What changed in this filing

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Item 9A. Controls and Procedures

2022-03-01 compared with 2021-03-23 · 115 added, 63 removed, 149 unchanged (54% of the section changed)

5 unchanged sentences

Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Based on the evaluation of our disclosure controls and procedures as of December 31, 2020, our principal executive and financial officer concluded that, as of such date, our disclosure controls and procedures were not effective at a reasonable assurance level as a result of the material weakness that existed in our internal control over financial reporting as described below.

Our management assessed the effectiveness of our internal control over financial reporting as of December 31, 2021 based on the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in its 2013 Internal Control — Integrated Framework.

Based on this assessment, our management has concluded that our internal control over financial reporting was effective as of December 31, 2021.

Pursuant to Section 404(c) of the Sarbanes-Oxley Act, our independent registered public accounting firm has issued an attestation report on the effectiveness of our internal control over financial reporting for the year ended December 31, 2021, which is included below.

Management's Annual Report on Internal Control over Financial Reporting

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Internal control over financial reporting is a process designed under the supervision and with the participation of our management, including our principal executive and financial officer, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with accounting principles generally accepted in the United States of America.

As the acquisition of Lineagen occurred in the third quarter of 2020, we excluded the internal control over financial reporting of Lineagen from the scope of our assessment of the effectiveness of the Company’s internal controls.

As the acquisition of BioDiscovery occurred in the fourth quarter of 2021, we excluded the internal control over financial reporting of BioDiscovery 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.

Lineagen's total net assets excluded from our assessment constituted approximately 1% of the Company’s total assets as of December 31, 2020, and Lineagen's revenues and net loss excluded from our assessment represented approximately 24% and 4%, respectively, of the Company’s total revenue and net loss for the year ended December 31, 2020.

Material Weaknesses in Internal Control over Financial Reporting

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that a reasonable possibility exists that a material misstatement of our annual or interim financial statements would not be prevented or detected on a timely basis.

For the year ended December 31, 2020, our management assessed the effectiveness of our internal control over financial reporting using the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in Internal Control-Integrated Framework (2013 Framework).

Based on this assessment, our management determined that, as of December 31, 2020, there was a material weakness in our internal control environment over financial reporting because we did not have a sufficient number of resources to support the growth and complexity of our financial reporting requirements.

This material weakness contributed to a material weakness in our control activities based on the criteria set forth in the 2013 Framework.

BioDiscovery's total net assets excluded from our assessment constituted approximately 3% of the Company’s total assets as of December 31, 2021, and BioDiscovery revenues excluded from our assessment represented approximately 6% of the Company’s total revenue for the year ended December 31, 2021.

Remediation of Previously Disclosed Material Weakness

As disclosed in Item 9A in our Annual Report on Form 10-K for the year ended December 31, 2020 filed with the SEC on March 23, 2021, our management previously identified material weaknesses in our internal control environment over financial reporting related to an insufficient number of resources to support the growth and complexity of our financial reporting requirements.

Specifically, the design of certain controls did not adequately provide appropriate segregation of duties.

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The material weaknesses did not result in any identified material misstatements to our financial statements, and there were no changes to previously released financial results.

Remediation of Material Weaknesses

Management has been actively engaged in developing and implementing a remediation plan to address the material weaknesses described above.

The remediation efforts that are in process or expected to be implemented include the following:

• Management has engaged external consultants to assist with our internal accounting functions and further enhance our internal controls which has increased the number of personnel involved in financial reporting.

• We recently hired a new Chief Financial Officer and are in the process of hiring additional qualified individuals that will increase the number of personnel involved in financial reporting and the control environment.

The additional resources and procedures described above are designed to enable us to broaden the scope and quality of our internal review of underlying information related to financial reporting and to formalize and enhance our internal control procedures.

While the implementation of improved controls and procedures is ongoing, we have determined that as of December 31, 2020 that the material weaknesses described above have not been fully remediated.

During 2021, our management, with the oversight of the Audit Committee of our Board of Directors, engaged in efforts to remediate the material weaknesses identified and previously disclosed.

We completed these remediation measures in the quarter ended December 31, 2021, including testing of the design and concluding on the operating effectiveness of the related controls.

