What changed in this filing

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Item 9A. Controls and Procedures

2024-03-05 compared with 2023-03-09 · 129 added, 45 removed, 168 unchanged (51% of the section changed)

12 unchanged sentences

Based on this assessment, our management concluded that, as of December 31, 2023, our internal control over financial reporting was effective based on those criteria.

As the acquisition of Purigen occurred in the fourth quarter of 2022, we excluded the internal control over financial reporting of Purigen from the scope of our assessment of the effectiveness of the Company’s internal controls.

This exclusion is in accordance with the general guidance issued by the Staff of the SEC that an assessment of a recently-acquired business may be omitted from our scope in the year of acquisition, if specified conditions are satisfied.

Goodwill and net intangibles assets acquired were not excluded from our assessment.

Purigen's total net assets excluded from our assessment constituted approximately 2% of the Company’s total assets as of December 31, 2022, and Purigen’s revenues excluded from our assessment represented approximately 0.1% of the Company’s total revenue for the year ended December 31, 2022.

Changes in Internal Control over Financial Reporting

Except as described below, there were no changes to our internal control over financial reporting (as defined in Rules 13a-15(f) and 15-d-15(f) under the Exchange Act) that occurred during the quarter ended December 31, 2023 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

In October 2021, we acquired BioDiscovery LLC.

We have integrated the internal controls of the acquired business into our overall system of internal control over financial reporting as of December 31, 2022.

In November 2022, we acquired Purigen Biosystems Inc..

We have completed our integration of internal controls of the acquired business into our overall system of internal control over financial reporting as of December 31, 2023.

OTHER INFORMATION

During the three months ended December 31, 2023, no director or officer of the Company adopted , terminated or modified a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” as defined in Item 408(a) of Regulation S-K of the Exchange Act.

DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS

1 unchanged sentence

DIRECTORS, EXECUTIVE OFFICERS, AND CORPORATE GOVERNANCE

The information required by this item will be set forth under the captions “Proposal 1 – Election of Directors,” “Information Regarding the Board of Directors and Corporate Governance,” “Information Regarding Committees of the Board of Directors,” “Executive Officers,” and “Delinquent Section 16(a) Reports,” if any, in our definitive proxy statement to be filed with the Securities and Exchange Commission in connection with our 2023 Annual Meeting of Stockholders, or the Proxy Statement, which is expected to be filed not later than 120 days after the end of our fiscal year ended December 31, 2022, and is incorporated in this Annual Report by reference.

The information required by this item will be set forth under the captions “Proposal 1 – Election of Directors,” “Information Regarding the Board of Directors and Corporate Governance,” “Information Regarding Committees of the Board of Directors,” “Executive Officers,” and “Delinquent Section 16(a) Reports,” if any, in our definitive proxy statement to be filed with the SEC in connection with our 2024 Annual Meeting of Stockholders, or the Proxy Statement, which is expected to be filed not later than 120 days after the end of our fiscal year ended December 31, 2023, and is incorporated in this Annual Report by reference.

We have adopted a code of business conduct and ethics, or the Ethics Code, that applies to all our employees, officers and directors.

4 unchanged sentences

EXECUTIVE COMPENSATION

The information required by this item will be set forth under the caption “Executive and Director Compensation” in the Proxy Statement and is incorporated in this Annual Report by reference.

The information required by this item will be set forth under the caption “Executive and Director Compensation” and “Item 402(v) Pay Versus Performance Disclosure” in the Proxy Statement and is incorporated in this Annual Report by reference.

SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

1 unchanged sentence

CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information required by this item will be set forth under the captions “Transaction With Related Persons and Indemnification” and “Information Regarding the Board of Directors and Corporate Governance” in the Proxy Statement and is incorporated in this Annual Report by reference.

The information required by this item will be set forth under the captions “Transactions With Related Persons and Indemnification” and “Information Regarding the Board of Directors and Corporate Governance” in the Proxy Statement and is incorporated in this Annual Report by reference.

PRINCIPAL ACCOUNTANT FEES AND SERVICES

The information required by this item will be set forth under the caption “Principal Accountant Fees and Services” and “Pre-Approval Policies and Procedures” in the Proxy Statement and is incorporated in this Annual Report by reference.

The information required by this item will be set forth under the captions “Principal Accountant Fees and Services” and “Pre-Approval Policies and Procedures” in the Proxy Statement and is incorporated in this Annual Report by reference.

EXHIBIT AND FINANCIAL STATEMENT SCHEDULES

15 unchanged sentences

Number Description

2.1^€ (1)

Agreement and Plan of Merger, dated October 8, 2021, by and among the Company, Starship Merger Sub I, Inc., Starship Merger Sub II, LLC, BioDiscovery, Inc.

and Soheil Shams.

