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”, our principal executive officer) and chief financial officer (“CFO”, our principal 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, 2021. Based on such evaluation, our CEO and CFO have concluded that as of December 31, 2021, 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, 2021. This assessment was performed under the direction and supervision of our CEO and CFO 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, 2021, based on criteria established in the COSO 2013 framework. 102 ​ Table of Contents ​ 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, 2021. Their report is filed within this Annual Report on Form 10-K. ​ Inherent Limitations of Internal Controls Our management, including our CEO and CFO, 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. ​ Changes in internal control over financial reporting During the fourth quarter of 2021, 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. ​ Item 9B. Other Information ​ None. ​ ​ 103 ​ 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 2022 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 2022 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 2022 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 2022 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 2022 Annual Meeting of Shareholders or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 104 ​ 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. 107 Consolidated Balance Sheets as of December 31, 2021 and 2020 110 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2021, 2020 and 2019 111 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2021, 2020 and 2019 112 Consolidated Statements of Cash Flows for the Years Ended December 31, 2021, 2020 and 2019 113 Notes to Consolidated Financial Statements for the Years Ended December 31, 2021, 2020 and 2019 114 ​ (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. ​ ​ 105 ​ Table of Contents ​ ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS FOR THE YEARS ENDED DECEMBER 31, 2021, 2020 AND 2019 ​ ​ ​ Page Report of Independent Registered Public Accounting Firm - KPMG Accountants N.V. , Amstelveen, The Netherlands (PCAOB ID 1012 ) 107 Consolidated Balance Sheets as of December 31, 2021 and 2020 110 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2021, 2020 and 2019 111 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2021, 2020 and 2019 112 Consolidated Statements of Cash Flows for the Years Ended December 31, 2021, 2020 and 2019 113 Notes to Consolidated Financial Statements 114 ​ ​ ​ 106 ​ 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, 2021 and 2020, the related consolidated statement of operations and comprehensive loss, shareholders’ equity, and cash flows for each of the years in the three-year period ended December 31, 2021, 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, 2021, 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, 2021 and 2020, and the results of its operations and its cash flows for each of the years in the three year-period ended December 31, 2021, 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, 2021 based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. 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. 107 ​ 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 Matter 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 f inancial 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. Evaluation of the acquisition of Corlieve as a business combination As discussed in Notes 2.3.5 and 3 to the consolidated financial statements, the Company acquired 97.7% of the outstanding ordinary shares of Corlieve for a total purchase price of EUR 65.8 million. The Company applied the applicable accounting guidance which requires the acquirer to assess whether the acquisition should be accounted for as an asset acquisition or a business combination. ​ We identified the evaluation of the acquisition as a business combination to be a critical audit matter. This evaluation required significant auditor judgement to assess whether or not substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets based on the similarities of risks associated with managing and creating outputs from the assets, including the acquired workforce and identification of intangible assets. ​ The following are the primary procedures we performed to address this critical audit matter: ​ ‒ We evaluated the design and tested the operating effectiveness of certain internal controls related to the business combination process, including controls related to technical accounting review and over the completeness of assets and liabilities acquired. ‒ We read the sale and purchase agreement and performed inquires with management and business development personnel to understand the business rationale for acquiring Corlieve. ‒ We read the employment terms and inquired of management and business development personnel to challenge management’s judgement that the employees acquired represent an organized workforce. ‒ We involved valuation professionals with specialized skills and knowledge, who assisted us in evaluating the Company’s identification of intangible assets acquired. 108 ​ Table of Contents ​ /s/ KPMG Accountants N.V. ​ We have served as the Company’s auditor since 2019. Amstelveen , The Netherlands February 25, 2022 ​ ​ ​ ​ ​ 109 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 556,256 ​ $ 244,932 Accounts receivable and contract asset ​ ​ 58,768 ​ ​ 6,618 Prepaid expenses ​ ​ 10,540 ​ ​ 4,337 Other current assets and receivables ​ ​ 2,675 ​ ​ 3,024 Total current assets ​ ​ 628,239 ​ ​ 258,911 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 43,505 ​ ​ 32,328 Operating lease right-of-use assets ​ ​ 25,573 ​ ​ 26,086 Intangible assets, net ​ ​ 62,686 ​ ​ 3,361 Goodwill ​ ​ 27,633 ​ ​ 542 Deferred tax assets, net ​ ​ 15,647 ​ ​ 16,419 Other non-current assets ​ ​ 5,897 ​ ​ 2,748 Total non-current assets ​ ​ 180,941 ​ ​ 81,484 Total assets ​ $ 809,180 ​ $ 340,395 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 2,502 ​ $ 3,772 Accrued expenses and other current liabilities ​ ​ 28,487 ​ ​ 18,038 Current portion of operating lease liabilities ​ ​ 5,774 ​ ​ 5,524 Total current liabilities ​ ​ 36,763 ​ ​ 27,334 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 100,963 ​ ​ 35,617 Operating lease liabilities, net of current portion ​ ​ 28,987 ​ ​ 30,403 Contingent consideration ​ ​ 29,542 ​ ​ — Deferred tax liability, net ​ ​ 12,913 ​ ​ — Other non-current liabilities ​ ​ 4,236 ​ ​ 3,136 Total non-current liabilities ​ ​ 176,641 ​ ​ 69,156 Total liabilities ​ ​ 213,404 ​ ​ 96,490 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of December 31, 2021 and 60,000,000 shares authorized as of December 31, 2020 and 46,298,635 and 44,777,799 ordinary shares issued and outstanding as of December 31, 2021 and December 31, 2020, respectively ​ ​ 2,802 ​ ​ 2,711 Additional paid-in-capital ​ ​ 1,076,972 ​ ​ 1,016,018 Accumulated other comprehensive (loss) / income ​ ​ ( 28,856 ) ​ ​ 9,907 Accumulated deficit ​ ​ ( 455,142 ) ​ ​ ( 784,731 ) Total shareholders' equity ​ ​ 595,776 ​ ​ 243,905 Total liabilities and shareholders' equity ​ $ 809,180 ​ $ 340,395 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 110 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2021 2020 ​ 2019 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 517,400 ​ $ 4,352 ​ $ - License revenues from related party ​ ​ — ​ ​ 32,967 ​ ​ 4,988 Collaboration revenues ​ ​ 6,602 ​ ​ 59 ​ ​ — Collaboration revenues from related party ​ ​ — ​ ​ 136 ​ ​ 2,293 Total revenues ​ ​ 524,002 ​ ​ 37,514 ​ ​ 7,281 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of contract revenues ​ ​ ( 24,976 ) ​ ​ — ​ ​ — Research and development expenses ​ ​ ( 143,548 ) ​ ​ ( 122,400 ) ​ ​ ( 94,737 ) Selling, general and administrative expenses ​ ​ ( 56,290 ) ​ ​ ( 42,580 ) ​ ​ ( 33,544 ) Total operating expenses ​ ​ ( 224,814 ) ​ ​ ( 164,980 ) ​ ​ ( 128,281 ) Other income ​ ​ 12,306 ​ ​ 3,342 ​ ​ 1,888 Other expense ​ ​ ( 876 ) ​ ​ ( 1,302 ) ​ ​ ( 2,028 ) Income / (loss) from operations ​ ​ 310,618 ​ ​ ( 125,426 ) ​ ​ ( 121,140 ) Interest income ​ ​ 162 ​ ​ 938 ​ ​ 3,547 Interest expense ​ ​ ( 7,474 ) ​ ​ ( 3,825 ) ​ ​ ( 3,810 ) Foreign currency gains / (losses), net ​ ​ 29,660 ​ ​ ( 13,613 ) ​ ​ ( 268 ) Other non-operating (losses) / gains, net ​ ​ ( 160 ) ​ ​ 483 ​ ​ ( 2,530 ) Income / (loss) before income tax (expense) / benefit ​ $ 332,806 ​ $ ( 141,443 ) ​ $ ( 124,201 ) Income tax (expense) / benefit ​ ​ ( 3,217 ) ​ ​ 16,419 ​ ​ — Net income / (loss) ​ $ 329,589 ​ $ ( 125,024 ) ​ $ ( 124,201 ) Other comprehensive (loss) / gain: ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation adjustments ​ ​ ( 38,763 ) ​ ​ 16,596 ​ ​ 570 Total comprehensive gain / (loss) ​ $ 290,826 ​ $ ( 108,428 ) ​ $ ( 123,631 ) Earnings per ordinary share - basic ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net income / (loss) per ordinary share ​ $ 7.17 ​ $ ( 2.81 ) ​ $ ( 3.11 ) Earnings per ordinary share - diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ Diluted net income / (loss) per ordinary share ​ $ 7.04 ​ $ ( 2.81 ) ​ $ ( 3.11 ) Weighted average shares - basic ​ ​ 45,986,467 ​ ​ 44,466,365 ​ ​ 39,999,450 Weighted average shares - diluted ​ ​ 46,840,972 ​ ​ 44,466,365 ​ ​ 39,999,450 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 111 ​ 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) deficit equity ​ ​ (in thousands, except share data) 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 loss ​ — ​ ​ — ​ ​ — ​ ​ 570 ​ ​ — ​ ​ 570 Follow-on public offering ​ 5,625,000 ​ ​ 311 ​ ​ 242,363 ​ ​ — ​ ​ — ​ ​ 242,674 Hercules warrants exercise ​ 37,175 ​ ​ 2 ​ ​ 1,271 ​ ​ — ​ ​ — ​ ​ 1,273 Exercises 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 Income for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ 329,589 ​ ​ 329,589 Other comprehensive loss ​ — ​ ​ — ​ ​ — ​ ​ ( 38,763 ) ​ ​ — ​ ​ ( 38,763 ) Issuance of ordinary shares ​ 921,730 ​ ​ 55 ​ ​ 29,509 ​ ​ — ​ ​ — ​ ​ 29,564 Income tax benefit of past share issuance cost ​ — ​ ​ — ​ ​ 3,047 ​ ​ — ​ ​ — ​ ​ 3,047 Exercise of share options ​ 241,496 ​ ​ 15 ​ ​ 2,638 ​ ​ — ​ ​ — ​ ​ 2,653 Restricted and performance share units distributed during the period ​ 352,886 ​ ​ 21 ​ ​ ( 21 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 25,635 ​ ​ — ​ ​ — ​ ​ 25,635 Issuance of ordinary shares relating to employee stock purchase plan ​ 4,724 ​ ​ — ​ ​ 146 ​ ​ — ​ ​ — ​ ​ 146 Balance at December 31, 2021 ​ 46,298,635 ​ $ 2,802 ​ $ 1,076,972 ​ $ ( 28,856 ) ​ $ ( 455,142 ) ​ $ 595,776 ​ The accompanying notes are an integral part of these consolidated financial statements ​ 112 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Net income / (loss) ​ $ 329,589 ​ $ ( 125,024 ) ​ $ ( 124,201 ) Adjustments to reconcile net income / (loss) to net cash generated from / (used in) operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ 7,299 ​ ​ 10,648 ​ ​ 6,669 Share-based compensation expense ​ ​ 25,635 ​ ​ 21,831 ​ ​ 17,533 Deferred tax expense / (income) ​ ​ 3,210 ​ ​ ( 16,419 ) ​ ​ - Changes in fair value of contingent consideration and derivative financial instruments ​ ​ 6,843 ​ ​ ( 483 ) ​ ​ 2,530 Unrealized foreign exchange (gains) / losses, net ​ ​ ( 31,335 ) ​ ​ 14,730 ​ ​ 891 Change in deferred revenue ​ ​ - ​ ​ ( 33,642 ) ​ ​ ( 4,999 ) Other non-cash items, net ​ ​ ( 2,800 ) ​ ​ - ​ ​ - Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract asset related to CSL Behring milestone payments ​ ​ ( 55,000 ) ​ ​ - ​ ​ - Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 3,959 ) ​ ​ ( 6,967 ) ​ ​ ( 4,769 ) Accounts payable ​ ​ ( 727 ) ​ ​ ( 2,701 ) ​ ​ 1,652 Accrued