Attached files
UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
FORM 10-K/A
(Amendment No. 1)
|
(Mark One)
|
|
|
x
|
ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|
|
FOR THE FISCAL YEAR ENDED DECEMBER 31, 2009
|
|
OR
|
|
o
|
TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|
|
FOR THE TRANSITION PERIOD FROM TO
|
|
COMMISSION FILE NUMBER 0-28218
|
AFFYMETRIX, INC.
(Exact name of registrant as specified in its charter)
|
DELAWARE
|
77-0319159
|
|
|
(State or other jurisdiction of
|
(IRS Employer Identification Number)
|
|
|
incorporation or organization)
|
||
|
3420 CENTRAL EXPRESSWAY
|
||
|
SANTA CLARA, CALIFORNIA
|
95051
|
|
|
(Address of principal executive offices)
|
(Zip Code)
|
|
|
(408) 731-5000
|
||
|
(Registrant’s telephone number, including area code)
|
||
|
Title of Each Class
|
Name of Each Exchange on Which Registered
|
|
|
Common Stock, $0.01 par value
|
The Nasdaq Global Select Market
|
|
|
Preferred Stock Purchase Rights
|
The Nasdaq Global Select Market
|
Securities registered pursuant to Section 12(g) of the Act:
None
Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes o No x
Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes o No x
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 the preceding 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 past 90 days. Yes x No o
Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes o No o
Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. o
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one).
|
Large accelerated filer o
|
Accelerated filer x
|
|
|
Non-accelerated filer o (Do not check if a smaller reporting company)
|
Smaller reporting company o
|
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No x
The aggregate market value of the registrant’s common stock held by non-affiliates of the registrant at June 30, 2009, based on the closing price of such stock on The Nasdaq Global Select Market on such date, was approximately $413 million. The number of shares of the registrant’s Common Stock, $0.01 par value, outstanding on February 22, 2010, was 70,901,491.
DOCUMENTS INCORPORATED BY REFERENCE
Certain sections of the Proxy Statement filed in connection with the 2010 Annual Meeting of Stockholders are incorporated by reference into Part III of the registrant’s Annual Report on Form 10-K for the fiscal year ended December 31, 2009.
EXPLANATORY NOTE
This Amendment No. 1 on Form 10-K/A (this “Amendment No. 1”) to our Annual Report on Form 10-K for the fiscal year ended December 31, 2009, which was filed with the U.S. Securities and Exchange Commission (the “Commission”) on March 1, 2010 (the “Original Filing” and, together with Amendment No.1, the “Annual Report”), is being filed solely for the purposes of correcting Management’s Report on Internal Control Over Financial Reporting in Item 9A to provide management’s conclusion on the effectiveness of its internal control over financial reporting as of December 31, 2009 and to file as an exhibit to our Annual Report the consent of Ernst & Young LLP, our independent registered public accounting firm. These items were inadvertently omitted from the Original Filing. In accordance with the rules of the Commission, Items 9A and 15 have been included in this Amendment No. 1 in their entirety.
This Amendment No. 1 does not amend or otherwise update any other information in the Original Filing. Accordingly, this Amendment No. 1 should be read in conjunction with the Original Filing and with our filings with the SEC subsequent to the Original Filing. This Amendment No. 1 does not reflect events occurring after the filing of the Original Filing or modify or update disclosures, including the exhibits to the Original Filing, affected by subsequent events.
AFFYMETRIX, INC.
FORM 10-K
DECEMBER 31, 2009
|
Item No.
|
Page
|
|||
ITEM 9A. CONTROLS AND PROCEDURES
Disclosure Controls and Procedures
As required by paragraph (b) of Exchange Act Rules 13a-15 or 15d-15, Affymetrix’ management, including our Chief Executive Officer and Chief Financial Officer, conducted an evaluation as of the end of the period covered by this report, of the effectiveness of Affymetrix’ disclosure controls and procedures as defined in Exchange Act Rule 13a-15(e) and 15d-15(e). Based on that evaluation, our Chief Executive Officer and Chief Financial Officer concluded that Affymetrix’ 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) and 15d-15(f). Under the supervision of our Chief Executive Officer and Chief Financial Officer and with the participation of our management, we conducted an evaluation of the effectiveness of our internal control over financial reporting as of December 31, 2009 based on the framework in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). Based on that evaluation, our management concluded that our internal control over financial reporting was effective as of December 31, 2009.