2.2^€ (2)

Agreement and Plan of Merger, dated November 23, 2022, by and among the Company, Mazdan Merger Sub, Inc., Purigen Biosystems, Inc.

and Shareholder Representative Services LLC.

2.3^€ (3)

First Amendment to Agreement and Plan of Merger, dated March 4, 2023, by and between the Company and Soheil Shams, as the Securityholders’ Representative.

2.4^€ (4)

Second Amendment to Agreement and Plan of Merger, dated July 15, 2023, by and among the Company, Starship Merger Sub I, Inc., Starship Merger Sub II, LLC, BioDiscovery, Inc.

and Soheil Shams

3.1^€ (5)

Certificate of Elimination of Series A Preferred Stock.

Amended and Restated Certificate of Incorporation, as amended.

Amended and Restated Bylaws.

Amendment to Amended and Restated Bylaws .

Form of Common Stock Certificate.

Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust.

Form of Warrant to Purchase Common Stock Issued to Underwriters (attached to Underwriting Agreement).

Form of Warrant Certificate (included in Exhibit 4.

Form of Warrant Agent Agreement by and between the Registrant and American Stock Transfer & Trust Company LLC, as warrant agent.

Form of Warrant to Purchase Common Stock for Service Providers.

Registration Rights Agreement, dated March 14, 2019, by and among the Company and the Innovatus Investors.

Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering.

1 unchanged sentence

Description of the Company’s Securities.

Bionano Genomics, Inc.

Amended and Restated 2006 Equity Compensation Plan (the “2006 Plan”).

Forms of grant notice, stock option agreement and notice of exercise under the 2006 Plan.

Form of Note, representing the Company’s Senior Secured Convertible Notes due 2025.

Form of Warrant to Purchase Common Stock issued to Purchaser in October 2023 Offering.

Amendmen t to Initial Registered Note issued to Purchaser dated February 27, 2024

Bionano Genomics, Inc.

2018 Equity Incentive Plan, as amended (the “2018 Plan”).

10.2A+ Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan.

10.2B+ Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan.

10.2C+ Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of international grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of r estricted s tock u nit g rant n otice and r estricted s tock u nit a ward a greement under the Bionano Genomics, Inc.

Forms of restricted stock unit grant notice and restricted stock unit award agreement under the Bionano Genomics, Inc.

2018 Equity Incentive Plan.

23 unchanged sentences

Lease, dated August 22, 2016, by and between SFF BBC, LLC and Purigen Biosystems, Inc.

10.14A First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016

First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016

Sales Agreement, dated March 23, 2021, by and between the Company and Cowen and Company, LLC.

Amendment No.

1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC.

License Agreement by and between Princeton University and the Registrant, dated January 7, 2004.

13 unchanged sentences

Amended and Restated Exclusive License Agreement with Equity, dated July 16, 2021, by and between The Board of Trustees of the Leland Stanford Junior University and Purigen Biosystems, Inc.

10.22A^€ Amendment No.

10.21A^€

Amendment No.

1 to the Amended and Restated Exclusive License Agreement Effective the 16th Day of July 2021 Between Stanford University and Purigen Biosystems, Inc., dated November 14, 2022, by and between The Board of Trustees of the Leland Stanford Junior University and Purigen Biosystems, Inc.

Employment Agreement, effective as of September 11, 2023, by and between Gülsen Kama and the Company.

Transition, Separation and Consulting Agreement dated as of August 11, 2023, by and between Christopher Stewart and the Company.

Securities Purchase Agreement, dated October 11, 2023, by and among the Company and the Purchaser named therein.

Letter Agreement between the Company and the Purchaser named therein, dated February 27, 2024.

21.1 Subsidiaries of the Registrant.

23.1 Consent of BDO USA LLP, independent registered public accounting firm .

Affiliates whose securities collateralize securities of the registrant

23.1 Consent of BDO USA , P.

, independent registered public accounting firm .

24.1 Power of Attorney (included on signature page).

5 unchanged sentences

Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

Bionano Genomics, Inc.

Incentive Compensation Recoupment Policy

101.INS Inline XBRL Instance Document—the instance document does not appear in the Interactive Data File as its XBRL tags are embedded within the Inline XBRL document.

3 unchanged sentences

101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document.

Number Description

101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document.

104 Cover Page Interactive Data File (formatted in Inline XBRL and contained in Exhibit 101)

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 19, 2021.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on November 28, 2022.

Incorporated by reference to the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021

Incorporated by reference to Exhibit 2.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 19, 2021.