Specifically, remediation efforts that we implemented during 2021 include the following:

• Management engaged external consultants to assist with our internal accounting functions and further enhance our internal controls, which increased the number of external personnel involved in financial reporting.

• We hired a new Chief Financial Officer, a Senior Manager SEC Reporting & Technical Accounting, a Senior Manager of Accounting, and a Senior Accountant, which has increased the number of qualified full-time employees involved in our financial reporting and the control environment.

Accordingly, we have determined that the material weaknesses are considered to be remediated.

The financial statements and internal control over financial reporting have been audited by BDO USA LLP, an independent registered public accounting firm.

BDO’s reports with respect to fairness of the presentation of the financial statements, and the effectiveness of internal control over financial reporting, are included herein.

Changes in Internal Control over Financial Reporting

Other than the continuation of the implementation of measures described above, there were no material changes in our internal control over financial reporting during the quarter ended December 31, 2020 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Attestation Report of the Registered Public Accounting Firm

This Annual Report on Form 10-K does not include an attestation report of our registered public accounting firm due to an exemption for “emerging growth companies.”

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, 2021 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Report of Independent Registered Public Accounting Firm

Stockholders and Board of Directors

Bionano Genomics, Inc.

San Diego, CA

Opinion on Internal Control over Financial Reporting

We have audited Bionano Genomic, Inc’s.

(the “Company’s”) internal control over financial reporting as of December 31, 2021, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (the “COSO criteria”).

In our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2021, based on the COSO criteria.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (“PCAOB”), the consolidated balance sheets of the Company as of December 31, 2021 and 2020, the related consolidated statements of operations and comprehensive loss, stockholders’ equity, and cash flows for the years then ended, and the related notes and our report dated March 1, 2022 expressed an unqualified opinion thereon.

Basis for Opinion

The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Item 9A, Management’s Annual Report on Internal Control over Financial Reporting.

Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit.

We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with U.S.

federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit of internal control over financial reporting in accordance with the standards of the PCAOB.

Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects.

Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk.

Our audit also included performing such other procedures as we considered necessary in the circumstances.

We believe that our audit provides a reasonable basis for our opinion.

As indicated in the accompanying Item 9A, Management’s Annual Report on Internal Control over Financial Reporting, management’s assessment of and conclusion on the effectiveness of internal control over financial reporting did not include the internal controls of BioDiscovery, LLC., which was acquired during the fourth quarter of 2021, and which is included in the consolidated balance sheet of the Company as of December 31, 2021, and the related consolidated statements of operations and comprehensive loss, stockholders’ equity, and cash flows for the year then ended.

BioDiscovery, LLC.

constituted approximately 3% of the Company’s total assets as of December 31, 2021 and approximately 6% of revenues for the year then ended.

Management did not assess the effectiveness of internal control over financial reporting of BioDiscovery, LLC.

because of the timing of the acquisition.

Our audit of internal control over financial reporting of the Company also did not include an evaluation of the internal control over financial reporting of BioDiscovery, LLC.

Definition and Limitations of Internal Control over Financial Reporting

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles.

A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and

dispositions of the assets of the company;

(2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company;

and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements.

Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

/s/ BDO USA, LLP

San Diego, CA

March 1, 2022

OTHER INFORMATION

Forgiveness of Paycheck Protection Program Loan

As previously reported, on April 17, 2020, we received loan proceeds of approximately $1.77 million, or the PPP Loan, pursuant to the Paycheck Protection Program under the Coronavirus Aid, Relief, and Economic Security Act administered by the U.S.

Small Business Administration, or the SBA.

The PPP Loan was evidenced by a promissory note, dated as of April 17, 2020, issued by East West Bank.

We applied for forgiveness of the PPP Loan and on March 18, 2021, we received a notice from East West Bank confirming the SBA’s forgiveness of the PPP Loan together with all accrued interest in full, effective as of March 15, 2021.

DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS

Not applicable.

DIRECTORS, EXECUTIVE OFFICERS, AND CORPORATE GOVERNANCE

The information required by this item and not set forth below will be set forth in our definitive proxy statement to be filed with the Securities and Exchange Commission in connection with our 2021 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, 2020, and is incorporated in this Annual Report on Form 10-K by reference.

The information required by this item will be set forth under the captions “Election of Directors,” “Delinquent Section 16(a) Reports,” “Information Regarding the Board of Directors and Corporate Governance,” in our definitive proxy statement to be filed with the Securities and Exchange Commission in connection with our 2022 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, 2021, 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.

2 unchanged sentences

If we make any substantive amendments to the Ethics Code or grant any waiver from a provision of the Ethics Code to any executive officer or director, we will promptly disclose the nature of the amendment or waiver on our website or in a Current Report on Form 8-K.

Information contained in, or that can be accessed through, our website is not incorporated by reference herein, and you should not consider information on our website to be part of this Annual Report on Form 10-K.

EXECUTIVE COMPENSATION

The information required by this item will be set forth in the Proxy Statement and is incorporated in this Annual Report on Form 10-K by reference.

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.

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

The information required by this item will be set forth in the Proxy Statement and is incorporated in this Annual Report on Form 10-K by reference.

The information required by this item will be set forth under the captions “Security Ownership of Certain Beneficial Owners and Management” and “Equity Compensation Plan Information” in the Proxy Statement and is incorporated in this Annual Report by reference.

CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information required by this item will be set forth in the Proxy Statement and is incorporated in this Annual Report on Form 10-K by reference.

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.

PRINCIPAL ACCOUNTING FEES AND SERVICES

The information required by this item will be set forth in the Proxy Statement and is incorporated in this Annual Report on Form 10-K by reference.

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

EXHIBITS, FINANCIAL STATEMENT SCHEDULES

2 unchanged sentences

The response to this portion of Item 15 is set forth under Item 8 above.

The following consolidated financial statements of Bionano Genomics, Inc are included in Item 8 of this report:

◦ Reports of Independent Registered Public Accounting Firm

◦ Consolidated Balance Sheets — December 31, 2021 and 2020

◦ Consolidated Statements of Operations — Years ended December 31, 2021 and 2020

◦ Consolidated Statements of Comprehensive Income — Years ended December 31, 2021 and 2020

◦ Consolidated Statements of Cash Flows — Years ended December 31, 2021 and 2020

◦ Notes to Consolidated Financial Statements

(2) Financial statement schedule.

5 unchanged sentences

and Michael S.

3.1 Amended and Restated Certificate of Incorporation.

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.

Amended and Restated Certificate of Incorporation, as amended.

Amended and Restated Bylaws.

Form of Common Stock Certificat e .

Form of Common Stock Certificate .

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

3 unchanged sentences

Form of Warrant to Purchase Common Stock for Service Providers.

Registration Rights Agreement, dated March 14, 2019, between the Company and Aspire Capital Fund, LLC.

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.

Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering.

Underwriting Agreement, dated January 8, 2021, by and among Bionano Genomics, Inc.

and Oppenheimer & Co.

Inc., as representatives of the several underwriters named therein.

Underwriting Agreement, dated January 20, 2021, by and among Bionano Genomics, Inc.

and Oppenheimer & Co.

Inc., as representatives of the several underwriters named therein.

Description of the Company’s Securities.

Fifth Amended and Restated Investors’ Rights Agreement, dated August 5, 2016 as amended.

Bionano Genomics, Inc.

2 unchanged sentences

Bionano Genomics, Inc.

2018 Equity Incentive Plan (the “2018 Plan”).

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

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

3 unchanged sentences

10.7+ Bionano Genomics, Inc.

Non-Employee Director Compensation Policy.

Credit and Security Agreement by and between the Registrant, Midcap Financial Trust and the Lenders listed on the Schedule of Lenders attached thereto, dated June 29, 2018.

Non-Employee Director Compensation Policy, as amended

Number Description

Employment Agreement by and between the Registrant and R.

3 unchanged sentences

Employment Agreement by and between the Registrant and Mark Oldakowski, dated November 7, 2017.

Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated March 8, 2016 .

Number Description

First Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated December 9, 2016.

Second Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated May 2, 2017.

Third Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated November 20, 2017.

Forbearance and Fourth Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated February 9, 2018.

Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012.

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Fourth Amendment License Agreement by and between Princeton University and the Registrant, dated February 9, 2012.

Agreement by and between the Registrant and Berry Genomics Co., Ltd.

dated August 2, 2016.

Sublicense Agreement by and between the Registrant and Industry 3200 dated December 27, 2013.