The effectiveness of our internal control over financial reporting as of December 31, 2009, has been audited by Ernst &Young LLP, our independent registered public accounting firm, as stated in their report which is included as follows.
REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
To the Board of Directors and Stockholders of Affymetrix, Inc.
We have audited Affymetrix, Inc.’s internal control over financial reporting as of December 31, 2009, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (the “COSO criteria”). Affymetrix, Inc.’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 conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). 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.
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.
In our opinion, Affymetrix, Inc. maintained, in all material respects, effective internal control over financial reporting as of December 31, 2009, based on the COSO criteria.
We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the consolidated balance sheets of Affymetrix, Inc. as of December 31, 2009 and 2008, and the related consolidated statements of operations, comprehensive income (loss), stockholders’ equity, and cash flows for each of the three fiscal years in the period ended December 31, 2009 of Affymetrix, Inc. and our report dated March 1, 2010 expressed an unqualified opinion thereon.
/s/ Ernst & Young LLP
San Jose, California
March 1, 2010
Changes in Internal Control Over Financial Reporting
There were no changes in our internal control over financial reporting identified in connection with the evaluation required by paragraph (d) of Exchange Act Rules 13a-15 or 15d-15 that occurred during the fourth fiscal quarter of 2009 that have materially affected or are reasonably likely to materially affect, our internal control over financial reporting.
ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
(a)(1) Financial Statements. The financial statements required to be filed in our Annual Report on Form 10-K are set forth in Part II, Item 8 of the Original Filing.
(a)(2) Financial Statement Schedules. The financial statement schedule required to be filed in our Annual Report on Form 10-K is set forth in Schedule II—Valuation and Qualifying Accounts to the Original Filing. All other schedules have been omitted as they are not required, not applicable or the information is otherwise included.
(a)(3) Exhibits:
|
EXHIBIT
NUMBER
|
DESCRIPTION OF DOCUMENT
|
|
2.1(1)
|
Agreement and Plan of Merger by and among Panomics, Inc., the Company, Panda Acquisition Corporation and the Equityholders’ Representative dated as of November 11, 2008.
|
|
3.1(2)
|
Restated Certificate of Incorporation.
|
|
3.2(3)
|
Amended and Restated Bylaws.
|
|
4.1(4)
|
Indenture dated as of December 15, 2003, between the Company and The Bank of New York, as Trustee.
|
|
4.2(5)
|
Indenture dated as of November 16, 2007, between the Company and the Bank of New York Trust Company, N.A. as Trustee.
|
|
10.1(6)‡
|
1993 Stock Plan, as amended.
|
|
10.2(6)‡
|
1996 Nonemployee Directors Stock Option Plan.
|
|
10.3(7)
|
Lease between Sobrato Interests and the Company dated June 12, 1996 (3380 Central Expressway, Santa Clara, CA).
|
|
10.4(7)
|
Lease between Sobrato Interests and the Company dated May 31, 1996 (3450 Central Expressway, Santa Clara, CA).
|
|
10.5(8)‡
|
1998 Stock Incentive Plan.
|
|
10.6(8)‡
|
Form of Officer and Director Indemnification Agreement.
|
|
10.7(9)‡
|
Amendment No. 1 to the 1996 Nonemployee Directors Stock Option Plan of the Company
|
|
10.8(10)‡
|
Amended and Restated 1996 Non-Employee Directors Stock Plan.
|
|
10.9(11)*
|
Common Terms Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.10(11)*
|
License Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.11(11)*
|
Affymetrix Instrument and Chip Supply Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.12(11)*
|
Research & Development Collaboration Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.13(11)*
|
Diagnostic Product and Instrument Agency Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.14(11)*
|
Affymetrix Instrument Agency Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.15(12)
|
Lease between Sobrato Interests and the Company dated July 3, 2002 (3420 Central Expressway, Santa Clara, CA).
|
|
10.16(12)
|
First Amendment to Lease between Sobrato Interests and the Company dated September 30, 2003 (3420 Central Expressway, Santa Clara, CA).
