<PAGE>   1


                                                                    EXHIBIT 10.4


          Confidential Materials omitted and filed separately with the
      Securities and Exchange Commission. Asterisks denote such omission.








                          SPONSORED RESEARCH AGREEMENT

                                     BETWEEN

                  WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH,

                                AFFYMETRIX, INC.,

                          BRISTOL-MYERS SQUIBB COMPANY

                                       AND

                        MILLENNIUM PHARMACEUTICALS, INC.


<PAGE>   2


                                TABLE OF CONTENTS


Article I.    DEFINITIONS...................................................   1
              1.1.     "Additional Consortium Members" .....................   2
              1.2.     "Advisory Board".....................................   2
              1.3.     "Affiliate"..........................................   2
              1.4.     "AFFX Contribution"..................................   2
              1.5.     "AFFX Materials".....................................   2
              1.6.     "Annual Research Program"............................   2
              1.7.     "Annual Research Program Plan".......................   2
              1.8.     "Background Know-How"................................   2
              1.9.     "Background Patent Rights" ..........................   3
              1.10.    "Consortium Member Agreement"........................   3
              1.11.    "Consortium Members".................................   3
              1.12.    "Consortium Member Contribution".....................   3
              1.13.    "Contract Year"......................................   3
              1.14.    "Contributed Technology Upgrade".....................   3
              1.15.    "Core License Field".................................   3
              1.16.    "Existing Research Agreement"........................   3
              1.17.    "Field"..............................................   4
              1.18.    "GAAP"...............................................   4
              1.19.    "Initial Consortium Members".........................   4
              1.20.    "Institute Director".................................   4
              1.21.    "Invention Notice"...................................   4
              1.22.    "IP Owning Consortium Member" .......................   4
              1.23.    "Licensee Consortium Members"........................   4
              1.24.    "License Field"......................................   4
              1.25.    "Millennium Contributed Technology"..................   4
              1.26.    "Minimum Contribution Level".........................   5
              1.27.    "Product Technology License Agreement"...............   5
              1.28.    "Program Copyrights".................................   5
              1.29.    "Program Know-How"...................................   5
              1.30.    "Program Materials"..................................   5
              1.31.    "Program Patent Rights"..............................   5
              1.32.    "Requisite Majority".................................   6
              1.33.    "Research Program"...................................   6
              1.34.    "Research Program Director"..........................   6
              1.35.    "Research Project"...................................   6
              1.36.    "Research Project Plan"..............................   6
              1.37.    "Research Technology License Agreement"..............   6

Article II.   THE CONSORTIUM................................................   7
              2.1.     Consortium Members...................................   7


<PAGE>   3


              2.2.     Advisory Board.......................................   7
              2.3.     Consortium Member Agreement..........................   8

Article III.  THE RESEARCH PROGRAM..........................................   9
              3.1.     General..............................................   9
              3.2.     Research Program Director. ..........................   9
              3.3.     Annual Research Program Plans........................  12
              3.4.     Records..............................................  14
              3.5.     Meetings.............................................  15
              3.6.     Reports..............................................  15
              3.7.     Technology Transfer..................................  16
              3.8.     Research Program Administrator.......................  16
              3.9.     Conduct of the Research Program by the Institute.....  16

Article IV.   RESEARCH PROGRAM FUNDING, THIRD PARTY ACTIVITIES AND
              TECHNOLOGY CONTRIBUTIONS......................................  17
              4.1.     Consortium Members' Commitments. ....................  17
              4.2.     Funding Mechanics....................................  18
              4.3.     Financial Records....................................  18
              4.4.     Third Party Activities...............................  18
              4.5.     Consortium Member License Grants
                       and Technology Transfer..............................  22


Article V.    INTELLECTUAL PROPERTY RIGHTS..................................  22
              5.1.     Background Know-How..................................  22
              5.2.     Program Know-How, Program Materials
                       and Program Copyrights...............................  22
              5.3.     Ownership of Intellectual Property Rights............  23
              5.4.     Research Technology License Option...................  23
              5.5.     Product Technology License Option....................  24
              5.6.     Institute Rights.....................................  26
              5.7.     Patent Filing, Prosecution and Maintenance...........  27
              5.8      Program Materials....................................  29
              5.9.     Employee Agreements..................................  30
              5.10.    No Implied Licenses..................................  30

Article VI.   CONFIDENTIAL INFORMATION......................................  30
              6.1.     Confidentiality......................................  30
              6.2.     Term.................................................  31
              6.3.     Return of Materials..................................  32

Article VII.  PUBLICATION AND ACADEMIC RIGHTS...............................  32
              7.1.     Use of Information...................................  32


<PAGE>   4


              7.2.     Publication or Public Disclosure of Information......  32

Article VIII. WITHDRAWAL....................................................  33
              8.1.     Voluntary Withdrawal.................................  33
              8.3.     Effect of Withdrawal.................................  33


Article IX.   TERM; TERMINATION AND RENEWAL.................................  35
              9.1.     Term.................................................  35
              9.2.     Termination for Breach by the Institute..............  36
              9.3.     Termination Rights of the Institute. ................  36
              9.4.     Additional Termination Event.........................  36
              9.5.     Return of Funds; Continued Funding Obligation........  37
              9.6.     Survival.............................................  37
              9.7.     Renewal..............................................  37

Article X.    REPRESENTATIONS AND WARRANTIES................................  38
              10.1.    Representations and Warranties of All Parties........  38
              10.2.    Representations and Warranties of the Institute......  38
              10.3.    Limitations..........................................  38

Article XI.   LIABILITY AND INDEMNIFICATION.................................  38
              11.1.    Release from Liability...............................  39
              11.2.    Indemnification......................................  39

Article XII.  GENERAL PROVISIONS............................................  40
              12.1.    Dispute Resolution...................................  40
              12.2.    Governing Law........................................  40
              12.3.    Independent Contractors..............................  41
              12.4.    Parties Bound........................................  41
              12.5.    Assignment...........................................  41
              12.6.    Entire Agreement.....................................  41
              12.7.    Further Assurances...................................  41
              12.8.    Right to Develop Independently.......................  41
              12.9.    Notices..............................................  42
              12.10.   Amendment............................................  43
              12.11.   Waiver...............................................  43
              12.12.   Limitation of Liability. ............................  43
              12.13.   Section Headings.....................................  43
              12.14.   Severability.........................................  43
              12.15.   Counterparts.........................................  43
              12.16.   Public Announcements.................................  43
              12.17.   No Third Party Beneficiary Rights....................  44


<PAGE>   5


                          SPONSORED RESEARCH AGREEMENT

         AGREEMENT made as of the 28th day of April, 1997 (the "Effective Date")
by and among Whitehead Institute for Biomedical Research, a Delaware corporation
("Institute"), Affymetrix, Inc., a California corporation ("AFFX"),
Bristol-Myers Squibb Company, a Delaware corporation ("BMS"), and Millennium
Pharmaceuticals, Inc., a Delaware corporation ("Millennium") (the "Agreement").

                                  INTRODUCTION

         1. In the pursuit of its objective of expanding human knowledge in the
biomedical sciences, the Institute has proposed a program of research in the
Field (as hereinafter defined). The Institute has research facilities and
experienced scientists and other personnel which enable it to conduct research
activities in the Field through the Whitehead Center for Genome Research.

         2. The Consortium Members (as hereinafter defined) desire to sponsor
the Research Program (as hereinafter defined) in the Field.

         3. The Consortium Members recognize that the Institute as a recipient
of U.S. government research funds is subject to certain federal guidelines and
regulations regarding use of federal funds, conflicts of interest and other
areas of concern to the federal government, and acknowledge that the Institute
will continue to follow its policies and procedures that ensure adherence to
such guidelines and regulations. The Consortium Members recognize that the
Institute is engaged in the Human Genome Project, aimed at determining the
genomic sequence of the human and mouse genomes. This project is supported by
the United States government and the Institute has committed to placing the
fruits of this work in the public domain on a rapid basis without patents or
other restrictions and without advance access to any party. The Consortium
Members acknowledge the Institute's commitment and seek no rights or special
access to the results of the Human Genome Project.

         4. In consideration of the sponsorship by the Consortium Members of the
Research Program, the Institute is willing to grant the Consortium Members
certain licenses and options to license patents, patent applications and other
intellectual property rights arising out of the Research Program.

         In consideration of the mutual covenants and promises contained in this
Agreement and other good and valuable consideration, the receipt of which is
hereby acknowledged, the Institute and each of the Consortium Members agree as
follows:

Article I    DEFINITIONS

         (a) Defined Terms. As used in this Agreement, the following terms,
whether used in the singular or plural, shall have the following respective
meanings:


<PAGE>   6


         1.1. "Additional Consortium Members" means Consortium Members, other
than the Initial Consortium Members, who become parties to this Agreement
pursuant to the procedures specified in Section 2.1.

         1.2. "Advisory Board" means the committee comprising the Research
Program Director, the Institute Director and representatives of the Consortium
Members established pursuant to Section 2.2.

         1.3. "Affiliate" means, with respect to a specified party to this
Agreement, any corporation, company, partnership, joint venture and/or firm
which now or hereafter controls, is controlled by or is under common control
with such specified party. For purposes of this Section 1.3, "control" shall
mean (a) in the case of corporate entities, direct or indirect ownership of at
least 50% of the stock or shares entitled to vote for the election of directors;
and (b) in the case of non-corporate entities, direct or indirect ownership of
at least 50% of the equity interest with the power to direct the management and
policies of such noncorporate entities.

         1.4. "AFFX Contribution" means the technology rights and other
contributions of AFFX set forth on Schedule I to this Agreement. AFFX
Contribution shall not include any AFFX Materials provided to the Institute
pursuant to Section 4.1.2 of this Agreement.

         1.5. "AFFX Materials" means the chips, hardware, chip design services
and software to be provided by AFFX to the Institute, as specifically set forth
in each Annual Research Program Plan and related Annual Research Program Budget.

         1.6. "Annual Research Program" means the research undertaken during a
Contract Year by the Institute pursuant to this Agreement as part of the
Research Program as provided in Article III.

         1.7. "Annual Research Program Plan" means the annual written research
plan for the conduct of the applicable Annual Research Program as prepared and
approved pursuant to Section 3.3.1.

         1.8. "Background Know-How" means all discoveries, inventions, data,
software, biological materials, information, trade secrets and other technology
developed or generated by the Institute or its employees or contractors prior to
the Effective Date that satisfy all of the following conditions: (a) are
relevant to the Field, (b) are used by the Institute in the conduct of the
Research Program, and (c) are not subject to any contractual restrictions as of
the Effective Date that would prohibit the Institute from granting to the
Licensee Consortium Members the license set forth in Section 5.1.


                                       -2-


<PAGE>   7


         1.9.  "Background Patent Rights" means any and all patent applications
and patents covering any invention included within the Background Know-How, as
set forth on Schedule VI to this Agreement, as Schedule VI may be amended from
time to time.

         1.10. "Consortium Member Agreement" means the agreement, effective as
of the Effective Date of this Agreement, between and among the Consortium
Members governing the relations of the Consortium Members among themselves with
respect to the Research Program and their respective rights in and to the
Background Know-How, Program Know-How, Program Materials, Program Copyrights and
Program Patent Rights.

         1.11. "Consortium Members" means the Initial Consortium Members and the
Additional Consortium Members.

         1.12. "Consortium Member Contribution" means the AFFX Contribution
and/or the Millennium Contributed Technology.

         1.13. "Contract Year" means (a) with respect to the first Contract
Year, the period commencing on the Effective Date and ending on June 30, 1998,
and (b) each subsequent twelve (12) months period commencing on each July 1
during the term of this Agreement.

         1.14. "Contributed Technology Upgrade" means any invention, process,
revision, update, modification, addition and other improvement related thereto,
whether patentable or not, including but not limited to new hardware and
software, technical data, information, material and know-how (a) which is
necessary or useful to make, develop or otherwise utilize Millennium Contributed
Technology (b) which is developed or acquired by Millennium during the period
that Millennium is obligated to provide the Institute with Contributed
Technology Upgrades pursuant to the applicable Annual Research Program Plan and,
if applicable, Article VIII, and (c) to which Millennium has the right to grant
licenses or sublicenses without violating the terms of any agreement or other
arrangement with a third party.

         1.15. "Core License Field" means all uses or applications of Program
Know-How, Program Materials, Program Copyrights, Program Patent Rights and
Background Know-How with respect to (a) the diagnosis, prediction, prevention
and/or treatment of human or animal diseases or medical conditions, (b) analysis
of nucleic acid samples and management of data relating thereto, and (c)
agriculture and related endeavors.

         1.16. "Existing Research Agreement" means the Sponsored Research
Agreement effective as of October 21, 1996 between the Institute, Millennium and
Dr. Thomas Hudson.


                                       -3-


<PAGE>   8


         1.17. "Field" means the identification and development of new genomics
technologies and genetic information to, among other things, ascertain, process,
integrate and interpret genomic information in a high throughput, massively
parallel fashion, thereby enabling functional annotation of genomes (biological
function and disease relevance).

         1.18. "GAAP" means United States generally accepted accounting
principles.

         1.19. "Initial Consortium Members" means AFFX, BMS and Millennium.

         1.20. "Institute Director" means the individual serving as the Director
of the Institute.

         1.21. "Invention Notice" means a notice given by the Institute pursuant
to Section 5.3.2 or by the Institute or an IP Owning Consortium Member pursuant
to Section 5.3.3 of an invention covered by, or able to be covered by, a patent
or patent application within the Program Patent Rights, which includes a
description of the invention sufficient to permit each Consortium Member to
evaluate its interest in such invention.

         1.22. "IP Owning Consortium Member" means a Consortium Member that (a)
jointly owns with the Institute or one or more other Consortium Members certain
patents or patent applications included in Program Patent Rights as a result of
joint conception and/or reduction to practice in the course of the Research
Program or (b) is the sole owner of certain patents or patent applications
included in Program Patent Rights as a result of that Consortium Member's
conception and/or reduction to practice in the course of the Research Program.

         1.23. "Licensee Consortium Members" means the Consortium Member or
Members which, pursuant to the Consortium Member Agreement, are the designated
licensee or licensees of particular Program Know-How, Program Materials, Program
Copyrights, Program Patent Rights or Background Know-How.

         1.24. "License Field" means all uses or applications of Program
Know-How, Program Materials, Program Copyrights, Program Patent Rights and
Background Know-How, as applicable.

         1.25. "Millennium Contributed Technology" means such technology rights
developed or acquired by Millennium of the type set forth on Schedule II to this
Agreement as may be contributed by Millennium to the Institute pursuant to the
provisions of Section 4.5 of this Agreement.


                                       -4-


<PAGE>   9


          Confidential Materials omitted and filed separately with the
       Securities and Exchange commission. Asterisks denote such omission.

         1.26. "Minimum Contribution Level" means (a) for the first Contract
Year, ***********, and (b) for each subsequent Contract Year,
**************************** *****, of which *****************, of which ******
is in the form of cash, provided that (a) the amount specified shall be subject
to adjustment, not to exceed five percent (5%) in any Contract Year, to reflect
the increase, if any, in the U.S. Consumer Price Index (or any comparable
successor index thereto) during the immediately preceding Contract Year, and (b)
no Consortium Member Contributions shall be considered in determining whether
the Minimum Contribution Level has been achieved, but the price of AFFX
Materials (as determined pursuant to Schedule III to this Agreement) shall be so
considered.

         1.27. "Product Technology License Agreement" means a license agreement
substantially in the form of Exhibit A hereto, entered into by the Institute
(and, if applicable, any IP Owning Consortium Members), as licensor(s) and the
Licensee Consortium Members, as licensees.

         1.28. "Program Copyrights" means any and all copyrights worldwide
developed or acquired by the Institute covering any written, oral, visual or
multimedia materials (including any assemblages of data and software in source
code or object code form) created or acquired by (a) the Institute or its
employees or contractors (either alone or jointly with one or more employees of
one or more Consortium Members) or (b) one or more contractors or employees of
one or more Consortium Members in the course of the Research Program.

         1.29. "Program Know-How" means all discoveries, inventions, data,
software, information, trade secrets and other technology developed or generated
by (a) the Institute or its employees or contractors (either alone or jointly
with one or more contractors or employees of one or more Consortium Members) or
(b) one or more contractors or employees of one or more Consortium Members in
the course of the Research Program, provided that any discovery, invention,
data, software, information, trade secret or other technology constituting
Program Know-How shall cease to constitute Program Know-How from and after the
date it is (i) made generally available to the public by the Institute through
publication thereof in accordance with the procedures set forth in Article VII,
or (ii) is otherwise made generally available to the public without breach of
this Agreement. Program Know-How does not include Program Materials.

         1.30. "Program Materials" means any and all biological materials,
including without limitation blood, plasma, DNA and RNA which are obtained
and/or developed in the course of the Research Program.