expenses, other liabilities, and operating leases ​ ​ 9,204 ​ ​ 3,199 ​ ​ 6,010 Net cash generated from / (used in) operating activities ​ ​ 287,959 ​ ​ ( 134,828 ) ​ ​ ( 98,684 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Acquisition of Corlieve, net of cash acquired ​ ​ ( 49,949 ) ​ ​ - ​ ​ - Purchases of intangible assets ​ ​ - ​ ​ ( 2,213 ) ​ ​ ( 996 ) Purchases of property, plant, and equipment ​ ​ ( 17,438 ) ​ ​ ( 7,271 ) ​ ​ ( 5,651 ) Net cash used in investing activities ​ ​ ( 67,387 ) ​ ​ ( 9,484 ) ​ ​ ( 6,647 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds from loan increment, net of debt issuance costs ​ ​ 64,067 ​ ​ - ​ ​ - Proceeds from public offering of shares, net of issuance costs ​ ​ - ​ ​ - ​ ​ 242,718 Proceeds from issuance of ordinary shares ​ ​ 30,899 ​ ​ - ​ ​ - Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 2,798 ​ ​ 7,444 ​ ​ 5,603 Repayment of debt acquired through acquisition of Corlieve ​ ​ ( 1,572 ) ​ ​ - ​ ​ - Share issuance costs from issuance of ordinary shares ​ ​ ( 1,334 ) ​ ​ - ​ ​ - Proceeds from exercise of warrants ​ ​ - ​ ​ - ​ ​ 500 Net cash generated from financing activities ​ ​ 94,858 ​ ​ 7,444 ​ ​ 248,821 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 3,757 ) ​ ​ 3,822 ​ ​ ( 106 ) Net increase / (decrease) in cash, cash equivalents and restricted cash ​ ​ 311,673 ​ ​ ( 133,046 ) ​ ​ 143,384 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 247,680 ​ ​ 380,726 ​ ​ 237,342 Cash, cash equivalents and restricted cash at the end of period ​ $ 559,353 ​ $ 247,680 ​ $ 380,726 Cash and cash equivalents ​ $ 556,256 ​ $ 244,932 ​ $ 377,793 Restricted cash related to leasehold and other deposits ​ ​ 3,097 ​ ​ 2,748 ​ ​ 2,933 Total cash, cash equivalents and restricted cash ​ $ 559,353 ​ $ 247,680 ​ $ 380,726 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 6,539 ) ​ $ ( 4,131 ) ​ $ ( 3,117 ) Non-cash increase in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ 1,488 ​ $ 630 ​ $ 313 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 113 ​ 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 ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25, 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 trade 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, 2021 and the Company’s budgeted cash flows for the twelve months following the issuance date. ​ 114 ​ Table of Contents 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 share and purchase agreement (“SPA”) entered into on June 21, 2021 to acquire all of the outstanding ordinary shares of Corlieve Therapeutics SAS (“Corlieve”), a privately held French gene therapy company (“Corlieve Transaction”), the treatment of the commercialization and license agreement entered into (“CSL Behring Agreement”) between the Company and CSL Behring LLC (“CSL Behring”), the assessment of a valuation allowance on the Company’s deferred tax assets in the Netherlands and the U.S., and 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”). 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. ​ 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. and Corlieve AG) 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 ($) and the functional currency of Corlieve AG is the Swiss Franc. The consolidated financial statements are presented in U.S. dollars. ​ 115 ​ Table of Contents 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. ​ 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 5, “ 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. ​ 116 ​ Table of Contents 2.3.5 Corlieve transaction ​ On July 30, 2021 (“Acquisition Date”), the Company acquired Corlieve. The Company evaluated the Corlieve transaction as to whether or not the transaction should be accounted for as a business combination or asset acquisition. Refer to Note 3 “ Corlieve transaction ” for further detail. ​ a. Goodwill ​ Goodwill represents the excess of the fair value of the consideration transferred over the fair value of the net assets assumed in a business combination. Goodwill is not amortized but is evaluated for impairment on an annual basis and between annual tests if we become aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the reporting unit below its carrying amount. As of December 31, 2021, the Company has not recognized any impairment charges related to goodwill. ​ Refer to Note 3 “ Corlieve transaction ” for further detail. ​ b. Acquired research and development ​ The Company identified various licenses that combined with the results of the research and development activities conducted in relation to AMT-260 since incorporation of Corlieve in 2019 constitute an In-process research and development intangible asset (“IPR&D Intangible Asset”). The IPR&D Intangible Asset is considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts and is not amortized. If and when development is completed, which generally occurs when regulatory approval to market a product is obtained, the associated asset would be deemed finite-lived and would then be amortized based on its respective useful life at that point in time. As of December 31, 2021, the Company has not recognized any impairment charges related to the IPR&D Intangible Asset. ​ In case of abandonment, the IPR&D Intangible Asset will be written-off. In accordance with ASC 350, Intangibles – Goodwill and Other, the Company tests indefinite-lived intangible assets for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate the fair value of the IPR&D Intangible Asset is below its carrying amount. ​ Refer to Note 3 “ Corlieve transaction ” for further detail. ​ c. Contingent consideration ​ Each reporting period, the Company revalues the contingent consideration obligations associated with the Corlieve transaction to their fair value and records changes in the fair value within research and development expenses. Changes in contingent consideration result from changes in assumptions regarding the probabilities of achieving the relevant milestones, or probability of success (“POS”), the estimated timing of achieving such milestones, and the interest rate to discount the payments. Payments made soon after the acquisition date are recorded as cash flows from financing activities, and payments, or the portion of the payments, not made soon after the acquisition date are recorded as cash flows from operating activities. ​ Refer to Note 3 “ Corlieve transaction ” for further detail. ​ 2.3.6 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. 117 ​ Table of Contents ​ 2.3.7 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. ​ 2.3.8 Net income / (loss) per share ​ The Company follows the provisions of ASC 260, Earnings Per Share . In accordance with these provisions, net income / (loss) per share is calculated by dividing net income / (loss) by the weighted average number of ordinary shares outstanding during the period. ​ Diluted net income / (loss) per share reflects the dilution that would occur if share options or warrants to issue ordinary shares were exercised, performance or restricted share units were distributed, or shares under the employee share purchase plan were issued. However, potential ordinary shares are excluded if their effect is anti-dilutive. ​ Refer to Note 16 “ Basic and diluted earnings per share ” for further information. ​ 2.3.9 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, Property, Plant, and Equipment . 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. The Company performs the same quantitative analysis discussed above for long-lived assets and finite-lived intangible assets ​ Refer to Note 2.3.5 “ Corlieve transaction ” for information on impairment testing related to goodwill and acquired research and development intangible assets. ​ 2.3.10 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 ​ 118 ​ Table of Contents 2.3.11 Leases ​ The Company adopted ASC 842, Leases 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. ​ 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. ​ For leases recognized after the adoption date, the Company determines if an arrangement is a lease at inception. Operating lease right-of-use assets and lease liabilities are initially recognized based on the present value of future minimum lease payments over the lease term at commencement date calculated using an incremental borrowing rate applicable to the lease asset, unless the implicit rate is readily available. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Leases with a term of twelve months or less are not recognized on the consolidated balance sheets. ​ 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 within cash flows from operations within the Consolidated statements of cash flows. ​ 2.3.12 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. ​ 2.3.13 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. ​ 2.3.14 Accounts receivable ​ Accounts receivables include amounts due from services provided to the Company’s licensing and collaboration partners as well as unconditional rights to consideration from its licensing and collaboration partners. ​ ​ 2.3.15 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. ​ 119 ​ Table of Contents 2.3.16 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. ​ 2.3.17 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. ​ In 2016, the Company adopted a qualified 401(k) Plan for all employees located in the United States. The 401(k) Plan offers both a pre-tax and post-tax (Roth) component. Employees may contribute up to the IRS statutory limit 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. ​ 2.3.18 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. Compensation expense related to Performance Share Units is recognized when the Company considers achievement of the milestones to be probable. 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. ​ 2.3.19 Revenue recognition ​ The Company primarily generates revenue from its commercialization and license agreement with CSL Behring and its collaboration, research, and license agreements with BMS for the development and commercialization of product candidates. ​ CSL Behring collaboration ​ On June 24, 2021 (“Signing Date”), the Company entered into a commercialization and license agreement pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec (“Product”). The Company concluded that CSL Behring is a customer in accordance with ASC 606, Revenue from Contracts with Customers and identified two material performance obligations related to the CSL Behring Agreement: ​ (i) Sale of the exclusive global rights to the Product (“License Sale”); and (ii) Generate information to support the regulatory approval of the current and next generation manufacturing process of Product and to provide any such information generated to CSL Behring (“Manufacturing Development”). 120 ​ Table of Contents These performance obligations are considered distinct from one another, as CSL Behring can benefit from the identified service either on its own or together with other resources that are readily available to CSL Behring, and as the performance obligations are separately identifiable from other performance obligations in the CSL Behring Agreement. ​ Refer to Note 4 “ Collaboration arrangements and concentration of credit risk ” for further detail. ​ Bristol-Myers Squib collaboration ​ The Company initially entered into collaboration, research, and license agreements with BMS in 2015 and amended them in 2020. ​ 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 4, “ 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 4, “Collaboration arrangements and concentration of credit risk” , for a detailed discussion). ​ Collaboration and Manufacturing Revenue ​ The Company recognizes Collaboration Revenues associated with 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. ​ 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. ​ 2.3.20 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. ​ 121 ​ Table of Contents The Company’s other income also consists of employee retention credits received under the U.S. Coronavirus Aid, Relief, and Economic Security Act, income related to a settlement agreement that the Company and VectorY B.V. entered into in April 2021, as well as income from subleasing part of the Company’s Amsterdam facility. Other expense consists of expenses incurred in relation to the subleasing income. ​ 2.3.21 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. ​ 2.3.22 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, 2021, and 2020, the Company did not have any significant unrecognized tax benefits. ​ 2.3.23 Recently Adopted Accounting Pronouncements ​ Recent Accounting Pronouncements Not Yet Effective ​ ASU 2021-10: Government Assistance ​ In November 2018, the FASB issued ASU 2021-10, Government Assistance (Topic 832) which discusses the requirements for disclosures related to transactions with a government. ASU 2021-10 is effective for fiscal years beginning after December 15, 2021. The new disclosure requirements will require disclosures around 1) information about the nature of the transactions and the related accounting policy used to account for the transactions, 2) the line items on the balance sheet and income statement that are affected by the transactions, and the amounts applicable to each financial statement line item, and 3) significant terms and conditions of the transactions, including commitments and contingencies. An entity should apply the updates prospectively or retrospectively. The Company currently includes information on government grants and does not expect these amendments to have a material impact on the Company’s consolidated financial statements. ​ ​ 122 ​ Table of Contents 3. Corlieve transaction ​ At the Acquisition Date, the Company acquired Corlieve. Following Corlieve’s formation in November 2019, Corlieve obtained exclusive licenses to certain patents from two French research institutions that continue to collaborate with the Company. Corlieve also obtained an exclusive license from Regenxbio Inc. (“Regenxbio”) to use AAV9 to deliver any sequence that affects the expression of the Glutamate inotropic receptor kainate type subunit 2 (“GRIK 2”) gene sequence in humans. Corlieve and Regenxbio simultaneously entered into a collaboration plan related to agreed joint preclinical research and development activities. At the Acquisition Date, Corlieve and its Swiss subsidiary, Corlieve Therapeutics AG, employed seven employees. Corlieve’s result for the full year 2021 was a $ 7.3 million loss. The result included in the Company’s consolidated results for the year ended December 31, 2021 is a $ 4.1 million loss. ​ The Company evaluated the Corlieve transaction as to whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen test to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. Based on the fair values of the gross assets acquired, the Company determined the screen test was not met. The Company further analyzed whether or not the acquired inputs and processes that have the ability to create outputs would meet the definition of a business. Significant judgment is required in the application of the screen test to determine whether an acquisition is a business combination or an acquisition of assets. ​ Identifiable assets and liabilities of Corlieve, including identifiable intangible assets, were recorded at their fair values as of the Acquisition Date, when the Company obtained control. The excess of the fair value of the consideration transferred over the fair value of the net assets acquired was recorded as goodwill. ​ The following table summarizes the fair values assigned to assets acquired and the liabilities assumed by the Company, along with the resulting goodwill, as of the Acquisition Date: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allocation ​ ​ € ​ (in thousands) Consideration ​ ​ Cash € 44,876 Contingent consideration ​ 20,165 Liability related to Mandatorily Redeemable Shares (see below) ​ 719 Fair value of total consideration € 65,760 ​ ​ ​ Recognized amounts of identifiable assets acquired and liabilities assumed ​ ​ Current assets including € 2.8 million of cash € 2,902 Property, plant and equipment ​ 34 Identifiable intangible asset ​ 53,564 Current liabilities ​ ( 1,132 ) Deferred tax liability, net ​ ( 11,915 ) Debt ​ ( 1,352 ) Other non-current liabilities ​ ( 260 ) Fair value of net assets acquired ​ 41,841 Goodwill ​ 23,919 ​ € 65,760 ​ Consideration ​ On the Acquisition Date, the Company acquired 97.7 % of the outstanding ordinary shares of Corlieve in return for EUR 44.9 million ($ 53.3 million as of the Acquisition Date). As is contractually required the Company acquired the remaining outstanding ordinary shares on February 9, 2022 following the expiration of a minimum holding period. The Company recorded a liability related to these Mandatorily Redeemable Shares for an amount of EUR 0.7 million ($ 0.9 million) as of the Acquisition Date. The Company financed the Corlieve Transaction from its cash on hand. ​ 123 ​ Table of Contents In addition to the payments to acquire 100 % of the outstanding ordinary shares, Corlieve’s former shareholders are eligible to receive up to EUR 35.8 million ($ 40.6 million as of December 31, 2021) upon achievement of certain development milestones through Phase I/II and EUR 143.1 million ($ 162.3 million as of December 31, 2021) upon achievement of certain milestones associated with Phase III development and obtaining approval to commercialize Corlieve’s target candidate for the treatment of temporal lobe epilepsy (“AMT-260” or “TLE”) in the United States of America and the European Union. The Company may elect to pay up to 25 % of such milestone payments through the issuance of the Company’s ordinary shares. ​ As of the Acquisition Date, the Company recorded EUR 20.2 million ($ 24.0 million) as a contingent liability (presented as “Non-current liability”) for the fair value of these milestone payments. The fair value of the contingent liability as of December 31, 2021 amounted to EUR 26.0 million ($ 29.5 million). Changes in fair value of the contingent liability are recognized within research and development expenses in the consolidated statements of operations. ​ Identified intangible assets ​ The Company identified various licenses that combined with the results of the research and development activities conducted in relation to AMT-260 since incorporation of Corlieve in 2019 constitute an In-process research and development intangible asset (“IPR&D Intangible Asset”). ​ The Company determined the fair value of the IPR&D Intangible Asset using a present value model based on expected cash flows. Estimating the amounts and timing of cash flows required to complete the development of AMT-260 as well as net sales, cost of goods sold, and sales and marketing costs involved considerable judgment and uncertainty. The expected cash flows are materially impacted by the probability of successfully completing the various stages of development (i.e., dosing of first patient in clinical trial, advancing into late-stage clinical development and obtaining approval to commercialize a product candidate) as well as the weighted average cost of capital of 10.4 % used to discount the expected cash flows. Based on all such information and its judgment the Company estimated the fair value of the IPR&D Intangible Asset at EUR 53.6 million ($ 63.6 million) as of the Acquisition Date. ​ Deferred tax liability, net ​ Corlieve’s deferred tax assets at the time of acquisition amounted to EUR 1.5 million ($ 1.7 million). Recognition of the IPR&D Intangible Asset gave rise to a deferred tax liability of EUR 13.4 million ($ 15.9 million) at the enacted French corporate income tax rate of 25.0 %. The Company consequently recorded a net deferred tax liability of EUR 11.9 million ($ 14.2 million as of the Acquisition Date). Changes in the net deferred tax liability after the Acquisition Date will be recorded in income tax expense in the consolidated statements of operations. ​ Goodwill ​ Goodwill represents the excess of total consideration over the estimated fair value of net assets acquired. The Company recorded EUR 23.9 million ($ 28.4 million) of goodwill in the consolidated balance sheet as of the Acquisition Date. The goodwill primarily relates to the recognition of a deferred tax liability recognized in association with the IPR&D Intangible asset of EUR 13.4 million ($ 15.9 million as of Acquisition Date) as well as the fair market value of the experienced workforce and potential synergies from the acquisition. The Company allocated the goodwill to its reporting unit. The Company does not expect any portion of this goodwill to be deductible for income tax purposes. ​ Debt As of the Acquisition Date, Corlieve held a loan with outstanding amount equal to EUR 1.0 million ($ 1.2 million), which loan was repaid in its entirety in September 2021. As of the Acquisition Date, Corlieve also held a loan with outstanding amount equal to EUR 0.4 million ($ 0.4 million), which was repaid in its entirety in December 2021. ​ Other As of the Acquisition Date, the Company also acquired other assets and assumed other liabilities, which included among others, EUR 2.9 million ($ 3.4 million) of current assets, which consisted of EUR 2.8 million ($ 3.3 million) of cash, and EUR 1.1 million ($ 1.3 million) of current liabilities. ​ 124 ​ Table of Contents ​ 4. Collaboration arrangements and concentration of credit risk ​ CSL Behring collaboration ​ On the Signing Date, uniQure biopharma B.V., a wholly-owned subsidiary of uniQure N.V., entered into the CSL Behring Agreement with CSL Behring, pursuant to which CSL Behring received exclusive global rights to the Product. On May 6, 2021, a day after the expiration of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, the CSL Behring Agreement became fully effective (“Closing”). ​ Pursuant to the CSL Behring Agreement, the Company received a $ 450.0 million upfront cash payment and $ 12.4 million in other payments related to the Closing and the transfer of the license. The Company is eligible to receive up to $ 1.6 billion in additional payments based on the achievement of 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. ​ On the Signing Date, 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 commensurate with the SSP. The Company will be responsible for supplying development and commercial Product until such time that these capabilities may be transferred to CSL Behring or a designated contract manufacturing organization. The Company will be completing the HOPE-B clinical trial and the validation of the manufacturing process on behalf of CSL Behring, as well as provide further development services if requested by CSL Behring. Activities related to on-demand development services as well as activities related to the completing the HOPE-B clinical trial will be reimbursed by CSL Behring at an agreed full-time-employee rate (“FTE-rate”) and CSL Behring will also reimburse agreed third-party expenses incurred in relation to performing these activities. The validation of the manufacturing process as well as Manufacturing Development will be reimbursed through a future milestone payment. If completed after certain contractually agreed upon dates, the milestone payment will be reduced in accordance with a pre-specified mechanism. ​ The Company concluded that CSL Behring is a customer in accordance with Topic 606. The Company identified two material performance obligations related to the CSL Behring Agreement: (i) License Sale; and (ii) Manufacturing Development. These performance obligations are considered distinct from one another, as CSL Behring can benefit from the identified service either on its own or together with other resources that are readily available to CSL Behring, and as the performance obligations are separately identifiable from other performance obligations in the CSL Behring Agreement. The Company continued to develop the Product between the Signing Date and Closing and performed certain reimbursable activities to fulfill the transfer of the global rights (“Additional Covenants” and together with the License the “License Sale”). The Additional Covenants are not considered distinct from the performance obligation to sell the license to CSL Behring as CSL Behring could not benefit from the Additional Covenants on their own, or have these activities be performed with readily available resources. 