|
|
10.17(13)‡
|
Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan, as adopted effective March 9, 2000 and amended through June 23, 2008.
|
|
10.18(14)‡
|
Form of Non-Qualified Stock Option Agreement under the Affymetrix, Inc. Amended and Restated 1996 Non-Employee Directors Stock Plan.
|
|
10.19(1)‡
|
Form of Stock Option Agreement under the Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan.
|
|
10.20(A)(15)‡
|
Nonqualified Supplemental Deferred Compensation Plan of the Company
|
|
10.20(B)(15)‡
|
Nonqualified Supplemental Deferred Compensation Plan Adoption Agreement.
|
|
10.21(16)
|
Fifth Amendment to Lease between Sobrato Interests and the Company dated July 3, 2002 (3380 Central Expressway, Santa Clara, CA).
|
|
10.22(16)
|
First Amendment to Lease between Sobrato Interests and the Company dated July 3, 2002 (3450 Central Expressway, Santa Clara, CA).
|
|
10.23(17)
|
Lease between Keppel Logistics Pte Ltd. and Affymetrix Pte Ltd. dated as of January 1, 2006 (7 Gul Circle, Singapore 629363).
|
|
10.24(1)‡
|
Form of Restricted Stock Agreement under the Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan.
|
|
10.25(18)‡
|
Offer Letter from the Company to Kevin M. King dated December 18, 2006.
|
|
10.26(19)**
|
Amendment Agreement dated December 22, 2006 by and among F. Hoffmann-La Roche Ltd., Roche Molecular Systems, Inc. and the Company
|
|
10.27(20)‡
|
Offer Letter from the Company to John C. Batty dated May 16, 2007.
|
|
10.28(21)
|
Settlement and Release Agreement dated January 9, 2008 between the Company and Illumina, Inc.
|
|
10.29(22)‡
|
Affymetrix, Inc. Change of Control Plan, as amended through November 5, 2008.
|
|
10.30(22)‡
|
Offer Letter from the Company to John F. (Rick) Runkel dated October 6, 2008.
|
|
10.31(1)‡
|
Offer Letter from the Company to Frank Witney dated November 7, 2008
|
|
10.32(23)‡
|
First Amendment to Affymetrix, Inc. 1998 Stock Incentive Plan.
|
|
10.33(24)
|
Stipulation of Settlement regarding the Affymetrix Derivative Litigation in the United States District Court, Northern District of California.
|
|
10.34(25)‡
|
Offer Letter from the Company to Andrew J. Last, Ph.D., dated November 2, 2009.
|
|
10.35(25)
|
Lease Agreement between SBP Limited Partnership and the Company dated August 10, 2008(26309 Miles Road, Warrensville Heights, OH).
|
|
10.36(25)
|
First Amendment and Lease Expansion Agreement between SBP Limited Partnership and the Company dated May 20, 2009 (26309 Miles Road, Warrensville Heights, OH).
|
|
10.37(25)
|
Lease Agreement between OTR, acting as the duly authorized nominee of The State Teacher Retirement System of Ohio and Anatrace, Inc. dated February 14, 2001 (434 Dussel Drive, Maumee, OH).
|
|
10.38(25)
|
Assignment and Assumption of Lease between Anatrace, Inc. and USB Acquisition dated April 30, 2005 (434 Dussel Drive, Maumee, OH).
|
|
21(25)
|
List of Subsidiaries.
|
|
23
|
Consent of Independent Registered Public Accounting Firm.
|
|
31.1(25)
|
Certification of Chief Executive Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002 with respect to the Original Filing.
|
|
31.2(25)
|
Certification of Chief Financial Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002 with respect to the Original Filing.
|
|
31.3
|
Certification of Chief Executive Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002 with respect to this Amendment No. 1.
|
|
31.4
|
Certification of Chief Financial Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002 with respect to this Amendment No. 1.
|
|
32(25)
|
Certification of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002.
|
|
(1)
|
Incorporated by reference to Registrant’s form 10-K as filed on March 2, 2009 (File. No. 000-28218).
|
|
(2)
|
Incorporated by reference to Registrant’s Form 8-K as filed on June, 13, 2000 (File No. 000-28218).
|
|
(3)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on August 7, 2009 (File No. 000-28218).
|
|
(4)
|
Incorporated by reference to Registrant’s Form S-3 as filed on January 29, 2004 (File No. 333-112311).
|
|
(5)
|
Incorporated by reference to Registrant’s Form 8-K as filed on November 19, 2007 (File No. 000-28218).
|
|
(6)
|
Incorporated by reference to Registrant’s Registration Statement on Form S-1 (File No. 333-03648), as amended.
|
|
(7)
|
Incorporated by reference to Registrant’s Quarterly Report on Form 10-Q as filed on August 14, 1996 (File No. 000-28218).
|
|
(8)
|
Incorporated by reference to Registrant’s Report on Form 10-K as filed on March 31, 1999 (File No. 000-28218).
|
|
(9)
|
Incorporated by reference to Registrant’s Registration Statement on Form S-3 as filed on July 12, 1999 (File No. 333-82685), as amended.
|
|
(10)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on May 15, 2001 (File No. 000-28218).
|
|
(11)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on May 15, 2003 (File No. 000-28218).
|
|
(12)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 15, 2004 (File No. 000-28218).
|
|
(13)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on August 8, 2008 (File No. 000-28218).
|
|
(14)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on November 9, 2004 (File No. 000-28218).
|
|
(15)
|
Incorporated by reference to Registrant’s Form 8-K as filed on November 7, 2008 (File No. 000-28218).
|
|
(16)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 16, 2005 (File No. 000-28218).
|
|
(17)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 9, 2006 (File No. 000-28218).
|
|
(18)
|
Incorporated by reference to Registrant’s Form 8-K as filed on December 19, 2006 (File No. 000-28218).
|
|
(19)
|
Incorporated by reference to Registrant’s Form 8-K as filed on December 22, 2006 (File No. 000-28218).
|
|
(20)
|
Incorporated by reference to Registrant’s Form 8-K as filed on June 6, 2007 (File No. 000-28218).
|
|
(21)
|
Incorporated by reference to Registrant’s Form 10-K as filed on February 29, 2008 (File No. 000-28218).
|
|
(22)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on November 7, 2008 (File No. 000-28218).
|
|
(23)
|
Incorporated by reference to Registrant’s Form S-8 as filed on April 18, 2001 (File No. 333-59158).
|
|
(24)
|
Incorporated by reference to Registrant’s Form 8-K as filed on May 20, 2009 (File No. 000-28218).
|
|
(25)
|
Incorporated by reference to the Original Filing.
|
|
‡
|
Management contract, compensatory plan, contract or arrangement
|
|
*
|
Confidential treatment granted
|
|
**
|
Confidential treatment requested
|
Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.
|
AFFYMETRIX, INC.
(Registrant)
|
||
|
By:
|
/s/ KEVIN M. KING
|
|
|
January 6, 2011
|
Kevin M. King
|
|
|
DIRECTOR, PRESIDENT AND
CHIEF EXECUTIVE OFFICER
|
||
INDEX TO EXHIBITS
|
EXHIBIT
NUMBER
|
DESCRIPTION OF DOCUMENT
|
|
2.1(1)
|
Agreement and Plan of Merger by and among Panomics, Inc., the Company, Panda Acquisition Corporation and the Equityholders’ Representative dated as of November 11, 2008.
|
|
3.1(2)
|
Restated Certificate of Incorporation.
|
|
3.2(3)
|
Amended and Restated Bylaws.
|
|
4.1(4)
|
Indenture dated as of December 15, 2003, between the Company and The Bank of New York, as Trustee.
|
|
4.2(5)
|
Indenture dated as of November 16, 2007, between the Company and the Bank of New York Trust Company, N.A. as Trustee.
|
|
10.1(6)‡
|
1993 Stock Plan, as amended.
|
|
10.2(6)‡
|
1996 Nonemployee Directors Stock Option Plan.
|
|
10.3(7)
|
Lease between Sobrato Interests and the Company dated June 12, 1996 (3380 Central Expressway, Santa Clara, CA).
|
|
10.4(7)
|
Lease between Sobrato Interests and the Company dated May 31, 1996 (3450 Central Expressway, Santa Clara, CA).
|
|
10.5(8)‡
|
1998 Stock Incentive Plan.
|
|
10.6(8)‡
|
Form of Officer and Director Indemnification Agreement.
|
|
10.7(9)‡
|
Amendment No. 1 to the 1996 Nonemployee Directors Stock Option Plan of the Company
|
|
10.8(10)‡
|
Amended and Restated 1996 Non-Employee Directors Stock Plan.
|
|
10.9(11)*
|
Common Terms Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.10(11)*
|
License Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.11(11)*
|
Affymetrix Instrument and Chip Supply Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.12(11)*
|
Research & Development Collaboration Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.13(11)*
|
Diagnostic Product and Instrument Agency Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.14(11)*
|
Affymetrix Instrument Agency Agreement between F. Hoffmann-La Roche Ltd. and the Company dated January 29, 2003.
|
|
10.15(12)
|
Lease between Sobrato Interests and the Company dated July 3, 2002 (3420 Central Expressway, Santa Clara, CA).
|
|
10.16(12)
|
First Amendment to Lease between Sobrato Interests and the Company dated September 30, 2003 (3420 Central Expressway, Santa Clara, CA).
|
|
10.17(13)‡
|
Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan, as adopted effective March 9, 2000 and amended through June 23, 2008.
|
|
10.18(14)‡
|
Form of Non-Qualified Stock Option Agreement under the Affymetrix, Inc. Amended and Restated 1996 Non-Employee Directors Stock Plan.
|
|
10.19(1)‡
|
Form of Stock Option Agreement under the Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan.
|
|
10.20(A)(15)‡
|
Nonqualified Supplemental Deferred Compensation Plan of the Company
|
|
10.20(B)(15)‡
|
Nonqualified Supplemental Deferred Compensation Plan Adoption Agreement.
|
|
10.21(16)
|
Fifth Amendment to Lease between Sobrato Interests and the Company dated July 3, 2002 (3380 Central Expressway, Santa Clara, CA).
|
|
10.22(16)
|
First Amendment to Lease between Sobrato Interests and the Company dated July 3, 2002 (3450 Central Expressway, Santa Clara, CA).
|
|
10.23(17)
|
Lease between Keppel Logistics Pte Ltd. and Affymetrix Pte Ltd. dated as of January 1, 2006 (7 Gul Circle, Singapore 629363).
|
|
10.24(1)‡
|
Form of Restricted Stock Agreement under the Affymetrix, Inc. Amended and Restated 2000 Equity Incentive Plan.
|
|
10.25(18)‡
|
Offer Letter from the Company to Kevin M. King dated December 18, 2006.
|
|
10.26(19)**
|
Amendment Agreement dated December 22, 2006 by and among F. Hoffmann-La Roche Ltd., Roche Molecular Systems, Inc. and the Company
|
|
10.27(20)‡
|
Offer Letter from the Company to John C. Batty dated May 16, 2007.
|
|
10.28(21)
|
Settlement and Release Agreement dated January 9, 2008 between the Company and Illumina, Inc.
|
|
10.29(22)‡
|
Affymetrix, Inc. Change of Control Plan, as amended through November 5, 2008.
|
|
10.30(22)‡
|
Offer Letter from the Company to John F. (Rick) Runkel dated October 6, 2008.
|
|
10.31(1)‡
|
Offer Letter from the Company to Frank Witney dated November 7, 2008
|
|
10.32(23)‡
|
First Amendment to Affymetrix, Inc. 1998 Stock Incentive Plan.
|
|
10.33(24)
|
Stipulation of Settlement regarding the Affymetrix Derivative Litigation in the United States District Court, Northern District of California.
|
|
10.34(25)‡
|
Offer Letter from the Company to Andrew J. Last, Ph.D., dated November 2, 2009.
|
|
10.35(25)
|
Lease Agreement between SBP Limited Partnership and the Company dated August 10, 2008(26309 Miles Road, Warrensville Heights, OH).
|
|
10.36(25)
|
First Amendment and Lease Expansion Agreement between SBP Limited Partnership and the Company dated May 20, 2009 (26309 Miles Road, Warrensville Heights, OH).
