Bionano Genomics Inc 2025年度报告

(Mark One) ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THETRANSITION PERIOD FROM Commission File Number 001-38613 Bionano Genomics, Inc. (Exact name of Registrant as specified in its Charter) Indicate by check mark if the Registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes☐No☒ Indicate by check mark whether the Registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during thepreceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to such filing requirements for the past90 days. Yes☒No☐ Indicate by check mark whether the Registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of RegulationS-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the Registrant was required to submit such files). Yes☒No☐Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2of the Exchange Act. Large accelerated filer☐Non-accelerated filer☒Emerging growth company☐If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised Accelerated filer☐Smaller reporting company☒ financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control overfinancial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its auditreport☐ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflectthe correction of an error to previously issued financial statements.☐Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant’s executive officers during the relevant recovery period pursuant to § 240.10D-1(b).☐ The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant as of June 30, 2025 (the last business day of theregistrant’s most recently completed second fiscal quarter) was approximately $12,154,000 based on the closing price of the registrant’s common stock on June 30,2025 of $3.28 per share, as reported by the Nasdaq Capital Market.As of March 19, 2026, the Registrant had 11,092,000 shares of common stock, $0.0001 par value per share, outstanding. DOCUMENTS INCORPORATED BY REFERENCE Portions of the definitive proxy statement, or the Proxy Statement, for the Registrant’s 2026 Annual Meeting of Stockholders are incorporated by reference into PartIII of this Annual Report on Form 10-K. The Proxy Statement will be filed with the Securities and Exchange Commission within 120 days of the Registrant’s fiscalyear ended December 31, 2025. Table of Contents PART I Item 1.BusinessItem 1A.Risk FactorsItem 1B.Unresolved Staff CommentsItem 1C.CybersecurityItem 2.PropertiesItem 3.Legal ProceedingsItem 4.Mine Safety Disclosures PART II Item 5.Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of EquitySecurities102Item 6.[Reserved]102Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations103Item 7A.Quantitative and Qualitative Disclosures About Market Risk118Item 8.Financial Statements and Supplementary Data118Item 9.Changes in and Disagreements With Accountants on Accounting and Financial Disclosure170Item 9A.Controls and Procedures170Item 9B.Other Information171Item 9C.Disclosure Regarding Foreign Jurisdictions that Prevent Inspections171 PART III Item 10.Directors, Executive Officers and Corporate Governance172Item 11.Executive Compensation172Item 12.Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters172Item 13.Certain Relationships and Related Transactions, and Director Independence172Item 14.Principal Accountant Fees and Services172 PART IVItem 15. Exhibit and Financial Statement Schedules173Item 16.Form 10-K Summary179Signatures180 As used in this Form 10-K, “Bionano,” the “Company,” “we,” “our,” and “us” refer to Bionano Genomics, Inc. and itssubsidiariesor,as the context may require,Bionano Genomics,Inc.only.“Lineagen”(doing business as“BionanoLaboratories”), “BioDiscovery” and “Pur