uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. ​ UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2021 2020 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 578,464 ​ $ 244,932 Accounts receivable ​ ​ 3,771 ​ ​ 6,618 Prepaid expenses ​ ​ 10,345 ​ ​ 4,337 Other current assets and receivables ​ ​ 1,184 ​ ​ 3,024 Total current assets ​ ​ 593,764 ​ ​ 258,911 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 35.9 million as of September 30, 2021 and $ 35.2 million as of December 31, 2020, respectively ​ ​ 41,215 ​ ​ 32,328 Operating lease right-of-use assets ​ ​ 26,194 ​ ​ 26,086 Intangible assets, net ​ ​ 64,005 ​ ​ 3,361 Goodwill ​ ​ 28,060 ​ ​ 542 Deferred tax assets, net ​ ​ 15,719 ​ ​ 16,419 Other non-current assets ​ ​ 5,668 ​ ​ 2,748 Total non-current assets ​ ​ 180,861 ​ ​ 81,484 Total assets ​ $ 774,625 ​ $ 340,395 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 5,373 ​ $ 3,772 Accrued expenses and other current liabilities ​ ​ 30,746 ​ ​ 18,038 Current portion of operating lease liabilities ​ ​ 5,798 ​ ​ 5,524 Total current liabilities ​ ​ 41,917 ​ ​ 27,334 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 71,490 ​ ​ 35,617 Operating lease liabilities, net of current portion ​ ​ 29,733 ​ ​ 30,403 Contingent consideration ​ ​ 23,781 ​ ​ — Deferred tax liabilities, net ​ ​ 13,141 ​ ​ — Other non-current liabilities ​ ​ 3,808 ​ ​ 3,136 Total non-current liabilities ​ ​ 141,953 ​ ​ 69,156 Total liabilities ​ ​ 183,870 ​ ​ 96,490 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of September 30, 2021 and 60,000,000 shares authorized as of December 31, 2020 and 46,207,776 and 44,777,799 ordinary shares issued and outstanding as of September 30, 2021 and December 31, 2020, respectively ​ ​ 2,797 ​ ​ 2,711 Additional paid-in-capital ​ ​ 1,069,191 ​ ​ 1,016,018 Accumulated other comprehensive (loss) / income ​ ​ ( 17,883 ) ​ ​ 9,907 Accumulated deficit ​ ​ ( 463,350 ) ​ ​ ( 784,731 ) Total shareholders' equity ​ ​ 590,755 ​ ​ 243,905 Total liabilities and shareholders' equity ​ $ 774,625 ​ $ 340,395 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ ​ 2 Table of Contents ​ uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2021 2020 2021 2020 ​ ​ (in thousands, except share and per share amounts) ​ (in thousands, except share and per share amounts) License revenues ​ ​ — ​ ​ — ​ ​ 462,400 ​ ​ — License revenues from related party ​ ​ — ​ ​ 1,776 ​ ​ — ​ ​ 3,353 Collaboration revenues ​ ​ 1,989 ​ ​ — ​ ​ 3,911 ​ ​ — Collaboration revenues from related party ​ ​ — ​ ​ 13 ​ ​ — ​ ​ 75 Total revenues ​ ​ 1,989 ​ ​ 1,789 ​ ​ 466,311 ​ ​ 3,428 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of contract revenues ​ ​ — ​ ​ — ​ ​ ( 23,178 ) ​ ​ — Research and development expenses ​ ​ ( 36,432 ) ​ ​ ( 36,302 ) ​ ​ ( 101,209 ) ​ ​ ( 90,716 ) Selling, general and administrative expenses ​ ​ ( 12,023 ) ​ ​ ( 10,789 ) ​ ​ ( 42,323 ) ​ ​ ( 31,372 ) Total operating expenses ​ ​ ( 48,455 ) ​ ​ ( 47,091 ) ​ ​ ( 166,710 ) ​ ​ ( 122,088 ) Other income ​ ​ 1,680 ​ ​ 1,032 ​ ​ 9,622 ​ ​ 2,558 Other expense ​ ​ ( 214 ) ​ ​ ( 220 ) ​ ​ ( 673 ) ​ ​ ( 1,059 ) (Loss) / income from operations ​ ​ ( 45,000 ) ​ ​ ( 44,490 ) ​ ​ 308,550 ​ ​ ( 117,161 ) Interest income ​ ​ 46 ​ ​ 13 ​ ​ 123 ​ ​ 916 Interest expense ​ ​ ( 1,924 ) ​ ​ ( 942 ) ​ ​ ( 5,377 ) ​ ​ ( 2,887 ) Foreign currency gains / (losses), net ​ ​ 10,436 ​ ​ ( 8,681 ) ​ ​ 21,645 ​ ​ ( 7,724 ) Other non-operating gains, net ​ ​ — ​ ​ 325 ​ ​ — ​ ​ 2,531 (Loss) / income before income tax expense ​ $ ( 36,442 ) ​ $ ( 53,775 ) ​ $ 324,941 ​ $ ( 124,325 ) Income tax expense ​ ​ ( 89 ) ​ ​ — ​ ​ ( 3,560 ) ​ ​ — Net (loss) / income ​ $ ( 36,531 ) ​ $ ( 53,775 ) ​ $ 321,381 ​ $ ( 124,325 ) Other comprehensive (loss) / gain: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation adjustments ​ ​ ( 13,288 ) ​ ​ 9,652 ​ ​ ( 27,790 ) ​ ​ 9,022 Total comprehensive (loss) / gain ​ $ ( 49,819 ) ​ $ ( 44,123 ) ​ $ 293,591 ​ $ ( 115,303 ) Earnings per ordinary share - basic ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net (loss) / income per ordinary share ​ $ ( 0.79 ) ​ $ ( 1.21 ) ​ $ 7.00 ​ $ ( 2.80 ) Earnings per ordinary share - diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Diluted net (loss) / income per ordinary share ​ $ ( 0.79 ) ​ $ ( 1.21 ) ​ $ 6.87 ​ $ ( 2.80 ) Weighted average shares - basic ​ ​ 46,152,404 ​ ​ 44,471,844 ​ ​ 45,888,769 ​ ​ 44,379,924 Weighted average shares - diluted ​ ​ 46,152,404 ​ ​ 44,471,844 ​ ​ 46,780,963 ​ ​ 44,379,924 ​ ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 3 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY FOR THE THREE-MONTH PERIOD ENDED SEPTEMBER 30 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital (loss) deficit equity ​ (in thousands, except share and per share amounts) Balance at June 30, 2020 44,444,405 ​ $ 2,692 ​ $ 1,000,389 ​ $ ( 7,319 ) ​ $ ( 730,257 ) ​ $ 265,505 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 53,775 ) ​ ​ ( 53,775 ) Other comprehensive income — ​ ​ — ​ ​ — ​ ​ 9,652 ​ ​ — ​ ​ 9,652 Exercise of share options 7,348 ​ ​ — ​ ​ 139 ​ ​ — ​ ​ — ​ ​ 139 Restricted share units distributed during the period 35,480 ​ ​ 2 ​ ​ ( 2 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 6,372 ​ ​ — ​ ​ — ​ ​ 6,372 Issuance of ordinary shares relating to employee stock purchase plan 277 