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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549
   FORM 10-K/A Amendment No. 1
 x
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2003 OR o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 Commission file number 0-22570 LYNX THERAPEUTICS, INC.  Delaware
    
    94-3161073(State or other jurisdiction of
    
    (I.R.S. Employer Identification No.)incorporation or organization)
 25861 Industrial Blvd., Hayward, CA 94545
(Address of principal executive offices, including zip code) (510) 670-9300
(Registrants telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: None Securities registered pursuant to Section 12(g) of the Act: Common Stock, $.01
par value per share 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 and 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 [  ] 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. [X] Indicate by check mark whether the Registrant is an accelerated filer (as
defined in Exchange Act Rule 12b-2). Yes [  ] No [X] State the aggregate market value of the voting and non-voting common
equity held by non-affiliates of the Registrant computed by reference to the
price at which the common equity was last sold, or the average bid and asked
price of such common equity, as of the last business day of the registrants
most recently completed second fiscal quarter: $10,920,824.1 The number of shares of common stock of the Registrant outstanding as of
March 9, 2004, was 6,199,245. The aggregate market value of the common stock of
the Registrant held by non-affiliates of the Registrant, based upon the closing
price of the common stock reported on the Nasdaq National Market on March 9,
2004, was $30,264,929.2      1
    
    Based on a closing price of $3.79 per share on June 30, 2003 and
4,654,245 shares outstanding (as adjusted to reflect the Registrants
reverse stock split effected in January 2003). Excludes 1,772,761 shares
of the Registrants common stock held by executive officers, directors and
stockholders whose ownership exceed 5% of the common stock outstanding at
June 30, 2003.2
    
    Based on a closing price of $6.30 per share on March 9, 2004 and
6,199,245 shares outstanding. Excludes 1,395,288 shares of the
Registrants common stock held by executive officers, directors and
stockholders whose ownership exceed 5% of the common stock outstanding at
March 9, 2004.




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DOCUMENTS INCORPORATED BY REFERENCE None. EXPLANATORY NOTE Lynx Therapeutics, Inc. is filing this Amendment No. 1 on Form 10-K/A to our
Annual Report on Form 10-K, originally filed with the Securities and Exchange
Commission on March 30, 2004, solely for the purpose of amending and restating
certain portions of such Annual Report on Form 10-K. Each of the following
sections of the Annual Report is amended and restated in its entirely, and
current as of April 29, 2004: Part III, Item 10. Directors and Executive Officers of the Registrant; and Part III, Item 14. Principal Accountant Fees and Services. In addition, we have filed the following exhibits herewith: 32.3
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.32.4
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.
 Except as specifically indicated herein, no other information included in the
Annual Report on Form 10-K is amended by this Amendment No. 1 on Form 10-K/A.




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LYNX THERAPEUTICS, INC. FORM 10-K/A ANNUAL REPORT
FOR THE FISCAL YEAR ENDED
DECEMBER 31, 2003 TABLE OF CONTENTS PagePART IIIItem 10. Directors and Executive Officers of the Registrant
    
    
    1Item 14. Principal Accountant Fees and Services
    
    
    4SIGNATURESEXHIBIT 31.3EXHIBIT 31.4




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PART III 
 Item 10. Directors and Executive Officers of the Registrant Our executive officers and directors, and their ages as of February 18,
2004, are as follows: Name
    
    Age
    
    PositionKevin P. Corcoran
    
    
    45
    
    
    President, Chief Executive Officer and DirectorJen-i Mao, Ph.D.
    
    
    51
    
    
    Vice President, Genetic AnalysisKathy A. San Roman
    
    
    50
    
    
    Vice President, Human Resources &
Administration and Acting Chief Financial
OfficerThomas J. Vasicek, Ph.D.
    
    
    45
    
    
    Vice President, Business DevelopmentCraig C. Taylor (1) (2)
    
    
    53
    
    
    Chairman of the BoardSydney Brenner, M.B., D. Phil
    
    
    77
    
    
    Director and Principal Scientific AdvisorLeroy Hood, M.D., Ph.D.
    
