchange Commission). 10.5 t ​ Form of Performance Stock Unit Award under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.5 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2017 filed with the Securities and Exchange Commission). 10.6 t ​ Employment Agreement dated December 9, 2014 between uniQure, Inc. and Matthew Kapusta (incorporated by reference to Exhibit 10.6 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 10.7 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated March 14, 2017 (incorporated by reference to Exhibit 10.7 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 10.8 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated October 26, 2017 (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 31, 2017 filed with the Securities and Exchange Commission). 10.10 ​ Patent License Agreement (L-107-2007), effective as of May 2, 2007, by and between the Company and the National Institutes of Health, as amended on December 31, 2009, May 31, 2013, and November 11, 2013 (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on March 31, 2017 filed with the Securities and Exchange Commission). 10.11 ​ Patent License Agreement (L-116-2011), effective as of August 10, 2011, by and between the Company and National Institutes of Health, as amended on May 31, 2013 and November 11, 2013 (incorporated by reference to Exhibit 10.2 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on March 31, 2017 filed with the Securities and Exchange Commission). 10.18 ​ Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between the Company and King113 Hartwell LLC (incorporated by reference to Exhibit 10.28 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the Securities and Exchange Commission). 10.19 ​ Business Acquisition Agreement, dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding N.V., the Company and the other Parties listed therein (incorporated by reference to Exhibit 10.29 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the Securities and Exchange Commission). 153 ​ Table of Contents 10.20 ​ Deed of Assignment of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of April 5, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.30 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the Securities and Exchange Commission). 10.21 ​ Agreement for Transfer of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.31 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the Securities and Exchange Commission). 10.26 ​ Second Amended and Restated Loan and Security Agreement, dated as of May 6, 2016 by and among uniQure Biopharma B.V., uniQure, Inc., uniQure IP B.V., the Company's subsidiaries listed therein, and Hercules Technology Growth Capital, Inc (incorporated by reference to Exhibit 10.30 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission . 10.27† ​ Collaboration and License Agreement by and between uniQure Biopharma B.V. and Bristol-Myers Squibb Company dated April 6, 2015 (incorporated by reference to Exhibit 4.30 of the Company's annual report on Form 20-F (file no. 001-36294) filed with the Securities and Exchange Commission). 10.29† ​ Investor Agreement by and between uniQure Biopharma B.V. and Bristol-Myers Squibb Company dated April 6, 2015 (incorporated by reference to Exhibit 4.32 of the Company's annual report on Form 20-F (file no. 001-36294) filed with the Securities and Exchange Commission). 10.32 ​ Lease relating to Paasheuvelweg 25, dated as of March 7, 2016, by and between 52 IFH GmbH & Co. KG and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.36 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 10.34 t ​ Employment Agreement dated August 4, 2017 between uniQure biopharma B.V. and Sander van Deventer (incorporated by reference to Exhibit 10.2 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2017 filed with the Securities and Exchange Commission). 10.36 t ​ Employment Agreement dated July 15, 2017 between uniQure biopharma B.V. and Christian Klemt (incorporated by reference to Exhibit 10.4 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2017 filed with the Securities and Exchange Commission). 10.37† ​ Assignment and License Agreement dated April 17, 2017 between Professor Paolo Simioni and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.1 of the Company’s periodic report on Form 8-K (file no. 001-36294) filed on October 19, 2017 with the Securities and Exchange Commission). 10.38t Employment Agreement dated August 20, 2018 by and between uniQure, Inc. and Dr. Robert Gut (incorporated by reference to Exhibit 10.38 of the Company’s annual report on Form 10-K for the year ended December 31, 2018 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.39 ​ Amendment No. 1 to Second Amended and Restated Loan and Security Agreement dates as of December 6, 2018 by and among uniQure Biopharma B.V., uniQure, Inc., uniQure IP B.V., the Company, and Hercules Technology Growth Capital, Inc (incorporated by reference to Exhibit 10.1 of the Company's current report on Form 8-K (file no. 001-36294) filed with the Securities and Exchange Commission) filed on December 10, 2018. 10.40 ​ First Amendment Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between the Company and King113 Hartwell LLC (incorporated by reference to Exhibit 10.1 of the Company's current report on form 8-K (file no. 001-36294) filed with the Securities and Exchange Commission) filed on November 15, 2018. 10.41t ​ Employee Share Purchase Plan (incorporated by reference to Exhibit 4.2 of the Company's registration statement on Form S-8 (file no. 333-225629) filed with the Securities and Exchange Commission) filed on June 14, 2018. 154 ​ Table of Contents 10.42 ​ Second Amendment Lease relating to 113 Hartwell Avenue, Lexington Massachusetts, dated as of June 17, 2019, by and between the Company and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.42 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2019 filed with the Securities and Exchange Commission). 10.43 ​ Form of Share Option Agreement, effective June 18, 2019, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.43 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2019 filed with the Securities and Exchange Commission). 10.44t ​ Amended and Restated Employment Agreement, executed September 17, 2019, by and between the Company and Dr. Kuta (incorporated by reference to Exhibit 10.1 of the Company’s current report on Form 8-K (file no. 001-36294) filed with the Securities and Exchange Commission) filed on September 20, 2019. 10.45t ​ Employment Agreement, executed September 17, 2019, by and between the Company and Dr. Sander van Deventer (incorporated by reference to Exhibit 10.2 of the Company’s current report on form 8-K (file no. 001-36294) filed with the Securities and Exchange Commission) filed on September 20, 2019. 10.47 ​ Amended and Restated Collaboration and License Agreement by and between 4D Molecular Therapeutics, Inc and uniQure biopharma B.V., dated August 6, 2019 (incorporated by reference to Exhibit 10.4 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 30, 2019 filed with the Securities and Exchange Commission). 10.48 ​ Collaboration and License Agreement by and between 4D Molecular Therapeutics, Inc and uniQure biopharma B.V., dates August 6, 2019 (incorporated by reference to Exhibit 10.5 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 30, 2019 filed with the Securities and Exchange Commission). 10.49t ​ Amended and Restated Employment Agreement, executed March 1, 2020 by and between uniQure biopharma B.V. and Christian Klemt (incorporated by reference to Exhibit 10.49 of the Company’s annual report on Form 10-K for the year ended December 31, 2019 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.50t ​ Amended and Restated Employment Agreement, executed March 1, 2020 by and between uniQure Inc. and Dr. Robert Gut (incorporated by reference to Exhibit 10.50 of the Company’s annual report on Form 10-K for the year ended December 31, 2019 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.51t ​ Amended and Restated Employment Agreement, executed March 1, 2020 by and between uniQure Inc. and Maria Cantor (incorporated by reference to Exhibit 10.51 of the Company’s annual report on Form 10-K for the year ended December 31, 2019 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.52t ​ Amended and Restated Employment Agreement, executed March 1, 2020 by and between uniQure Inc. and Jonathan Garen (incorporated by reference to Exhibit 10.52 of the Company’s annual report on Form 10-K for the year ended December 31, 2019 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.53† ​ Commercialization and License Agreement by and between uniQure biopharma B.V. and CSL Behring LLC dated June 24, 2020 (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2020 filed with the Securities and Exchange Commission). 10.54t ​ Separation agreement, executed August 25, 2020, by and between uniQure biopharma B.V. and Sander van Deventer (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 30, 2020 filed with the Securities and Exchange Commission). 10.55t ​ Separation agreement, executed August 25, 2020, by and between uniQure Inc. and Robert Gut (incorporated by reference to Exhibit 10.2 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 30, 2020 filed with the Securities and Exchange Commission). 10.56t ​ Employment agreement, executed September 14, 2020, by and between uniQure Inc. and Ricardo Dolmetsch (incorporated by reference to Exhibit 10.3 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on September 30, 2020 filed with the Securities and Exchange Commission). 155 ​ Table of Contents 10.57*† ​ Amendment to Collaboration and License Agreement by and between uniQure Biopharma B.V. and Bristol-Myers Squibb Company dated December 1, 2020. 10.58* ​ Amendment No. 2 to Second Amended and Restated Loan and Security Agreement as of January 29, 2021 by and among uniQure Biopharma B.V., uniQure, Inc., uniQure IP B.V., the Company and Hercules Capital Inc. 14.1 ​ Code of Ethics (incorporated by reference to Exhibit 14.1 of the Company's annual report on Form 10-K (file no. 001-36294) for the period ending December 31, 2016 filed with the Securities and Exchange Commission). 21.1* ​ Subsidiaries of the Company . 23.1* ​ Consent of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 23.2* ​ Consent of Independent Registered Public Accounting Firm – PricewaterhouseCoopers Accountants N.V. 24.1* ​ Power of Attorney (incorporated by reference to the signature page of this Annual Report on Form 10-K) . 31.1* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Executive Officer . 31.2* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Financial Officer . 32.1* ​ Section 1350 Certification . 101* ​ The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2020, formatted in Inline XBRL (eXtensible Business Reporting Language): (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations and Comprehensive Income (Loss), (iii) Consolidated Statements of Shareholders’ Equity, (iv) Consolidated Statements of Cash Flows and (v) Notes to Consolidated Financial Statements. 104* ​ The cover page from the Company’s Annual Report on Form 10-K for the year ended December 31, 2020, has been formatted in Inline XBRL. ​ ​ † Confidential treatment requested as to certain portions, which portions have been omitted and filed separately with the Securities and Exchange Commission ​ * Filed herewith ​ t Indicates a management contract or compensatory plan or arrangement. ​ ​ ​ 156 ​ Table of Contents SIGNATURES ​ Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ​ ​ ​ ​ ​ UNIQURE, N.V. ​ ​ ​ ​ By: /s/ MATTHEW KAPUSTA ​ ​ Matthew Kapusta ​ ​ Chief Executive Officer (Principal Executive and Financial Officer) ​ POWER OF ATTORNEY ​ KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Matthew Kapusta and Christian Klemt, jointly and severally, his or her attorney-in-fact, with the power of substitution, for him or her in any and all capacities, to sign any amendments to this Annual Report on Form 10-K and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact, or his or her substitute or substitutes, may do or cause to be done by virtue hereof. ​ Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated. ​ Signatures Title Date ​ ​ ​ ​ ​ /s/ MATTHEW KAPUSTA ​ Chief Executive Officer, Chief Financial Officer and Director (Principal Executive and Financial Officer) ​ March 1, 2021 Matthew Kapusta ​ ​ ​ ​ ​ ​ ​ /s/ CHRISTIAN KLEMT ​ Chief Accounting Officer ​ March 1, 2021 Christian Klemt ​ ​ ​ ​ ​ ​ ​ /s/ PHILIP ASTLEY SPARKE ​ Director ​ March 1, 2021 Philip Astley Sparke ​ ​ ​ ​ ​ ​ ​ /s/ MADHAVAN BALACHANDRAN ​ Director ​ March 1, 2021 Madhavan Balachandran ​ ​ ​ ​ ​ ​ ​ /s/ ROBERT GUT ​ Director ​ March 1, 2021 Robert Gut ​ ​ ​ ​ ​ ​ ​ /s/ JACK KAYE ​ Director ​ March 1, 2021 Jack Kaye ​ ​ ​ ​ ​ ​ ​ /s/ DAVID MEEK ​ Director ​ March 1, 2021 David Meek ​ ​ ​ ​ ​ ​ ​ /s/ LEONARD POST ​ Director ​ March 1, 2021 ​ Leonard Post ​ ​ ​ ​ ​ ​ ​ /s/ PAULA SOTEROPOULOS ​ Director ​ March 1, 2021 Paula Soteropoulos ​ ​ ​ ​ ​ ​ ​ ​ ​ /s/ JEREMY P. SPRINGHORN ​ Director ​ March 1, 2021 Jeremy P. Springhorn ​ ​ ​ ​ ​ 157 ​