                                       -5-


<PAGE>   10


         1.31. "Program Patent Rights" means any and all patent applications and
patents covering any invention conceived and/or reduced to practice by (a) the
Institute or its employees or contractors (either alone or jointly with one or
more employees of one or more Consortium Members) either (i) in the course of
the Research Program, or (ii) at any time prior to the first anniversary of the
expiration or termination of the Research Program to the extent such invention
was developed using or otherwise employs Program Know-How, Program Materials
and/or inventions disclosed in Program Patent Rights conceived and/or reduced to
practice in the course of the Research Program; or (b) one or more contractors
or employees of one or more Consortium Members in the course of the Research
Program.

         1.32. "Requisite Majority" means (a) at least one (1) representative of
each Consortium Member, and (b) the Research Program Director, and (c) the
Institute Director.

         1.33. "Research Program" means the research conducted by the Institute
pursuant to this Agreement, including without limitation pursuant to Article
III, consisting of the Annual Research Programs, each of which shall consist of
a series of Research Projects.

         1.34. "Research Program Director" means a tenured faculty member of the
Institute who has primary responsibility to direct the activities of the
Research Program and is designated pursuant to Section 3.2.

         1.35. "Research Project" means a research project conducted by the
Institute as part of the Research Program involving matters of general interest
and utility to the Consortium Members.

         1.36. "Research Project Plan" means the annual written research plan
for the conduct of a Research Project.

         1.37. "Research Technology License Agreement" means a license agreement
substantially in the form of Exhibit B hereto, entered into between the
Institute (and, if applicable, any IP Owning Consortium Members), as licensor(s)
and the Licensee Consortium Members, as licensees.

         (b)   Cross-Reference to Other Defined Terms. The following terms are
defined in the Sections of this Agreement set forth below:

<TABLE>
<CAPTION>
                Defined Term                                         Section
                ------------                                         -------
<S>                                                                  <C>
         Additional Field Program                                     4.4.1
         Announcements                                                12.16
         Annual Research Program Budget                               3.3.2
</TABLE>


                                       -6-


<PAGE>   11


<TABLE>
<S>                                                              <C>
         Cash Commitment                                         4.1
         Commercial Third Party Project                          4.4.2
         Confidential Information                                6.1
         Disclosing Party                                        6.1
         Effective Date                                          Introduction
         Excess Funding Amount                                   3.3.2
         Executive Officers                                      2.2.4
         Indemnitee                                              11.2.4
         Indemnitors                                             11.2.4
         Initial Product Technology Option Period                5.5
         Initial Research Technology Option Period               5.4
         Patent Administrator                                    5.7.1
         Patent Portfolio Administration                         5.7.1
         Product Technology License                              5.5
         Product Technology Option Extension Period              5.5
         Receiving Party                                         6.1
         Research Program Director Death/Disability Notice       3.2.2
         Research Program Director Termination Notice            3.2.2
         Research Technology License                             5.4
         Research Technology Option Extension Period             5.4
         Shortfall Amount                                        3.3.2
         Total Cash Commitments                                  4.1
</TABLE>

Article II.       THE CONSORTIUM

         2.1.     Consortium Members. As of the date of this Agreement, the sole
Consortium Members are the Initial Consortium Members. The Initial Consortium
Members agree to consider the advisability of including Additional Consortium
Members in the Consortium, in consultation with the Institute. The addition of
any such Additional Consortium Members to this Agreement shall require the
written approval of the Institute and all of the other then existing Consortium
Members. If a proposed Additional Consortium Member receives such approval, it
shall become a party to this Agreement by executing a counterpart hereof, which
counterpart shall include an appropriate amendment of Schedule III specifying
the funding commitment of such Additional Consortium Member for purposes of
Section 4.1, as well as a party to an amended version of the Consortium Member
Agreement.

         2.2.     Advisory Board.

                  2.2.1. Establishment of Advisory Board. The Institute and the
Consortium Members shall establish an Advisory Board consisting of the Institute
Director, the Research Program Director and two (2) representatives of each
Consortium Member. Each Consortium Member has designated the two (2)


                                       -7-


<PAGE>   12


representatives to serve on its behalf on the Advisory Board listed on Schedule
IV to this Agreement. Each Consortium Member may change any of its
representatives on the Advisory Board at any time upon notice to the Institute
and all other Consortium Members, provided that each Consortium Member agrees
that at all times at least one of its representatives on the Advisory Board
shall be a senior officer of such Consortium Member (it being understood that a
senior officer of BMS shall include senior officers of the Pharmaceutical
Research Institute of BMS). In addition, each Consortium Member, with the prior
approval of the Institute and all other Consortium Members, and the Institute,
with the prior approval of all Consortium Members, may invite non-voting
employees, consultants or scientific advisors to attend the meetings of the
Advisory Board (provided that any such attendees shall be bound by obligations
of confidentiality).

                  2.2.2. Advisory Board Responsibilities. The purpose of the
Advisory Board shall be to provide guidance to the Research Program Director and
the Institute relating to the overall strategic direction of the Research
Program and the allocation of resources among Research Projects within the
Research Program. The Advisory Board shall also discharge the various tasks and
functions assigned to it under this Agreement.

                  2.2.3. Meetings of the Advisory Board. The Advisory Board
shall meet no less frequently than once each calendar quarter, and shall meet at
such other times as may be deemed appropriate by the Advisory Board. Unless
otherwise determined by the Advisory Board, meetings of the Advisory Board shall
rotate among the Institute's facility in Cambridge, Massachusetts and locations
specified by each Consortium Member in turn, with the initial meeting to be held
at the Institute's facility.

                  2.2.4. Advisory Board Decisions. All decisions of the Advisory
Board shall require the approval of a Requisite Majority of the Advisory Board.
In the event that the approval of a Requisite Majority cannot be obtained on a
particular issue, the Advisory Board shall refer such issue to designated senior
management representatives of the Consortium Members (the "Executive Officers")
and the Institute Director for resolution. It is the intention of the parties
that any issue referred to the Executive Officers and the Institute Director
shall be resolved by negotiation in good faith as soon as practicable, but no
later than thirty (30) days after its referral. Such resolution, if any, of a
referred issue shall be final and binding on the Consortium Members and the
Institute. The parties shall make reasonable efforts to maintain the efforts of
the Research Program pending resolution of the unresolved issue.

         2.3.     Consortium Member Agreement.  In addition to being a party to
this Agreement, each Consortium Member shall, simultaneously with its becoming a
Consortium Member, become a party to the Consortium Member Agreement. The


                                       -8-


<PAGE>   13


Institute has been provided with a copy of the Consortium Member Agreement
redacted to exclude financial terms and other confidential matters, and shall be
provided with a similarly redacted copy of all amendments thereto. The
Consortium Member Agreement shall govern the relations of the Consortium Members
among themselves relating to the Research Program, including with respect to
such matters as the distribution of Program Know-How, Program Materials, Program
Copyrights, Program Patent Rights and/or Background Know-How among such Licensee
Consortium Members. To the extent that the provisions of this Agreement refer to
determinations made pursuant to the Consortium Member Agreement, or otherwise
require the Institute to take certain actions based upon the terms or provisions
of the Consortium Member Agreement, the Consortium Members shall advise the
Institute in writing concerning any such determinations, terms or provisions.

Article III.      THE RESEARCH PROGRAM

         3.1.     General. Subject to renewal as provided in Section 9.7, the
Research Program will consist of five Annual Research Programs, one Annual
Research Program for each Contract Year during the term of this Agreement. The
Research Program, including each Research Project encompassed therein, will be
conducted under the general supervision and direction of the Research Program
Director.

         3.2.     Research Program Director.

                  3.2.1. Commitment of Research Program Director. The Research
Program Director will be Dr. Eric Lander. The Institute agrees that the
management of the Research Program will be a major focus of the energies,
activities and time of the Research Program Director, it being understood by the
Institute and Dr. Lander that the active participation of Dr. Lander in the
management of the Research Program is a material factor in the determination by
the Consortium Members to participate in and fund the Research Program. However,
the Consortium Members recognize that Dr. Lander has, and will continue to have,
other important responsibilities, including (a) as Director of the Whitehead
Center for Genome Research (where Dr. Lander is responsible for the effort to
map and sequence human and mouse genomes under the sponsorship of the National
Institutes of Health and the Department of Energy), which will continue to be a
major focus of Dr. Lander's energies, activities and time; (b) as a laboratory
head at the Institute (where Dr. Lander has responsibilities to oversee student
and postdoctoral research and administrative responsibilities); and (c) as a
Professor at the Massachusetts Institute of Technology (where Dr. Lander has
teaching responsibilities). In the event that any Consortium Member believes
that the Research Program Director is not fulfilling the commitment to the
Research Program set forth above, it shall provide a written notice to the
Institute and all other Consortium Members setting forth its concerns and
requesting that a meeting of the Advisory Board be held to discuss the matter.
Such Advisory Board meeting shall be held on a mutually agreeable date and at a


                                       -9-


<PAGE>   14


mutually agreeable location within (30) days after the date of such notice. The
purpose of such meeting shall be to review the concerns set forth in the notice
and seek to reach agreement on a mutually acceptable course of action to address
such concerns. If any Consortium Member, following such Advisory Board meeting,
believes that the Research Program Director has not fulfilled the commitment set
forth above and is not satisfied with the results of the Advisory Board meeting,
such Consortium Member shall have the right to submit a notice of material
breach to the Institute pursuant to Section 9.2 of this Agreement (subject to
the Institute's rights to remedy such breach pursuant to the provisions of
Section 9.2).

                  3.2.2. Research Program Director Termination. In the event
that the Research Program Director notifies the Institute that he does not
intend to continue serving as the Research Program Director, or the Institute
determines to terminate the employment of the Research Program Director or to
remove him from his role as Research Program Director, the Institute shall
provide written notice of such event within seven (7) days after receipt or
determination thereof to all Consortium Members (a "Research Program Director
Termination Notice"). In the event that the Research Program Director dies or
becomes disabled for a period in excess of sixty (60) days to the extent that he
is incapable of fulfilling his commitment to serve as Research Program Director,
the Institute shall provide written notice of such event to all Consortium
Members promptly following the occurrence thereof (a "Research Program Director
Death/Disability Notice"). Promptly following the receipt of a Research Program
Director Termination Notice or Research Program Director Death/Disability
Notice, the Institute and the Consortium Members shall confer concerning the
feasibility of appointing a successor Research Program Director, and the
Consortium Members shall consider in good faith proposals in this regard made by
the Institute, and the Institute shall consider in good faith proposals in this
regard made by any Consortium Member. Following consultation with the Consortium
Members, the Institute may appoint a new Research Program Director and shall
notify all Consortium Members of such appointment. Notwithstanding the
foregoing, each Consortium Member shall have the right to withdraw as a
Consortium Member by providing notice to the Institute and all other Consortium
Members within sixty (60) days after receipt of a Research Program Director
Termination Notice or a Research Program Director Death/Disability Notice. If a
Consortium Member elects to withdraw as a Consortium Member pursuant to this
Section 3.2.2 (irrespective of whether the Institute has appointed a new
Research Program Director), such Consortium Member shall continue to support the
then current Annual Research Program at the levels (in terms of cash and, in the
case of AFFX, AFFX Materials, subject to Section 8.3.2(e)) set forth in the
applicable Annual Research Program Budget (at the times and in the manner set
forth in Section 4.2) for the period ending nine (9) months after the date of
the applicable Research Program Director Termination Notice or Research Program
Director Death/Disability Notice. In the event that all Consortium Members elect
to withdraw pursuant to this Section 3.2.2, the Institute shall expeditiously
seek to shut down the Research Program and each


                                      -10-


<PAGE>   15


Consortium Member shall be obligated to continue to fund the lesser of such shut
down costs or the funding for such nine (9) month period at the levels set forth
in the applicable Annual Research Program Plan (it being agreed that (a) funding
in the case of a shut down of the Research Program shall consist primarily of
cash, and (b) the period during which the Institute may actually disburse such
funds may extend for a twelve (12) month period, and the rights of Licensee
Consortium Members shall apply to Program Know-How, Program Copyrights, Program
Materials and Program Patent Rights discovered, developed, conceived and/or
reduced to practice during such disbursement period). If the continued support
or funding obligation of a Consortium Member upon a withdrawal pursuant to this
Section 3.2.2 above would extend beyond the conclusion of an Annual Research
Program, such support or funding obligation shall continue for the remainder of
the continued support or funding period with respect to the following Annual
Research Program, provided that the amount of such support or funding obligation
shall not exceed the amount that would have been applicable for such period of
time under the prior Annual Research Program.

                  3.2.3. New Research Program Director. If at least one
Consortium Member does not elect to withdraw as a Consortium Member pursuant to
Section 3.2.2, the Institute shall as expeditiously as possible appoint a new
Research Program Director. Each Consortium Member shall have the right to
withdraw as a Consortium Member by providing notice to the Institute and all
other Consortium Members within sixty (60) days after the date that the
Consortium Members have received notice from the Institute of the appointment of
such new Research Program Director. If a Consortium Member elects to withdraw as
a Consortium Member pursuant to this Section 3.2.3, such Consortium Member shall
continue to support the then current Annual Research Program at the levels (in
terms of cash and, in the case of AFFX, AFFX Materials, subject to Section
8.3.2(e)) set forth in the applicable Annual Research Program Budget (at the
times and in the manner set forth in Section 4.2) for the period ending six (6)
months after the date that such Consortium Member provides notice of withdrawal
pursuant to this subsection. In the event that all then remaining Consortium
Members elect to withdraw pursuant to this subsection, the Institute shall
expeditiously seek to shut down the Research Program and each Consortium Member
shall be obligated to continue to fund the lesser of such shut down costs or the
funding for such six (6) month period at the levels set forth in the applicable
Annual Research Program Plan (it being agreed that (a) funding in the case of a
shut down of the Research Program shall consist primarily of cash, and (b) the
period during which the Institute may actually disburse such funds may extend
for a twelve (12) month period after the date of notice of withdrawal, and the
rights of Licensee Consortium Members shall apply to Program Know-How, Program
Copyrights, Program Materials and Program Patent Rights discovered, developed,
conceived and/or reduced to practice during such disbursement period). If the
continued support or funding obligation of a Consortium Member upon a withdrawal
pursuant to this Section 3.2.3 would extend beyond the conclusion of an


                                      -11-


<PAGE>   16


Annual Research Program, such support or funding obligation shall continue for
the remainder of the continued funding period with respect to the following
Annual Research Program, provided that the amount of such support or funding
obligation shall not exceed the amount that would have been applicable for such
period of time under the prior Annual Research Program.

         3.3.     Annual Research Program Plans.

                  3.3.1. General. The Annual Research Program Plan, encompassing
specific Research Project Plans, for each Annual Research Program shall be as
proposed by the Research Program Director in consultation with the Advisory
Board. Except as provided below with respect to the Annual Research Program Plan
for the first Contract Year, each Annual Research Program Plan shall be approved
by a Requisite Majority of the Advisory Board at least thirty (30) days prior to
the commencement of the relevant Contract Year. The Annual Research Program Plan
for the first Contract Year shall be approved by the Institute and each
Consortium Member on the Effective Date. Each Annual Research Program Plan shall
be subject to amendment from time to time by the approval of a Requisite
Majority of the Advisory Board. At such time as each Annual Research Program
Plan (other than the Annual Research Program Plan for the first Contract Year)
is approved as provided in this Section 3.3.1, such Annual Research Program Plan
shall be initialled by the Research Program Director and an authorized
representative of each Consortium Member. Each Annual Research Program Plan
shall describe in reasonable detail the work to be undertaken by the Institute
pursuant thereto, including the staffing for and goals and timetable of the
specific Research Projects to be undertaken as part of the Annual Research
Program.

                  3.3.2. Annual Research Program Budget. Each Annual Research
Program Plan shall include a budget for the estimated direct expenses to be
incurred by the Institute in carrying out such Annual Research Program plus
indirect costs at the Institute's indirect cost rate approved by the United
States government (the "Annual Research Program Budget"). The direct expenses of
the Institute shall include without limitation any travel and other expenses
incurred by the Institute in fulfilling its obligations pursuant to Section
2.2.3 (Meetings of the Advisory Board) and Section 3.7 (Technology Transfer).
The indirect cost rate shall be applied to the direct expenses in the manner
approved by the United States government, which shall be disclosed by the
Institute to the Advisory Board. The Institute shall not incur financial
obligations with respect to the Research Program except as authorized under an
Annual Research Program Budget, or make long-term financial commitments not
authorized under an Annual Research Program Budget, without the prior approval
of a Requisite Majority of the Advisory Board. Each Annual Research Program
Budget (other than for the first Contract Year) shall include a reconciliation
of the funding provided pursuant to Article IV for the preceding Contract Year
versus the amount actually expended by the Institute in the Research Program
during the preceding


                                      -12-


<PAGE>   17


Contract Year. Any amount funded but not expended during the preceding Contract
Year shall be referred to as the "Shortfall Amount". All Shortfall Amounts shall
be carried forward and be available for use in the Research Program in
subsequent Contract Years, subject to Section 4.3. However, if the Shortfall
Amount exceeds twenty-five percent (25%) of the funding provided in the
preceding Contract Year (such excess referred to as the "Excess Funding
Amount"), the Consortium Members shall receive a credit in the amount of the
Excess Funding Amount in the Annual Research Program Budget for the Contract
Year following the Contract Year in which there exists an Excess Funding Amount,
such credit to be allocated among the Consortium Members in accordance with the
Consortium Member Agreement and reflected in an amendment to Schedule III.