    
    65
    
    
    DirectorJames C. Kitch (2)
    
    
    56
    
    
    DirectorMarc D. Kozin (1)
    
    
    42
    
    
    DirectorJames V. Mitchell
    
    
    53
    
    
    DirectorDavid C. UPrichard, Ph.D. (1)
    
    
    55
    
    
    DirectorRichard P. Woychik, Ph.D.
    
    
    51
    
    
    Director
   (1)
    
    Member of the Audit Committee.(2)
    
    Member of the Compensation Committee. Kevin P. Corcoranhas served as a director of Lynx since July 2002. Mr.
Corcoran was appointed President and Chief Executive Officer of Lynx in June
2002. He joined Lynx in September 1995 as Staff Software Engineer, and from
January 1999 to June 2002, Mr. Corcoran served as Vice President, Operations.
Prior to joining Lynx, Mr. Corcoran held various managerial positions with
Applied Biosystems, Inc., an instrumentation company, from July 1992 to
September 1995. His most recent role at Applied Biosystems, Inc. was Group
Leader for Genetic Analysis software. Mr. Corcoran received a B.S. in Computer
Science from California State University, Hayward. Jen-i Mao, Ph.D.,has served as Vice President, Genetic Analysis of Lynx
since June 1998. Prior to joining Lynx, from 1981 to 1998, Dr. Mao held various
management positions at Genome Therapeutics, Inc., a biotechnology company. Her
most recent role at Genome Therapeutics, Inc. was as Vice President of Genetics
and Technology Development. From 1991 through 1998, Dr. Mao also served as
Principal Investigator of the National Institute of Health-funded Genome
Science Technology Center to map and sequence human chromosome 10. Dr. Mao
received a B.S. in Agricultural Chemistry from the National Taiwan University
and a Ph.D. in Molecular Biophysics and Biochemistry from Yale University. Dr.
Mao will be leaving the company in April 2004. Kathy A. San Romanjoined Lynx in August 1992 as Director of
Administration and was appointed Vice President, Human Resources and
Administration in January 1999 and Acting Chief Financial Officer in March
2004. Prior to joining Lynx, from June 1982 through July 1989, Ms. San Roman
held numerous positions at Applied Biosystems, Inc., including most recently as
Corporate Secretary. From February 1991 to July 1992, Ms. San Roman was
Associate Director, Investor Relations at Informix Corporation, a software
development company. Thomas J. Vasicek, Ph.D., joined Lynx in June 2002 as Vice President,
Business Development. Prior to joining Lynx, Dr. Vasicek served as Chief
Scientific Officer at LabSeek Scientific Collaborative, a biotech company, from
May 2000 to October 2001. He also served as the Director, Commercial Technology
for the Corning Advanced Life Sciences Products Division of Corning, Inc. a
manufacturing company, from January 1999 to May 2000, and was a Sr. Scientist
at Millennium Pharmaceuticals, a pharmaceutical company, from June 1996 to
January 1999. Dr. Vasicek received a B.S. in chemistry from the Massachusetts
Institute of Technology and a Ph.D. in Genetics from Harvard University. 1