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Balance at September 30, 2020 44,487,510 ​ $ 2,694 ​ $ 1,006,898 ​ $ 2,333 ​ $ ( 784,032 ) ​ $ 227,893 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at June 30, 2021 46,050,250 ​ $ 2,788 ​ $ 1,062,234 ​ $ ( 4,595 ) ​ $ ( 426,819 ) ​ $ 633,608 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 36,531 ) ​ ​ ( 36,531 ) Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 13,288 ) ​ ​ — ​ ​ ( 13,288 ) Exercise of share options 84,811 ​ ​ 5 ​ ​ 909 ​ ​ — ​ ​ — ​ ​ 914 Restricted share units distributed during the period 69,165 ​ ​ 4 ​ ​ ( 4 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 5,955 ​ ​ — ​ ​ — ​ ​ 5,955 Issuance of ordinary shares relating to employee stock purchase plan 3,550 ​ ​ — ​ ​ 97 ​ ​ — ​ ​ — ​ ​ 97 Balance at September 30, 2021 46,207,776 ​ $ 2,797 ​ $ 1,069,191 ​ $ ( 17,883 ) ​ $ ( 463,350 ) ​ $ 590,755 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 4 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY FOR THE NINE-MONTH PERIOD ENDED SEPTEMBER 30 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2019 43,711,954 ​ $ 2,651 ​ $ 986,803 ​ $ ( 6,689 ) ​ $ ( 659,707 ) ​ $ 323,058 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 124,325 ) ​ ​ ( 124,325 ) Other comprehensive income — ​ ​ — ​ ​ — ​ ​ 9,022 ​ ​ — ​ ​ 9,022 Exercise of share options 211,288 ​ ​ 12 ​ ​ 3,529 ​ ​ — ​ ​ — ​ ​ 3,541 Restricted and performance share units distributed during the period 560,986 ​ ​ 31 ​ ​ ( 31 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 16,450 ​ ​ — ​ ​ — ​ ​ 16,450 Issuance of ordinary shares relating to employee stock purchase plan 3,282 ​ ​ — ​ ​ 147 ​ ​ — ​ ​ — ​ ​ 147 Balance at September 30, 2020 44,487,510 ​ $ 2,694 ​ $ 1,006,898 ​ $ 2,333 ​ $ ( 784,032 ) ​ $ 227,893 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2020 44,777,799 ​ $ 2,711 ​ $ 1,016,018 ​ $ 9,907 ​ $ ( 784,731 ) ​ $ 243,905 Income for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ 321,381 ​ ​ 321,381 Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 27,790 ) ​ ​ — ​ ​ ( 27,790 ) Issuance of ordinary shares 921,730 ​ ​ 55 ​ ​ 29,510 ​ ​ — ​ ​ — ​ ​ 29,565 Tax benefit past share issuance cost — ​ ​ — ​ ​ 2,977 ​ ​ — ​ ​ — ​ ​ 2,977 Exercise of share options 156,787 ​ ​ 10 ​ ​ 1,814 ​ ​ — ​ ​ — ​ ​ 1,824 Restricted and performance share units distributed during the period 346,736 ​ ​ 21 ​ ​ ( 21 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 18,747 ​ ​ — ​ ​ — ​ ​ 18,747 Issuance of ordinary shares relating to employee stock purchase plan 4,724 ​ ​ — ​ ​ 146 ​ ​ — ​ ​ — ​ ​ 146 Balance at September 30, 2021 46,207,776 ​ $ 2,797 ​ $ 1,069,191 ​ $ ( 17,883 ) ​ $ ( 463,350 ) ​ $ 590,755 ​ ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 5 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine months ended September 30, ​ 2021 2020 ​ ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net income / (loss) ​ $ 321,381 ​ $ ( 124,325 ) Adjustments to reconcile net income / (loss) to net cash generated from / (used in) operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ 5,447 ​ ​ 8,354 Share-based compensation expense ​ ​ 18,747 ​ ​ 16,450 Deferred tax expense ​ ​ 3,560 ​ ​ - Changes in fair value of contingent consideration and derivative financial instruments ​ ​ 416 ​ ​ ( 2,531 ) Unrealized foreign exchange (gains) / loss, net ​ ​ ( 23,242 ) ​ ​ 7,758 Other non-cash items, net ​ ​ ( 2,862 ) ​ ​ ( 2,082 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 1,993 ) ​ ​ ( 1,183 ) Accounts payable ​ ​ 2,003 ​ ​ ( 3,724 ) Accrued expenses, other liabilities, and operating leases ​ ​ 11,592 ​ ​ 3,630 Net cash generated from / (used in) operating activities ​ ​ 335,049 ​ ​ ( 97,653 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Acquisition of Corlieve, net of cash acquired ​ ​ ( 49,949 ) ​ ​ - Purchases of intangible assets ​ ​ - ​ ​ ( 2,314 ) Purchases of property, plant, and equipment ​ ​ ( 13,885 ) ​ ​ ( 4,475 ) Net cash used in investing activities ​ ​ ( 63,834 ) ​ ​ ( 6,789 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from loan increment, net of debt issuance costs ​ ​ 34,603 ​ ​ - Proceeds from issuance of ordinary shares ​ ​ 30,899 ​ ​ - Share issuance costs from issuance of ordinary shares ​ ​ ( 1,334 ) ​ ​ - Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 1,971 ​ ​ 3,688 Repayment of debt acquired through acquisition of Corlieve ​ ​ ( 1,175 ) ​ ​ - Net cash generated from financing activities ​ ​ 64,964 ​ ​ 3,688 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 2,589 ) ​ ​ 2,235 Net increase / (decrease) in cash, cash equivalents and restricted cash ​ ​ 333,590 ​ ​ ( 98,519 ) Cash, cash equivalents and restricted cash at beginning of period ​ ​ 247,680 ​ ​ 380,726 Cash, cash equivalents and restricted cash at the end of period ​ $ 581,270 ​ $ 282,207 Cash and cash equivalents ​ $ 578,464 ​ $ 279,493 Restricted cash related to leasehold and other deposits ​ ​ 2,806 ​ ​ 2,714 Total cash, cash equivalents and restricted cash ​ $ 581,270 ​ $ 282,207 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 4,503 ) ​ $ ( 3,342 ) Non-cash increase in accounts payables and accrued expenses and other current liabilities related to purchases of intangible assets and property, plant, and equipment ​ $ 415 ​ $ 116 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ 6 Table of Contents 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 (AMT) Holding N.V (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability ( naamloze vennootschap ) and changed its legal name from uniQure B.V. to uniQure N.V. ​ The Company is registered in the trade register of the Chamber of Commerce ( Kamer van Koophandel ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. ​ 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 these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the Securities and Exchange Commission (“SEC”) regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). ​ The unaudited consolidated financial statements are presented in U.S. dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. ​ 2.2 Unaudited interim financial information ​ The interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the period presented. ​ Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the nine months ended September 30, 2021, are not necessarily indicative of the results to be expected for the full year ending December 31, 2021, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2020, filed with the SEC on March 1, 2021 . ​ 2.3 Use of estimates ​ The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates. ​ 7 Table of Contents 2.4 Accounting policies ​ The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2020, and the notes thereto, which are included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2020, filed with the SEC on March 1, 2021 . There have been no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2021, except as noted below. ​ Revenue recognition – CSL Behring Agreement ​ The Company determined its revenue recognition policies related to the CSL Behring Agreement (defined below) when the CSL Behring Agreement became fully effective on May 6, 2021. Refer to Note 4 “Collaboration arrangements and concentration of credit risk” for further detail. ​ Earnings per ordinary share ​ The Company recognized net income for the first time in 2021. The Company had a net loss for the three months ended September 30, 2021. Net income / (loss) per ordinary share was calculated in accordance with ASC 260, Earnings Per Share. Refer to Note 13 “Basic and diluted earnings per share” for further detail. ​ Corlieve transaction ​ The Company acquired Corlieve Therapeutics SAS (“Corlieve”) on July 30, 2021. The Company determined the accounting for this transaction in accordance with ASC 805, Business Combination. Refer to Note 3 “Corlieve transaction” for further detail. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the nine months ended September 30, 2021, as compared to the recent accounting pronouncements described in Note 2.3.22 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2020 , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ ​ 8 Table of Contents 3 Corlieve transaction ​ On July 30, 2021 (“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. At the same time Corlieve also obtained an exclusive license from Regenxbio Inc. 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 Inc. 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. ​ 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 provisional 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 provisional 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 ​ 720 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 ​ 53,267 Current liabilities ​ ( 1,129 ) Deferred tax liability, net ​ ( 11,472 ) Debt ​ ( 1,352 ) Other non-current liabilities ​ ( 260 ) Fair value of net assets acquired ​ 41,990 Goodwill ​ 23,770 ​ € 65,760 ​ Consideration ​ On the Acquisition Date, the Company acquired 97.7 % of the outstanding ordinary shares of Corlieve for EUR 44.9 million ($ 53.3 million). The Company is contractually required to acquire the remaining outstanding ordinary shares in February 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 transaction from its cash on hand. ​ 9 Table of Contents In addition, Corlieve’s former shareholders are eligible to receive up to EUR 35.8 million ($ 42.5 million) upon achievement of certain development milestones through Phase I/II and EUR 143.1 million ($ 169.9 million) 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 liability for the contingent consideration was determined using unobservable inputs with respect to (i) the probability of achieving the relevant milestones, or probability of success (“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 based on the estimated timing of achieving the milestones. The unobservable inputs were estimated within a range of inputs. Varying the inputs within the range of inputs considered by the Company would not result in a material change of the fair value of contingent consideration as of the Acquisition Date. Increasing the POS of AMT-260 advancing into clinical development by 5 % would increase the fair value of contingent consideration by $ 1.9 million to $ 25.9 million as of the Acquisition Date. Similarly reducing the estimated timing of achieving such milestones by six months would reduce the fair value of contingent consideration by $ 1.3 million to $ 25.3 million as of the Acquisition Date. The Company subsequently measures the contingent liability at its fair value. The fair value of the contingent liability as of September 30, 2021 amounted to EUR 20.5 million ($ 23.8 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 53.3 million ($ 63.3 million) as of the Acquisition Date. ​ 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. ​ 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. ​ Deferred tax liability, net ​ Corlieve’s deferred tax assets at the time of acquisition amounted to EUR 1.8 million ($ 2.2 million). Recognition of the IPR&D intangible asset gave rise to a deferred tax liability of EUR 13.3 million ($ 15.8 million) at the enacted French corporate income tax rate of 25.0 %. The Company consequently recorded a net deferred tax liability of EUR 11.5 million ($ 13.6 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. ​ 10 Table of Contents Goodwill ​ Goodwill represents the excess of total consideration over the estimated fair value of net assets acquired. The Company recorded EUR 23.8 million ($ 28.2 million) of goodwill in the consolidated balance sheet as of the Acquisition Date. The Company allocated the goodwill to its only reporting unit. The Company does not expect any portion of this goodwill to be deductible for tax purposes. Goodwill is not amortized but is evaluated for impairment on an annual basis and between annual tests, in accordance with ASC 350, Intangibles – Goodwill and Other, if the Company becomes aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the corporate reporting unit below its carrying amount. ​ Provisional fair values ​ The provisional determination of the fair value for the IPR&D intangible asset required considerable judgment. As of September 30, 2021, the valuation of this item has not yet been finalized. The Company will adjust the provisional valuation of identifiable assets and assumed liabilities for any material additional information regarding the fair values that becomes available until it finalized its valuation. Any such adjustments might also impact the deferred tax liability as well as goodwill. The finalization of the valuation might change the outcome of the screen test requiring the Company to treat the transaction as an asset acquisition. In accordance with ASC 805, the Company in this case, among others, would not record any goodwill and expense all identifiable intangible assets without alternative future use. 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. ​ ​ 11 Table of Contents ​ 4 Collaboration arrangements and concentration of credit risk ​ CSL Behring collaboration ​ On June 24, 2020, (the “Signing Date”), uniQure biopharma B.V., a wholly-owned subsidiary of uniQure N.V., entered into a commercialization and license agreement (the “CSL Behring Agreement”) with CSL Behring LLC, (“CSL Behring”), pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec, the Company’s investigational gene therapy for patients with hemophilia B, (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 stand-alone selling price (“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 the development and validation of a next generation manufacturing process (“Manufacturing Development Services”) 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) Sale of the exclusive global rights to the Product (“License”); 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”). 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. 12 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 sale of the License 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 recognized nil and $ 462.4 million of revenues related to the License Sale in the three and nine months ended September 30, 2021, respectively, compared to nil in the same periods in the prior year. The costs associated with fulfilling this performance obligation are presented as “Cost of contract revenue” with the exception of the cost incurred prior to the Closing, which had been presented as “Research and development expenses ”. The Company determined that the variable milestone payment related to Manufacturing Development Services 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 did not recognize any revenue related to Manufacturing Development during the three and nine months ended September 30, 2021. The Company recognized $ 0.5 million and $ 0.9 million of collaboration revenue in the three and nine months ended September 30, 2021, respectively, compared to nil in the same periods in the prior year. 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. As of September 30, 2021, the Company has accounts receivable of $ 1.9 million from CSL Behring. 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. Bristol-Myers Squibb collaboration In May 2015, the Company and Bristol-Myers Squibb (“BMS”) entered into a collaboration and license agreement and various related agreements with BMS (“BMS CLA”). ​ The initial four-year research term under the collaboration terminated on May 21, 2019. On December 1, 2020, the Company and BMS amended the BMS CLA (“amended BMS CLA”). Under the amended BMS CLA, BMS is limited to four Collaboration Targets. BMS may until November 30, 2021 replace up to two of these four Collaboration Targets with up to two new targets in the field of cardiovascular disease. The Company continues to be eligible to receive research, development, and regulatory milestone payments of up to $ 217.0 million for each Collaboration Target if defined milestones are achieved. ​ 13 Table of Contents 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. BMS may place purchase orders to provide limited services primarily related to analytical and development efforts in respect of the four Collaboration Targets. BMS may request such services for a period not to exceed the earlier of (i) the completion of all activities under a Research Plan and (ii) either (A) three years after the last replacement target has been designated by BMS during the one-year replacement period ending on November 30, 2021, or (B) November 30, 2023, if no replacement targets are designated. BMS continues to reimburse the Company for these services. ​ The Company evaluated the impact of the amended BMS CLA in relation to its performance obligation to provide access to BMS to its technology and know-how in the field of gene therapy and to participate in joint steering committee and other governing bodies (“License Revenue”). ​ The Company 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. 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 no t generally consider this probable and did not record any License Revenue during the three and nine months ended September 30, 2021. ​ ​ 5 Intangible assets, net and Goodwill ​ The following table presents the Company’s acquired licenses and acquired IPR&D intangible asset: ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, December 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Acquired licenses ​ $ 4,858 ​ $ 5,660 Less accumulated amortization ​ ​ ( 2,587 ) ​ ​ ( 2,299 ) Acquired licenses, net ​ $ 2,271 ​ $ 3,361 Acquired in-process research and development intangible asset ​ 61,734 ​ — Intangibles, net ​ $ 64,005 ​ $ 3,361 ​ 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.” ​ ​ ​ ​ ​ 14 Table of Contents 6 Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. U.S. GAAP requires disclosure of methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: ​ Level 1 – Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. ​ Level 2 – Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. ​ Level 3 – Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. ​ To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. ​ The carrying amount of cash and cash equivalents, accounts receivable, prepaid expenses, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Consolidated balance sheets approximate their fair values due to their short-term maturities. ​ The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2021, and December 31, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Quoted prices in active markets (Level 1) Significant other observable inputs (Level 2) Significant unobservable inputs (Level 3) Total Classification in Consolidated balance sheets ​ ​ ​ (in thousands) ​ ​ At December 31, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash, cash equivalents and restricted cash ​ $ 247,680 ​ $ — ​ $ — ​ $ 247,680 ​ Cash and cash equivalents; other non-current assets Total assets ​ $ 247,680 ​ $ — ​ $ — ​ $ 247,680 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative financial instruments ​ ​ — ​ ​ — ​ ​ 2,645 ​ ​ 2,645 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 2,645 ​ $ 2,645 ​ ​ At September 30, 2021 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash, cash equivalents and restricted cash ​ $ 581,270 ​ $ — ​ $ — ​ $ 581,270 ​ Cash and cash equivalents; other non-current assets Total assets ​ $ 581,270 ​ $ — ​ $ — ​ $ 581,270 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 23,781 ​ ​ 23,781 ​ Contingent consideration Derivative financial instruments ​ ​ — ​ ​ — ​ ​ 2,645 ​ ​ 2,645 ​ Other non-current liabilities Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 280 ​ ​ 280 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 26,706 ​ $ 26,706 ​ ​ ​ Derivative financial instruments ​ The Company issued derivative financial instruments related to its collaboration with BMS. ​ In 2015, the Company granted BMS two warrants that were subsequently terminated in connection with the amendment to the BMS CLA on December 1, 2020. ​ 15 Table of Contents 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 September 30, 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 September 30, 2021 and December 31, 2020. The Company obtained reasonably available market information that it believed market participants would use in determining the likelihood of the occurrence of a change-of control transaction within the biotechnology industry. Selecting and evaluating market information involves considerable judgement and uncertainty. Based on all such information and its judgment, the Company estimated that the fair market value of the derivative financial liability (presented within “Other non-current liabilities”) as of September 30, 2021 and December 31, 2020 was $ 2.6 million. ​ Contingent consideration ​ The Company is required to pay up to EUR 178.8 million ($ 212.4 million) 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). 