                  3.3.3. Millennium Contributed Technology. Each Annual Research
Program Plan shall include a detailed description of the Millennium Contributed
Technology to be contributed to the Institute in connection with the Annual
Research Program.

                  3.3.4. AFFX Materials. Each Annual Research Program shall
include a detailed description of the expected requirements of the Institute for
AFFX Materials in connection with the Annual Research Program, broken down on a
quarterly basis.

                  3.3.5. Existing Research Agreement.

                         (a) The Institute and the Consortium Members agree that
the Research Program (as defined in the Existing Research Agreement) undertaken
by Millennium, the Institute and Dr. Thomas Hudson, as the principal
investigator, pursuant to the Existing Research Agreement shall constitute a
Research Project under this Agreement for the first Contract Year (and
thereafter if approved by the Advisory Board), and all research conducted
thereunder, and all results and findings therefrom, including any of the
foregoing that occurred prior to the Effective Date of this Agreement, shall be
deemed to be from the Research Program conducted under this Agreement. All
Program Materials (as defined in the Existing Research Agreement) shall be
deemed to be Program Materials under this Agreement, all Program Technology (as
defined in the Existing Research Agreement) shall be deemed to be Program
Know-How under this Agreement, and all Patent Rights (as defined in the Existing
Research Agreement) shall be deemed to be Program Patent Rights under this
Agreement.

                         (b) Millennium and the Institute agree that all
rights that Millennium has under the Existing Research Agreement shall be deemed
to be rights of the Consortium Members or the Advisory Board, as appropriate,
and, where applicable, any elections, options or other rights which are
exercisable by Millennium shall be exercisable by the Consortium Members,
including, without limitation, the following: (i) all data and information to be
provided to Millennium under the


                                      -13-


<PAGE>   18


Existing Research Agreement shall be provided to the Advisory Board, (ii) all
meetings at which Millennium has the right or obligation to attend shall be
attended by a designee of the Advisory Board, who shall confer and consult with
other members of the Advisory Board about the agendas and discussions at such
meetings, (iii) all decisions regarding the scope of, and funding for, the
Research Program under the Existing Research Agreement shall become part of the
Annual Research Program Budget review and approval procedure under this
Agreement, (iv) the license and option granted to Millennium for the Program
Technology and the Patent Rights, respectively, under the Existing Research
Agreement are terminated, and each of the Licensee Consortium Members shall have
the rights with respect to such Program Technology and Patent Rights as the
Consortium Members have with respect to Program Know-How and Program Patent
Rights under this Agreement, (v) any rights or obligations of Millennium with
respect to patent filing, prosecution or maintenance of Patent Rights under the
Existing Research Agreement shall be terminated, and such rights and obligations
shall be governed by the terms of this Agreement applicable to Program Patent
Rights, (vi) Millennium's option with respect to New Opportunities (as defined
in the Existing Research Agreement) shall be terminated and such New
Opportunities shall be presented to the Advisory Board for consideration as part
of the Research Program, (vii) all rights of Millennium with respect to Program
Materials under the Existing Research Agreement shall be deemed to be granted to
each Consortium Member, (viii) all rights of Millennium with respect to review
and comment of proposed publications under the Existing Research Agreement shall
be terminated, and such rights shall be governed by the terms of Article VII of
this Agreement, (ix) any rights Millennium has to terminate the Existing
Research Agreement may only be exercised by the unanimous consent of the
Consortium Members, (x) any funds which may be required to be returned to
Millennium under the Existing Research Agreement shall be paid, instead, to the
Consortium Members, pro rata, in accordance with their Applicable Contribution
Percentage (as defined in the Consortium Member Agreement), (xi) each of the
benefits and protections granted by the Institute to Millennium under Sections
6.3 (with respect to collaborations), VII (with respect to confidentiality
obligations), X (with respect to representations and warranties made by the
Institute), and XI (with respect to release from liability and indemnification
by the Institute) shall be terminated, and such benefits and protections shall
be governed by the applicable provisions of this Agreement, and (xii) all
notices given by either the Institute or Millennium pursuant to the Existing
Research Agreement shall also be given to each of BMS and AFFX at their
respective addresses as set forth in this Agreement.

                           (c) The Institute and Millennium agree to execute
such amendments, assignments or other documents relating to the Existing
Research Agreement as may be required to effectuate this Section 3.3.5;
provided, however, that they shall not modify, amend or terminate the Existing
Research Agreement without the prior written consent of BMS and AFFX.


                                      -14-


<PAGE>   19


         3.4.     Records. The Institute shall use reasonable efforts to
maintain records, in sufficient detail and in good scientific manner, which
shall be complete and accurate and shall fully and properly reflect all work
done and results achieved in the performance of each Research Project (including
all data in the form required under all applicable laws and regulations). It is
understood that such records shall include detailed, witnessed laboratory
notebooks sufficient to document any patentable inventions made in the course of
such Research Project. Upon request by the Advisory Board or a Consortium
Member, the Institute will provide copies of all such materials to the Advisory
Board or a Consortium Member, as the case may be (e.g., in order to assist the
appropriate Consortium Members in the preparation of patent applications related
to such inventions pursuant to Section 5.7.2).

         3.5.     Meetings. Joint scientific meetings between appropriate
representatives of the Institute (including the Research Program Director) and
the Consortium Members, shall occur on a regular basis during the course of each
Research Project to discuss the results generated under the Research Project and
to consider modifications to the Research Project based upon such results. Such
meetings shall occur at least on a quarterly basis in person or by
teleconference, as agreed by the Institute and the Consortium Members. The
Institute agrees to provide to the Advisory Board copies of any written
materials prepared or used by the Institute's representatives in connection with
such joint scientific meetings.

         3.6.     Reports.

                  3.6.1. Research Project Reports. The Institute shall promptly
disclose data and information obtained under each Research Project to the
Advisory Board. To the extent reasonably available, such disclosure will include
documentation necessary or useful in the development, manufacture or sale of
products or services based upon inventions or technology developed in the
Research Project. As part of the regular quarterly meetings described in Section
3.5, the Institute shall submit a written technical report to the Advisory Board
summarizing all activities under each Research Project, including without
limitation the number of scientists and other staff who worked on each Research
Project, and the research results and know-how obtained during the just-ended
quarter in connection with such Research Project. The Institute shall also
submit to the Advisory Board a comprehensive final report within ninety (90)
days after termination or expiration of each Research Project.

                  3.6.2. Quarterly Reports. Within thirty (30) days after the
end of each three (3) month period during each Contract Year, the Institute
shall submit to the Advisory Board a reporting of expenses incurred through the
end of such quarter in the Research Program (including a breakdown for each
Research Project). Within sixty (60) days after the end of each Contract Year,
the Institute shall submit to the Advisory Board a final report which will
include a detailed reporting of expenses


                                      -15-


<PAGE>   20


incurred in the Research Program. To the extent applicable, such expense reports
shall comply with GAAP.

         3.7.     Technology Transfer. The Advisory Board shall establish
guidelines and procedures for the transfer of Background Know-How, Program
Know-How and Program Materials from the Institute to the Licensee Consortium
Members in order to ensure a prompt and continuous flow of technical information
from the Institute to the Licensee Consortium Members. Such guidelines and
procedures shall, at a minimum, include (a) delivery and periodic updating of
software programs, (b) access to hardware systems, and (c) technical assistance
rendered by employees of the Institute to Licensee Consortium Members in
utilizing and implementing transferred technology. The Institute agrees to
transfer the Background Know-How, Program Know-How and Program Materials
following such guidelines and procedures and to provide training to employees
and consultants of the Consortium Members at its facility located in Cambridge,
Massachusetts or at such other facility as approved by a Requisite Majority of
the Advisory Board to enable such technology transfer.

         3.8.     Research Program Administrator. The Institute shall retain a
research program administrator selected by the Research Program Director and
acceptable to a Requisite Majority of the Advisory Board, for the purposes of
(a) facilitating effective communication among the Research Program Director,
the Institute and the Consortium Members, (b) assisting in the scheduling of
Advisory Board meetings and joint scientific meetings pursuant to Section 3.5,
(c) coordination with the Patent Administrator (as defined in Section 5.7.1) and
the Consortium Members relating to intellectual property matters consistent with
Article V, and (d) undertaking such other administrative responsibilities as
shall be assigned by the Research Program Director or the Advisory Board. All
expenses relating to the research program administrator shall be included in the
budget for each Annual Research Program.

         3.9.     Conduct of the Research Program by the Institute.  Subject to
the funding of the Research Program in accordance with the provisions of Article
IV, during the term of this Agreement, the Institute shall:

                  3.9.1. Use all reasonable efforts and proceed diligently to
perform the Research Program, including the Research Projects, as set forth in
the Annual Research Program Plans and Research Project Plans, including, without
limitation, by using its good faith efforts to allocate a sufficient number of
Institute scientists per year, using personnel with sufficient skills and
experience, together with sufficient equipment and facilities, to carry out its
obligations under the Research Program, including the Research Projects, and to
accomplish the objectives of the Research Program, including the Research
Projects;

                  3.9.2.   Conduct the Research Program, including the Research
Projects, in good scientific manner, and in compliance in all material respects
with all


                                      -16-


<PAGE>   21


requirements of applicable laws, rules and regulations, and all other
requirements of any applicable good laboratory practices to attempt to achieve
its objectives efficiently and expeditiously;

                  3.9.3. Subject to the provisions of Section 5.8.1, furnish
each Consortium Member with Program Materials, as the Consortium Members from
time to time shall reasonably request, in accordance with the procedures set
forth in Section 3.7;

                  3.9.4. Promptly provide an Invention Notice to each Consortium
Member with respect to any Program Patent Rights;

                  3.9.5. Allow representatives of each of the Consortium
Members, upon reasonable notice and during normal business hours, to visit the
facilities where the Research Program or any Research Project is being
conducted, and consult informally, during such visits and by telephone, with the
Institute personnel performing work on the Research Program or such Research
Project;

                  3.9.6. Maintain liability insurance with respect to the work
it is performing under the Research Program in such amounts as it customarily
maintains with respect to similar research programs, which insurance shall
designate each Consortium Member as an "insured", and to pay the premiums due
thereunder. Each Consortium Member shall receive a certificate indicating
coverage as an insured and the amount of such coverage; and

                  3.9.7. Apply all research funds received from the Consortium
Members pursuant to this Agreement to fund the Research Program, carry out its
obligations in connection therewith and accomplish the goals and objectives of
the Research Program as determined by the Advisory Board.


Article IV.       RESEARCH PROGRAM FUNDING, THIRD PARTY ACTIVITIES AND
                  TECHNOLOGY CONTRIBUTIONS

         4.1.     Consortium Members' Commitments.

                  4.1.1. Cash Commitments. The maximum cash commitment of each
Consortium Member to fund each Annual Research Program is as set forth opposite
such Consortium Member's name on Schedule III hereto. Schedule III also sets
forth the cash commitment of each Consortium Member to fund the Annual Research
Program for the first Contract Year, and shall be amended for each subsequent
Contract Year to reflect the Annual Research Program Budget for such Contract
Year and the allocation of the resulting cash commitment among the Consortium
Members in accordance with the terms of the Consortium Member Agreement (the
cash commitment for each Contract Year being referred to as each Consortium
Member's


                                      -17-


<PAGE>   22


"Cash Commitment" and, collectively, as the "Total Cash Commitments"). All
funding shall be provided by check or by wire transfer, except as otherwise
agreed by the Institute and all of the Consortium Members and as outlined in
Schedule III. Notwithstanding anything in this Agreement to the contrary, each
Consortium Member shall be severally (and not jointly) liable for its funding
commitment pursuant to this Agreement.

                  4.1.2. AFFX Materials. AFFX hereby agrees to supply to the
Institute the AFFX Materials set forth in each Annual Research Program Plan at
the times specified therein.

         4.2.     Funding Mechanics. On or before the first day of each calendar
quarter during each Contract Year (other than the first Contract Year), each
Consortium Member shall pay to the Institute, by check or wire transfer, an
amount equal to twenty five percent (25%) of the Cash Commitment of such
Consortium Member for such Contract Year. With respect to the first Contract
Year, each Consortium Member shall pay to the Institute the amounts set forth on
Schedule III within ten (10) days after the Effective Date, and thereafter
during such first Contract Year shall make the quarterly payments set forth in
the preceding sentence on the first day of October, January and April. In the
event that during any Contract Year the Advisory Board approves a modification
to the Annual Research Program Budget for such Contract Year, the payments to be
made during the remainder of the Contract Year shall be appropriately adjusted.

         4.3.     Financial Records. The Institute shall maintain funds with
respect to each Research Project in a separate account and shall expend such
funds for wages, supplies and other operating expenses incurred in the
performance of such Research Project. The Institute shall keep and maintain
adequate books and records (in compliance with GAAP, to the extent applicable)
so as to be able to furnish complete and accurate information to the Advisory
Board regarding funds provided for the conduct of Research Projects, including
the quarterly reports provided pursuant to Section 3.6.2. Representatives of
each Consortium Member shall be permitted to examine such books and records
during normal business hours and upon reasonable prior written notice to the
Institute. It is understood that funds which are not used or otherwise committed
prior to the completion or termination of a Research Project shall be retained
by the Institute and shall be utilized by the Institute for future expenditures
for other Research Projects. Upon the completion or termination of the Research
Program, any funds which have not previously been used or otherwise committed
shall be returned by the Institute to the appropriate Consortium Members within
sixty (60) days after such completion or termination in accordance with the
terms of the Consortium Member Agreement.

         4.4.     Third Party Activities.


                                      -18-


<PAGE>   23


                  4.4.1.   Non-Commercial Activities.

                           (a) The Institute and the Consortium Members
acknowledge that receipt of funding support from governmental or non-commercial
sources could be beneficial to the conduct of the Research Program. The
Institute may seek to obtain funding from governmental or non-commercial sources
for research projects in the Field in consultation with the Advisory Board,
provided that the Institute shall not be obligated to do so. With respect to
research projects in the Field that are not part of the Research Program but are
to be conducted by Institute personnel who are participants in the Research
Program (including, but not limited to, the Research Program Director), the
Institute agrees (i) to inform and consult with the Advisory Board prior to
undertaking any research projects in the Field which involve governmental or
non-commercial sources of funding, and to formally designate any such research
project in the Field as an "Additional Field Program", (ii) not to undertake any
such Additional Field Program (other than projects funded through governmental
sources) unless the project and the terms thereof are approved by a Requisite
Majority of the Advisory Board, and (iii) to continue to report to the Advisory
Board on a quarterly basis concerning the status and results of any Additional
Field Program undertaken by the Institute. However, the Institute shall not use
or otherwise apply Program Know-How, Program Materials, Program Copyrights or
Program Patent Rights in any Additional Field Program unless all intellectual
property resulting or derived from the use or application in any such Additional
Field Program of Program Know-How, Program Materials, Program Copyrights or
Program Patent Rights are exclusively licensed to Consortium Members to the same
extent, and upon the same terms, as if such intellectual property rights
constituted Program Know-How, Program Materials, Program Copyrights and/or
Program Patent Rights. Notwithstanding the foregoing, the Consortium Members
acknowledge that intellectual property rights developed in connection with the
projects funded by the United States government may be subject to limited use
rights retained by the United States government.

                           (b) The Institute may (i) provide Program Know-How,
Program Materials and/or Program Copyrights to a non-commercial party for
purposes of conducting non-commercial research and collaborating with such
non-commercial party and (ii) use Program Know-How, Program Materials and/or
Program Copyrights for purposes of conducting non-commercial research with such
non-commercial party (it being understood that Program Materials do not include
AFFX Materials). Program Know-How, Program Materials and/or Program Copyrights
shall only be transferred by the Institute to such recipients who execute an
agreement substantially in the form of Exhibit D-1 or D-2 (as determined
pursuant to subsection (c)) attached hereto, provided that no substantive
changes shall be made with respect to provisions relating to Intellectual
Property (as such term is defined in Exhibit D-1) without the prior approval of
a Requisite Majority of the Advisory Board. The Institute shall promptly inform
the Advisory Board of any


                                      -19-


<PAGE>   24


Intellectual Property disclosed to it and shall take such actions with respect
thereto (including the exercise of an option to obtain a license thereto and the
negotiation of the terms thereof) as shall be determined by a Requisite Majority
of the Advisory Board. The Institute shall provide copies of agreements entered
into with recipients of Program Know-How, Program Materials and Program
Copyrights to the Advisory Board within fifteen days after execution thereof.
The Institute shall retain the right to use internally Program Know-How, Program
Materials, Program Copyrights and Program Patent Rights solely for purposes of
conducting non-commercial research.

                           (c) Attached as Exhibits D-1 and D-2 are alternative
forms of agreements to be used in connection with the transfer by the Institute
of Program Know-How, Program Materials and/or Program Copyrights pursuant to
subsection (b). Exhibit D-1 is intended for use in connection with the transfer
of significant Program Know-How, Program Materials and/or Program Copyrights,
while Exhibit D-2 is intended for use in connection with the transfer of less
significant Program Know-How, Program Materials and/or Program Copyrights. The
Advisory Board shall establish guidelines for determining the circumstances
under which the use of Exhibit D-1 is required, and the Institute agrees to
comply with such guidelines. In all other circumstances, the Institute may use
either Exhibit D-1 or Exhibit D-2.

                  4.4.2.   Commercial Activities.

                           (a) The Institute shall not perform services for, or
conduct collaborative research with, commercial third parties using (a) the
funds provided to the Institute pursuant to this Agreement, (b) Consortium
Member Contributions or Contributed Technology Upgrades licensed to the
Institute pursuant to this Agreement, or (c) Program Know-How, Program
Materials, Program Copyrights or Program Patent Rights. In addition to the
foregoing, if the Institute intends to undertake research projects in the Field
with commercial third parties (a "Commercial Third Party Project"), the
Institute shall provide notice to the Advisory Board of its intention to
undertake such Commercial Third Party Project and shall discuss with the
Advisory Board (i) in the event that Institute personnel (including Dr. Lander)
assigned to the Research Program are also expected to be participants in such
Commercial Third Party Project, the likelihood of potential subject matter
overlaps between the Research Program and the Commercial Third Party Project,
(ii) the risks that, notwithstanding the previous sentence, Program Know-How or
Program Materials may be used in such Commercial Third Party Project and the
Institute's plans for mitigating such risks, (iii) the impact of such Commercial
Third Party Project on the personnel resources of the Institute allocated to the
Research Program, and (iv) any other matters that might have an adverse impact
on the Research Program and/or the Institute's ability to perform the Research
Program. In addition, in the event that the Institute personnel assigned to any
Research Project are also expected to be participants in any Commercial Third
Party Project, the Institute shall, prior to engaging in such Commercial Third
Party Project, provide written notice to


                                      -20-


<PAGE>   25


the Consortium Members describing the proposed research project and the terms
(financial and otherwise) relating thereto, and, at the request of the
Consortium Members, shall enter into good faith negotiations with the Consortium
Members concerning the inclusion of such proposed research project in the
Research Program.

                           (b) The Institute shall not (i) distribute or
disclose, or knowingly allow to be distributed or disclosed, Program Know-How,
Program Materials and/or Program Copyrights to any third party commercial entity
or (ii) use Program Know-How, Program Materials and/or Program Copyrights in
research or consulting activities with any third party commercial entity.

                  4.4.3.   Withdrawal Rights. In the event that the Institute
either (a) undertakes an Additional Field Program pursuant to Section 4.4.1
funded through governmental sources, or (b) undertakes a Commercial Third Party
Project with a commercial third party pursuant to Section 4.4.2 in which
Institute personnel (including Dr. Lander) assigned to the Research Program are
also expected to be participants, each Consortium Member shall have the right to
withdraw as a Consortium Member in the event that it believes in good faith that
the undertaking by the Institute of any such Additional Field Program or
Commercial Third Party Project would be materially detrimental to the Research
Program. Any Consortium Member electing to withdraw pursuant to this Section
4.4.3 shall provide notice of withdrawal to the Institute and all other
Consortium Members within sixty (60) days after the designation of the
applicable Additional Field Program or the notification to the Advisory Board of
such Commercial Third Party Project, as applicable. If a Consortium Member
elects to withdraw as a Consortium Member pursuant to this Section 4.4.3, such
Consortium Member shall continue to support the then current Annual Research
Program at the levels (in terms of cash and, in the case of AFFX, AFFX
Materials, subject to Section 8.3.2(e)) set forth in the applicable Annual
Research Program Budget (at the times and in the manner set forth in Section
4.2) for the period ending six (6) months after the date that such Consortium
Member provides notice of withdrawal pursuant to this Section 4.4.3, provided
that in the event that all Consortium Members elect to withdraw pursuant to this
Section 4.4.3, the Institute shall expeditiously seek to shut down the Research
Program and each Consortium Member shall be obligated to continue to fund the
lesser of such shut down costs or the funding for such six (6) month period at
the levels set forth in the applicable Annual Research Program Budget (it being
agreed that (a) funding in the case of a shut down of the Research Program shall
consist primarily of cash, and (b) the period during which the Institute may
actually disburse such funds may extend for a twelve (12) month period after the
date of notice of withdrawal, and the rights of Licensee Consortium Members
shall apply to Program Know-How, Program Copyrights, Program Materials and
Program Patent Rights discovered, developed, conceived and/or reduced to
practice during such disbursement period). If the continued support or funding
obligation of a Consortium Member upon a withdrawal pursuant to this Section
4.4.3 would extend beyond the conclusion of an


                                      -21-


<PAGE>   26


Annual Research Program, such support or funding obligation shall continue for
the remainder of the continued support or funding period with respect to the
following Annual Research Program, provided that the amount of such support or
funding obligation shall not exceed the amount that would have been applicable
for such period of time under the prior Annual Research Program.

         4.5.     Consortium Member License Grants and Technology Transfer.

                  4.5.1. Millennium License Grant. Millennium hereby grants to
the Institute and each Consortium Member other than Millennium a worldwide,
paid-up, non-exclusive right and license, without the right to grant
sublicenses, to use the Millennium Contributed Technology only in the course of
the Research Program. Except as specifically provided herein, no rights to
Millennium Contributed Technology are being licensed or otherwise conveyed to
the Institute or Consortium Members other than Millennium.

                  4.5.2. AFFX License Grant. AFFX hereby grants to the Institute
and each Consortium Member other than AFFX a worldwide, paid-up non-exclusive
right and license, without the right to grant sublicenses, to use the AFFX
Materials only in the course of the Research Program. Except as specifically
provided herein, no rights to AFFX Materials are being licensed or otherwise
conveyed to the Institute or Consortium Members other than AFFX.

                  4.5.3. Technology Transfer. AFFX shall transfer to the
Institute the AFFX Materials, as specified in each Annual Research Program Plan.
Millennium shall transfer to the Institute the tangible manifestations of the
Millennium Contributed Technology, as specified in each Annual Research Program
Plan.

Article V     INTELLECTUAL PROPERTY RIGHTS

         5.1. Background Know-How. The Institute hereby grants to the Licensee
Consortium Members a perpetual, non-exclusive, worldwide, paid-up right and
license in the License Field, with a right to grant sublicenses, under
Background Know-How (i) to make, have made, import, distribute, use, offer for
sale and sell products, (ii) to use, practice, offer for sale and sell methods,
and (iii) to otherwise exploit Background Know-How. The rights in the Background
Know-How will be used by the Licensee Consortium Members only pursuant to, and
are subject to the limitations set forth in, the Consortium Member Agreement.

         5.2. Program Know-How, Program Materials and Program Copyrights.
Subject to the provisions of Section 5.6, the Institute and each IP Owning
Consortium Member hereby grant to the applicable Licensee Consortium Member(s) a
perpetual, exclusive, worldwide, paid-up right and license in the License Field,
with a right to grant sublicenses, under Program Know-How, Program Materials and
Program


                                      -22-


<PAGE>   27


Copyrights (i) to make, have made, import, distribute, use, offer for sale and
sell products, (ii) to use, practice, offer for sale and sell methods, and (iii)
to otherwise exploit Program Know-How, Program Materials and Program Copyrights,
provided that access to tangible manifestations of Program Materials shall be
subject to the limitations set forth in Section 5.8.1. The rights in the Program
Know-How, Program Materials and Program Copyrights will be used by the
Consortium Members only pursuant to, and are subject to the limitations set
forth in, the Consortium Member Agreement.

         5.3.     Ownership of Intellectual Property Rights.

                  5.3.1. Any and all (i) patents and patent applications
covering inventions conceived and reduced to practice, and (ii) copyrights in
any written, oral, visual or multimedia materials created solely by one or more
employees or contractors of one or more Consortium Members (but not an Institute
employee or contractor) in the course of the Research Program shall be the
property of and shall be owned by such Consortium Member(s), subject to the
rights granted to applicable Licensee Consortium Member(s) under this Agreement.
Such Consortium Member(s) shall be deemed to be (an) IP Owning Consortium
Member(s) with respect to such invention or copyright and shall promptly
disclose to the Advisory Board each such invention or copyright in writing (such
disclosures to be provided on at least a quarterly basis).

                  5.3.2. Any and all (i) patents and patent applications
covering inventions conceived or reduced to practice, and (ii) copyrights in any
written, oral, visual or multimedia materials created solely by one or more
employees or contractors of the Institute in the course of the Research Program
shall be the property of and shall be owned by the Institute, subject to the
rights granted to applicable Licensee Consortium Member(s) under this Agreement.
Institute shall promptly disclose to the Advisory Board each such invention or
copyright in writing (such disclosures to be provided on at least a quarterly
basis).

                  5.3.3. Any and all (i) patents and patent applications
covering inventions conceived and/or reduced to practice, and (ii) copyrights in
any written, oral, visual or multimedia materials created jointly by one or more
employees or contractors of the Institute and one or more employees or
contractors of one or more Consortium Members in the course of the Research
Program shall be the property of and shall be owned by the Institute and the
applicable IP Owning Consortium Members jointly, subject to the rights granted
to the applicable Licensee Consortium Member(s) by the Institute and any
applicable IP Owning Consortium Member under this Agreement. The Institute (and
any applicable IP Owning Consortium Member) shall promptly disclose to the
Advisory Board each such invention or copyright in writing (such disclosures to
be provided on at least a quarterly basis).


                                      -23-


<PAGE>   28


         5.4. Research Technology License Option. The Institute and each IP
Owning Consortium Member hereby grant to the applicable Licensee Consortium
Member(s) an option (exercisable on a Program Patent Right-by-Program Patent
Right basis) to obtain a co-exclusive (with the Institute (including any third
party to which the Institute has granted a license pursuant to the provisions of
Section 5.6 of this Agreement) and each other Consortium Member), worldwide,
paid-up right and license in the License Field, with a right to grant
sublicenses as provided below, under the Program Patent Rights: (i) to make,
have made and use products, (ii) to use and practice methods and (iii) to
otherwise exploit the Program Patent Rights, in all cases subject to the
limitation that the right and license granted under this Section 5.4 shall not
extend to the commercial sale of products or the commercial performance of
services (a "Research Technology License"). Such Research Technology License may
be sublicensed by a Licensee Consortium Member in the context of academic or
non-commercial relationships or to a commercial entity with which the Licensee
Consortium Member is conducting collaborative research activities only for use
in connection with such collaborative research activities. The rights in the
Program Patent Rights will be used by the Consortium Members only pursuant to,
and are subject to the limitations set forth in, the Consortium Member
Agreement. Each option to obtain a Research Technology License granted to the
applicable Licensee Consortium Member(s) pursuant to this Section shall extend
for a period of one hundred twenty (120) days after the date of receipt by the
applicable Licensee Consortium Member(s) of an Invention Notice (which Invention
Notice shall specifically indicate that such 120-day period commences upon such
receipt) (the "Initial Research Technology Option Period"). The Initial Research
Technology Option Period may be extended, at the election of one or more License
Consortium Members, by providing written notice to the Institute and all other
Consortium Members, prior to the expiration of the Initial Research Technology
Option Period, in which event the period during which the option may be
exercised shall be extended until such time, if ever, as the Institute grants a
license to a third party with respect to the applicable Program Patent Rights
pursuant to Section 5.6 (the "Research Technology Option Extension Period"),
provided that during the Research Technology Option Extension Period, the
Licensee Consortium Member(s) electing to extend the option period shall
reimburse the Institute for its reasonable out-of-pocket expenses incurred in
connection with the prosecution and maintenance of the applicable Program Patent
Rights, such reimbursement to be contributed to equally among all Licensee
Consortium Members electing to extend the option period and all Licensee
Consortium Members that have exercised such option during the Initial Research
Technology Option Period. Promptly following the exercise of the option granted
pursuant to this Section, the Institute, each IP Owning Consortium Member (if
any) and the applicable Licensee Consortium Member(s) shall execute and deliver
a Research Technology License Agreement covering the applicable Program Patent
Rights.


                                      -24-


<PAGE>   29


         5.5. Product Technology License Option. The Institute and each IP
Owning Consortium Member hereby grant to the applicable Licensee Consortium
Member(s) an option (exercisable on a Program Patent Right-by-Program Patent
Right basis) to obtain an exclusive, worldwide right and license in the License
Field, with a right to grant sublicenses, under the Program Patent Rights (and,
if applicable, Background Patent Rights): (i) to make, have made, use, offer for
sale, sell, import and distribute products, (ii) to use, practice, offer for
sale and sell methods, and (iii) to otherwise exploit the Program Patent Rights
(a "Product Technology License"). The rights in the Program Patent Rights will
be used by the Consortium Members only pursuant to, and are subject to the
limitations set forth in, the Consortium Member Agreement. The applicable
Licensee Consortium Member(s) shall be obligated to pay royalties to the
Institute and the other Consortium Members to the extent provided in the
applicable Product Technology License Agreement (with respect to the Institute
and any IP Owning Consortium Member) and the Consortium Member Agreement (with
respect to the other Consortium Members). The option to obtain a Product
Technology License granted to Licensee Consortium Members pursuant to this
Section may be exercised at any time from receipt by the applicable Licensee
Consortium Member(s) of an Invention Notice as to the particular Program Patent
Rights until one hundred fifty (150) days after receipt of such Invention Notice
(which Invention Notice shall specifically indicate that such 150-day period
commences upon such receipt) (the "Initial Product Technology Option Period").
The Initial Product Technology Option Period may be extended, at the election of
one or more Licensee Consortium Members, by providing written notice to the
Institute and all other Consortium Members prior to the expiration of the
Initial Product Technology Option Period, in which event the period during which
the option may be exercised shall be extended until such time, if ever, as the
Institute grants a license to a third party with respect to the applicable
Program Patent Rights pursuant to Section 5.6 (the "Product Technology Option
Extension Period"), provided that during the Product Technology Option Extension
Period, the Licensee Consortium Member(s) electing to extend the option period
shall reimburse the Institute for its reasonable out-of-pocket expenses incurred
in connection with the prosecution and maintenance of the applicable Program
Patent Rights, such reimbursement to be contributed to equally among all
Licensee Consortium Members electing to extend the option period and all
Licensee Consortium Members that have exercised such option during the Initial
Product Technology Option Period. Promptly following the exercise of the option
granted pursuant to this Section, the Institute and the applicable Licensee
Consortium Member(s) shall seek to agree upon the applicable royalty (which
royalty shall in any event be within the range specified on Schedule V hereto
and shall be split between the Institute and the applicable IP Owning Consortium
Member(s) in such manner as shall be determined by them in good faith based upon
the standards set forth in Schedule V and specified in the applicable Product
Technology License Agreement). In the event that the parties are unable to agree
upon such royalty, the matter shall be resolved by arbitration in accordance
with Section 12.1. Upon determination of the applicable royalty (by agreement of
the


                                      -25-


<PAGE>   30


parties or arbitration), the Institute, each IP Owning Consortium Member (if
any) and the applicable Licensee Consortium Member(s) shall execute and deliver
a Product Technology License Agreement covering such Program Patent Rights for
the License Field, provided that the applicable Licensee Consortium Member(s)
shall have the right to revoke the exercise of the option in the event that the
royalty rate is determined by means of arbitration (in which event, for purposes
of this Section 5.5, such option shall not be considered to have been
exercised). In the event that there are one or more significant product
opportunities derived from the Program Patent Rights that fall outside of the
Core License Field, the applicable Licensee Consortium Member(s) and the
Institute agree to discuss in good faith reasonable diligence criteria (in
addition to the provisions set forth in Exhibit A attached hereto) only with
respect to such product opportunities outside of the Core License Field, which
criteria may include mutually agreed upon minimum royalties.

         5.6.     Institute Rights.

                           (a) In the event that no Licensee Consortium Member
exercises the option with respect to any Program Patent Rights pursuant to
Section 5.4 during the Initial Research Technology Option Period or pursuant to
Section 5.5 during the Initial Product Technology Option Period, the Institute
may negotiate a license under its rights to such Program Patent Rights (and any
directly related Program Know-How, Program Materials and/or Program Copyrights)
with any third party, provided that the Institute shall not grant any such
license until the expiration of a thirty (30) day period commencing on the date
on which the Licensee Consortium Member(s) receive written notice from the
Institute stating the Institute's intention to grant a license to the applicable
Program Patent Rights (and any directly related Program Know-How, Program
Materials and/or Program Copyrights) and describing in such notice the
applicable terms of such license (during which 30-day period each Licensee
Consortium Member electing to extend the option period under Section 5.4 and/or
5.5 shall have the right to exercise the option to obtain a Research Technology
License or a Product Technology License). If the terms the Institute proposes to
offer to a third party would be more favorable to the third party than either
(x) the terms set forth in the form of Product Technology License Agreement
(including the applicable royalty range), or (y) in the event that a Licensee
Consortium Member has exercised the Product Technology License option but has
not reached agreement with the Institute with respect to royalties or has
revoked the exercise of the option based on a royalty rate determined by
arbitration, the most favorable terms (from the perspective of the Licensee
Consortium Member) offered by the Institute or by the arbitrators, then the
Institute must first offer in writing such more favorable terms to the
applicable Licensee Consortium Members, and such Licensee Consortium Member(s)
will have thirty (30) days to accept or reject such offer.


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<PAGE>   31


                  Confidential Materials omitted and filed separately with the
         Securities and Exchange commission. Asterisks denote such omission.


                           (b) All license fees, milestone payments and royalty
income derived by the Institute based on the licensing of Program Patent Rights
(and any directly related Program Know-How, Program Materials and/or Program
Copyrights) to third parties shall be divided as follows after deducting the
Institute's costs of licensing and enforcing such rights: (a) ********* to the
Institute, and (b) ***** ****** divided among the Consortium Members pursuant to
the terms of the Consortium Member Agreement. In the event that the Institute
grants a license pursuant to this Section 5.6 to any Program Know-How, Program
Materials and/or Program Copyrights, such license shall be non-exclusive, and
the licenses thereto to Licensee Consortium Members set forth in Section 5.2
shall remain exclusive except as to such license granted pursuant to this
Section 5.6.

         5.7.     Patent Filing, Prosecution and Maintenance.

                  5.7.1. Administration of Patent Portfolio. The Institute shall
designate an individual (the "Patent Administrator"), such individual to be
subject to the approval of a Requisite Majority of the Advisory Board, to be
responsible for Patent Portfolio Administration (as defined below). As used
herein, the term "Patent Portfolio Administration" means (a) the identification
of potentially patentable inventions in consultation with employees of and
contractors to the Institute; (b) communication of information regarding
potentially patentable inventions to designees of each Consortium Member and
patent counsel to the Institute; (c) coordination of discussions among
representatives of the Institute, each Consortium Member and Institute patent
counsel concerning the advisability of filing for patent protection on
potentially patentable inventions; (d) coordinating the preparation and filing
of appropriate patent applications, and providing copies thereof to Consortium
Members for comments prior to filing; (e) coordination of the preparation and
filing of corresponding foreign patent applications within required time
periods; (f) maintenance of databases concerning patent applications and patents
which indicate any critical dates for filings, responses, payments and other
patent-related actions (which databases shall, to the extent feasible, be
networked with Consortium Members in order to provide for access by Consortium
Members to such databases); (g) provision of Invention Notices to Consortium
Members, as well as notices concerning the commencement and expiration of the
option periods set forth in Sections 5.4 and 5.5; and (h) coordination of the
transition of responsibility for patent prosecution and maintenance with respect
to one or more Program Patent Rights from the Institute to the applicable
Licensee Consortium Member(s) pursuant to the provisions of Section 5.7.2.


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<PAGE>   32


                  5.7.2. Control by Licensee Consortium Members. Subject to the
rights of the applicable Licensee Consortium Member(s) set forth in this Section
5.7.2 and in any applicable Research Technology License Agreements and/or
Product Technology License Agreements, the Institute shall be responsible for
the filing and prosecution of patent applications, and the maintenance of
patents that may issue therefrom, within the Program Patent Rights. The
applicable Licensee Consortium Member(s) shall have the right, at their option
and expense, to control the filing and prosecution of patent applications, and
maintenance of patents that may issue therefrom, within the Program Patent
Rights. Such activities shall be conducted in the name of the owner of such
invention (as set forth in Section 5.3). The Institute and each IP Owning
Consortium Member shall cooperate with and provide assistance to the applicable
Licensee Consortium Member(s) in connection with such activities, including
without limitation execution of all documents, and performance of all acts
reasonably necessary, to prosecute such patent applications, and maintain,
enforce and defend such patents. Such Licensee Consortium Member(s) shall keep
the Institute and each IP Owning Consortium Member reasonably informed as to the
status of any patent application and any patent within the Program Patent
Rights. The applicable Licensee Consortium Member(s) shall provide the Institute
and each IP Owning Consortium Member copies of all correspondence concerning
patent prosecution in sufficient time prior to due dates to allow the parties
and their attorneys to review the correspondence and comment on the prosecution,
such comments to be reasonably considered. Copies of such correspondence being
forwarded to the Institute should also be sent to its patent attorney, Patricia
Granahan, Esq., Hamilton, Brook, Smith & Reynolds, Two Militia Drive, Lexington,
MA 02173, telephone (617) 861-6240, fax (617) 861-9540 or such other attorney as
may be designated by the Institute from time to time. Each Licensee Consortium
Member exercising its right to control filing, prosecution and maintenance of a
Program Patent Rights under this Section 5.7.2 shall provide such information to
the Patent Administrator in order to permit him or her to maintain the databases
referred to in Section 5.7.1.

                  5.7.3. Institute/IP Owning Consortium Member Rights. If the
applicable Licensee Consortium Member(s) exercise rights of control pursuant to
Section 5.7.2 but thereafter elect not to file or thereafter prosecute any
patent application within the Program Patent Rights, or elect not to pay any fee
required to maintain a patent within the Program Patent Rights, in any country,
such Licensee Consortium Member(s) shall promptly notify the Institute and each
IP Owning Consortium Member. In such event, the Institute and each IP Owning
Consortium Member, in its discretion and at its expense, shall (a) have the
right to file and prosecute such application, and/or maintain such patent, in
such country, and (b) subject to the following sentence, have the right to grant
exclusive licenses to third parties to such patent application and/or patent
limited to such country(ies), in which event the options set forth in Sections
5.4 and 5.5 shall terminate with respect to such country(ies), provided that the
Institute shall only have the right to grant


                                      -28-


<PAGE>   33


non-exclusive licenses to third parties to such patent application and/or patent
(and the options set forth in Sections 5.4 and 5.5 shall be for non-exclusive
rights for such country(ies)) in the event that the applicable License
Consortium Member(s) elect not to file, prosecute or pay fees as a result of
their good faith determination that seeking and/or maintaining patent protection
in such country(ies) would not be beneficial due to the existence of prior art
or previously issued patents, or because such patent protection would not
provide meaningful legal and/or business protection under the circumstances.
Prior to granting any such license to a third party, the Institute and each IP
Owning Consortium Member shall notify the applicable Licensee Consortium
Member(s) of its intent to grant such a license, and shall, at the request of
such Licensee Consortium Member(s), negotiate in good faith terms for the
maintenance of exclusivity under Sections 5.4 and 5.5 with respect to such
patent application and/or patent.

         5.8.     Program Materials.

                  5.8.1. Transfer of Program Materials. The Advisory Board shall
determine under which circumstances Program Materials shall be transferred to
Consortium Members. To the extent Program Materials are transferred, unless
otherwise determined by the Advisory Board, Program Materials relating to a
Research Project shall be transferred to all Consortium Members which wish to
receive such Program Materials. However, the Consortium Members acknowledge that
there may be situations in which the Institute enters into collaborations with
third parties to gain access to Program Materials under terms which limit the
dissemination of such Program Materials to third parties, including Consortium
Members; the Institute acknowledges that any such limitations need to be taken
into consideration when determining whether to enter into any such third party
agreements, and agrees to use reasonable efforts to obtain the rights to
disseminate such Program Materials to the Consortium Members.

                  5.8.2. Use of Biological Materials. (a) The Institute agrees
that biological materials to be obtained from human subjects for purposes of
conducting Research Projects shall be obtained only after all necessary review
and final approvals by the appropriate institutional review board, human
experimentation committee or similar body have been obtained, said process
specifically to include review and final approval of the consent form(s) to be
used to document that the human subject has had an opportunity to be informed
about the nature of and the potential risks and benefits associated with the
research and has decided to provide biological materials knowing that such
biological materials will be analyzed by the Institute and Consortium Members
and may be retained by Institute and/or Consortium Members.

                         (b) The Institute agrees that the Research Program
Director or an appropriately designated collaborator or assistant will enroll an
individual as a human subject only after he or she has provided said individual
full and complete


                                      -29-


<PAGE>   34


disclosure of: (i) any and all risks known or anticipated to be associated with
participation, (ii) any benefits that might be realized by the individual as a
consequence of his or her participation, (iii) any involvement of Consortium
Members in the research, specifically including a statement in the consent form
and any necessarily related documents that cells, blood, plasma or nucleic acid
samples may be analyzed, retained indefinitely, and subjected to other uses by
the Institute and Consortium Members and that the Institute and Consortium
Members may derive economic benefit from the study of said samples, no part of
which will be shared with the subject, and (iv) any other information required
pursuant to the research protocol that is finally approved by institutional
review board, human experimentation committee or similar body.

                           (c) The Institute agrees that no human subject will
be enrolled until he or she has consented in writing to his or her
participation. The Institute agrees that no child aged seven (7) or older shall
be enrolled unless, in addition to obtaining the informed consent of said
child's parent or guardian, the written assent of the child is obtained.

                           (d) The Institute agrees to use a consent/assent form
the same as or substantially similar to Exhibit C attached hereto. In the event
that an institutional review board, human experimental committee or similar body
requires significant changes in such language, the Institute shall promptly so
inform the Advisory Board and shall not enroll any human subjects unless the
Advisory Board has provided its prior written approval to such changes, such
approval not to be unreasonably withheld.

         5.9.     Employee Agreements. Each employee and contractor of the
Institute involved in the Research Program, as well as all students, research
fellows and similar participants engaged by the Institute in the Research
Program, shall execute and deliver to Institute an agreement, in form reasonably
satisfactory to the Advisory Board, under which such person will assign to the
Institute any inventions made or copyrightable materials created by such person
in connection with the Research Program and agree to abide by the provisions of
Section 4.4.1 (b) and 4.4.2 (b) and the confidentiality obligations of the
Institute specified in Article VI.

         5.10.    No Implied Licenses. Except for the licenses and options to
obtain a license expressly pursuant to this Agreement, no licenses, implied or
otherwise, are granted by the Institute to any Consortium Member or by any
Consortium Member to the Institute or any other Consortium Member, including
licenses to so-called "background" technology.

Article VI.       CONFIDENTIAL INFORMATION


                                      -30-


<PAGE>   35


         6.1. Confidentiality. Consortium Members may from time to time disclose
Confidential Information to the Institute in connection with the Research
Program, and the Institute may from time to time disclose Confidential
Information to one or more Consortium Members. For purposes of this Agreement,
(a) the term "Disclosing Party" means the Consortium Member or the Institute
which discloses Confidential Information as contemplated by the preceding
sentence, (b) the term "Receiving Party" means the Consortium Member or the
Institute to which Confidential Information is disclosed by a Disclosing Party,
and (c) the term "Confidential Information" means information and materials of a
Disclosing Party which are designated as confidential in writing by such
Disclosing Party, whether by letter or by use of an appropriate stamp or legend,
prior to or at the same time any such information or materials are disclosed by
such Disclosing Party to the Receiving Party. Notwithstanding the foregoing,
materials and other information which are orally, visually or electronically
disclosed by a Disclosing Party, or are disclosed in writing without an
appropriate letter, stamp, or legend, shall constitute Confidential Information
if such Disclosing Party, within 30 days after such disclosure, delivers to the
Receiving Party a written document or documents describing the material or
information and indicating that it is confidential, provided that any disclosure
of information by the Receiving Party prior to receipt of such notice shall not
constitute a breach by the Receiving Party of its obligations under this Section
6.1. The Receiving Party agrees, to the extent permitted by law, that
Confidential Information shall remain the property of the Disclosing Party, and
that, unless otherwise agreed to by the Disclosing Party, Confidential
Information shall not be disclosed, divulged or otherwise communicated by it to
third parties (including without limitation, other Consortium Members) or used
by it for any purposes other than in connection with the Research Program and
the exploitation of the licenses granted in Article 5; provided that the term
"Confidential Information" shall exclude materials or information that:

                           (a) are in possession of the Receiving Party at the
time of disclosure thereof as demonstrated by prior written records;

                           (b) are or later become part of the public domain
through no fault of the Receiving Party;

                           (c) are received by the Receiving Party from a third
party having no obligation of confidentiality to the Disclosing Party that made
the disclosure;

                           (d) are developed independently by the Receiving
Party without use of Confidential Information as evidenced by written records;
or

                           (e) are required by law or regulation to be
disclosed; provided, however, that the Receiving Party has provided written
notice to the


                                      -31-


<PAGE>   36


Disclosing Party promptly so as to enable such Disclosing Party to seek a
protective order or otherwise prevent disclosure of such information.

         6.2.     Term. The obligations of the Receiving Party under this
Article VI shall continue for a period of five (5) years after the expiration or
termination of this Agreement; provided, however, that in the case of a
Consortium Member that withdraws, or is deemed to have withdrawn, as such
pursuant to Article VIII, the Receiving Party's obligations with respect to such
Consortium Member's Confidential Information shall continue only for a period of
five (5) years after the effective date of such Consortium Member's withdrawal.

         6.3.     Return of Materials.  Upon request by a Consortium Member that
made a disclosure of Confidential Information to the Institute, the Institute
promptly shall return all copies and other tangible manifestations of the
Confidential Information disclosed.

Article VII.      PUBLICATION AND ACADEMIC RIGHTS

         7.1.     Use of Information. Subject to the provisions of Section 7.2,
the Institute (and its employees) shall have the right to publish or otherwise
disclose information and/or data developed by the Institute under the Research
Program. The Institute (or its employees) shall include an appropriate
acknowledgment of the sponsorship of the Research Program by the Consortium
Members in such publication or disclosure. The Consortium Members shall have the
right to use, disclose and exploit any such data and information in accordance
with the rights held by them pursuant to this Agreement.

         7.2.     Publication or Public Disclosure of Information.

                  7.2.1. Notice. To avoid disclosure of Confidential Information
of a Consortium Member and the loss of patent rights as a result of premature
public disclosure of patentable information, the Institute agrees to provide
notice to the (i) Advisory Board, and (ii) each Consortium Member at least
thirty (30) days prior to any submission for publication or disclosure, together
with any and all materials intended for publication or disclosure relating to
technical reports, data, or information developed by the Institute or its
employees during the term of and pursuant to this Agreement.

                  7.2.2. Filing of Patent Application. During the course of any
such 30-day period, the Advisory Board or any Consortium Member shall provide
notice to the Institute whether it desires that a patent application be filed on
any invention disclosed in such materials. In the event that the Advisory Board
or a Consortium Member desires that such a patent application be filed, the
Institute agrees to withhold publication and disclosure of such materials until
the occurrence of the first


                                      -32-


<PAGE>   37


of the following: (i) filing of a patent application covering such invention;
(ii) written agreement by the Advisory Board and/or the Consortium Member, as
the case may be, and the Institute that no patentable invention is disclosed in
such materials; or (iii) sixty (60) days after the date that such materials were
received by the Advisory Board and the Consortium Members from the Institute.
Further, during the course of any such 30-day period, any Consortium Member that
believes that any of its Confidential Information has been included in the
proposed publication or disclosure shall provide notice to the Institute of the
Confidential Information which should be removed from such proposed publication
or disclosure. The Institute agrees to remove all such Confidential Information
from the proposed publication or disclosure.

Article VIII.     WITHDRAWAL

         8.1.     Voluntary Withdrawal.  Any Consortium Member may voluntarily
withdraw as a Consortium Member under this Agreement by notice to the Institute
and the other Consortium Members as follows:

                  (i)      pursuant to the provisions of Section 3.2.2, 3.2.3 or
                           Section 4.4.3; and

                  (ii)     by notice of withdrawal given by such Consortium
                           Member (which it may elect to do in its sole
                           discretion) to the Institute and the other Consortium
                           Members no later than one (1) year prior to the
                           effective date of withdrawal, provided that the
                           effective date of withdrawal may be no earlier than
                           the last day of the third Contract Year.

In the case of a withdrawal pursuant to subsection (i) above, the effective date
of withdrawal shall be the expiration of the period during which the withdrawing
Consortium Member is required to fund the Research Program pursuant to Section
3.2.2, 3.2.3 or 4.4.3, as applicable, provided that if the Institute elects to
disburse funding over an extended period of time as permitted by such Sections,
the effective date of withdrawal for purposes of Section 8.3.1 only shall be the
last date upon which such funds were disbursed.

         8.2.     Involuntary Withdrawal.  If a Consortium Member materially
breaches any material warranty, term or condition of this Agreement and fails to
remedy such material breach within ninety (90) days after receipt of notice in
writing of such material breach from the Institute, the Institute shall have the
right to cause the involuntary withdrawal of such Consortium Member, such
withdrawal to be effective immediately upon delivery of a written notice from
the Institute to such Consortium Member indicating the Institute's election to
cause such involuntary withdrawal to occur. For purposes of this Section 8.2,
any failure of a Consortium Member to make


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<PAGE>   38


a funding payment pursuant to Article IV when due shall be deemed to be a
material breach of this Agreement by such Consortium Member pursuant to which
the Institute shall be entitled to send a 90-day notice under this Section 8.2.

         8.3.     Effect of Withdrawal.

                  8.3.1. Intellectual Property Rights. From and after the
effective date of withdrawal of a Consortium Member, such Consortium Member
shall cease to have any rights as a Consortium Member under this Agreement,
including rights as a Licensee Consortium Member to any Program Know-How,
Program Materials, Program Copyrights or Program Patent Rights arising after
such effective date of withdrawal. However, except in the event of an
involuntary withdrawal pursuant to Section 8.2, the withdrawing Consortium
Member shall retain its rights as a Licensee Consortium Member in Background
Know-How, Program Know-How, Program Materials, Program Copyrights and Program
Patent Rights arising prior to the effective date of such withdrawal as provided
in Article V and its rights under Article VI and Article VII, provided that in
the event that the remaining Consortium Members designate a successor Licensee
Consortium Member(s) pursuant to the Consortium Member Agreement, such
successor(s) shall have a non-exclusive license to such Background Know-How,
Program Know-How, Program Materials, Program Copyrights and Program Patent
Rights to the extent necessary to enable such successor(s) to develop and
commercialize products or services based upon Program Know-How, Program
Materials, Program Copyrights and/or Program Patent Rights arising after the
effective date of withdrawal. In the event of an involuntary withdrawal pursuant
to Section 8.2, the withdrawing Consortium Member's rights as a Licensee
Consortium Member in Background Know-How, Program Know-How, Program Materials,
Program Copyrights and Program Patent Rights arising prior to the effective date
of such withdrawal as provided in Article V shall terminate, effective as of the
effective date of such withdrawal.

                  8.3.2.   Funding and Technology Contributions.

                           (a) In the event of a withdrawal pursuant to Section
8.1(i) above, the withdrawing Consortium Member shall continue to support or
fund the Research Program to the extent and for the period set forth in Section
3.2.2, 3.2.3 or 4.4.3, as applicable. In addition, if such withdrawing
Consortium Member is Millennium, it shall continue, during such continued
support or funding period, to provide, in the case of Millennium, the Millennium
Contributed Technology set forth in the applicable Annual Research Program Plan.

                           (b) In the event of a withdrawal pursuant to Section
8.1(ii) above, the withdrawing Consortium Member shall continue to support or
fund the Research Program until the effective date of withdrawal at the levels
(in terms of cash and, in the case of AFFX, AFFX Materials, subject to Section
8.3.2(e)) set forth in the


                                      -34-


<PAGE>   39


applicable Annual Research Program Budget (at the times and in the manner set
forth in Section 4.2). In addition, if such withdrawing Consortium Member is
Millennium, it shall continue, during such continued support or funding period,
to provide the Millennium Contributed Technology set forth in the applicable
Annual Research Program Plan.

                           (c) In the event of an involuntary withdrawal
pursuant to Section 8.2 above, the withdrawing Consortium Member shall continue
to support or fund the Research Program until the later of (i) twelve (12)
months after the effective date of withdrawal, or (ii) the end of the third
Contract Year, at the levels (in terms of cash and, in the case of AFFX, AFFX
Materials, subject to Section 8.3.2(e)) set forth in the applicable Annual
Research Program Budget (at the times and in the manner set forth in Section
4.2). In addition, if such withdrawing Consortium Member is Millennium, it shall
continue, during such continued support or funding period, to provide the
Millennium Contributed Technology set forth in the applicable Annual Research
Program Plan.

                           (d) If the continued support/funding and technology
contribution obligations of a Consortium Member upon a withdrawal pursuant to
this Article VIII would extend beyond the conclusion of an Annual Research
Program, (i) such support or funding obligation shall continue for the remainder
of the continued support or funding period with respect to the following Annual
Research Program(s), provided that the amount of such support or funding
obligation shall not exceed the amount that would have been applicable for such
period of time under the prior Annual Research Program, and (ii) such technology
contribution obligation for the period beyond the conclusion of such Annual
Research Program shall be negotiated in good faith by the parties.

                           (e) In the event that AFFX withdraws pursuant to
Section 8.1 or 8.2, the Institute and the other Consortium Members shall have
the right to require that AFFX, in lieu of providing all or any portion of the
AFFX Materials to the Institute set forth in the applicable Annual Research
Program Plan, provide cash funding for the continued funding periods set forth
in subsections (a), (b) or (c) above, in an amount determined pursuant to the
Consortium Member Agreement.

                           (f) Such ongoing support/funding and technology
contributions, if any, by the withdrawing Consortium Member shall constitute
liquidated damages arising out of the withdrawal of such Consortium Member.

                  8.3.3.   In the event of the withdrawal of a Consortium Member
pursuant to this Article VIII, or the termination by any Consortium Member
pursuant to Section 9.2, the Institute and the remaining Consortium Members
agree to meet and negotiate in good faith the continuation of the Research
Program, including ongoing funding obligations.


                                      -35-


<PAGE>   40


Article IX.   TERM; TERMINATION AND RENEWAL

         9.1. Term. Subject to the provisions of Section 9.6, the term of this
Agreement shall commence on the Effective Date and continue in full force and
effect until the last day of the fifth Contract Year, unless this Agreement is
terminated in its entirety prior to such date in accordance with this Article
IX, or renewed as set forth in Section 9.7.

         9.2. Termination for Breach by the Institute. If the Institute
materially breaches any material warranty, term or condition of this Agreement
and fails to remedy such material breach within ninety (90) days after receipt
of notice of such material breach from a Consortium Member (it being further
agreed that a Consortium Member providing notice pursuant to this Section shall
also provide notice to all other Consortium Members), each Consortium Member
may, at its or their option, as the case may be, and in addition to any other
remedies that such Consortium Member may have in law or in equity, terminate
this Agreement with respect to such Consortium Member by sending notice of
termination to the Institute, such termination to be effective immediately,
subject to the provisions of Section 9.6. From and after the effective date of
such termination, the terminating Consortium Member shall have no further
obligation to make cash payments and technology contributions to the Institute.

         9.3. Termination Rights of the Institute. Subject to the provisions of
Section 9.6, the Institute may terminate this Agreement, at its option, by
notice to the Consortium Members, in the event that at any time:

                  (a) the cash funding commitments of the Consortium Members
total less than the Minimum Cash Funding Level for any Contract Year; or

                  (b) the Consortium Members default in their obligation to fund
Research Projects as provided in this Agreement and such default results in
total funding of any Annual Research Program being less than the Minimum Cash
Funding Level for the applicable Contract Year.

If the Institute desires to terminate this Agreement pursuant to this Section
9.3, it shall first give the Consortium Members notice of its intention to
terminate and afford the Consortium Members a period of ninety (90) days to
eliminate the factual circumstance that would permit the Institute to so
terminate. Such curative steps by the Consortium Members may include increasing
their funding commitments, paying the defaulted funding amount and/or arranging
for the addition of an Additional Consortium Member as provided in Section 2.1
(as to whose addition, the Institute shall not unreasonably withhold its
approval). In the event that the Consortium Members fail to eliminate the
factual circumstances that would permit the Institute to


                                      -36-


<PAGE>   41


          Confidential Materials omitted and filed separately with the
       Securities and Exchange commission. Asterisks denote such omission.

terminate this Agreement within such 90-day period, the Institute may terminate
this Agreement by notice to the Consortium Members, such termination to be
effective immediately.

         9.4. Additional Termination Event. Subject to the provisions of Section
9.6, the Institute or any Consortium Member may terminate this Agreement in the
event that at any time any material provisions of this Agreement violate a
binding law, statute, rule or regulation promulgated by the United States
government or any agency thereof, in which event the terminating party shall
provide notice to all other parties and, if within ninety (90) days after the
date of such notice, the Institute and the Consortium Members are unable to
negotiate an amendment that would cause this Agreement to be in compliance with
such regulation, this Agreement shall terminate effective immediately upon
further notice to all other parties from the terminating party (with any
termination by a Consortium Member being solely with respect to such Consortium
Member).

         9.5. Return of Funds; Continued Funding Obligation. Any funds paid to
the Institute by the Consortium Members which have not been expended or
committed upon the date of expiration or termination of this Agreement pursuant
to this Article IX shall be refunded to the Consortium Members within sixty (60)
days after the date of expiration or termination in accordance with the terms of
the Consortium Member Agreement. In the event that the total funds paid to the
Institute by the Consortium Members as of the date of a termination by the
Institute pursuant to Section 9.3 are not sufficient to cover costs and
non-cancelable commitments actually incurred by the Institute in connection with
the Research Program as of such date, the Consortium Members shall reimburse the
Institute the deficiency (with each Consortium Member being severally, and not
jointly, liable for its share of such deficiency determined in accordance with
the formula x/y where x is the amount of the deficiency and y is the number of
Consortium Members as of the date of termination), such reimbursement to be made
within thirty (30) days after the date of notice provided by the Institute to
the Consortium Members specifying the amount of the deficiency (with supporting
documentation therefor); provided, however, that the Consortium Members shall
not be obligated to reimburse the Institute pursuant to this sentence an amount
in excess of ****** of the total funding commitment of the Consortium Members
pursuant to Section 4.1 for the twelve (12) month period commencing on the date
of termination. The Institute will use its best efforts to minimize any costs
and non-cancelable commitments to be paid for by the Consortium Members pursuant
to the previous sentence, including without limitation by reassigning personnel
and transferring supplies.


                                      -37-


<PAGE>   42


         9.6.  Survival. The following articles and sections of this Agreement
shall survive the expiration or termination of this Agreement: Sections 3.4,
3.5, 3.6, 4.3 and 4.4 and Articles V, VI, VII, IX, XI and XII.

         9.7.  Renewal. Not later than the end of the third Contract Year, the
Consortium Members and the Institute shall meet (at a time and place designated
by the Institute in a notice to the Consortium Members and mutually agreed upon
by the Consortium Members) to consider a renewal of the term of this Agreement
for an additional five (5) Contract Years commencing at the end of the fifth
Contract Year. If the Institute and the Consortium Members shall so agree to
such a renewal, they shall enter into an appropriate amendment of this Agreement
reflecting the terms to be in effect during the renewal period, including the
funding commitments of the Consortium Members for each Contract Year in such
renewal term.

Article X      REPRESENTATIONS AND WARRANTIES

         10.1. Representations and Warranties of All Parties. Each party
represents and warrants to the other parties that: (i) it is free to enter into
this Agreement; (ii) in so doing, it will not violate any other agreement to
which it is a party; and (iii) it has taken all corporate action necessary to
authorize the execution and delivery of this Agreement and the performance of
its obligations under this Agreement.

         10.2. Representations and Warranties of the Institute. The Institute
hereby represents and warrants to each of the Consortium Members that: (a) it
has not entered into any agreement with any third party which is in conflict
with the rights granted to any of the Consortium Members pursuant to this
Agreement; (b) except as indicated on Schedule VI, it is the owner of, or is the
licensee of, all of the Background Know-How in existence on the date of this
Agreement, and has the right to grant licenses or sublicenses therefor to the
Licensee Consortium Members; (c) except as indicated on Schedule VI, it is the
owner of, or has exclusive rights to, all of the Background Patent Rights, and
has the exclusive right to grant licenses therefor; (d) to the best of its
knowledge, all such Background Patent Rights are in full force and effect and
have been maintained to date; (e) it is not aware of any asserted or unasserted
claim or demand which it believes can be enforced against the Background Patent
Rights; (f) it has no current knowledge that the practice of the Background
Patent Rights infringes upon or conflicts with any patent, patent application or
other proprietary right of any third party; and (g) the Institute has not
granted and will not grant any right or interest in and to Program Know-How,
Program Materials, Program Copyrights or Program Patent Rights that is
inconsistent with the grant of rights to the Consortium Members hereunder, and,
to the best of its knowledge, has disclosed all grants of rights that would
materially impact its right to grant licenses in the Background Know-How or
Background Patent Rights relevant to the work to be performed hereunder.


                                      -38-


<PAGE>   43


         10.3. Limitations. EXCEPT AS EXPRESSLY PROVIDED HEREIN, NO PARTY TO
THIS AGREEMENT MAKES ANY WARRANTY, EXPRESS OR IMPLIED, EITHER IN FACT OR BY
OPERATION OF LAW, BY STATUTE OR OTHERWISE, RELATING TO (i) ANY RESEARCH
CONDUCTED UNDER THIS AGREEMENT OR (ii) ANY INVENTION CONCEIVED AND/OR REDUCED TO
PRACTICE UNDER THIS AGREEMENT OR (iii) ANY OTHER INTELLECTUAL PROPERTY DEVELOPED
UNDER THIS AGREEMENT, AND EACH PARTY TO THIS AGREEMENT SPECIFICALLY DISCLAIMS
ANY IMPLIED WARRANTY OF MERCHANTABILITY OR WARRANTY OF FITNESS FOR A PARTICULAR
PURPOSE.

Article XI.    LIABILITY AND INDEMNIFICATION

         11.1. Release from Liability. The Institute agrees that no Consortium
Member shall be liable for, and hereby releases each Consortium Member from, any
liability as a result of damage to or loss of property or injury to or death of
any person as a result of or in connection with activities of the Institute and
the Institute's employees and agents relating to the Research Program, unless
such damage, loss, injury or death is the direct result of such Consortium
Member's negligence or willful acts or omissions.

         11.2. Indemnification.

               11.2.1. Indemnification by Consortium Members. Each Consortium
Member shall indemnify and hold each of the other Consortium Members and the
Institute, their respective Affiliates, licensees and sublicensees, and their
respective directors, officers, employees and agents, harmless from and against
any and all liabilities, damages to or loss or property or injury to or death of
any person or persons, costs and expenses (including reasonable attorneys' fees)
arising out of or resulting from such Consortium Member's (i) breach of any
representations or warranties set forth in this Agreement, or (ii) possession or
use of materials or information developed by the Institute in connection with
the Research Program, unless such damage, loss, injury or death is the direct
result of negligence or willful acts or omissions of the Institute, any other
Consortium Member or their employees or agents.

               11.2.2. Indemnification by the Institute. The Institute shall
indemnify and hold each Consortium Member, their respective Affiliates,
licensees and sublicensees, and their respective directors, officers, employees
and agents, harmless from and against any and all liabilities, damages to or
loss of property or injury to or death of any person or persons arising out of
the Institute's (i) breach of any representations or warranties set forth in
this Agreement, or (ii) possession or use of materials or information developed
by such Consortium Member in connection with the Research Program, unless such
damage, loss, injury or death is the direct


                                      -39-


<PAGE>   44


result of negligence or willful acts or omissions of such Consortium Member or
employees or agent thereof.

                  11.2.3. Costs and Expenses. As the parties intend to provide
complete indemnification, all costs and expenses of enforcing this Section 11.2
shall also be reimbursed by the indemnifying party.

                  11.2.4. Indemnification Procedures. A party that intends to
claim indemnification under this Section 11.2 (the "Indemnitee") shall promptly
notify the other parties (the "Indemnitors") of any loss, claim, damage,
liability or action in respect of which the Indemnitee intends to claim such
indemnification, and the Indemnitors shall assume the defense thereof with
counsel reasonably satisfactory to the Indemnitee whether or not such claim is
rightfully brought; provided, however, that an Indemnitee shall have the right
to retain its own counsel, with the fees and expenses to be paid by the
Indemnitors if the Indemnitors do not assume the defense, or if representation
of the Indemnitee by the counsel retained by the Indemnitors would be
inappropriate due to actual or potential differing interests between such
Indemnitee and any other person represented by such counsel in such proceedings.
The indemnity agreement in this Section 11.2 shall not apply to amounts paid in
settlement of any loss, claim, damage, liability or action if such settlement is
effected without the consent of the Indemnitors, which consent shall not be
withheld or delayed unreasonably. The failure to deliver notice to the
Indemnitors within a reasonable time after the commencement of any such action,
only if prejudicial to its ability to defend such action, shall relieve such
Indemnitors of any liability to the Indemnitee under this Section 11.2, but the
omission so to deliver notice to the Indemnitors will not relieve it of any
liability that it may have to any Indemnitee otherwise than under this Section
11.2. The Indemnitee under this Section 11.2, its employees and agents, shall
cooperate fully with the Indemnitors and its legal representatives in the
investigations of any action, claim or liability covered by this
indemnification.

Article XII.   GENERAL PROVISIONS

         12.1. Dispute Resolution. Any dispute or claim arising out of, or in
connection with, this Agreement shall be finally settled by binding arbitration
in accordance with the then current rules and procedures of the American
Arbitration Association. The arbitration shall be conducted by three (3)
arbitrators with experience with the issue under consideration (e.g., patent
experts in the case of patent-related disputes), one (1) to be appointed by the
Consortium Members, one to be appointed by the Institute and a third being
nominated by the two (2) arbitrators so selected or, if they cannot agree on a
third arbitrator, by the President of the American Arbitration Association. Such
arbitration will take place in Chicago, Illinois, unless otherwise determined by
a Requisite Majority of the Advisory Board. The arbitrators shall apply the law
of the Commonwealth of Massachusetts to the


                                      -40-


<PAGE>   45


merits of any dispute or claim, without reference to rules of conflicts of laws.
Judgment on any award rendered by the arbitrators may be entered in any court
having jurisdiction thereof. The parties agree that, any provision of applicable
law notwithstanding, they will not request, and the arbitrators shall have no
authority to award, punitive or exemplary damages against any party. Nothing in
this Section 12.1 shall limit a party's right to seek injunctive relief with
respect to a breach or threatened breach of this Agreement.

         12.2. Governing Law. This Agreement shall be governed by, construed,
and interpreted in accordance with the laws of the Commonwealth of
Massachusetts, without reference to principles of conflicts of laws.

         12.3. Independent Contractors. The relationship of the Consortium
Members and the Institute established by this Agreement is that of independent
contractors, and nothing contained in this Agreement shall be construed to (i)
give any of the parties hereto the power to direct or control the day-to-day
activities of another party hereto, (ii) constitute the parties as partners,
joint venturers, co-owners or otherwise as participants in a joint or common
undertaking, or (iii) allow any of the parties hereto to create or assume any
obligation on behalf of another party hereto for any purpose whatsoever.

         12.4. Parties Bound. This Agreement, including the indemnification
provisions, shall be binding upon and inure to the benefit of the parties
hereto, their respective successors, assigns, legal representatives and heirs.

         12.5. Assignment. This Agreement may not be assigned or transferred by
any of the parties hereto without the prior written consent of the other
parties; provided, however, that a Consortium Member may assign its rights and
delegate its obligations (i) to any Affiliate of such Consortium Member
(although, in the event of any such assignment and delegation, the assigning
Consortium Member shall remain primarily liable for its obligations hereunder)
and (ii) to a purchaser of all or substantially all of the business of such
Consortium Member to which this Agreement relates by merger, sale of assets or
otherwise.

         12.6. Entire Agreement. This Agreement (together with the Consortium
Member Agreement, in the case of the Consortium Members) constitutes the entire
and only agreement between the parties relating to the subject matter hereof,
and all prior negotiations, representations, agreements and understandings are
superseded hereby.

         12.7. Further Assurances. At any time or from time to time, the
Institute shall, at the request of the Advisory Board or any Consortium Member,
(i) deliver to the Advisory Board or such Consortium Member such records, data
or other documents consistent with the provisions of this Agreement, (ii)
execute, and deliver


                                      -41-


<PAGE>   46


or cause to be delivered, all such assignments, consents, documents or further
instruments of transfer or license, and (iii) take or cause to be taken all such
other actions, as the Consortium Members may reasonably deem necessary or
desirable in order for the Consortium Members to obtain the full benefits of
this Agreement and the transactions contemplated hereby.

         12.8. Right to Develop Independently. Nothing in this Agreement will
impair any Consortium Member's right to independently acquire, license, develop
or have developed, utilize or otherwise exploit similar information and
technology performing the same or similar functions as the information and
technology provided by the Institute or which is the subject of the Research
Program.

         12.9. Notices. Any notice or other communication required or permitted
under this Agreement shall be in writing and (i) personally delivered, (ii)
mailed, postage prepaid, first class, certified mail, return receipt requested,
or (iii) sent, shipping prepaid, return receipt requested by national overnight
courier service, to the appropriate party or parties at the addresses listed
below or at such other addresses as may be given from time to time in accordance
with the terms of this notice provision.

                  (a) Notice to the Consortium Members shall be addressed to
them as follows:

                      i.    In the case of BMS, to:

                            Bristol-Myers Squibb Company
                            P.O. Box 4000
                            Route 206 & Province Line Road
                            Princeton, New Jersey 08543-4000
                            Attention:  Vice President and Senior Counsel,
                            Pharmaceutical Research Institute and
                            Worldwide Strategic Business Development

                      ii.   In the case of Millennium, to:

                            Millennium Pharmaceuticals, Inc.
                            640 Memorial Drive
                            Cambridge, Massachusetts 02139
                            Attention:  Chief Business Officer


                      iii.  In the case of AFFX, to:

                            Affymetrix, Inc.


                                      -42-


<PAGE>   47


                             3380 Central Expressway
                             Santa Clara, California 95051
                             Attn:  President

                  (b) Notices to the Institute shall be addressed to:

                      Whitehead Institute for Biomedical Research
                      Nine Cambridge Center
                      Cambridge, Massachusetts
                      Attention:  Associate Director

                  (c) Notices to the members of the Advisory Board shall be
addressed to them as set forth in Schedule IV.

Any notice or other communication given by personal delivery shall be deemed
given on the date personally delivered; any notice or other communication given
by mail shall be deemed given three days after the date deposited in the United
States mail; and any notice or other communication given by national overnight
courier service shall be deemed given on the next business day after being sent.

         12.10. Amendment. This Agreement may only be amended by a written
instrument executed by the Institute and each of the Consortium Members, except
as provided in Schedule III.

         12.11. Waiver. No waiver of any rights shall be effective unless
assented to in writing by the party to be charged, and the waiver of any breach
or default shall not constitute a waiver of any other right hereunder or any
subsequent breach or default.

         12.12. Limitation of Liability. IN NO EVENT WILL ANY PARTY HERETO BE
LIABLE FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL OR INDIRECT DAMAGES ARISING IN
ANY WAY OUT OF THIS AGREEMENT, HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY.
THIS LIMITATION WILL APPLY EVEN IF THE OTHER PARTY OR PARTIES HERETO HAVE BEEN
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

         12.13. Section Headings. The headings of the several sections of this
Agreement are intended for convenience of reference only and are not intended to
be a part of, or to affect the meaning or interpretation of this Agreement.

         12.14. Severability. In the event that any provision of this Agreement
becomes or is declared by a court of competent jurisdiction to be illegal,
unenforceable or void, this Agreement shall continue in full force and effect
without said provision; provided that no such severability shall be effective if
the result of such action


                                      -43-


<PAGE>   48


materially changes the economic benefit of this Agreement to the Consortium
Members or the Institute.

         12.15.   Counterparts.  This Agreement may be executed in counterparts,
each of which shall be deemed an original, but all of which together shall
constitute one and the same instrument.

         12.16.   Public Announcements.

                  12.16.1. Any written announcements, press releases or similar
publicity (collectively, "Announcements") with respect to the execution of this
Agreement shall be agreed upon by the Institute and the Consortium Members in
advance of such Announcement. Each party agrees to provide to each other Party a
copy of any proposed public Announcement relating to this Agreement or the
Research Program as soon as reasonably practicable under the circumstances prior
to its scheduled release. Each party shall have the right to expeditiously
review and recommend changes to any Announcement regarding this Agreement or
developments under the Research Program. Except as otherwise required by law,
the party whose Announcement has been reviewed shall consider in good faith the
removal of any information any reviewing party reasonably deems to be
inappropriate for disclosure. In proposing, reviewing and considering comments
on Announcements, the interests of the Institute and all Consortium Members
shall be taken into consideration, with the overall goal being the furtherance
of the objectives of the Research Program and the harmonization of the interests
of all parties.

                  12.16.2. The parties agree that the terms of this Agreement
shall be maintained in confidence by all parties, except that (a) any party may
disclose the terms hereof to the extent required by law (including without
limitation pursuant to the requirements of U.S. securities laws), and (b) the
Institute may disclose the terms hereof to government agencies (such as the NIH)
or the U.S. Congress to the extent it deems such disclosure to be necessary or
desirable, provided that such disclosure under (a) and/or (b) of this Section
12.16.2 shall, to the extent legally permissible, be in the form of the redacted
version of this Agreement to be agreed upon by the Institute and the Consortium
Members.

         12.17. No Third Party Beneficiary Rights. The Institute and the
Consortium Members agree and acknowledge that the Institute is not intended to
be, and shall not constitute, a third party beneficiary of the Consortium Member
Agreement, which is intended exclusively as an agreement among, and for the
benefit of, the Consortium Members.


                                      -44-


<PAGE>   49


         IN WITNESS WHEREOF, the parties have caused this Agreement to be
executed by their duly authorized representatives as of the day and year first
above written.

WHITEHEAD INSTITUTE FOR                     BRISTOL-MYERS  SQUIBB COMPANY
BIOMEDICAL RESEARCH

By: /s/ Gerald R. Fink                      By: /s/ Peter S. Ringrose
   --------------------------------            ---------------------------------
Name: Gerald R. Fink                        Name: Peter S. Ringrose
     ------------------------------              -------------------------------
Title:                                      Title: President R & D
     ------------------------------              -------------------------------
Date:                                       Date: 4/28/97
     ------------------------------              -------------------------------

AFFYMETRIX, INC.                            MILLENNIUM PHARMACEUTICALS,
                                                  INC.

By: /s/ Stephen Fodor                       By: /s/ Steven H. Holzman
   --------------------------------            ---------------------------------
Name: Stephen Fodor                         Name: Steven H. Holzman
     ------------------------------              -------------------------------
Title: President/CEO                        Title: 
     ------------------------------              -------------------------------
Date: 28 April 97                           Date:
     ------------------------------             --------------------------------


                                 ACKNOWLEDGEMENT

         The undersigned has read, understands and agrees to be bound by those
provisions of this Agreement specifically applicable to him as the Research
Program Director.

                                            RESEARCH PROGRAM DIRECTOR


                                            /s/ Eric Lander
                                            -------------------------------
                                            Dr. Eric Lander


                                      -45-


<PAGE>   50


                                    EXHIBIT A

                      PRODUCT TECHNOLOGY LICENSE AGREEMENT







                               To be provided.









                                      -46-


<PAGE>   51


                                    EXHIBIT B

                      RESEARCH TECHNOLOGY LICENSE AGREEMENT









                               To be provided.









                                      -47-

<PAGE>   52


                                    EXHIBIT C

                           HUMAN SUBJECT CONSENT FORM


NOTE:    THE CONSENT FORM SHALL INCLUDE AT LEAST THE FOLLOWING CLAUSES, PLUS
         SUCH OTHER PROVISIONS AS MAY BE REQUIRED BY APPLICABLE INSTITUTIONAL
         REVIEW BOARDS AND AS MAY BE DETERMINED FROM TIME TO TIME BY THE
         ADVISORY BOARD.

I understand that the research project in which I will enroll is designed in
part to identify genes which may predispose individuals to develop
__________________________ and/or other related diseases. This will be attempted
by determining the presence or absence of certain deoxyribonucleic acid (DNA)
markers in cells removed from a blood sample that I will provide. The
information provided by these markers will be compared to the presence or
absence of certain clinical findings in me and other participating family
members who decide to enroll in the research project.

I understand that the blood sample that I provide pursuant to the research will
be sent to the Whitehead Institute for Biomedical Research ("Whitehead") located
in Cambridge, Massachusetts, and that the scientists at Whitehead will analyze
the DNA taken from my blood to help locate genes that may predispose to
__________________________________.

I understand that when Whitehead receives a blood sample from me it will be
devoid of any accompanying information that could permit persons working there
to link the findings made concerning any DNA obtained pursuant to the project
with my identity.

I understand that my DNA (and possibly, cell lines derived from my white blood
cells) will be retained indefinitely (banked) by Whitehead.

I understand that Whitehead may analyze my sample as part of other research
activities or share anonymous portions of it with other researchers working in
other institutions or companies, including, but not limited to, Affymetrix,
Inc., Bristol-Myers Squibb Company and Millennium Pharmaceuticals, Inc.

I understand that the analysis of my DNA sample may contribute to the creation
of new diagnostic tests, new medicines, or other events that may be commercially
valuable to Whitehead and licensees of Whitehead (including the companies listed
in the preceding paragraph) and that I will receive no financial benefits from
such developments.


                                      -48-


<PAGE>   53


I understand that the genetic mapping research of this type could possibly
discover sensitive facts about families such as, for example, non-paternity, or
that some other presumed biological relationship is not in the fact the case.

I understand that should I in the course of this research be informed by the
physician-investigator who enrolled me in the study that I am genetically
predisposed to develop one or more serious disorders that such knowledge could
compromise my ability to obtain health, life, disability or other insurance
standard rates, or, possibly, render me unable to obtain insurance at all.


                                      -49-


<PAGE>   54


                                   EXHIBIT D-1

                          MATERIALS TRANSFER AGREEMENT


         This Materials Transfer Agreement (the "Agreement"), effective as of
________________, 199___ ("Effective Date"), made by and between Whitehead
Institute for Biomedical Research, a Delaware corporation ("Whitehead"),
____________________, a not-for-profit organization (the "Institution"), and its
investigator, ________________ ("Principal Investigator"), shall govern the
terms and conditions of Whitehead's transfer of certain biological materials,
copyrighted materials and/or know-how to the Institution and the Principal
Investigator.

                                  INTRODUCTION

1.       Whitehead is the owner of the Materials (as defined below).

2.       The Institute has requested that Whitehead provide the Materials to the
Institution, and Whitehead is willing to do so in accordance with the terms of
this Agreement.

3.       The Materials constitute unique research materials developed at
considerable expense by Whitehead, and is subject to licensing rights granted to
third parties, which third party rights are intended to be protected by the
provisions of this Agreement.

NOW, THEREFORE, the parties hereto agree as follows:

         1. Biological Materials, Copyrighted Materials and Know-How.
"Biological Materials" shall mean the biological materials set forth on Exhibit
A hereto, together with any fragments, derivatives, modifications, variants,
progeny or improvements thereof; "Copyrighted Materials" shall mean the software
programs and other copyrighted materials set forth on Exhibit A hereto; and
"Know-How" shall mean the discoveries, inventions, data, software, information,
trade secrets and other technology set forth on Exhibit A hereto. The term
"Materials" shall mean the Biological Materials, Copyrighted Materials and
Know-How, as applicable.

         2. Transfer. Whitehead shall transfer the Materials to the Institution.
Acceptance of the Materials by the Institution shall be for the purpose
described in Section 3 only and shall not be deemed a grant by Whitehead to the
Institution of any rights in or to the Materials.

         3. Use of Materials. Whitehead will provide the Materials solely for
the purpose of allowing the Principal Investigator and anyone under his/her
direct


                                      -50-


<PAGE>   55


supervision to use the Materials for in vitro research or in vivo animal
research proposes only ("Research"). The Institution shall not disclose or
distribute the Materials to any third party without the express prior written
consent of Whitehead. The Institution shall not use the Materials for purposes
of conducting research with any third party. No commercial development will be
undertaken by the Institution with the Materials, and the Materials will not be
used in research sponsored or funded by a commercial entity or in research
programs to which any third party (other than the federal government) has
licensing rights. Institution and Principal Investigator acknowledge that the
Materials are experimental and will comply with all laws and regulations
applicable to their handling and use. Institution shall return all unused
Materials to Whitehead within thirty (30) days of the completion of the
Research.

         4. Report of Results. The Principal Investigator shall periodically
review results generated during the performance of the Research with Whitehead
for evaluation of patentable information and coordination of ongoing research
efforts. In addition, the Principal Investigator will provide Whitehead with
periodic written summaries of results generated during the performance of the
Research. A final report shall be delivered to Whitehead with periodic written
summaries of results generated during the performance of the Materials
transferred to the Institution pursuant to the performance of this Agreement
within thirty (30) days of the completion of the Research.

         5. Publications. It is acknowledged that the parties may desire to
publish and disclose the results of the Research. In order to balance this
interest with Whitehead's proprietary interests, Principal Investigator will
submit for Whitehead's review any manuscripts, abstracts, or presentations
intended for publication or other public disclosure. Whitehead will use
reasonable efforts to complete its review promptly and will complete its review
within thirty (30) days of receipt of the submitted documents. If during its
thirty (30) day review period, Whitehead notifies Principal Investigator and the
Institution that it desires patent applications to be filed on any results
disclosed or contained in the documents, Principal Investigator will defer
publication or other disclosure for a period, not to exceed sixty (60) days from
the date of submission to Whitehead, sufficient to permit any desired patent
applications to be filed. Further, during the course of any such 30-day period,
if the Whitehead believes that any Confidential Information (as defined in
Section 8) has been included in the proposed publication or disclosure, it shall
provide notice to the Principal Investigator and the Institution identifying
such information. The Principal Investigator and the Institution agree to remove
all such Confidential Information from the proposed publication or disclosure.


                                      -51-


<PAGE>   56


         6.       Intellectual Property Rights

                  (a) The Institution shall promptly and fully disclose in
writing to Whitehead any and all inventions, technology, improvements,
discoveries, developments, trade secrets or intellectual property conceived,
developed or reduced to practice by the Principal Investigator and/or anyone
under his or her direct supervision using the Materials ("Intellectual
Property"). Title to intellectual property rights, including patent applications
and patents issued thereon, in any invention or discovery arising out of the
Research invented solely by employees of the Institution shall be owned by the
Institution, subject to the rights granted to Whitehead under this Agreement.
Title to intellectual property rights, including patent applications and patents
issued thereon, in any invention or discovery invented jointly by employees of
the Institution and Whitehead arising out of the Research shall be owned jointly
by the Institution and Whitehead, subject to the rights granted to Whitehead
under this Agreement.

                  (b) The Institution hereby grants to Whitehead an option to
obtain an exclusive worldwide right and license, with a right to grant
sublicenses, under the Intellectual Property (i) to make, use, sell and import
products, (ii) to use, practice and sell methods, and (iii) to otherwise exploit
the Intellectual Property.