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Craig C. Taylorwas elected Chairman of the Board of Lynx in December
2000, has served as a director of Lynx since March 1994 and served as Acting
Chief Financial Officer from July 1994 to April 1997. He has been active in
venture capital since 1977, when he joined Asset Management Company, a venture
capital firm. He is a general partner of AMC Partners 89 L.P., which serves as
the general partner of Asset Management Associates 1989 L.P., a private venture
capital partnership. He currently serves as a director of Pharmacyclics, Inc.,
a biotechnology company, and several private companies. Sydney Brenner, M.B., D.Phil.,has served as a director of Lynx since
October 1993 and as Lynxs principal scientific advisor. He is a distinguished
Professor at the Salk Institute of Biological Studies in La Jolla, California.
He served as Director and President of The Molecular Sciences Institute, a
nonprofit research institute in Berkeley, California, from July 1996 to January
2001, when he retired as Director of Research. In September 1996, he retired
from his position of Honorary Professor of Genetic Medicine, University of
Cambridge School of Clinical Medicine, Cambridge, England. From 1986 to his
retirement in 1991, Dr. Brenner directed the Medical Research Council Unit of
Molecular Genetics. He was a member of the Scripps Research Institute in La
Jolla, California, until December 1994. Dr. Brenner is a Fellow of the Royal
Society (1995) and a Foreign Associate of the U.S. National Academy of Sciences
(1977) and has received numerous awards of recognition, including the Nobel
Prize in Physiology or Medicine for 2002, the Albert Lasker Medical Research
Award (2000 and 1991), the Genetics Society of America Medal (1987) and the
Kyoto Prize (1990). Dr. Brenner is the principal inventor of Lynxs bead-based
technologies. Leroy Hood, M.D., Ph.D.,has served as a director of Lynx since May 2000. In
December 1999, he founded the Institute for Systems Biology, a private
nonprofit research institute, and currently serves as the President and a
director. From 1992 to 1999, he was the chair of the Molecular Biotechnology
Department at the University of Washington and the William GatesIII Professor
of Biomedical Sciences. Dr. Hood received an M.D. from John Hopkins Medical
School and a Ph.D. from the California Institute of Technology. He has been a
member of the National Academy of Sciences and the American Academy of Arts and
Sciences since 1982. He currently serves as a director of Paradigm Genetics, a
biotechnology company. James C. Kitchhas served as a director of Lynx since February 1993 and as
Secretary of Lynx from February 1992 to December 1997. Since 1979, Mr. Kitch
has been a partner at Cooley Godward LLP, a law firm, which has provided legal
services to Lynx. Marc D. Kozinhas served as a director of Lynx since July 2002. Since
1996, Mr. Kozin has served as President of the North American practice for
L.E.K. Consulting LLC, a business consulting company. In this position, he
leads L.E.K.s life science strategic planning services. Mr. Kozin received a
B.A. in Economics from Duke University and an M.B.A. from The Wharton School,
University of Pennsylvania. He also serves as a member of the Board of
Governors at New England Medical Center. James V. Mitchellhas served as a director of Lynx since March 2003. Mr.
Mitchell co-founded Meier Mitchell & Company, a company active in the venture
lending area, in 1984 and sold the company in 1999. He subsequently served as
President of the acquired company until October 2002. Mr. Mitchell received a
B.A. in Economics from the University of California at Santa Barbara and an
M.B.A. from The Wharton School, University of Pennsylvania. David C. UPrichard, Ph.D.,has served as a director of Lynx since March
2001. Dr. UPrichard currently serves as a President of Druid Consulting LLC
and as a Venture Partner at Apax Partners Ltd. From September 1999 to March
2003, he served as the Chief Executive Officer of 3-Dimensional
Pharmaceuticals, Inc., a pharmaceutical company. From 1997 until 1999, he
served as the President, Research and Development, for SmithKline Beecham
Pharmaceuticals, a pharmaceutical company. Prior to joining SmithKline Beecham,
from 1994 to 1997, Dr. UPrichard served as International Research Director of
Zeneca Pharmaceuticals, Inc., and, from 1991 to 1994, he managed research
groups in the U.S. and U.K. at ICI Pharmaceuticals, Inc. and Zeneca, both of
which are pharmaceutical companies. Dr. UPrichard received a B.Sc. in
Pharmacology from the University of Glasgow and a Ph.D. in Pharmacology from
the University of Kansas. He currently serves as a director of Invitrogen
Corp., a biotechnology company, Guilford Pharmaceuticals Corp., a
pharmaceutical company and several private companies. 2




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Richard P. Woychik, Ph.D.,has served as a director of Lynx since July
2002. Since August 2002, Dr. Woychik has served as the director of The Jackson
Laboratory in Bar Harbor, Maine. Prior to joining The Jackson Laboratory, Dr.
Woychik served as Chief Scientific Officer at Lynx, a position that he held
since joining Lynx in January 2001. Prior to joining Lynx, from 1998 to 2000,
Dr. Woychik was Senior Director and Head of the Alameda Global R&D Molecular
Genetics Research Center at Pfizer Inc., a pharmaceutical company. From 1997 to
1998, Dr. Woychik was a Professor in the Departments of Pediatrics, Genetics
and Pharmacology and Vice Chairman for Research in Pediatrics at Case Western
Reserve University, and from 1987 to 1997, he was a research scientist at the
Oak Ridge National Laboratory. Dr. Woychik received a Ph.D. in Molecular
Biology from Case Western Reserve University. Audit Committee The Audit Committee of the Board of Directors oversees the Companys
corporate accounting and financial reporting process. For this purpose, the
Audit Committee performs several functions. The Audit Committee evaluates the
performance of and assesses the qualifications of the independent auditors;
determines and approves the engagement of the independent auditors; determines
whether to retain or terminate the existing independent auditors or to appoint
and engage new independent auditors; reviews and approves the retention of the
independent auditors to perform any proposed permissible non-audit services;
monitors the rotation of partners of the independent auditors on the Companys
audit engagement team as required by law; confers with management and the
independent auditors regarding the effectiveness of internal controls over
financial reporting; establishes procedures, as required under applicable law,
for the receipt, retention and treatment of complaints received by the Company
regarding accounting, internal accounting controls or auditing matters and the
confidential and anonymous submission by employees of concerns regarding
questionable accounting or auditing matters; reviews the financial statements
to be included in the Companys Annual Report on Form 10-K; and discusses with
management and the independent auditors the results of the annual audit and the
results of the Companys quarterly financial statements. Three directors
comprise the Audit Committee: Messrs. Taylor and Kozin and Dr. UPrichard.
The Board of Directors annually reviews the Nasdaq listing standards definition
of independence for Audit Committee members and has determined that all members
of the Companys Audit Committee are independent (as independence is currently
defined in Rule 4350(d)(2)(A)(i) and (ii) of the Nasdaq
listing standards). Audit Committee Financial Expert We currently do not have an audit committee financial expert as defined in
Item 401(h) of Regulation S-K. The Board believes that the interests of our
stockholders can be adequately served for the time being by the current members
but intends to add such an expert to the Board once a suitable candidate can be
identified and recruited. Section 16(a) Beneficial Ownership Reporting Compliance Section 16(a) of the Exchange Act requires our directors and executive
officers, and persons who own more than 10% of a registered class of our equity
securities, to file with the Securities and Exchange Commission initial reports
of ownership and reports of changes in ownership of our common stock and other
equity securities. Officers, directors and greater than 10% stockholders are
required by SEC regulation to furnish us with copies of all Section 16(a) forms
that they file. To our knowledge, based solely on a review of the copies of such reports
furnished to us, during the calendar year ended December 31, 2003, all Section
16(a) filing requirements applicable to our officers, directors and greater
than 10% beneficial owners were complied with. Code of Conduct We have adopted the Lynx Therapeutics, Inc. Code of Conduct that applies
to all officers, directors and employees. The Code of Conduct will be
available on our website at www.lynxgen.com no later than May 4, 2004. If the
Company makes any substantive amendments to the Code of Conduct or grants any
waiver from a provision of the Code to any executive officer or director, the
Company will promptly disclose the nature of the amendment or waiver on its
website. 3




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Stockholder Communications With The Board Of Directors Historically, we have not adopted a formal process for stockholder
communications with the Board of Directors. Nevertheless, every effort has been
made to ensure that the views of stockholders are heard by the Board of
Directors or individual directors, as applicable, and that appropriate
responses are provided to stockholders in a timely manner. We believe our
responsiveness to stockholder communications to the Board of Directors has been
excellent. Nevertheless, during the upcoming year the Board of Directors will
give full consideration to the adoption of a formal process for stockholder
communications with the Board of Directors and, if adopted, publish it promptly
and post it to our website 
 Item 14. Principal Accountant Fees and Services The following table represents aggregate fees billed to the Company for
fiscal years ended December 31, 2003 and December 31, 2002, by Ernst & Young
LLP, the Companys principal accountant. Fiscal Year Ended(in thousands)2003
    
    2002Audit Fees
    
    $
    166,460
    
    
    $
    128,750Audit-related Fees
    
    
    48,300
    
    
    
    45,186Tax Fees
    
    
    31,320
    
    
    
    31,000All Other Fees
    
    
    53,044
    
    
    
    21,456Total Fees
    
    $
    299,124
    
    
    $
    226,392
 Audit Fees:This category includes fees for the audit of our annual
financial statements, review of the financial statements included in our
quarterly reports on Form 10-Q and services that are normally provided by the
independent auditors in connection with statutory and regulatory filings or
engagements for those fiscal years. This category also includes advice on
audit and accounting matters that arose during, or as a result of, the audit or
the review of interim financial statements and statutory audits required by
non-U.S. jurisdictions. Audit-Related Fees:This category consists of assurance and related
services by Ernst & Young LLP that are reasonably related to the performance of
the audit or review of our financial statements and are not reported above
under Audit Fees. Tax Fees:This category consists of professional services rendered by
Ernst & Young LLP for tax compliance and tax advice. The services for the fees
disclosed under this category include tax return preparation and technical tax
advice. All Other Fees:This category consists of fees for professional services
rendered by Ernst & Young LLP in connection with registration statements filed
by Lynx and research and consultations regarding a foreign joint venture and
reorganization of Lynx GmbH. All of the fees described above were approved by the Audit Committee. The
Audit Committee has determined the rendering of non-audit services by Ernst &
Young LLP is compatible with maintaining their independence. 4




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Audit Committee Pre-Approval Policies and Procedures. The Audit Committee has adopted a policy and procedures for the
pre-approval of audit and non-audit services rendered by our independent
auditor, Ernst & Young LLP. The policy generally pre-approves specified
services in the defined categories of audit services, audit-related services,
and tax services up to specified amounts. Pre-approval may also be given as
part of the Audit Committees approval of the scope of the engagement of the
independent auditor or on an individual explicit case-by-case basis before the
independent auditor is engaged to provide each service. The pre-approval of
services may be delegated to one or more of the Audit Committees members, but
the decision must be reported to the full Audit Committee at its next scheduled
meeting. 5




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SIGNATURES Pursuant to the requirements of Section 13 or 15(d) Securities Exchange
Act of 1934, the Registrant has duly caused this report on Form 10-K/A to be
signed on its behalf by the undersigned, thereunto duly authorized, on April,
29, 2004. LYNX THERAPEUTICS, INC.By:
    
    /s/
    
    Kevin P. CorcoranKevin P. CorcoranPresident and Chief Executive Officer
 Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed by the following persons on behalf of the Registrant and
in the capacities and on the dates indicated. Signatures
    
    Title
    
    Date/s/ Kevin P. Corcoran
    
    President, Chief Executive Officer and Director
    
    April 29, 2004(Principal Executive Officer)Kevin P. Corcoran*
    
    Chairman of the Board
    
    April 29, 2004Craig C. Taylor/s/ Kathy A. San Roman
    
    Vice President Human Resources &
    
    April 29, 2004Administration and Acting Chief FinancialKathy A. San Roman
    
    Officer (Principal Financial and Accounting Officer)*
    
    Director
    
    April 29, 2004Sydney Brenner*
    
    Director
    
    April 29, 2004Leroy Hood*
    
    Director
    
    April 29, 2004James C. Kitch*
    
    Director
    
    April 29, 2004Marc D. Kozin*
    
    Director
    
    April 29, 2004James V. Mitchell*
    
    Director
    
    April 29, 2004David C. UPrichard*
    
    Director
    
    April 29, 2004Richard P. Woychik
 * By:
    
    /s/ Kevin P. CorcoranKEVIN P. CORCORANATTORNEY-IN-FACT




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Exhibit Index Exhibit No.
    
    Description of Document2.1
    
    Acquisition Agreement, dated as of February 4, 1998, by and between
the Company and Inex Pharmaceuticals Corporation, incorporated by
reference to the indicated exhibit of the Companys Current Report on
Form 8-K filed on March 24, 1998.3.1
    
    Amended and Restated Certificate of Incorporation of the Company,
incorporated by reference to the indicated exhibit of the Companys
Form 10-Q for the period ended June 30, 2000.3.1.1
    
    Certificate of Amendment to Amended and Restated Certificate of
Incorporation of the Company, incorporated by reference to the
indicated exhibit of the Companys Form 10-K for the period ended
December 31, 2002.3.2
    
    Bylaws of the Company, as amended, incorporated by reference to the
indicated exhibit of the Companys Form 10-Q for the period ended
June 30, 2000.4.1
    
    Form of Common Stock Certificate, incorporated by reference to
Exhibit 4.2 of the Companys Statement Form 10 (File No. 0-22570), as
amended (see the Statement Form 10).10.1
    
    Form of Indemnity Agreement entered into between the Company and its
directors and officers, incorporated by reference to Exhibit 10.7 of
the Companys Statement Form 10.10.2**
    
    The Companys 1992 Stock Option Plan (the Stock Option Plan),
incorporated by reference to Exhibit 10.8 of the Companys Statement
Form 10.10.3**
    
    Form of Incentive Stock Option Grant under the Stock Option Plan,
incorporated by reference to Exhibit 10.9 of the Companys Statement
Form 10.10.4**
    
    Form of Nonstatutory Stock Option Grant under the Stock Option Plan,
incorporated by reference to Exhibit 10.10 of the Companys Statement
Form 10.10.5
    
    Agreement of Assignment and License of Intellectual Property Rights,
dated June 30, 1992, by and between the Company and ABI, incorporated
by reference to Exhibit 10.11 of the Companys Statement Form 10.10.6
    
    Amended and Restated Investor Rights Agreement, dated as of November
1, 1995, incorporated by reference to Exhibit 10.30 of the Companys
Form 10-K for the period ended December 31, 1995.10.7+
    
    Technology Development and Services Agreement, dated as of October 2,
1995, by and among the Company, Hoechst Aktiengesellschaft and its
subsidiary, Hoechst Marion Roussel, Inc., incorporated by reference
to Exhibit 10.28 of the Companys Form 10-K for the period ended
December 31, 1995.10.7.1+
    
    Amended and Restated First Amendment to Technology Development and
Services Agreement, dated May 1, 1998, by and between the Company and
Hoechst Marion Roussel, Inc., incorporated by reference to Exhibit
10.36 of the Companys Form 10-Q for the period ended June 30, 1998.10.7.2+
    
    Second Amendment to Technology Development and Services Agreement,
dated March 1, 1999, by and among the Company, Hoechst Marion
Roussel, Inc. and its affiliate Hoechst Schering AgrEvo GmbH,
incorporated by reference to the indicated exhibit of the Companys
Form 10-K/A filed on August 24, 2001 for the period ended December
31, 2001.




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Exhibit No.
    
    Description of Document10.7.3+
    
    Third Amendment to Technology Development and Services Agreement,
dated December 20, 1999, by and among the Company, Aventis
Pharmaceutical Inc. and its affiliate Aventis CropScience GmbH,
incorporated by reference to the indicated exhibit of the Companys
Form 10-K/A filed on August 24, 2001 for the period ended December
31, 2001.10.7.4+
    
    Fourth Amendment to Technology Development and Services Agreement,
dated March 31, 2002, by and between the Company and Aventis
CropScience GmbH, incorporated by reference to the indicated exhibit
of the Companys Form 10-Q for the period ended March 31, 2002.10.7.5+
    
    Fifth Amendment to Technology Development and Services Agreement,
dated as of September 30, 2002, by and between the Company and Bayer
CropScience GmbH, incorporated by reference to the indicated exhibit
of the Companys Form 10-Q for the period ended September 30, 2002.10.10
    
    Lease, dated as of February 27, 1998, by and between the Company and
SimFirst, L.P., Limited Partnership, incorporated by reference to
Exhibit 10.35 of the Companys Form 10-Q for the period ended March
31, 1998.10.11**
    
    The Companys 1998 Employee Stock Purchase Plan (the Purchase
Plan), incorporated by reference to Exhibit 99.1 of the Companys
Form S-8 (File No. 333-59163).10.12+
    
    Research Collaboration Agreement, dated as of October 29, 1998, by
and between the Company and E.I. Dupont de Nemours and Co.,
incorporated by reference to Exhibit 10.13 of the Companys Form
10-K/A filed on August 24, 2001 for the period ended December 31,
2001.10.12.1+
    
    Letter Amendment, dated March 1, 2002, to Research Collaboration
Agreement by and between the Company and E.I. DuPont De Nemours and
Co., incorporated by reference to the indicated exhibit of the
Companys Form 10-Q for the period ended March 31, 2002.10.13
    