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. The unobservable inputs were estimated within a range of inputs. Varying the inputs within the range of inputs considered by the Company would not result in a material change of the fair value of contingent consideration as of September 30, 2021. Increasing the POS of AMT-260 advancing into clinical development by 5 % would increase the fair value of contingent consideration by $ 1.9 million to $ 25.7 million as of September 30, 2021. Similarly reducing the estimated timing of achieving such milestones by six months would reduce would increase the fair value of contingent consideration by $ 1.3 million to $ 25.1 million as of September 30, 2021. ​ The following table presents the changes in fair value of contingent consideration between the July 30, 2021 Acquisition Date and September 30, 2021: ​ ​ ​ ​ ​ ​ Amount of ​ contingent ​ consideration ​ ​ 2021 ​ (in thousands) Amount recorded on Acquisition Date $ 23,950 Change in fair value (included within research and development expenses) ​ 416 Currency translation effects ​ ( 585 ) Balance at September 30, 2021 $ 23,781 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 16 Table of Contents 7 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2021 2020 ​ ​ (in thousands) Accruals for services provided by vendors-not yet billed ​ $ 19,846 ​ $ 8,269 Personnel related accruals and liabilities ​ ​ 10,900 ​ ​ 7,687 Contract liability ​ ​ — ​ ​ 2,082 Total ​ $ 30,746 ​ $ 18,038 ​ ​ ​ ​ 8 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-only period was initially extended from November 2018 to January 1, 2021 and was further extended to January 1, 2022 as a result of raising more than $ 90.0 million in equity financing in September 2019. The interest only period was again further extended to June 1, 2023 as a result of the January 2021 amendment (see below). 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. 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. The Company may draw down the remaining $ 65.0 million under the Tranche B in a series of one or more advances of not less than $ 20.0 million each until December 15, 2021. Advances under Tranche B bear interest at a rate equal to the greater of (i) 8.25 % or (ii) 8.25 % plus the prime rate, less 3.25 % per annum. The principal balance and all accrued but unpaid interest on advances under Tranche B is due on June 1, 2023, which date may be extended by the Company by up to two twelve-month periods. Advances under Tranche B may now be prepaid without charge as six months have passed since the Company drew down the $ 35.0 million of Tranche B. The Company owes a back-end fee of 4.85 % of amounts outstanding under Tranche B. The back-end fee is reduced if prepayment occurs at an earlier date. The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2018 Amended Facility and 2021 Amended Facility was $ 71.6 million as of September 30, 2021, compared to $ 35.9 million amortized cost 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 facilities in the three months ended September 30, 2021, was $ 1.8 million and the foreign currency loss on the facilities in the nine months ended September 30, 2021, was $ 4.0 million, compared to a foreign currency gain of $ 1.5 million and $ 1.5 million during the same periods in 2020 for the 2018 Amended Facility. Interest expense associated with the 2018 Amended Facility and 2021 Amended Facility during the three and nine months ended September 30, 2021, was $ 1.9 million and $ 5.2 million, compared to $ 0.9 million and $ 2.7 million, respectively, during the same periods in 2020 for the 2018 Amended Facility. 17 Table of Contents As a covenant in the 2018 Amended Facility and 2021 Amended Facility, the Company has periodic reporting requirements and is required to keep a minimum cash balance deposited in bank accounts in the United States, equivalent to the lesser of (i) 65 % of the outstanding balance of principal due or (ii) 100% of worldwide cash and cash equivalents. This restriction on cash and cash equivalents only relates to the location of the cash and cash equivalents, and such cash and cash equivalents can be used at the discretion of the Company. In combination with other covenants, the 2018 Amended Facility and 2021 Amended Facility restricts the Company’s ability to, among other things, incur future indebtedness and obtain additional debt financing, to make investments in securities or in other companies, to transfer assets, to perform certain corporate changes, to make loans to employees, officers, and directors, and to make dividend payments and other distributions to its shareholders. The Company secured the facilities by directly or indirectly pledging its total assets of $ 774.6 million with the exception of $ 103.5 million of cash and cash equivalents and other current assets held by uniQure N.V. The 2018 Amended Facility and 2021 Amended 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 September 30, 2021, the Company was in material compliance with all covenants and provisions. ​ 9 Shareholders’ equity ​ 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 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 three and nine months ended September 30, 2021, nil and $ 1.3 million, respectively, of direct, incremental costs were deducted from additional paid-in capital. ​ Following the Closing of the CSL Behring transaction, the Company released and consumed its prior year net operating tax losses carry forward for the years 2011 to 2018. The Company allocated a part of the release to the tax benefit of share issuance costs incurred in 2014, 2015, 2017 and 2018. This resulted in an increase of additional paid-in capital of nil and $ 3.0 million in the three and nine