|
|
10.37(25)
|
Lease Agreement between OTR, acting as the duly authorized nominee of The State Teacher Retirement System of Ohio and Anatrace, Inc. dated February 14, 2001 (434 Dussel Drive, Maumee, OH).
|
|
10.38(25)
|
Assignment and Assumption of Lease between Anatrace, Inc. and USB Acquisition dated April 30, 2005 (434 Dussel Drive, Maumee, OH).
|
|
21(25)
|
List of Subsidiaries.
|
|
23
|
Consent of Independent Registered Public Accounting Firm.
|
|
31.1(25)
|
Certification of Chief Executive Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002 with respect to the Original Filing.
|
|
31.2(25)
|
Certification of Chief Financial Officer Pursuant to Section 302 of Sarbanes-Oxley Act of 2002 with respect to the Original Filing.
|
|
31.3
|
Certification of Chief Executive Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002 with respect to this Amendment No. 1.
|
|
31.4
|
Certification of Chief Financial Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002 with respect to this Amendment No. 1.
|
|
32(25)
|
Certification of Chief Executive Officer Pursuant to Section 906 of Sarbanes-Oxley Act of 2002.
|
|
(1)
|
Incorporated by reference to Registrant’s form 10-K as filed on March 2, 2009 (File. No. 000-28218).
|
|
(2)
|
Incorporated by reference to Registrant’s Form 8-K as filed on June, 13, 2000 (File No. 000-28218).
|
|
(3)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on August 7, 2009 (File No. 000-28218).
|
|
(4)
|
Incorporated by reference to Registrant’s Form S-3 as filed on January 29, 2004 (File No. 333-112311).
|
|
(5)
|
Incorporated by reference to Registrant’s Form 8-K as filed on November 19, 2007 (File No. 000-28218).
|
|
(6)
|
Incorporated by reference to Registrant’s Registration Statement on Form S-1 (File No. 333-03648), as amended.
|
|
(7)
|
Incorporated by reference to Registrant’s Quarterly Report on Form 10-Q as filed on August 14, 1996 (File No. 000-28218).
|
|
(8)
|
Incorporated by reference to Registrant’s Report on Form 10-K as filed on March 31, 1999 (File No. 000-28218).
|
|
(9)
|
Incorporated by reference to Registrant’s Registration Statement on Form S-3 as filed on July 12, 1999 (File No. 333-82685), as amended.
|
|
(10)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on May 15, 2001 (File No. 000-28218).
|
|
(11)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on May 15, 2003 (File No. 000-28218).
|
|
(12)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 15, 2004 (File No. 000-28218).
|
|
(13)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on August 8, 2008 (File No. 000-28218).
|
|
(14)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on November 9, 2004 (File No. 000-28218).
|
|
(15)
|
Incorporated by reference to Registrant’s Form 8-K as filed on November 7, 2008 (File No. 000-28218).
|
|
(16)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 16, 2005 (File No. 000-28218).
|
|
(17)
|
Incorporated by reference to Registrant’s Form 10-K as filed on March 9, 2006 (File No. 000-28218).
|
|
(18)
|
Incorporated by reference to Registrant’s Form 8-K as filed on December 19, 2006 (File No. 000-28218).
|
|
(19)
|
Incorporated by reference to Registrant’s Form 8-K as filed on December 22, 2006 (File No. 000-28218).
|
|
(20)
|
Incorporated by reference to Registrant’s Form 8-K as filed on June 6, 2007 (File No. 000-28218).
|
|
(21)
|
Incorporated by reference to Registrant’s Form 10-K as filed on February 29, 2008 (File No. 000-28218).
|
|
(22)
|
Incorporated by reference to Registrant’s Form 10-Q as filed on November 7, 2008 (File No. 000-28218).
|
|
(23)
|
Incorporated by reference to Registrant’s Form S-8 as filed on April 18, 2001 (File No. 333-59158).
|
|
(24)
|
Incorporated by reference to Registrant’s Form 8-K as filed on May 20, 2009 (File No. 000-28218).
|
|
(25)
|
Incorporated by reference to the Original Filing.
|
|
‡
|
Management contract, compensatory plan, contract or arrangement
|
|
*
|
Confidential treatment granted
|
|
**
|
Confidential treatment requested
|