    Master Loan and Security Agreement, dated as of October 26, 1998, by
and between the Company and Transamerica Business Credit Corporation,
incorporated by reference to Exhibit 10.14 of the Companys Form
10-K/A filed on August 24, 2001 for the period ended December 31,
2001.10.14
    
    Promissory Note No. 7, dated as of September 29, 2000, issued by the
Company to Transamerica Business Credit Corporation, incorporated by
reference to Exhibit 10.15 of the Companys Form 10-K/A filed on
August 24, 2001 for the period ended December 31, 2001.10.15+
    
    Collaboration Agreement, dated as of September 30, 1999, by and
between the Company and Hoechst Schering AgrEvo GmbH, incorporated by
reference to Exhibit 10.16.10.16**
    
    Employment Agreement, dated as of October 18, 1999, by and between
the Company and Norman John Wilkie Russell, Ph.D., incorporated by
reference to Exhibit 10.13 of the Companys Form 10-Q for the period
ended September 30, 1999.10.17+
    
    Collaboration Agreement, dated as of October 1, 2000, by and between
the Company and Takara Shuzo Co., Ltd. incorporated by reference to
Exhibit 10.18 of the Companys Form 10-K/A filed on August 24, 2001
for the period ended December 31, 2001.10.17.1+
    
    Amendment No. 1 to Collaboration Agreement, dated December 19, 2002,
by and between the Company and Takara Bio Inc., incorporated by
reference to the indicated exhibit of the Companys Form 10-K for the
period ended December 31, 2002.




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Exhibit No.
    
    Description of Document10.17.2+
    
    Amendment No. 2 to Collaboration Agreement, dated June 30, 2003, by
and between the Company and Takara Bio Inc., incorporated by
reference to the indicated exhibit of the Companys Form 10-Q for the
period ended September 30, 2003.10.18
    
    Securities Purchase Agreement, dated as of May 24, 2001, by and among
the Company and the investors listed therein, incorporated by
reference to Exhibit 10.1 of the Companys Current Report on Form
8-K, filed on June 4, 2001.10.19
    
    Registration Rights Agreement, dated as of May 24, 2001, by and among
the Company and the investors listed therein, incorporated by
reference to Exhibit 10.2 of the Companys Current Report on Form
8-K, filed on June 4, 2001.10.20
    
    Form of Warrant issued by the Company in favor of each investor
thereto, incorporated by reference to Exhibit 10.3 of the Companys
Current Report on Form 8-K, filed on June 4, 2001.10.21+
    
    Joint Venture Agreement, dated as of June 29, 2001, by and between
the Company and BASF Aktiengesellschaft, incorporated by reference to
Exhibit 10.18 of the Companys Form 10-Q for the period ended June
30, 2001.10.22+
    
    First Amendment to Joint Venture Agreement, by and between the
Company and BASF Aktiengesellschaft, dated as of August 14, 2001,
incorporated by reference to Exhibit 10.22.2 of the Companys Form
10-Q for the period ended September 30, 2001.10.23+
    
    Technology License Agreement, dated as of June 1, 2001, by and
between the Company and BASF-LYNX Bioscience AG, incorporated by
reference to Exhibit 10.19 of the Companys Form 10-Q for the period
ended June 30, 2001.10.24
    
    Common Stock Purchase Agreement, by and between the Company and
Takara Shuzo Co., Ltd., dated as of October 1, 2001, incorporated by
reference to Exhibit 10.24 of the Companys Form 10-Q for the period
ended September 30, 2001.10.25+
    
    Purchase Agreement, dated as of March 5, 2002, by and between Geron
Corporation and Lynx Therapeutics, Inc., incorporated by reference to
the indicated exhibit of the Companys Current Report on Form 8-K
filed on March 18, 2002.10.26+
    
    Common Stock Purchase Agreement, dated as of March 5, 2002, by and
between Geron Corporation and Lynx Therapeutics, Inc., incorporated
by reference to the indicated exhibit of the Companys Current Report
on From 8-K filed on March 18, 2002.10.27
    
    Form of Securities Purchase Agreement by and among the Company and
the investors listed therein, incorporated by reference to the
indicated exhibit of the Companys Current Report on Form 8-K, as
amended, filed on April 30, 2002.10.28
    
    Form of Registration Rights Agreement by and among the Company and
the investors listed therein, incorporated by reference to the
indicated exhibit of the Companys Current Report on Form 8-K, as
amended, filed on April 30, 2002.10.29
    
    Form of Warrant issued by the Company in favor or each investor party
to the Securities Purchase Agreement and Friedman, Billings, Ramsey &
Co., Inc., incorporated by reference to the indicated exhibit of the
Companys Current Report on Form 8-K, as amended, filed on April 30,
2002.




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##### Table of Contents



Exhibit No.
    
    Description of Document10.30**
    
    Employment Agreement, dated as of June 3, 2002, by and between the
Company and Kevin P. Corcoran, incorporated by reference to the
indicated exhibit of the Companys Form 10-Q for the period ended
June 30, 2002.10.31**
    
    Employment Agreement, dated as of June 10, 2002, by and between the
Company and Thomas J. Vasicek, Ph.D., incorporated by reference to
the indicated exhibit of the Companys Form 10-Q for the period ended
June 30, 2002.10.32**
    
    Letter Agreement, dated as of July 9, 2002, by and between the
Company and Norman John Wilkie Russell, Ph.D., incorporated by
reference to the indicated exhibit of the Companys Form 10-Q for the
period ended June 30, 2002.10.33
    
    Common Stock Purchase Agreement, dated as of September 25, 2002, by
and between the Company and Takara Shuzo Co., Ltd., incorporated by
reference to the indicated exhibit of the Companys Form 10-Q for the
period ended September 30, 2002.10.34
    
    Loan and Security Agreement, dated October 23, 2002, by and between
the Company and Comerica Bank-California, incorporated by reference
to the indicated exhibit of the Companys Form 10-Q for the period
ended September 30, 2002.10.35
    
    Common Stock Purchase Agreement, dated as of December 26, 2002, by
and between the Company and Takara Shuzo Co., Ltd., incorporated by
reference to the indicated exhibit of the Companys Form 10-K for the
period ended December 31, 2002.10.39
    
    Securities Purchase Agreement by and among the Company and the
investors listed therein, incorporated by reference to the indicated
exhibit of the Companys Form 8-K filed on September 25, 2003.10.40
    
    Form of Warrant issued by the Company in favor of each investor,
incorporated by reference to the indicated exhibit of the Companys
Form 8-K filed on September 25, 2003.10.41+
    
    Services Agreement, by and between E.I. DuPont de Nemours and Company.10.42
    
    Securities Purchase Agreement by and among the Company and the
investors listed therein, incorporated by reference to the indicated
exhibit of the Companys Form 8-K filed on January 2, 2004.10.43
    
    Form of Warrant issued by the Company in favor of each investor,
incorporated by reference to the indicated exhibit of the Companys
Form 8-K filed on January 2, 2004.21.1
    
    Subsidiaries of the Company.23.1
    
    Consent of Ernst & Young LLP, Independent Auditors.24.1
    
    Power of Attorney.31.1
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the
Securities Exchange Act of 1934, as amended.31.2
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the
Securities Exchange Act of 1934, as amended .




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##### Table of Contents



Exhibit No.
    
    Description of Document31.3*
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the
Securities Exchange Act of 1934, as amended.31.4*
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) of the
Securities Exchange Act of 1934, as amended.32.1++
    
    Certification required by Rule 13a-14(a) or Rule 15d-14(a) and
Section 1350 of Chapter 63 of Title 18 of the United States Code (18
U.S.C. 1350).++
    
    This certification accompanies the Annual Report on Form 10-K which
it relates, pursuant to Section 906 of the Sarbanes Oxley Act of
2002, and is not deemed filed with the Securities and Exchange
Commission and is not to be incorporated by reference into any filing
of Lynx Therapeutics, Inc. under the Securities Act or the Exchange
Act (whether made before or after the date of the Annual Report on
Form 10-K), irrespective of any general incorporation language
contained in such filing.
   *
    
    Being filed herewith; all other exhibits previously filed.**
    
    Management contract or compensatory plan or arrangement.(+)
    
    Portions of this agreement have been deleted pursuant to our request for
confidential treatment.