months ended September 30, 2021, respectively. ​ 10 Share-based compensation ​ 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”). At the annual general meeting of shareholders in June 2021, the Company’s shareholders approved an increase in the number of shares authorized for issuance under the 2014 Plan from 8,601,471 to 12,601,471 . ​ a) 2014 Plans ​ Share-based compensation expense recognized by classification included in the Consolidated statements of operations and comprehensive loss in relation to the 2014 Plans for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2021 2020 ​ 2021 ​ 2020 ​ ​ (in thousands) ​ (in thousands) Research and development ​ $ 3,245 ​ $ 3,906 ​ $ 9,205 ​ $ 9,177 Selling, general and administrative ​ ​ 2,705 ​ ​ 2,457 ​ ​ 9,520 ​ ​ 7,240 Total ​ $ 5,950 ​ $ 6,363 ​ $ 18,725 ​ $ 16,417 ​ ​ ​ 18 Table of Contents Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2021 2020 ​ 2021 ​ 2020 ​ ​ (in thousands) ​ (in thousands) Award type ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 2,965 ​ $ 3,994 ​ $ 9,155 ​ $ 8,948 Restricted share units ​ ​ 2,582 ​ ​ 1,525 ​ ​ 8,364 ​ ​ 5,178 Performance share units ​ ​ 403 ​ ​ 844 ​ ​ 1,206 ​ ​ 2,291 Total ​ $ 5,950 ​ $ 6,363 ​ $ 18,725 ​ $ 16,417 ​ As of September 30, 2021, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 31,952 ​ 2.93 Restricted share units ​ ​ 21,887 ​ 2.16 Performance share units ​ ​ 1,359 ​ 0.76 Total ​ $ 55,198 ​ 2.57 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares. ​ Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. The following tables summarize option activity under the Company’s 2014 Plans for the nine months ended September 30, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2020 ​ 2,659,279 ​ $ 28.13 Granted ​ 1,088,843 ​ $ 36.37 Forfeited ​ ( 233,777 ) ​ $ 40.81 Expired ​ ( 14,146 ) ​ $ 45.59 Exercised ​ ( 156,787 ) ​ $ 11.65 Outstanding at September 30, 2021 ​ 3,343,412 ​ $ 30.63 Thereof, fully vested and exercisable at September 30, 2021 ​ 1,792,291 ​ $ 23.14 Thereof, outstanding and expected to vest after September 30, 2021 ​ 1,551,121 ​ $ 39.28 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 23.2 Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 1.8 ​ 19 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: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, Nine months ended September 30, Assumptions 2021 2020 2021 2020 Expected volatility ​ 75 % ​ 70 % ​ 75 % ​ 70 % Expected terms ​ 10 years ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 1.47 % ​ 0.84 % ​ 1.21 % - 1.85 % ​ 0.76 % - 1.44 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ 0 % ​ Restricted share units (“RSUs”) ​ The following table summarizes the RSUs activity for the nine months ended September 30, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 467,344 ​ $ 43.56 Granted ​ 547,271 ​ $ 36.48 Vested ​ ( 214,368 ) ​ $ 40.48 Forfeited ​ ( 102,697 ) ​ $ 40.94 Non-vested at September 30, 2021 ​ 697,550 ​ $ 39.34 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 20.0 ​ RSUs vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. ​ Performance share units (“PSUs”) ​ The following table summarizes the PSUs activity for the nine months ended September 30, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 212,614 ​ $ 42.32 Granted ​ 66,600 ​ ​ 36.39 Vested ​ ( 132,368 ) ​ $ 33.09 Forfeited ​ ( 2,916 ) ​ $ 57.56 Non-vested at September 30, 2021 ​ 143,930 ​ $ 47.76 ​ The PSUs granted in 2019 vest on the third anniversary of the grant, subject to the grantee’s continued employment. ​ The Company granted shares to certain employees in September 2021 that will be earned upon the later of one year of service period or the achievement of certain defined milestones, subject to the grantee’s continued employment. The Company recognized the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. ​ 20 Table of Contents b) 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 ordinary shares on each purchase date is equal to 85 % of the lower of the closing market price on the offering date and the closing market price on the purchase date of each three-month offering period. During the nine months ended September 30, 2021, 4,724 ordinary shares were issued under the ESPP compared to 3,282 during the same period in 2020. As of September 30, 2021, a total of 127,302 ordinary shares remain available for issuance under the ESPP plan compared to a total of 134,925 as of September 30, 2020. ​ 11 Other income ​ Other income during the three and nine months ended September 30, 2021, was $ 1.7 million and $ 9.6 million, respectively, compared to $ 1.0 million and $ 2.6 million during the same periods in 2020. ​ Other income in 2020 and 2021 includes income from payments received from European authorities to subsidize the Company’s research and development efforts in the Netherlands as well as income from subleasing part of the Amsterdam facility. ​ In addition, other income includes $ 1.3 million and $ 2.6 million of employee retention credits received under the U.S. Coronavirus Aid, Relief, and Economic Security Act, during the three and nine months ended September 30, 2021, respectively. Additionally, $ 3.0 million related to the acquisition 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. This $ 3.0 million was recorded in other income for the nine months ended September 30, 2021 ( nil for three months ended September 30, 2021). No such income was recorded in 2020. ​ ​ 21 Table of Contents 12 Income taxes ​ The Company recorded $ 0.1 million in income tax expense in the three months ended September 30, 2021, and $ 3.6 million in the nine months ended September 30, 2021. The Company recorded no income tax expense during the same periods in 2020. ​ 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 intends to record such revenue in its Dutch tax return related to the 12-month period ended December 31, 2020. As such, the Company expects to file a return showing a taxable profit in the Netherlands in 2020, which would result 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 would relate to 2019. 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 including 2021. As such, the Company retained its full valuation allowance related to the net deferred assets as of September 30, 2021. The adjustment to the Company’s 2020 filing position resulting in the release and consumption of prior year net operating tax losses carried forward was treated as a discrete event in the nine months ended September 30, 2021. The Company allocated part of the release to the tax benefit of share issuance cost incurred in 2014, 2015, 2017 and 2018. This resulted in an increase of additional paid-in capital as well as deferred tax expenses of $ 3.0 million. ​ The Company released its valuation allowance against the Company’s deferred tax assets in the United States as of December 31, 2020. The Company recorded $ 0.2 million and $ 0.7 million deferred tax expense in relation to its operations in the United States during the three and nine months ended September 30, 2021, respectively. The Company recorded a nil net deferred tax expense in the prior year as it had recorded a valuation allowance against its net deferred tax assets in the United States as of September 30, 2020. ​ In connection with the Corlieve acquisition, the Company recognized a deferred tax liability related to acquired identifiable intangible assets net of net operating tax losses carried forward of EUR 11.5 million ($ 13.6 million) as of the Acquisition Date. The Company recorded deferred tax income of $ 0.2 million related to reduction of the net deferred tax liability between the Acquisition Date and September 30, 2021 as a result of incurring net operating losses in France. ​ The effective income tax rates of 0.2 % and - 1.1 % during the three and nine months ended September 30, 2021, respectively, are substantially lower than the enacted rate of 25 % in the Netherlands. This is a result of the Company recording a valuation allowance against its remaining net deferred tax assets in the Netherlands as of December 31, 2020 and September 30, 2021. ​ ​ ​ 13 Basic and diluted earnings per share ​ Basic net (loss) / income per ordinary share is computed by dividing net (loss) / income 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 three months and nine months ended September 30, 2021, dilutive net (loss) / income per ordinary share is computed using the treasury method. 22 Table of Contents ​ The following table provides the calculation of basic and diluted earnings per ordinary share: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2021 2020 ​ 2021 ​ 2020 ​ ​ (in thousands) ​ (in thousands) Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net (loss) / income attributable to ordinary shares ​ $ ( 36,531 ) ​ $ ( 53,775 ) ​ $ 321,381 ​ $ ( 124,325 ) ​ ​ ​ ( 36,531 ) ​ ​ ( 53,775 ) ​ ​ 321,381 ​ ​ ( 124,325 ) Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average number of ordinary shares outstanding - basic ​ ​ 46,152,404 ​ ​ 44,471,844 ​ ​ 45,888,769 ​ ​ 44,379,924 Stock options under 2014 Plans and previous plan ​ ​ — ​ ​ — ​ ​ 784,942 ​ ​ — Non-vested RSUs and PSUs ​ ​ — ​ ​ — ​ ​ 105,870 ​ ​ — Employee share purchase plan ​ ​ — ​ ​ — ​ ​ 1,382 ​ ​ — Weighted-average number of ordinary shares outstanding - diluted ​ ​ 46,152,404 ​ ​ 44,471,844 ​ ​ 46,780,963 ​ ​ 44,379,924 ​ The following table presents ordinary share equivalents that were excluded from the calculation of diluted net (loss) / income per ordinary share for the three and nine months ended September 30, 2021 and 2020 as the effect of their inclusion would have been anti-dilutive. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2021 2020 ​ 2021 ​ 2020 ​ ​ (in thousands) ​ (in thousands) Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 3,357,412 ​ ​ 2,960,158 ​ ​ 2,572,470 ​ ​ 2,960,158 Non-vested RSUs and PSUs ​ ​ 841,480 ​ ​ 672,805 ​ ​ 735,610 ​ ​ 672,805 Employee share purchase plan ​ ​ 1,219 ​ ​ 1,997 ​ ​ 1,219 ​ ​ 1,997 BMS warrants (derecognized as of December 1, 2020 - refer to Note 6, "Fair value measurement" ) ​ ​ — ​ ​ 8,071,000 ​ ​ — ​ ​ 8,071,000 Total anti-dilutive ordinary share equivalents ​ ​ 4,200,111 ​ ​ 11,705,960 ​ ​ 3,309,299 ​ ​ 11,705,960 ​ 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 September 30, 2020. In addition, the BMS warrants were not exercisable as of September 30, 2020. 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. ​ ​ ​ ​ ​ ​ ​ 14 Subsequent events ​ 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”). Ms. Jacques will also serve as a member of the Audit Committee of the Board effective as of October 21, 2021. ​ ​ ​ 23 Table of Contents