Incorporated by reference to Exhibit 2.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on November 28, 2022.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2023.

Incorporated by reference to the Registrant’s Registration Statement on Form S-1 (File No.

Incorporated by reference to Exhibit 3.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021

Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018.

Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on April 14, 2023.

Incorporated by reference to Exhibit 3.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021

Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018.

Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on April 14, 2023.

Incorporated by reference to Exhibit 4.13 of the Registrant’s Registration Statement on Form S-1 (File No.

333-233828), as amended.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on November 21, 2018.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on March 14, 2019.

Incorporated by reference to Exhibit 4.16 of the Registrant’s Registration Statement on Form S-1 (File No.

333-237074), as amended, filed with the SEC on March 24, 2020.

Incorporated by reference to Exhibit 4.10 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 4.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023.

Incorporated by reference to Exhibit 4.2 of the Registrant’s Registration Statement on Form S-3 (File No.

Incorporated by reference to Exhibit 10.2 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.3 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 99.1 of the Registrant’s Registration Statement on Form S-8 (File No.

333-245764), filed with the SEC on August 14, 2020.

Incorporated by reference to Exhibit 10.2A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.2B of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.2C of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.5 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 99.5 of the Registrant’s Registration Statement on Form S-8 (File No.

333-227073), filed with the SEC on August 28, 2018.

Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on November 28, 2022.

Incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2020.

Incorporated by reference to Exhibit 10.7 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022.

Incorporated by reference to Exhibit 10.7 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.10 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.6 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020.

Number Description

Incorporated by reference to the Registrant’s Registration Statement on Form S-1 (File No.

333-233828), as amended.

Incorporated by reference to the Registrant’s Registration Statement on Form S-1 (File No.

Incorporated by reference to the Registrant’s Registration Statement on Form S-8 (File No.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on August 4, 2021.

Incorporated by reference to the Registrant’s Registration Statement on Form S-8 (File No.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2020.

Incorporated by reference to the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on March 24, 2021.

Incorporated by reference to Exhibit 10.7 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020.

Incorporated by reference to Exhibit 10.14 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.20 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.21 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.22 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.22 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021

Incorporated by reference to Exhibit 10.23 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021

Incorporated by reference to Exhibit 10.39 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022.

Incorporated by reference to Exhibit 10.33 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022.

Incorporated by reference to Exhibit 10.38 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022.

Incorporated by reference to Exhibit 10.14 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.14A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 1.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on March 24, 2021.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023

Incorporated by reference to Exhibit 10.25 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.26 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.27 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.28 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.29 to the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.23 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.34 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.32 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.33 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.24 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.35 of the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, filed with the SEC on August 17, 2018.

Incorporated by reference to Exhibit 10.22 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.22A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.1 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023.

Incorporated by reference to Exhibit 10.2 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023.

Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023.

Number Description

Incorporated by reference to Exhibit 21.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023.

Incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024

Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024

Certain exhibits and schedules have been omitted pursuant to Item 601(a)(5) of Regulation S-K.

4 unchanged sentences

Pursuant to Item 601(b)(10) of Regulation S-K, certain portions of this exhibit have been omitted (indicated by “[***]”) because the Company has determined that the information is not material and is the type that the Company treats as private or confidential.

This certification is deemed not filed for purpose of section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

This certification is furnished herewith and deemed not filed for purpose of section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act (whether made before or after the date of this Annual Report on Form 10-K), irrespective of any general incorporation language contained in such filing.

FORM 10-K SUMMARY

8 unchanged sentences

Erik Holmlin, Ph.D.

and Christopher Stewart as his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign this Annual Report on Form 10-K of Bionano Genomics, Inc., and any or all amendments thereto, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorney-in-fact and agent full power and authority to do and perform each and every act and thing requisite or necessary to be done in and about the premises hereby ratifying and confirming all that said attorney-in-fact and agent, or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

and Gülsen Kama as his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign this Annual Report on Form 10-K of Bionano Genomics, Inc., and any or all amendments thereto, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorney-in-fact and agent full power and authority to do and perform each and every act and thing requisite or necessary to be done in and about the premises hereby ratifying and confirming all that said attorney-in-fact and agent, or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, this Annual Report has been signed below by the following persons on behalf of the Registrant in the capacities and on the dates indicated.

5 unchanged sentences

Erik Holmlin, Ph.D.

/s/ Christopher Stewart Chief Financial Officer

/s/ Gülsen Kama

Chief Financial Officer

(Principal Financial and Accounting Officer)

March 5, 2024

Christopher Stewart

Barker, Ph.D.

22 unchanged sentences

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures