PACIFIC BIOSCIENCES OF CALIFORNIA, INC. 10-K

ITEM 9A. CONTROLS AND PROCEDURES Evaluation of Disclosure Controls and Procedures Our management, with the participation of our chief executive officer, our chief financial officer, and our principal accounting officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a–15(e) and 15d–15(e) of the Exchange Act) as of the end of the period covered by this Annual Report on Form 10–K. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to our management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. 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 judgement in evaluating the cost-benefit relationship of possible controls and procedures. Based on this evaluation, our chief executive officer, chief fina ncial officer and our principal accounting officer concluded that our disclosure controls and procedures were effective as of the end of the period covered by this report. Management’s Report on Internal Control Over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as such term is defined in Exchange Act Rules 13a-15(f). Pacific Biosciences of California, Inc’s internal control over financial reporting is designed to provide reasonable assurance to the Company’s management and board of directors regarding the preparation and fair presentation of published financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Therefore, even those systems determined to be effective can provide only reasonable assurance with respect to financial statement preparation and presentation. Management assessed the effectiveness of the Company’s internal control over financial reporting as of December 31, 2021. In making this assessment, management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). Based on our assessment, we concluded that, as of December 31, 2021, the Company’s internal control over financial reporting was effective based on those criteria. Management’s assessment of and conclusion on the effectiveness of internal control over financial reporting did not include the internal controls of Omniome, Inc. and Circulomics, Inc., which are included in our 2021 consolidated financial statements and constituted 2% of total assets as of December 31, 2021 and approximately 1% of consolidated revenues for the year then ended. The Company’s internal control over financial reporting as of December 31, 2021 has been audited by Ernst &Young LLP, the independent registered public accounting firm who also audited the Company’s financial statements. Ernst &Young’s attestation report on the Company’s internal control over financial reporting appears on page 106 hereof. Changes in Internal Control Over Financial Reporting An evaluation was performed under the supervision and with the participation of our management, including our Chief Executive Officer, Chief Financial Officer and Principal Accounting Officer to determine whether any change in our internal control over financial reporting occurred during the fiscal quarter ended December 31, 2021 that materially affected, or is reasonably likely to materially affect, our internal control over financial reporting. There were no material changes in our internal control over financial reporting during the year ended December 31, 2021, that have materially affected, or were reasonably likely to materially affect, our internal control over financial reporting. ‎ 105 Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of Pacific Biosciences of California, Inc. Opinion on Internal Control over Financial Reporting We have audited Pacific Biosciences of California, Inc.’s internal control over financial reporting as of December 31, 2021, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). In our opinion, Pacific Biosciences of California, Inc. (the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2021, based on the COSO criteria. As indicated in the accompanying Management’s 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 Omniome, Inc. and Circulomics, Inc., which are included in the 2021 consolidated financial statements of the Company and constituted 2% of total assets as of December 31, 2021 and 1% of revenues for the year then ended. 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 Omniome, Inc. and Circulomics, Inc. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the 2021 consolidated financial statements of the Company and our report dated February 28, 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 Management’s 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 the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit 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, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. 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. 106 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/ Ernst & Young LLP Redwood City, California February 28, 2022  ‎ 107 ITEM 9B. OTHER INFORMATION None. ITEM 9C. DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS Not applicable. ‎ 108 PART III ITEM 10. DIRECTORS , EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE Information responsive to this item is incorporated herein by reference to our definitive proxy statement with respect to our 2022 Annual Meeting of Stockholders to be filed with the SEC within 120 days after the end of the fiscal year covered by this Annual Report on Form 10-K. ITEM 11. EXECUTIVE COMPENSATION Information responsive to this item is incorporated herein by reference to our definitive proxy statement with respect to our 2022 Annual Meeting of Stockholder to be filed with the SEC within 120 days after the end of the fiscal year covered by this Annual Report on Form 10-K. ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS Information responsive to this item is incorporated herein by reference to our definitive proxy statement with respect to our 2022 Annual Meeting of Stockholders to be filed with the SEC within 120 days after the end of the fiscal year covered by this Annual Report on Form 10-K. ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE Information responsive to this item is incorporated herein by reference to our definitive proxy statement with respect to our 2022 Annual Meeting of Stockholders to be filed with the SEC within 120 days after the end of the fiscal year covered by this Annual Report on Form 10-K. ITEM 14. PRINCIPAL ACCOUNTING FEES AND SERVICES Information responsive to this item is incorporated herein by reference to our definitive proxy statement with respect to our 2022 Annual Meeting of Stockholders to be filed with the SEC within 120 days after the end of the fiscal year covered by this Annual Report on Form 10-K. ‎ 109 PART IV ITEM 15. EXHIBITS , FINANCIAL STATEMENT SCHEDULES. (a) The following documents are filed as part of, or incorporated by reference into, this Annual Report on Form 10-K: 1. Financial Statements : See Index to Consolidated Financial Statements under Item 8 of this Annual Report on Form 10-K. 2. Financial Statement Schedules : All schedules are omitted because they are not required, are not applicable or the information is included in the consolidated financial statements or notes thereto. 3. Exhibits : We have filed or incorporated by reference into this Annual Report on Form 10-K, the exhibits listed on the accompanying Exhibit Index immediately below. (b) Financial Statement Schedules: See Item 15(a)(2), above. (c) Exhibits: Refer to the Exhibit Index that follows. ‎ 110 Exhibit Ind ex Incorporated by reference herein Exhibit ‎ Number Description Form Exhibit No. Filing Date 3.1 Amended and Restated Certificate of Incorporation 10-K 3.1 March 23, 2011 3.2 Second Amended and Restated Bylaws of Pacific Biosciences of California, Inc. 8-K 3.1 November 5, 2018 4.1 Specimen Common Stock Certificate S-1/A 4.1 October 1, 2010 4.2 Description of Registrant’s securities registered under Section 12 of the Exchange Act 10-K 4.2 February 28, 2020 4.3 Indenture, dated February 16, 2021, between Pacific Biosciences of California, Inc. and U.S. Bank National Association, as Trustee 8-K 4.1 February 17, 2021 4.4 Form of 1.50% Convertible Senior Notes due 2028 (included in Exhibit 4.3) 8-K 4.1 February 17, 2021 10.1 + Form of Director and Executive Officer Indemnification Agreement S-1 10.1 August 16, 2010 10.2 + 2010 Equity Incentive Plan S-1 10.4 August 16, 2010 10.3 + 2010 Equity Incentive Plan forms of agreement 10-Q 10.1 May 2, 2018 10.4 + 2010 Employee Stock Purchase Plan and forms of agreement thereunder S-1 10.5 August 16, 2010 10.5 + 2010 Outside Director Equity Incentive Plan S-1 10.6 August 16, 2010 10.6 + 2010 Outside Director Equity Incentive Plan forms of agreement 10-Q 10.2 May 2, 2018 10.7 + 2020 Equity Incentive Plan and related forms of agreement 8-K 10.1 August 5, 2020 10.8 + Pacific Biosciences of California, Inc. 2020 Inducement Equity Incentive Plan, as amended, and forms of agreement thereunder 8-K 10.1 April 19, 2021 10.12 + Letter Relating to Employment Terms by and between the Registrant and Susan G. Kim effective September 28, 2020 10-Q 10.2 November 3, 2020 10.13 + Change in Control and Severance Agreement by and between the Registrant and Susan G. Kim effective September 28, 2020 10-Q 10.3 November 3, 2020 10.14 + Form of Change in Control and Severance Agreement for executive officers 10-K 10.14 February 26, 2021 10.15 + Letter Relating to Employment Terms by and between the Registrant and Christian O. Henry effective September 14, 2020 10-K 10.15 February 26, 2021 10.16 + Change in Control and Severance Agreement by and between the Registrant and Christian O. Henry effective September 14, 2020 10-K 10.16 February 26, 2021 10.17 + Amended Change in Control and Severance Agreement by and between the Registrant and Christian O. Henry dated February 3, 2021 10-K 10.17 February 26, 2021 10.18 + Letter Relating to Employment Terms by and between the Registrant and Mark Van Oene effective January 8, 2021 10-K 10.18 February 26, 2021 10.19 + Letter Relating to Employment Terms by and between the Registrant and Peter Fromen effective January 8, 2021 10-K 10.19 February 26, 2021 10.20 + Lease Agreement by and between the Registrant and Menlo Park Portfolio II, LLC, dated July 22, 2015. 10-Q 10.2 August 5, 2015 10.21 † First Amendment to Lease Agreement by and between the Registrant and Menlo Park Portfolio II, LLC, dated December 23, 2016. 