125 ​ Table of Contents The Company determined that the fixed upfront payment of $ 450.0 million and the $ 12.4 million that the Company received in relation to the Additional Covenants should be allocated to the License Sale. In addition, the Company concluded that variable milestone payments, sales milestone payments and royalties should be allocated to the License Sale performance obligation as well. The Company determined that the License Sale was completed on May 6, 2021, when it transferred the license and CSL Behring assumed full responsibility for the development and commercialization of the Product. At Closing, the Company evaluated the amounts of potential payments and the likelihood that the payments will be received. The Company utilized the most likely amount method to estimate the variable consideration to be included in the transaction price. Since the Company cannot control the achievement of regulatory and first commercial sales milestones, the Company concluded that the potential payments are constrained as of Closing. The Company determined that it would recognize revenue related to these payments only to the extent that it becomes probable that no significant reversal of recognized cumulative revenue will occur thereafter. Similarly, the Company will record expenses related to its existing license and other agreements as well as its financial advisor for a high single digit percentage of any such revenue recognized associated to meeting a milestone. The Company will include payments related to sales milestones in the transaction price when their achievement becomes probable, and it will include royalties on the sale of Product once these have been earned. The Company determined that achievement of a total of $ 55.0 million of milestone payments related to the submissions of a biologics license application (“BLA”) and market authorization application (“MAA”) is probable as of the time of filing these financial statements and hence recorded these as license revenue in the year ended December 31, 2021. In making the determination, the Company considered that after Closing, it believes to successfully have completed the validation of its manufacturing process for the Product in December 2021 and that CSL Behring announced the accomplishment of the primary clinical endpoint for the Product in December 2021. The Company recognized $ 517.4 million of revenues related to the License Sale in the year ended December 31, 2021. The Company determined that the variable milestone payment related to Manufacturing Development should be allocated to the Manufacturing Development performance obligation. The Company concluded that this milestone payment represents the SSP of the services based on the estimated cost of providing the services including a reasonable margin. The services related to Manufacturing Development will be provided between Closing and the completion of an agreed manufacturing development plan. The variable consideration will be reduced if the Company does not complete the development by pre-agreed dates. The Company utilized the most likely amount method to estimate the variable consideration to be included in the transaction price. Completion of Manufacturing Development is partially dependent on the timing of regulatory submissions by CSL Behring as well as regulatory approvals of the developed manufacturing processes. Since the Company cannot control the timing or outcome of any regulatory decisions, the Company concluded that it would recognize revenue related to this payment when it becomes probable that the milestone has been achieved. The Company has not recognized any revenue related to Manufacturing Development. The Company recognized $ 2.4 million of collaboration revenue in the year ended December 31, 2021, respectively, compared to nil in the same periods in 2020 and 2019. The Company generates such collaboration revenue from services rendered in relation to completing the HOPE-B clinical trial on behalf of CSL Behring. CSL Behring may request additional development services or request the Company to support the transfer of manufacturing to a party designated by CSL Behring. These collaboration services will be reimbursed at the pre-agreed FTE-rate. The Company concluded that these rights at Closing do not represent material rights. The Company incurred $ 2.1 million of expenses for 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 the Company could not recognize any license revenue related to the CSL Behring Agreement in the period ended December 31, 2020. Following the Closing, the Company collected the $ 2.1 million of accounts receivable related to reimbursable contract fulfillment costs that was outstanding as of December 31, 2020 . As of December 31, 2021, the Company has recorded accounts receivable of $ 2.9 million from CSL Behring related to clinical development services as well as a contract asset of $ 55.0 million related to BLA and MAA submission milestone payments considered probable. 126 ​ 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. ​ 2020 Amendment ​ 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 was able to replace up to two of the four active Collaboration Targets with 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. ​ Since the December 2020 amendment, 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 also 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 four-year research term that expired in May 2019. 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) November 30, 2023, if no replacement targets are designated. BMS continues to reimburse the Company for these services. ​ During the year ended December 31, 2020, the Company evaluated the impact of the amendment of the BMS CLA had in relation to its performance obligation related to 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 had on its measure of progress towards the completion of its performance obligation related to License Revenue and determined that its remaining performance obligation under the amended BMS CLA was immaterial and recognized the remaining balance of unrecognized License Revenue as of November 30, 2020. ​ 127 ​ Table of Contents 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 up until the effective date of the amended BMS CLA and presented as revenue after the effective date): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 ​ ​ 2020 ​ ​ 2019 ​ ​ (in thousands) Bristol Myers Squibb $ 4,176 ​ $ 37,514 ​ $ 7,281 ​ $ 4,176 ​ $ 37,514 ​ $ 7,281 ​ Amounts owed by BMS in relation to the Collaboration and License Revenue are as follows (presented as “Accounts receivables” as of December 31, 2021 and 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands) Bristol Myers Squibb ​ $ 914 ​ $ 4,536 Total ​ $ 914 ​ $ 4,536 ​ 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 $ 4.2 million collaboration revenue for the year ended December 31, 2021 (December 31, 2020: $ 0.2 million; December 31, 2019: $ 2.3 million). ​ License Revenue ​ The Company recognized no License Revenue for the year ended December 31, 2021 (December 31, 2020: $ 33.0 million, December 31, 2019: $ 5.0 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 recognized 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 determined such progress by comparing activities performed at the end of each reporting period with total activities expected to be performed. The Company estimated 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 judgment. 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 consider this probable. However, there was a milestone that was recorded as license revenue in the year ended December 31, 2020 (see below). ​ 128 ​ Table of Contents On December 17, 2020 BMS designated one of the four Collaboration Targets as a candidate to advance into Investigational New Drug-enabling studies (“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 year 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. ​ 5. Fair value measurement and Other non-operating (losses) / gains ​ 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 and restricted cash. Restricted cash is included within “Other non-current assets” within the consolidated balance sheets. ​ The following table sets forth the balances and changes in fair values of liabilities that are measured at fair value using Level 3 inputs: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative ​ ​ ​ ​ ​ Contingent ​ financial ​ ​ ​ ​ consideration instruments Total ​ ​ (in thousands) 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 BMS 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 Amount recorded for contingent consideration on Acquisition Date of Corlieve ​ ​ 23,950 ​ ​ — ​ ​ 23,950 Net losses recognized in profit or loss ​ ​ 6,683 ​ ​ 160 ​ ​ 6,843 Currency translation effects ​ ​ ( 1,091 ) ​ ​ — ​ ​ ( 1,091 ) Balance at December 31, 2021 ​ $ 29,542 ​ $ 2,805 ​ $ 32,347 ​ 129 ​ Table of Contents 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. ​ The Company recorded the following results in other non-operating (losses) / gains related to the changes in the fair value of derivative financial instruments. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Other non-operating gains: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative gains ​ $ — ​ $ 483 ​ $ — Total other non-operating gains: ​ ​ — ​ ​ 483 ​ ​ — Other non-operating losses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative losses ​ ​ ( 160 ) ​ ​ — ​ ​ ( 2,530 ) Total other non-operating losses: ​ ​ ( 160 ) ​ ​ — ​ ​ ( 2,530 ) Other non-operating (losses) / gains, net ​ $ ( 160 ) ​ $ 483 ​ $ ( 2,530 ) ​ 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). ​ 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 (losses) / gains (December 31, 2019: $ 2.3 million loss) 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. ​ 130 ​ Table of Contents 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 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, the Company (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, 2021 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 transaction within the biotechnology industry. The Company estimated this unobservable input using the best information available as of December 1, 2020, and December 31, 2020 and 2021, respectively. 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 judgment 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 31, 2021 was $ 2.8 million (December 1, 2020 and December 31, 2020: $ 2.6 million). The Company recorded a $ 2.6 million loss within “Other non-operating (losses) / gains” in the year ended December 31, 2020 related to the initial recognition of this derivative financial liability. The increase of the fair market value of the derivative financial liability of $ 0.2 million in the year ended December 31, 2021 was recorded in Other non-operating (losses) / gains. ​ Hercules loan facility ​ In 2013 the Company entered into a venture debt loan facility with Hercules (see Note 10, “ Long-term debt ”) 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 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 years ended December 31, 2021 and 2020, respectively, the Company recognized no more gains or losses in Other non-operating (losses) / gains related to fair value changes of the Hercules warrants (December 31, 2019: $ 0.2 million loss). ​ 131 ​ Table of Contents Contingent consideration ​ Corlieve transaction ​ The Company is required to pay up to EUR 178.8 million ($ 202.8 million at the December 31, 2021 foreign exchange rate) to the former shareholders of Corlieve upon the achievement of contractually defined milestones in connection with the Company’s acquisition of Corlieve (refer to Note 3 “Corlieve transaction” ). The Company recorded a liability for the fair market value of the contingent consideration of EUR 20.2 million ($ 24.0 million) at the Acquisition Date. The fair market value was determined using unobservable initial inputs with respect to (i) the probability of achieving the relevant milestones, or POS, (ii) the estimated timing of achieving such milestones, and (iii) the interest rate used to discount the payments. The Company determined the fair market value of the contingent consideration by calculating the probability-adjusted payments based on each milestone’s probability of achievement. The probability-adjusted payments were then discounted to present value using a discount rate representing the Company’s credit risk. This discount rate was determined using the effective interest rate of the Company’s existing debt facility adjusted for difference in maturity dates based on CCC yield curve. ​ The fair value of the contingent consideration as of December 31, 2021 was $ 29.5 million using discount rates ranging from 10.9 % to 11.9 % as well as a 55 % likelihood of AMT-260 advancing into clinical development by no later than early 2024. The Company increased the likelihood of advancing into clinical development from 40 % to 55 % following the designation of a lead candidate in late October 2021, which resulted in EUR 5.0 million ($ 5.8 million) increase of the contingent liability. If as of December 31, 2021 the Company had assumed a 100 % likelihood of AMT-260 advancing into clinical development, then the fair value of the contingent consideration would have increased to $ 47.0 million. If as of December 31, 2021 the Company assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would be released to income. Changes in fair value of the contingent liability are recognized within research and development expenses in the consolidated statements of operations. ​ ​ Other ​ As of December 31, 2021, the Company recorded $ 0.8 million related to consideration for post-acquisition services, presented within Other non-current liabilities in connection with the Company’s acquisition of Corlieve. ​ Other ​ ​ ​ 6. Property, plant, and equipment, net ​ The following table presents the Company’s property, plant, and equipment as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands) Leasehold improvements ​ $ 45,372 ​ $ 37,849 Laboratory equipment ​ ​ 25,499 ​ ​ 22,106 Office equipment ​ ​ 4,465 ​ ​ 5,025 Construction-in-progress ​ ​ 5,069 ​ ​ 2,574 Total property, plant, and equipment ​ ​ 80,405 ​ ​ 67,554 Less accumulated depreciation ​ ​ ( 36,900 ) ​ ​ ( 35,226 ) Property, plant and equipment, net ​ $ 43,505 ​ $ 32,328 ​ Total depreciation expense was $ 6.1 million for the year ended December 31, 2021 (December 31, 2020: $ 5.7 million, December 31, 2019: $ 6.0 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. ​ 132 ​ Table of Contents The following table summarizes property, plant, and equipment by geographic region. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Lexington, Massachusetts (United States of America) ​ $ 17,311 ​ $ 15,949 Amsterdam (the Netherlands) ​ 26,160 ​ 16,379 Other ​ ​ 34 ​ ​ - Total ​ $ 43,505 ​ $ 32,328 ​ ​ 7. Right-of-use asset and lease liabilities ​ 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. ​ In December 2021, the Company entered into a new lease for an additional facility in Lexington, Massachusetts, United States of approximately 13,501 square feet of space. The lease is expected to commence in the second half of 2022, is set for seven years starting from the rent commencement date and is non-cancellable. The lease is renewable for one five-year term. ​ 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 lease for the 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 $ 5.4 million (EUR 4.7 million) as of December 31, 2021. ​ In May 2021, the Company entered into a sublease agreement to let an additional approximately 1,080 square meters of office space to accommodate the hiring of additional full-time employees. The lease expires in October 2028 and includes an option to break the lease on October 31, 2023. ​ 133 ​ Table of Contents Operating lease liabilities ​ The components of lease cost in accordance with the new lease accounting standard were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) ​ ​ ​ Operating lease cost ​ $ 5,306 ​ $ 5,052 ​ $ 4,474 Variable lease cost ​ ​ 698 ​ ​ 607 ​ ​ 507 Sublease income ​ ​ ( 907 ) ​ ​ ( 904 ) ​ ​ ( 1,053 ) Total lease cost ​ $ 5,097 ​ $ 4,755 ​ $ 3,928 ​ The table below presents the lease-related assets and liabilities recorded on the Consolidated balance sheets in accordance with the new lease accounting standard. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Assets ​ ​ ​ ​ ​ ​ Operating lease right-of-use assets ​ $ 25,573 ​ ​ 26,086 Liabilities ​ ​ ​ ​ ​ ​ Current ​ ​ ​ ​ ​ ​ Current operating lease liabilities ​ ​ 5,774 ​ ​ 5,524 Non-current ​ ​ ​ ​ ​ ​ Non-current operating lease liabilities ​ ​ 28,987 ​ ​ 30,403 Total lease liabilities ​ $ 34,761 ​ ​ 35,927 ​ Other information The weighted-average remaining lease term as of December 31, 2021, is 8.3 years, compared to 9.4 years as of December 31, 2020, and the weighted-average discount rate as of December 31, 2021 is 11.34 % , compared to 11.37 % as of December 31, 2020. The Company uses an incremental borrowing rate applicable to the lease asset. The table below presents supplemental cash flow and non-cash information related to leases. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Cash paid for amounts included in the measurement of lease liabilities ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating cash flows for operating leases 1) ​ $ 5,738 ​ $ 5,769 ​ $ 4,717 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use asset obtained in exchange for lease obligation ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease 2) ​ $ 1,699 ​ $ — ​ $ 9,002 1) The Company received $ 1.5 million of landlord incentive payments for the year ended December 31, 2019, which are not included in the cash paid amounts. 2) The Company capitalized $ 19.0 million of operating right-of-use assets upon adoption of ASC 842 Leases on January 1, 2019 that are not included in the movement for the year ended December 31, 2019. 134 ​ Table of Contents Undiscounted cash flows The table below reconciles the undiscounted cash flows as of December 31, 2021, 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, 2021. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Lexington ​ Amsterdam (1) ​ Total ​ (in thousands) 2022 $ 3,552 ​ $ 2,222 ​ $ 5,774 2023 ​ 3,650 ​ ​ 2,668 ​ ​ 6,318 2024 ​ 4,146 ​ ​ 2,112 ​ ​ 6,258 2025 ​ 4,465 ​ ​ 2,112 ​ ​ 6,577 2026 ​ 4,600 ​ ​ 2,112 ​ ​ 6,712 Thereafter ​ 11,680 ​ ​ 9,736 ​ ​ 21,416 Total lease payments $ 32,093 ​ $ 20,962 ​ $ 53,055 ​ ​ ​ ​ ​ ​ ​ ​ ​ Less: amount of lease payments representing interest payments ​ ( 10,251 ) ​ ​ ( 8,043 ) ​ ​ ( 18,294 ) Present value of lease payments ​ 21,842 ​ ​ 12,919 ​ ​ 34,761 Less: current operating lease liabilities ​ ( 3,552 ) ​ ​ ( 2,222 ) ​ ​ ( 5,774 ) Non-current operating lease liabilities $ 18,290 ​ $ 10,697 ​ $ 28,987 (1) Payments are due in EUR and have been translated at the foreign exchange rate as of December 31, 2021, of $ 1.13 / €1.00) ​ 8. Intangible assets, net and Goodwill ​ The following table presents the Company’s acquired licenses and acquired IPR&D as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Acquired licenses ​ $ 4,755 ​ $ 5,660 Less accumulated amortization ​ ​ ( 2,827 ) ​ ​ ( 2,299 ) Acquired licenses, net ​ $ 1,928 ​ $ 3,361 Acquired IPR&D Intangible Asset ​ 60,758 ​ — Intangibles, net ​ $ 62,686 ​ $ 3,361 ​ a. Acquired licenses ​ All acquired licenses are owned by uniQure biopharma B.V, a subsidiary of the Company. The acquired licenses have a weighted average remaining life of 10.8 years as of December 31, 2021. ​ 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. ​ 135 ​ Table of Contents As of December 31, 2021, the estimated future amortization expense for each of the five succeeding years and the period thereafter is as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2022 ​ $ 395 2023 ​ 133 2024 ​ 133 2025 ​ 133 2026 ​ 133 Thereafter ​ 1,001 Total ​ $ 1,928 ​ The amortization expense related to licenses for the year ended December 31, 2021 was $ 1.2 million (December 31, 2020: $ 4.6 million; December 31, 2019: $ 0.6 million). The impairment expense related to licenses for the year ended December 31, 2021 was $ 0.0 million (December 31, 2020: $ 0.3 million; December 31, 2019 $ 0.0 million). ​ b. Acquired in-process research and development ​ As part of its acquisition of Corlieve as of July 30, 2021, the Company identified certain intangible assets related to an IPR&D Intangible Asset. Refer to Note 3 “Corlieve transaction” . ​ c. Goodwill ​ As part of its acquisition of Corlieve as of July 30, 2021, the Company recorded goodwill. Refer to Note 3 “Corlieve transaction” . ​ ​ 9. Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands) Accruals for goods received from and services provided by vendors-not yet billed ​ $ 13,012 ​ $ 8,269 Personnel related accruals and liabilities ​ ​ 12,603 ​ ​ 7,687 Accrued contract fulfillment costs and costs to obtain a contract ​ ​ 2,872 ​ ​ — Contract liability (see Note 4. "Collaboration arrangements and concentration of credit risk") ​ ​ — ​ ​ 2,082 Total ​ $ 28,487 ​ $ 18,038 ​ ​ 10. Long-term debt ​ On June 14, 2013, the Company entered into a venture debt loan facility with Hercules Capital, Inc. (formerly known as Hercules Technology Growth Capital, Inc.) (“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 that both refinanced the then-existing $ 20.0 million 2016 Amended Facility and allowed the Company to draw down an additional $ 15.0 million (“2018 Amended Facility”). The 2018 Amended Facility extended the loan’s maturity date from May 1, 2020 until June 1, 2023. The interest rate is adjustable and is the greater of (i) 8.85 % and (ii) 8.85 % plus the prime rate less 5.50 % per annum. Under the 2018 Amended Facility, the Company 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. ​ 136 ​ Table of Contents On January 29, 2021, the Company and Hercules amended the 2018 Amended Facility (“2021 Amended Facility”). Pursuant to the 2021 Amended Facility, Hercules agreed to an additional Facility of $ 100.0 million (“Tranche B”) increasing the aggregate principal amount of the term loan facilities from $ 35.0 million to up to $ 135.0 million. On January 29, 2021, the Company drew down $ 35.0 million of the Tranche B. Advances under Tranche B bore 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 of $ 70.0 million and all accrued but unpaid interest on advances under Tranche B was due on June 1, 2023, which date could had been extended by the Company by up to two twelve-month periods. Advances under the 2021 Amended Facility could have been prepaid without charge after July 29, 2021. The back-end fee in respect of advances under the 2021 Amended Facility ranged from 1.65 % to 6.85 %, depending on the repayment date. In addition to Tranche B, the 2021 Amended Facility had also extended the interest only payment period of the previously funded $ 35.0 million term loan (“Tranche A”) from January 1, 2022 to June l, 2023. ​ On December 15, 2021, the Company and Hercules amended and restated the 2021 Amended Facility (“2021 Restated Facility”). Pursuant to the 2021 Restated Facility, Tranche A and Tranche B of the 2021 Amended Facility with a total outstanding balance of $ 70.0 million were consolidated into one tranche with a total commitment of $ 100.0 million. The Company drew down an additional $ 30.0 million, resulting in total principal outstanding as of December 31, 2021 of $ 100.0 million. The 2021 Restated Facility extended the loan’s maturity date from June 1, 2023 until December 1, 2025. The interest-only period is extended from January 1, 2023 to December 1, 2024, or December 1, 2025 if, prior to June 30, 2024, either (a) the BLA for AMT-061 is approved by the FDA or (b) AMT-130 is advanced into a pivotal trial. The interest rate is adjustable and is the greater of (i) 7.95 % and (ii) 7.95 % plus the prime rate less 3.25 % per annum. Under the 2021 Restated Facility, the Company owes a back-end fee of 4.85 % of the outstanding debt. 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 Company continues to owe a $ 2.5 million back-end fee related to the 2021 Amended Facility which is due on June 1, 2023. ​ The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2021 Amended Facility was $ 101.6 million as of December 31, 2021, compared to an amortized cost of $ 35.9 million for the 2018 Amended Facility as of December 31, 2020, and is recorded net of discount and debt issuance costs. The foreign currency loss on the loan was $ 5.3 million in 2021 (2020: gain of $ 3.1 million; 2019: loss of $ 0.7 million). The fair value of the loan approximates its carrying amount. Inputs to the fair value of the loan are considered Level 3 inputs. ​ Interest expense recorded during the years ended December 31 was as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in millions) 2021 ​ $ 7.2 2020 ​ 3.7 2019 ​ ​ 3.7 ​ As a covenant in the 2021 Restated 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. The Company, beginning on April 1, 2023, is also required to keep a minimum of unrestricted cash of at least 50 % of the loan amount outstanding. If, prior to June 30, 2024, either (a) the BLA for AMT-061 is approved by the FDA or (b) AMT-130 is advanced into a pivotal trial, the minimum cash covenant will be lowered to at least 30 % of the loan amount outstanding and its effectiveness will be deferred to April 1, 2024. In combination with other covenants, the 2021 Restated 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 to its shareholders. The Company secured the facilities by directly or indirectly pledging its total assets of $ 809.2 million with the exception of $ 103.2 million of cash and cash equivalents and other current assets held by uniQure N.V. ​ 137 ​ Table of Contents The 2021 Restated Facility contain 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, 2021, the Company was in material compliance with all covenants and provisions. ​ The aggregate maturities of the loans, including $ 35.6 million of coupon interest payments and financing fees, for each of the 47 months after December 31, 2021, are as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2022 ​ $ 7,984 2023 ​ ​ 10,580 2024 ​ ​ 15,474 2025 ​ 101,549 Total ​ $ 135,587 ​ ​ ​ 11. Shareholders’ equity ​ As of December 31, 2021, the Company’s authorized share capital is € 4.0 million (or $ 4.5 million when translated at an exchange rate as of December 31, 2021, of $ 1.13 / €1.00), divided into 80,000,000 ordinary shares, each with a nominal value of € 0.05 . The Company’s shareholders, at the 2021 Annual General Meeting of Stockholders held on June 16, 2021, approved an increase in the number of authorized ordinary shares by 20,000,000 to 80,000,000 million. ​ 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, 2021, and 2020 and 2019 the Company’s other comprehensive result was restricted for payment of dividends for an accumulated other comprehensive loss of $ 28.9 million in 2021, an accumulated other comprehensive gain of $ 9.9 million in 2020, and an accumulated other comprehensive loss of $ 6.7 million in 2019. ​ On March 1, 2021, the Company entered into a Sales Agreement with SVB Leerink LLC (“SVB Leerink”) with respect to an at-the-market (“ATM”) offering program, under which the Company may, from time to time in its sole discretion, offer and sell through SVB Leerink, acting as agent, its ordinary shares, up to an aggregate offering price of $ 200.0 million. The Company will pay SVB Leerink a commission equal to 3 % of the gross proceeds of the sales price of all ordinary shares sold through it as sales agent under the Sales Agreement. In March and April 2021, the Company issued an aggregate of 921,730 ordinary shares at a weighted average price of $ 33.52 per ordinary share, with net proceeds of $ 29.6 million, after deducting underwriting discounts and net of offering expenses. The Company defers direct, incremental costs associated to this offering, except for the commission costs to SVB Leerink, which are a reduction to additional paid-in capital, and will deduct these costs from additional paid-in capital in the consolidated balance sheets proportionately to the amount of proceeds raised. During the year ended December 31, 2021, $ 1.3 million of direct, incremental costs were deducted from additional paid-in capital. ​ Following the Closing of the CSL Behring transaction, the Company consumed its tax net operating loss carryforwards from the years 2011 to 2018. The Company allocated the tax benefit from the release of the valuation allowance related to net operating loss carryforwards generated by share issuance costs incurred in 2014, 2015, 2017 and 2018 to additional paid-in capital. This resulted in an increase of additional paid-in capital of $ 3.0 million in the year ended December 31, 2021. ​ 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. 138 ​ Table of Contents ​ 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. ​ 12. 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, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Research and development ​ $ 12,813 ​ $ 11,965 ​ $ 8,029 Selling, general and administrative ​ ​ 12,794 ​ ​ 9,823 ​ ​ 9,439 Total ​ $ 25,607 ​ $ 21,788 ​ $ 17,468 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Award type ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 12,477 ​ $ 11,434 ​ $ 7,896 Restricted share units ​ ​ 11,347 ​ ​ 7,364 ​ ​ 4,117 Performance share units ​ ​ 1,783 ​ ​ 2,990 ​ ​ 5,455 Total ​ $ 25,607 ​ $ 21,788 ​ $ 17,468 ​ ​ As of December 31, 2021, 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 ​ $ 29,513 ​ 2.79 Restricted share units ​ ​ 19,348 ​ 2.00 Performance share units ​ ​ 781 ​ 0.63 Total ​ $ 49,642 ​ 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, 2021, 14,000 fully vested share options are outstanding (December 31, 2020: 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, 2018 and 2021, 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, 3,000,000 shares in 2018 and 4,000,000 shares in 2021 for a total of 12,601,471 shares. 139 ​ Table of Contents 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. 2014 Plan The following tables summarize option activity under the Company’s 2014 Plans for the year ended December 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2020 ​ 2,659,279 ​ $ 28.13 ​ 7.18 ​ $ 32,729 Granted ​ 1,174,893 ​ $ 35.85 ​ ​ ​ ​ ​ Forfeited ​ ( 258,718 ) ​ $ 40.78 ​ ​ ​ ​ ​ Expired ​ ( 25,633 ) ​ $ 42.81 ​ ​ ​ ​ ​ Exercised ​ ( 241,496 ) ​ $ 10.98 ​ ​ ​ ​ ​ Outstanding at December 31, 2021 ​ 3,308,325 ​ $ 31.02 ​ 7.05 ​ ​ 8,660 Thereof, fully vested and exercisable at December 31, 2021 ​ 1,786,825 ​ $ 24.47 ​ 5.49 ​ ​ 8,640 Thereof, outstanding and expected to vest after December 31, 2021 ​ 1,521,500 ​ $ 38.71 ​ 8.88 ​ ​ 20 Outstanding and expected to vest at December 31, 2020 ​ 1,116,874 ​ $ 42.06 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 24.6 ​ ​ ​ ​ ​ Granted to directors and officers during the period (options, grant date fair value $ in millions) ​ 312,704 ​ $ 6.5 ​ ​ ​ ​ ​ Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 2.7 ​ ​ ​ ​ ​ ​ 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, 2021 1,174,893 ​ $ 20.95 Granted, 2020 653,852 ​ ​ 28.08 Granted, 2019 647,526 ​ ​ 23.57 Vested, 2021 ​ 507,503 ​ ​ 22.17 Forfeited, 2021 ​ ( 258,718 ) ​ ​ 23.60 ​ 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, 2021 1,521,500 ​ $ 22.52 Outstanding and expected to vest, 2020 1,116,874 ​ ​ 24.25 ​ ​ ​ ​ ​ 140 ​ Table of Contents 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 2021 2020 ​ 2019 Expected volatility ​ 75 % ​ 70 % ​ 70 % - 75 % Expected terms ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 1.21 - 1.86 % ​ 0.76 % - 1.44 % ​ 1.92 % - 2.87 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ 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) 2021 241,496 ​ $ 5,046 2020 498,678 ​ 11,927 2019 434,665 ​ 17,700 ​ Restricted Share Units ​ The following table summarizes the RSU activity for the year ended December 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 467,344 ​ $ 43.56 Granted ​ 574,921 ​ $ 36.14 Vested ​ ( 220,518 ) ​ $ 40.56 Forfeited ​ ( 111,130 ) ​ $ 40.98 Non-vested at December 31, 2021 ​ 710,617 ​ $ 38.89 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 20.8 Granted to directors and officers during the period (shares, $ in millions) ​ 167,230 ​ $ 6.1 ​ 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 2021 574,921 ​ $ 36.14 2020 376,799 ​ ​ 48.18 2019 198,504 ​ ​ 38.63 ​ 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) 2021 $ 8,063 2020 12,156 2019 10,152 ​ 141 ​ Table of Contents RSUs generally vest over one to three years . RSUs granted to non-executive directors will vest one year from the date of grant. ​ Performance Share Units ​ The following table summarizes the PSU activity for the year ended December 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 212,614 ​ $ 42.32 Granted ​ 555,600 ​ ​ 30.19 Vested ​ ( 132,368 ) ​ $ 33.09 Forfeited ​ ( 2,916 ) ​ $ 57.56 Non-vested at December 31, 2021 ​ 632,930 ​ $ 33.54 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of PSUs granted during the period (in $ millions) ​ ​ ​ $ 16.8 ​ The Company granted shares to certain employees in September and December 2021 that will be earned upon achievement of defined milestones. Earned shares will vest upon the later of a minimum service period of one year or three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, portions of the December 2021 granted to executives and other members of senior management are subject to achieving a minimum total shareholder return relative to the Nasdaq biotechnology index. The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. ​ In January 2018 and January and February 2019, the Company awarded PSUs to its executives and other members of senior management. These PSUs were earned in January 2019 and January 2020, based on the Board’s assessment of the level of achievement of agreed upon performance targets through December 31, 2018, and December 31, 2019, respectively. The PSUs awarded for the year ended December 31, 2018 vested in February 2021 and the PSUs awarded for the year ended December 31, 2019 vested in January 2022. ​ The following table summarizes information about the weighted average grant-date fair value of the PSUs determined as of the date these were earned for the 2018 and 2019 PSUs, and the date of the grant for the 2021 PSUs: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2021 555,600 ​ $ 30.19 2020 91,003 ​ $ 57.56 2019 132,362 ​ $ 31.71 ​ 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) 2021 $ 5,074 2020 21,852 2019 1,056 ​ 142 ​ Table of Contents 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, 2021, 4,724 shares have been issued (December 31, 2020: 6,181 and December 31, 2019: 9,202 ). As of December 31, 2021, a total of 127,302 ordinary shares remains available for issuance under the ESPP plan. ​ ​ 13. Expenses by nature ​ Operating expenses excluding expenses presented in other expenses included the following expenses by nature: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Employee-related expenses ​ $ 96,161 ​ $ 75,926 ​ $ 59,130 Laboratory and development expenses ​ 36,014 ​ 35,977 ​ 30,130 Legal and advisory expenses ​ ​ 24,767 ​ 17,370 ​ 11,297 Office and housing expenses ​ 14,638 ​ 13,388 ​ 10,588 Other operating expenses ​ ​ 10,528 ​ 8,772 ​ 8,813 Depreciation and amortization expenses ​ 7,299 ​ 10,648 ​ 6,669 Fair value loss - Corlieve contingent consideration ​ ​ 6,683 ​ ​ - ​ ​ - Patent and license expenses ​ 3,748 ​ 2,899 ​ 1,654 Total ​ $ 199,838 ​ $ 164,980 ​ $ 128,281 ​ Details of employee-related expenses for the years ended December 31 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Wages and salaries ​ $ 53,078 ​ $ 40,919 ​ $ 32,029 Share-based compensation expenses ​ 25,635 ​ 21,831 ​ 17,533 Other employee expenses ​ ​ 4,570 ​ ​ 2,635 ​ ​ 1,392 Social security costs ​ 4,496 ​ 4,068 ​ 2,727 Contractor expenses ​ 3,170 ​ 2,423 ​ 2,464 Health insurance ​ 3,161 ​ 2,271 ​ 1,933 Pension costs - defined contribution plans ​ 2,051 ​ 1,779 ​ 1,052 Total ​ $ 96,161 ​ $ 75,926 ​ $ 59,130 ​ ​ ​ ​ 14. Other income ​ Other income during the year ended December 31, 2021 was $ 12.3 million compared to $ 3.3 million and $ 1.9 million during the same periods in 2020 and 2019, respectively. ​ Other income in 2021, 2020 and 2019 includes income from payments received from European authorities to subsidize the Company’s research and development efforts in the Netherlands. The amount recognized in the year ended December 31, 2021 was $ 5.3 million compared to $ 1.9 million in 2020 and $ 0.7 million in 2019. ​ In addition, other income includes $ 2.6 million of employee retention credits received under the U.S. Coronavirus Aid, Relief, and Economic Security Act, during the year ended December 31, 2021. An additional $ 3.0 million of other income was recorded in the year ended December 31, 2021, related to the receipt by the Company of 69,899 shares of VectorY B.V. in conjunction with a settlement agreement that the Company and VectorY B.V. entered into in April 2021. No such income was recorded in 2020 and 2019. ​ 143 ​ Table of Contents In 2021, 2020 and 2019 the Company’s other income also consisted of income from the subleasing of a portion of the Amsterdam facility while other expense consists of expenses incurred in relation to the subleasing income. ​ ​ ​ 15. Income taxes ​ a. Income tax expense / (benefit) ​ Due to the uncertainty surrounding the realization of favorable tax attributes in future tax returns, the Company has recorded a valuation allowance against the Company’s net deferred tax assets in the Netherlands. The Company released full valuation allowance against the Company’s net deferred tax assets in the United States as of December 31, 2020. ​ In connection with the Corlieve acquisition, the Company recognized a deferred tax liability related to acquired identifiable intangible assets and a deferred tax asset for net operating tax loss carryforwards for a net of EUR 11.9 million ($ 14.2 million) as of the Acquisition Date. ​ There are no significant unrecognized tax benefits as of December 31, 2021 and 2020. ​ For the years ended December 31, 2021, 2020 and 2019, income / (loss) before income tax (expense) / benefit consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Dutch operations ​ $ 348,400 ​ $ ( 130,493 ) ​ $ ( 111,820 ) U.S. operations ​ ( 12,737 ) ​ ( 10,950 ) ​ ( 12,381 ) Other ​ ​ ( 2,857 ) ​ ​ — ​ ​ — Total ​ $ 332,806 ​ $ ( 141,443 ) ​ $ ( 124,201 ) ​ The income tax benefit / (expense) for the years ended December 31, 2021, 2020 and 2019, consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) Current tax (expense) ​ ​ ​ ​ ​ ​ ​ ​ ​ Other ​ $ ( 7 ) ​ $ — ​ $ — Total current tax (expense) ​ $ ( 7 ) ​ $ — ​ $ — Deferred tax (expense) / benefit ​ ​ ​ ​ ​ ​ Dutch operations ​ $ ( 3,047 ) ​ $ — ​ $ — U.S. operations ​ ( 771 ) ​ 16,419 ​ — Other ​ ​ 608 ​ ​ — ​ ​ — Total deferred tax (expense) / benefit ​ $ ( 3,210 ) ​ $ 16,419 ​ $ — Total income tax (expense) / benefit ​ $ ( 3,217 ) ​ $ 16,419 ​ $ — ​ 144 ​ Table of Contents b. Tax rate reconciliation ​ The reconciliation of the amount of income tax (expense) / benefit that would result from applying the Dutch statutory income tax rate to the Company’s reported amount of income tax (expense) / benefit for the years ended December 31, 2021, 2020 and 2019, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Income / (loss) before income tax (expense) / benefit for the period ​ $ 332,806 ​ $ ( 141,443 ) ​ $ ( 124,201 ) Expected income tax (expense) / benefit at the tax rate enacted in the Netherlands ( 25 %) ​ ( 83,201 ) ​ 35,361 ​ 31,050 Non-deductible expenses ​ ( 9,182 ) ​ ( 5,041 ) ​ ( 4,972 ) Other net change in valuation allowance ​ 88,857 ​ ( 30,568 ) ​ ( 25,583 ) Difference in tax rates between the Netherlands and the U.S. as well as other foreign countries ​ 309 ​ 247 ​ ( 495 ) Release of valuation allowance related to expected future taxable income of U.S. operations ​ ​ — ​ ​ 16,419 ​ ​ — Income tax (expense) / benefit ​ $ ( 3,217 ) ​ $ 16,419 ​ $ — ​ Non-deductible expenses predominantly relate to share-based compensation expenses and affected the effective tax rate by an amount of $ 6.7 million in 2021 (2020: $ 5.8 million; 2019: $ 4.4 million). The fair value loss on contingent consideration affected the effective tax rate by an amount of $ 2.0 million in 2021 ( nil in 2020 and 2019). ​ 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 as of December 31, 2021 and 2020 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Deferred tax assets: ​ ​ Net operating loss carryforwards ​ $ 71,917 ​ $ 158,614 Operating lease liabilities ​ ​ 9,300 ​ ​ 9,515 Intangible assets ​ 2,039 ​ 1,702 Accrued expenses and other current liabilities ​ ​ 1,312 ​ ​ 1,118 Property, plant and equipment ​ 971 ​ 1,072 Inventory ​ ​ 148 ​ ​ — Research and development tax credit carryforwards ​ ​ 105 ​ ​ - Interest carryforwards ​ ​ — ​ ​ 1,597 Derivative financial instrument ​ ​ — ​ ​ 661 Total deferred tax assets ​ $ 85,792 ​ $ 174,279 Less valuation allowance ​ ( 60,289 ) ​ ( 150,113 ) Deferred tax assets, net of valuation allowance ​ $ 25,503 ​ $ 24,166 Acquired IPR&D Intangible Asset (see Note 3, "Corlieve transaction") ​ ​ ( 15,189 ) ​ ​ — Operating lease right-of-use assets ​ ​ ( 7,493 ) ​ ​ ( 7,702 ) Other current assets and receivables ​ ​ ( 87 ) ​ ​ ( 45 ) Deferred tax liability ​ $ ( 22,769 ) ​ $ ( 7,747 ) Net deferred tax asset ​ $ 2,734 ​ $ 16,419 ​ 145 ​ Table of Contents Changes in the valuation allowance were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2021 2020 2019 ​ ​ (in thousands) January 1, ​ $ 150,113 ​ $ 109,856 ​ $ 85,100 Changes recorded in the statement of operations ​ ​ ( 88,858 ) ​ ​ 30,568 ​ ​ 25,583 Increase related to 2021, 2020 and 2019 Dutch tax reforms ​ 1,897 ​ 18,287 ​ 4,059 Valuation allowance assumed in Corlieve acquisition ​ ​ 545 ​ ​ — ​ ​ — Release of valuation allowance related to expected current year and future periods recorded in profit and loss ​ ​ — ​ ​ ( 16,419 ) ​ ​ — Other changes including currency translation adjustments ​ ( 3,408 ) ​ 7,821 ​ ​ ( 4,886 ) December 31, ​ $ 60,289 ​ $ 150,113 ​ $ 109,856 ​ The Company released the full valuation allowance against the Company’s net deferred assets in the United States as of December 31, 2020. Included within changes recorded in the statement of operations for the year ended December 31, 2020 and December 31, 2019 are benefits of $ 1.2 million and $ 0.8 million, respectively, from the utilization of U.S. net operating loss carryforwards. ​ The valuation allowance as of December 31, 2021 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. Management considered reversing taxable temporary differences, projected future taxable income and tax-planning strategies in making this assessment. A valuation allowance was recorded against deferred tax assets if it is more likely than not that some or all the deferred tax assets will not be realized. ​ Netherlands ​ As of December 31, 2020, the Company had recorded a full valuation allowance against its Dutch net deferred tax assets. On May 6, 2021, the CSL Behring Agreement became effective (refer to Note 4 “Collaboration arrangements and concentration of credit risk” ). The Company recorded $ 462.4 million of license revenue related to closing the transaction. The Company recorded such revenue in its Dutch tax return related to the 12-month period ended December 31, 2020, which it filed on February 10, 2022. As such, the Company filed a return showing a taxable profit in the Netherlands in 2020, which resulted in the consumption of substantially all of its Dutch net operating losses for the years 2011 to 2018. The Company’s remaining Dutch net operating tax losses carried forward relate to 2019 and 2021. The Dutch government on June 4, 2021 enacted legislation, whereby such net operating tax losses can be carried forward indefinitely. The Company expects to continue incurring tax losses for the foreseeable future. As such, the Company retains its valuation allowance related to the deferred assets as of December 31, 2021. The Company allocated the tax benefit from the release of the valuation allowance related to net operating loss carryforwards generated by share issuance cost incurred in 2014, 2015, 2017 and 2018 to additional paid-in capital. This resulted in an increase of additional paid-in capital as well as deferred tax expenses of $ 3.0 million. ​ A portion of the valuation allowance for deferred tax assets relates to follow-on offering costs incurred in 2019 and costs related to the at-the-market offering in 2021. Any subsequently recognized tax benefits will be credited directly to contributed capital. As of December 31, 2021, that amount was $ 4.5 million ($ 7.7 million as of December 31, 2020). ​ The Dutch corporate tax rate for fiscal years 2019, 2020 and 2021 was 25 %. During 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 income tax rate at 25 % from 2021 onwards. In December 2021, even further changes were enacted that raised the corporate income tax rate from 25 % to 25.8 % from 2022 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. ​ In June 2021 legislation was enacted allowing for an indefinite carryforward from fiscal year 2022 onwards of existing and future net operating loss carryforwards subject to a limit of offsetting taxable profit in excess of EUR 1.0 million to 50% of the taxable profit. 146 ​ Table of Contents ​ The Dutch fiscal unity as of December 31, 2021 has an estimated $ 228.5 million (2020: $ 588.2 million; 2019: $ 414.0 million) of taxable losses that are available for carry forward indefinitely. In the year ended December 31, 2019, unused tax losses of $ 20.7 million expired. ​ The fiscal periods from 2019 onwards 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 income taxes resulting in a combined tax rate of 27.32 % for its U.S. operation. As of December 31, 2021, an estimated $ 39.1 million of net operating losses remain to be carried forward. These losses will expire between 2035 and 2037. ​ The Company’s U.S. operations generated taxable income in the fiscal years 2018 to 2021. 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. ​ 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 from 2018 are still open for inspection by the Internal Revenue Service (“IRS”). To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the IRS or Massachusetts Department of Revenue to the extent utilized in a future period. The Company is currently not under examination by the IRS for any tax years. ​ France ​ The French corporate tax rate for fiscal years 2021 was 26.5 %, as of January 1, 2022 the tax rate is decreased to 25 %. ​ The Company’s French operation has incurred losses since incorporation and is expected to continue incurring tax losses for the foreseeable future. ​ The French operation as of December 31, 2021 has an estimated $ 9.1 million of taxable losses that are available for carry forward indefinitely. ​ ​ ​ 16. Basic and diluted earnings per share ​ Basic net income / (loss) per ordinary share is computed by dividing net income / (loss) for the period by the weighted average number of ordinary shares outstanding during the period. Diluted earnings per ordinary share are calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. For the year ended December 31, 2021, dilutive net income / (loss) per ordinary share is computed using the treasury method. As the Company has incurred a loss in the years ended December 31, 2020 and December 31, 2019, all potentially dilutive ordinary shares for these years would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share for the years ended December 31, 2020 and December 31, 2019. ​ 147 ​ Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Net income / (loss) attributable to ordinary shares ​ $ 329,589 ​ $ ( 125,024 ) ​ $ ( 124,201 ) ​ ​ ​ 329,589 ​ ​ ( 125,024 ) ​ ​ ​ Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average number of ordinary shares outstanding - basic ​ ​ 45,986,467 ​ ​ 44,466,365 ​ ​ 39,999,450 Stock options under 2014 Plans and previous plan ​ ​ 746,044 ​ ​ — ​ ​ — Non-vested RSUs and PSUs ​ ​ 107,162 ​ ​ — ​ ​ — Employee share purchase plan ​ ​ 1,299 ​ ​ — ​ ​ — Weighted-average number of ordinary shares outstanding - diluted ​ ​ 46,840,972 ​ ​ 44,466,365 ​ ​ 39,999,450 ​ The following table presents ordinary share equivalents that were excluded from the calculation of diluted net income / (loss) per ordinary share for the years ended December 31, 2021, 2020 and 2019 as the effect of their inclusion would have been anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2021 ​ 2020 ​ 2019 ​ ​ (in thousands) Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 2,576,281 ​ ​ 2,673,279 ​ ​ 2,697,104 Non-vested RSUs and PSUs ​ ​ 1,236,385 ​ ​ 679,958 ​ ​ 850,252 Employee share purchase plan ​ ​ 1,842 ​ ​ 560 ​ ​ 485 BMS warrants (derecognized as of December 1, 2020 - refer to Note 5, "Fair value measurement" ) ​ ​ — ​ ​ — ​ ​ 8,893,000 Total anti-dilutive ordinary share equivalents ​ ​ 3,814,508 ​ ​ 3,353,797 ​ ​ 12,440,841 ​ The anti-dilutive ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that exceeded the price of the Company’s ordinary shares as of December 31, 2020 and December 31, 2019. In addition, the BMS warrants were not exercisable as of December 31, 2019, since this would have required the prior designation of Collaboration Targets by BMS. This would 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. ​ ​ ​ 17. 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. The Company also has obligations to make future payments that become due and payable upon the collection of milestone payments from CSL Behring. The achievement and timing of these milestones is not fixed and determinable. Relevant commitments and contingencies are further discussed in other sections of this form 10-K, such as, Note 3 “ Corlieve transaction ” and Note 4 “ Collaboration arrangements and concentration of credit risk ”, amongst others. ​ 18. 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, 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 4 “Collaboration arrangements and concentration of credit risk” ) as well as the elimination of the BMS warrants (see Note 5, “Fair value measurement” ). ​ 148 ​ Table of Contents On October 21, 2021, the Company held an Extraordinary General Meeting of its shareholders and Rachelle Jacques was appointed to the Board of Directors (the “Board”) as a non-executive director. Ms. Jacques will also serve as a member of the Audit Committee of the Board effective as of October 21, 2021. ​ On June 16, 2021, the Company’s shareholders voted to approve the reappointment of Mr. David Meek and Ms. Paula Soteropoulos as non-executive directors of the Board. Mr. Meek has been appointed chairman of the Board. Mr. Philip Astley-Sparke did not stand for reappointment and retired from the Board on June 16, 2021. ​ On June 15, 2021, Christian Klemt was appointed as Chief Financial Officer. Mr. Klemt was our Chief Accounting Officer from August 2017 to June 2021, and he will continue to serve as general manager of our Amsterdam site. Matthew Kapusta, who has been our Chief Executive Officer since December 2016 and had been our Chief Financial Officer from January 2015 to June 2021, will continue to serve as our Chief Executive Officer. In connection with his transition to Chief Financial Officer, Mr. Klemt will also serve as our Principal Financial Officer. ​ On May 17, 2021, Pierre Caloz was appointed as Chief Operating Officer. Mr. Caloz oversees all manufacturing operations, global CMC development and innovation, supply chain, and facilities. ​ 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. ​ 19. Subsequent events ​ None. ​ ​ 149 ​ Table of Contents EXHIBIT INDEX ​ Exhibit No. Description 2.1† ​ Sale and Purchase Agreement, executed June 21, 2021, by and between uniQure N.V. and Corlieve Therapeutics SAS (incorporated by reference to Exhibit 2.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2021 filed with the Securities and Exchange Commission). 3.1 ​ Amended Articles of Association of the Company (incorporated by reference to Exhibit 3.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2021 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 Plan (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). 10.6 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). 150 ​ Table of Contents 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). 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). 10.27† ​ 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). 10.36 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). 10.40 ​ 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. 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). 151 ​ Table of Contents 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. 10.49t ​ 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). 10.53† ​ 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). 10.57† ​ Amendment to Collaboration and License Agreement by and between uniQure biopharma B.V. and Bristol-Myers Squibb Company dated December 1, 2020 (incorporated by reference to Exhibit 10.57 of the Company’s annual report on Form 10-K for the year ended December 31, 2020 (file no. 0001-36294) filed with the Securities and Exchange commission). 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. (incorporated by reference to Exhibit 10.58 of the Company’s annual report on Form 10-K for the year ended December 31, 2020 (file no. 0001-36294) filed with the Securities and Exchange commission). 10.59 ​ Cooperation Agreement, dated as of April 16, 2021, by and among uniQure N.V., ForUniqure B.V., Forbion 1 Management B.V., Forbion International Management B.V., and Forbion Capital Partners Management Holding B.V. (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, 2021 filed with the Securities and Exchange Commission). 10.60t ​ 2014 Share Incentive Plan, Amended and Restated, effective as of June 16, 2021 (incorporated by reference to Exhibit 4.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ending on June 30, 2021 filed with the Securities and Exchange Commission). 10.61t ​ Employment Agreement, effective May 17, 2021, by and between uniQure biopharma B.V. and Pierre Caloz (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, 2021 filed with the Securities and Exchange Commission). 152 ​ Table of Contents 10.62t ​ Equity Side Letter, effective May 17, 2021, by and between uniQure N.V. and Pierre Caloz (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, 2021 filed with the Securities and Exchange Commission). 10.63t ​ Amended and Restated Employment Agreement, effective June 15, 2021, by and between uniQure biopharma B.V. and Christian Klemt (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 June 30, 2021 filed with the Securities and Exchange Commission). 10.64 ​ Consent and Amendment No. 3 to Second Amended and Restated Loan and Security Agreement, dated July 30, 2021, by and among the Registrant, Hercules Capital Inc., and the other parties named therein (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, 2021 filed with the Securities and Exchange Commission). 10.65t* ​ Form of Share Option Agreement, effective December 8, 2021, under the 2014 Share Incentive Plan. 10.66t* ​ Form of Restricted Stock Unit Award, effective December 8, 2021, under the 2014 Share Incentive Plan. 10.67†t* ​ Form of Performance Stock Unit Award, effective December 8, 2021 under the 2014 Share Incentive Plan. 10.68†* ​ Third Amended and Restated Loan and Security Agreement as of December 15, 2021, by and among uniQure biopharma B.V., uniQure Inc., uniQure IP B.V., the Company and Hercules Capital Inc. 10.69†* ​ Lease Agreement relating to 20 Maguire Road, Lexington, Massachusetts, dated as of December 22, 2021, by and between uniQure Inc. and G&I IX/GP4 20 Maguire LLC. 10.70†* ​ Lease Agreement relating to 91 Hartwell Avenue, Lexington, Massachusetts, dated as of February 1, 2022, by and between uniQure Inc. and NRL 91 Hartwell LLC. 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. 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* ​ Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 101* ​ The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2021, 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, 2021, 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. ​ 153 ​ 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 Officer) ​ ​ ​ ​ By: /s/ CHRISTIAN KLEMT ​ ​ Christian Klemt ​ ​ Chief Financial Officer (Principal 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 and Director (Principal Executive Officer) ​ February 25, 2022 Matthew Kapusta ​ ​ ​ ​ ​ ​ ​ /s/ CHRISTIAN KLEMT ​ Chief Financial Officer (Principal Financial Officer) ​ February 25, 2022 Christian Klemt ​ ​ ​ ​ ​ ​ ​ /s/ MADHAVAN BALACHANDRAN ​ Director ​ February 25, 2022 Madhavan Balachandran ​ ​ ​ ​ ​ ​ ​ /s/ ROBERT GUT ​ Director ​ February 25, 2022 Robert Gut ​ ​ ​ ​ ​ ​ ​ /s/ RACHELLE JACQUES ​ Director ​ February 25, 2022 Rachelle Jacques ​ ​ ​ ​ ​ ​ ​ /s/ JACK KAYE ​ Director ​ February 25, 2022 Jack Kaye ​ ​ ​ ​ ​ ​ ​ /s/ DAVID MEEK ​ Director ​ February 25, 2022 David Meek ​ ​ ​ ​ ​ ​ ​ /s/ LEONARD POST ​ Director ​ February 25, 2022 Leonard Post ​ ​ ​ ​ ​ ​ ​ /s/ PAULA SOTEROPOULOS ​ Director ​ February 25, 2022 Paula Soteropoulos ​ ​ ​ ​ ​ ​ ​ ​ ​ /s/ JEREMY P. SPRINGHORN ​ Director ​ February 25, 2022 Jeremy P. Springhorn ​ ​ ​ ​ ​ ​ 154 ​