License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014.

3 unchanged sentences

dated February 2, 2016.

Fifth Amendment to Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated June 13, 2018.

Amendment to Patent Sublicense Agreement by and between the Registrant and Industry 3200, dated June 28, 2018.

Common Stock Purchase Agreement, dated March 14, 2019, by and among the Company and the Innovatus Investors.

Loan and Security Agreement, dated March 14, 2019, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and the Lenders listed on Schedule 1.1 thereto.

Waiver and First Amendment to Loan and Security Agreement, dated June 25, 2019, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and East West Bank.

Second Amendment to Loan Agreement, dated March 6, 2020, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and East West Bank.

Consent and Third Amendment to Loan and Security Agreement, dated August 21, 2020, by and among the Company, Lineagen, Inc., Innovatus Life Sciences Lending Fund I, LP and East West Bank.

Fourth Amendment to Loan and Security Agreement, dated December 30, 2020, by and among the Company, Lineagen, Inc., Innovatus Life Sciences Lending Fund I, LP and East West Bank.

Common Stock Purchase Agreement, dated March 14, 2019, by and among the Company and the Innovatus Investors.

At Market Issuance Sales Agreement, dated August 13, 2020, by and between the Company and Ladenburg Thalmann & Co.

Bionano Genomics, Inc.

2020 Inducement Plan.

2020 Inducement Plan, as amended.

Form of Stock Option Grant Notice and Stock Option Agreement under the Bionano Genomics, Inc.

2020 Inducement Plan.

Forms of Restricted Stock Unit Grant Notice and Restricted Stock Unit Award Agreement under the Bionano Genomics, Inc.

2018 Equity Incentive Plan.

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

Standard Industrial/Commercial Single-Tenant Lease, made effective as of November 23, 2021, by and between the Company and 6777 Nancy Ridge LLC.

Employment Agreement , dated October 8, 2021 and effective October 18 , 2021, by and between the Company and Soheil Shams .

Stock Restriction Agreement , dated O c tober 8, 2021 and effective October 18, 2021, by and between the Company and Soheil Sham s.

10.36+ Employment Agreement, dated June 14, 2021, by and between the Company and Richard Shippy

Common Stock Purchase Agreement, dated March 14, 2019, between the Company and Aspire Capital Fund, LLC

10.38 Commercial Single-Tenant Lease – Net, dated February 28, 2016, by and between Tesa Beach LLC and BioDiscovery, Inc.

10.39 Fifth Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated January 12, 2022.

21.1 Subsidiaries of the Registrant.

Number Description

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

23.2 Consent of Deloitte & Touche LLP , independent registered public accounting firm.

24.1 Power of Attorney (included on signature page).

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31.2* Certification of Principal Financial Officer pursuant to Rules 13a-14(a) and 15d-14(a) promulgated under the Securities Exchange Act of 1934, as amended.

Number Description

32.1* Certification of Principal Executive Officer pursuant to 18 U.S.C.

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

101.INS XBRL Instance Document.

101.SCH XBRL Taxonomy Extension Schema Document.

101.CAL XBRL Taxonomy Extension Calculation Linkbase Document.

101.DEF XBRL Taxonomy Extension Definition Linkbase Document.

101.LAB XBRL Taxonomy Extension Label Linkbase Document.

101.PRE XBRL Taxonomy Extension Presentation Linkbase Document.

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.

101.SCH Inline XBRL Taxonomy Extension Schema Document.

101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document.

101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document.

101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document.

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 Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020.

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Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2020.

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

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 the Registrant’s Current Report on Form 8-K, filed with the SEC on January 11, 2021.

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on January 21, 2021.

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

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 Current Report on Form 8-K, filed with the SEC on October 12, 2021.

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

3 unchanged sentences

Omitted portions have been filed separately with the SEC.

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.

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Hannah Mamuszka

/s/ Aleksandar Rajkovic, M.D., Ph.D

Director March 1, 2022

Aleksandar Rajkovic, M.D., Ph.D.

/s/ Christopher Twomey Director March 1, 2022

3 unchanged sentences

Kristiina Vuori, M.D., Ph.D.

/s/ Vincent Wong, J.D., M.B.A.

Director March 1, 2022

Vincent Wong, J.D., M.B.A.

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