10-K 10.50 March 6, 2017 10.22 †† Development and Commercialization Agreement by and between the Registrant and Invitae Corporation dated January 12, 2021 10-K 10.23 February 26, 2021 10.23 †† Amendment to Development and Commercialization Agreement, dated as of June 3, 2021, by and between Pacific Biosciences of California, Inc. and Invitae Corporation 10-Q 10.6 August 6, 2021 111 10.24 Investment Agreement, dated as of February 9, 2021, between Pacific Biosciences of California, Inc. and SB Northstar LP. 8-K 10.1 February 10, 2021 10.25 †† Exclusive License Agreement by and between the Registrant and Cornell Research Foundation, Inc., dated as of February 1, 2004 S-1/A 10.8 October 22, 2010 10.26 + Letter Relating to Employment Terms by and between the Registrant and Michele Farmer effective May 17, 2021 10-Q 10.2 August 6, 2021 10.27 Agreement and Plan of Merger of Reorganization among Pacific Biosciences of California, Inc., Apollo Acquisition Corp., Apollo Acquisition Sub, LLC, Omniome, Inc. and Shareholder Representative Services, LLC, as securityholder representative, dated as of July 19, 2021 8-K 10.1 July 20, 201 10.28 Securities Purchase Agreement, dated as of July 19, 2021, by and between Pacific Biosciences of California, Inc. and each of the Investors 8-K 10.2 July 20, 201 10.29 Registration Rights Agreement, dated as of July 19, 2021, by and between Pacific Biosciences of California, Inc. and each of the Investors 8-K 10.3 July 20, 2021 21.1 List of Subsidiaries of the Registrant Filed herewith 23.1 Consent of Independent Registered Public Accounting Firm Filed herewith 31.1 Certification of Chief Executive Officer pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 Filed herewith 31.2 Certification of Chief Financial Officer pursuant to Exchange Act Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 Filed herewith 32.1 * Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 Furnished herewith 32.2 * Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 Furnished herewith 101.INS XBRL Instance Document (the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document) Filed herewith 101.SCH XBRL Taxonomy Extension Schema Document Filed herewith 101.CAL XBRL Taxonomy Extension Calculation Linkbase Document Filed herewith 101.DEF XBRL Taxonomy Extension Definition Linkbase Document Filed herewith 101.LAB XBRL Taxonomy Extension Labels Linkbase Document Filed herewith 101.PRE XBRL Taxonomy Extension Presentation Linkbase Document Filed herewith 104 Cover Page Interactive File (formatted as inline XBRL and contained in Exhibit 101) Filed herewith _________________________ + Indicates management contract or compensatory plan. † Confidential treatment has been requested for portions of this exhibit. These portions have been omitted and have been filed separately with the Securities and Exchange Commission. †† Certain confidential information contained in this Exhibit was omitted by means of marking such portions with brackets because the identified confidential information (i) is not material and (ii) would be competitively harmful if publicly disclosed. * The certifications attached as Exhibit 32.1 and 32.2 that accompany this Annual Report on Form 10-K are deemed furnished and not filed with the Securities and Exchange Commission and are not to be incorporated by reference into any filing of Pacific Biosciences of California, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, 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. ‎ 112 ITEM 16. FORM 10-K SUMMARY None. 113 Signatures Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended, the Registrant has duly caused this Annual Report on Form 10-K to be signed on its behalf by the undersigned, thereunto duly authorized. Pacific Biosciences of California, Inc. Date: February 28, 2022 By: /s/ Christian O. Henry Christian O. Henry Chief Executive Officer and President Date: February 28, 2022 By: /s/ S USAN G. Kim Susan G. Kim Chief Financial Officer Date: February 28, 2022 By: /s/ Michele Farmer Michele Farmer Vice President and Chief Accounting Officer ‎ 114 POWER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below hereby constitutes and appoints Christian O. Henry, Susan G. Kim, Brett Atkins and Michele Farmer, and each of them, as his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for each individual in any and all capacities, to sign any and all amendments to this Annual Report on Form 10-K, and to file the same, with all exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully for all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or the individual’s substitute, 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 report has been signed by the following persons on behalf of the Registrant in the capacities and on the dates indicated. Signature Title Date /s/ Christian O. Henry Christian O. Henry Director, Chief Executive Officer and President (Principal Executive Officer) February 28, 2022 /s/ Susan G. Kim Susan G. Kim Chief Financial Officer (Principal Financial Officer) February 28, 2022 /s/ Michele Farmer Michele Farmer Vice President and Chief Accounting Officer (Principal Accounting Officer) February 28, 2022 /s/ John F. Milligan John F. Milligan Chairman of the Board of Directors February 28, 2022 /s/ David Botstein David Botstein Director February 28, 2022 /s/ William W. Ericson William W. Ericson Director February 28, 2022 /s/ Hannah A. Valantine Hannah A. Valantine Director February 28, 2022 /s/ Randall S. Livingston Randall S. Livingston Director February 28, 2022 /s/ Marshall L. Mohr Marshall L. Mohr Director February 28, 2022 /s/ Kathy Ordoñez Kathy Ordoñez Director February 28, 2022 115 /s/ Lucy Shapiro Lucy Shapiro Director February 28, 2022 116