                  (c) The option granted to Whitehead pursuant to Section 6(b)
to obtain license rights shall extend for a period of one hundred eighty (180)
days after the date of Whitehead's receipt of a written notice given by the
Institution of an invention covered by, or able to be covered by, a patent or
patent application. Whitehead shall be deemed to have exercised such option if
it provides notice to the Institution of its decision to exercise the option
within such one hundred eighty (180) days period. Promptly following the
exercise of the option granted pursuant to Section 6(b), the parties shall
undertake good faith negotiations concerning the terms and conditions of any
such license. In the event that Whitehead does not exercise its option with
respect to any patent application or patent granted hereunder or the parties are
unable to agree upon the terms and conditions of any such license, the
Institution may enter into an agreement relating to such application or patent
with any third party; provided that the terms offered to a third party are not
more favorable to such third party than the terms offered to Whitehead and
rejected by Whitehead. If such terms offered to a third party are more favorable
to the third party, the Institution will offer such more favorable terms to
Whitehead, and Whitehead will have thirty (30) days to accept or reject such
offer.

                  (d) Institution hereby grants to Whitehead an exclusive,
worldwide, paid-up right and license, with the right to grant sublicenses, under
Intellectual Property, (i) to make and use products, (ii) to use and practice
methods and (iii) to otherwise exploit the Intellectual Property, in all cases
subject to the limitation that


                                      -52-


<PAGE>   57


the right and license granted under this Section 6(d) shall not extend to the
commercial sale of products or the commercial performance of services.

         7.  No Warranty. MATERIALS TRANSFERRED UNDER THIS AGREEMENT ARE
EXPERIMENTAL IN NATURE. MATERIALS PROVIDED BY WHITEHEAD TO THE INSTITUTION AND
THE PRINCIPAL INVESTIGATOR ARE "AS IS" AND WITHOUT ANY WARRANTIES, EXPRESS OR
IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE OR SAFETY. WHITEHEAD MAKES NO EXPRESS OR IMPLIED WARRANTY THAT THE USE
OF MATERIALS TRANSFERRED UNDER THIS AGREEMENT WILL NOT INFRINGE ANY PATENT OR
OTHER PROPRIETARY RIGHT OF ANY THIRD PARTY.

         8.  Confidentiality. As used herein, the term "Confidential
Information" means information received from Whitehead which is marked as being
confidential or which Whitehead, within 30 days after disclosure, indicates in
writing to the Institution is confidential. Subject to the provisions of Section
5, neither the Institution nor the Principal Investigator shall disclose,
divulge or otherwise transfer or communicate any of the Confidential Information
to third parties, unless and until such Confidential Information is in the
public domain through no fault of the Institution or the Principal Investigator.

         9.  Liability/Hold Harmless. In no event shall Whitehead or any
affiliate, be liable for any use of the Materials made by the Institution, and
the Institution hereby agrees to defend, indemnify, and hold Whitehead,
Whitehead's affiliates, and their respective successors in business harmless
from any loss, claim, damage, liability or expense (including reasonable
attorney's fees) that may arise from the Institution's use, storage, and
disposal of the Biological Materials, except to the extent such loss, claim,
damage, liability or expense is the direct result of Whitehead's gross
negligence or willful misconduct.

         10. Nonexclusivity. Whitehead's transfer of the Materials to the
Institution shall not restrict Whitehead from transferring the Materials to
other organizations or from using the Materials in any manner Whitehead desires.

         11. Ownership. Except as otherwise provided herein, no right, title or
interest in and to the Materials provided to the Institution is granted or
implied hereunder. Whitehead shall retain all right, title and interest in and
to the Materials.

         12. Assignment This Agreement may not be assigned or transferred by any
of the parties hereto without the prior written consent of the other parties.

         13. Notice. Notices (not including reports pursuant to Section 4, which
may be delivered by any reasonable means) required herein shall be given by
prepaid


                                      -53-


<PAGE>   58


certified or registered mail or courier requiring proof of receipt to the
address of the parties set forth on Exhibit B hereto.

         14. Term and Termination. The term of this Agreement shall commence on
the Effective Date and continue in full force and effect until the one (1) year
anniversary of the Effective Date, subject to extension by written agreement.
Either party may terminate this Agreement on thirty (30) days prior written
notice to the other party. Upon termination, Institution shall immediately
return to Whitehead the unused Materials, and all of Institution's and Principal
Investigator's rights to use the Materials shall end. Following termination,
neither party shall have any further obligations under this Agreement, except
that Sections 5 through 9 shall survive.

         15. No Conflict. The Institution and Principal Investigator warrant and
represent that to the best of their knowledge, each has the authority and
ability to enter into this Agreement and that no pre-existing or future
obligation, through contract or otherwise, would substantially interfere with,
and/or prohibit either party from performing all their respective obligations
and duties as described hereunder.

         16. Miscellaneous. This Agreement contains the entire understanding of
the parties with respect to the Materials, and supersedes any prior oral or
written agreements or understanding with respect thereto, all of which, to the
extent that any exist, are hereby terminated. No change, modification,
alteration or addition to any provision of this Agreement shall be binding
unless it is made in writing and is executed by duly authorized representatives
of both parties. This Agreement shall be governed by and construed under the
laws of the Commonwealth of Massachusetts, without reference to conflict of laws
principles. This Agreement may be executed in counterparts, each of which shall
be deemed an original, but all of which together shall constitute one and the
same instrument.

         IN WITNESS WHEREOF, the parties have caused this instrument to be
executed by their duly authorized representatives.

AGREED AND ACCEPTED FOR:

INSTITUTION

Signature:__________________________

Name:     __________________________

Title:    __________________________


                                      -54-


<PAGE>   59


PRINCIPAL INVESTIGATOR


Signature:__________________________

Name:     __________________________

Title:    __________________________


WHITEHEAD INSTITUTE
FOR BIOMEDICAL RESEARCH


Signature:__________________________

Name:     __________________________

Title:    __________________________


                                      -55-


<PAGE>   60


                                   EXHIBIT D-2

                          MATERIALS TRANSFER AGREEMENT


Date:

Subject: MATERIALS TRANSFER AGREEMENT

Dear

This is to acknowledge your request for certain material which will be provided
to you, for your use in non-commercial scientific research only, under the
following conditions:

         1.       The Material covered by this Agreement includes
                  ___________________________________________________, any
                  additional progeny or derivatives thereof which could not have
                  been made but for the material provided. You will use
                  reasonable effort to keep confidential any related information
                  and know-how which will be received under this agreement and
                  is marked "confidential".

         2.       The Material will be used only by you and by individuals
                  working under your direct supervision in your Institution, and
                  will not be transferred, distributed or released to any other
                  person.

         3.       You will inform the Whitehead Institute in confidence of
                  research results related to the Material, by personal
                  communication or by providing Dr. Eric Lander with a
                  manuscript describing the results of such research at the time
                  the manuscript is submitted for publication. If publication
                  results from research using the Material, acknowledgement of
                  and/or credit will be given to Dr. Lander as scientifically
                  appropriate.

         4.       The Material is made available for investigational use only in
                  laboratory animals or in vitro experiments and will not be
                  used in humans or for any other purpose.

         5.       All characteristics of the Material are not fully understood
                  and its use may involve risks or dangers that are not known or
                  fully appreciated. The Material is being provided without
                  warranty of any sort, express or implied. You and your
                  Institution will use the Material in compliance with all laws
                  and governmental regulations and guidelines applicable to the
                  Material and will comply with NIH guidelines.


                                      -56-


<PAGE>   61


         6.       [To the extent permitted by law,] You will hold the Whitehead
                  Institute and its employees harmless from any loss, claim,
                  damage or liability, of any kind, which may arise from or in
                  connection with this Agreement or your use, handling or
                  storage, of the Material. In no case shall the Whitehead
                  Institute or Dr. Lander be liable for any use by you, by
                  individuals working under your direct supervision or by your
                  Institution, of the Material or any loss, claim, damage or
                  liability, of any kind, which may arise from or in connection
                  with this Agreement or your use, handling or storage of the
                  Material.

         7.       Whitehead Institute (and its licensees of the Materials) are
                  hereby granted a right of first refusal to obtain an exclusive
                  license (a) to commercialize any substance produced that
                  incorporates the Material or progeny or derivative of the
                  Materials and/or (b) under any patent or other intellectual
                  property rights covering a new use of the Materials, the terms
                  of said exclusive license to be negotiated in good faith.

         8.       You understand that no other right or license to this Material
                  or to its use is granted or implied as a result of our sending
                  the Material to you.

         9.       At the request of the Whitehead Institute, unused Material
                  will be returned to the Whitehead Institute or destroyed.

If you agree to accept the Material under the above conditions, please sign the
Agreement, have it signed by an authorized representative of your Institution
and return it to:

                                    Mr. John Pratt
                                    Associate Director
                                    Whitehead Institute
                                    Nine Cambridge Center
                                    Cambridge, MA  02142

The Material will be sent to you as soon as possible after the receipt of the
signed Agreement.

                                   Sincerely,


                                   John Pratt




                                      -57-


<PAGE>   62


ACCEPTED:

                                    REQUESTER
                                    INSTITUTION:________________________________

By:______________________________   By:_________________________________________
      (Requester's Signature)       (Authorized Representative's Signature)

By:______________________________   By:_________________________________________
          (Printed Name)                  (Authorized Representative's Name)

Date:____________________________   Date:_______________________________________


                                      -58-


<PAGE>   63


                                   SCHEDULE I

                                AFFX CONTRIBUTION


         1. AFFX Commitment to Supply AFFX Materials. AFFX, as part of the AFFX
Contribution, hereby undertakes to supply to the Institute, in accordance with
the terms of each Annual Research Program Plan, the following types of AFFX
Materials at the fixed prices set forth in the Consortium Member Agreement
(which prices may not be modified without the approval of the Institute):

         Custom and Standard Probe Arrays ("chips"):

                  -        Expression monitoring custom probe arrays
                  -        Expression monitoring standard probe arrays
                  -        Genotyping custom probe arrays
                  -        Genotyping standard probe arrays

         GeneChip(R) Instruments

                  -        GeneChip Fluidics Station
                  -        GeneChip Scanner
                  -        GeneChip Workstation

         Software

                  -        GeneChip Software
                  -        GeneChip Analysis Software


         2. Waiver of Access Fees. AFFX shall, as part of the AFFX Contribution,
waive all access fees relating to the supply of the AFFX Materials.


         3. Grant of License. AFFX, hereby, as part of the AFFX Contribution,
grants rights to use to all AFFX Materials for use by the Institute and the
Consortium Members in the course of the Research Program.


                                      -59-


<PAGE>   64


                  Confidential Materials omitted and filed separately with the
         Securities and Exchange Commission. Asterisks denote such omission.

                                   SCHEDULE II

                        MILLENNIUM CONTRIBUTED TECHNOLOGY


I.       EXPRESSION PROFILING
         *********************
         *********************
         *********************
         *********************
         *********************

II.      HUMAN GENETICS
         *********************
         *********************
         *********************
         *********************
         *********************
         *********************
         *********************
         *********************
         *********************
         *********************

III.     DNA SEQUENCE ANALYSIS SOFTWARE
         *********************

IV.      HUMAN/ANIMAL SAMPLES
         *********************

         (As available and appropriate)

Note: To the extent set forth in the applicable Annual Research Program Plan,
Millennium shall promptly transfer to the Institute any Contributed Technology
Upgrades to the Millennium Contributed Technology. Any such Contributed
Technology Upgrades shall be deemed to be part of the Millennium Contributed
Technology to which they relate, shall be transferred pursuant to Section 4.5.3
and shall not obligate the Institute or the other Consortium Members to deliver
any additional consideration.


                                      -60-


<PAGE>   65


                  Confidential Materials omitted and filed separately with the
         Securities and Exchange Commission. Asterisks denote such omission.


                                  SCHEDULE III

                       CONSORTIUM MEMBER CASH COMMITMENTS

A.       BASIC FUNDING COMMITMENTS

<TABLE>
<CAPTION>
--------------------------------------------------------------------------------
                                     MAXIMUM               CONSORTIUM MEMBER
                                 CONSORTIUM MEMBER         CASH COMMITMENT
                                CASH COMMITMENT PER        FOR FIRST CONTRACT
CONSORTIUM MEMBER                CONTRACT YEAR (1)         YEAR (1)

--------------------------------------------------------------------------------
<S>                             <C>                        <C>
Affymetrix, Inc.                      *******                  ****** (2)

--------------------------------------------------------------------------------
BRISTOL-MYERS SQUIBB                  ******                   ******
COMPANY

--------------------------------------------------------------------------------
MILLENNIUM                            ******                   ****** (3)
PHARMACEUTICALS, INC.

--------------------------------------------------------------------------------
</TABLE>

         (1)      Subject to adjustment pursuant to part B of this Schedule III.

         (2)      Of this amount, ****** has previously been provided by AFFX to
                  the Institute (in the form of a *********). Accordingly,
                  AFFX's remaining cash funding commitment for the first
                  contract year is ******.

         (3)      Of this amount, ****** has previously been advanced by
                  Millennium to the Institute pursuant to the Existing Research
                  Agreement. Accordingly, Millennium's remaining funding
                  commitment for the first contract year is ******.

                (Schedule III is continued on the following page)


                                      -61-


<PAGE>   66



          Confidential Materials omitted and filed separately with the
       Securities and Exchange Commission. Asterisks denote such omission.

B.       Adjustments to Consortium Member Cash Commitments

         The Cash Commitments set forth in part A above are based upon the
assumption that each Annual Research Program Plan will require that AFFX supply
AFFX Materials to the Institute for use in connection with the Research Program.
In the event that for any Contract Year the amount of AFFX Materials to be
supplied by AFFX pursuant to the Annual Research Program Plan for such Contract
Year is greater or lesser than currently budgeted for the first Contract Year,
then the Cash Commitments set forth in part A above shall be subject to
adjustment as provided in the Consortium Member Agreement, provided that in no
event shall the Cash Commitments for any Contract Year exceed ********. The
Consortium Members shall notify the Institute concerning any adjustments made
pursuant to the Consortium Member Agreement, and the Institute agrees that any
such adjustments shall be considered to constitute an amendment to this Schedule
III and shall be binding upon the Institute, provided that no such adjustments
shall reduce the Total Cash Commitment of the Consortium Members set forth in
the applicable Annual Research Program Budget without the written consent of the
Institute. Furthermore, as provided in Section 4.1.1 of this Agreement, Schedule
III shall be amended for each Contract Year to reflect the Annual Research
Program Budget for such Contract Year, with the allocation of the Total Cash
Commitments among the Consortium Members to be determined pursuant to the terms
of the Consortium Member Agreement and set forth in such amended Schedule III.

         For purposes of determining whether the Minimum Contribution Level has
been satisfied, the price of AFFX Materials shall be determined in the manner
provided in the Consortium Member Agreement, notice of which determination shall
be provided to the Institute and shall be subject to audit and dispute by the
Institute. The Consortium Members agree not to amend provisions in the
Consortium Member Agreement relating to the price of AFFX Materials without the
Institute's written consent, such consent not to be unreasonably withheld.


                                      -62-


<PAGE>   67


          Confidential Materials omitted and filed separately with the
       Securities and Exchange Commission. Asterisks denote such omission.

C.       First Installment for First Contract Year

         Within ten (10) days after the Effective Date, the Consortium Members
shall provide the following funds to the Institute:

         Member            Amount
         ------            ------

                                          (reflecting the prior contribution
         AFFX              ******          described in footnote (2) above)

         BMS               ******

         Millennium        ******         (reflecting the prior ****** payment
                                          described in footnote (3) above)


                                      -63-


<PAGE>   68


                                   SCHEDULE IV

                             ADVISORY BOARD MEMBERS



Affymetrix:  Dr. Robert Lipshutz and Dr. Thomas Gingeras


Bristol-Myers Squibb:  Dr. Richard Gregg and Dr. William Koster


Millennium Pharmaceuticals, Inc.:  Dr. Frank Lee and Dr. Robert Tepper.


                                      -64-


<PAGE>   69


          Confidential Materials omitted and filed separately with the
       Securities and Exchange Commission. Asterisks denote such omission.

                                   SCHEDULE V

                  DETERMINATION OF ROYALTY RATES UNDER PRODUCT
                          TECHNOLOGY LICENSE AGREEMENTS



         A. The royalty rates for products or services that are royalty-bearing
under the terms of a Product Technology License Agreement shall range up to
******% of Net Sales (as defined in the Product Technology License Agreement) on
a per-product/service basis (i.e. only one royalty within the foregoing range
will be payable, irrespective of the number of patents/patent applications
licensed).

         In determining the appropriate royalty rate for a product or service,
all relevant factors shall be considered, including, but not limited to the
following:

         **************************************************************
******************

         **************************************************************
********************************************************************
******************

         **************************************************************
********************************************************************
********************************************************************
********************************************************************
******************

         **************************************************************
********************************************************************

         **************************************************************

         **************************************************************
********************************************************************
************************


                                      -65-


<PAGE>   70


         B. As provided in Section 5.5, the royalty rate determined pursuant to
the provisions of Part A above shall be split between the Institute and any
applicable IP Owning Consortium Member(s) based upon all relevant factors,
including, but not limited to, the relative contributions of the Institute and
the IP Owning Consortium Members to the Program Patent Rights and whether such
Program Patent Rights are owned solely by the IP Owning Consortium Member,
jointly by IP Owning Consortium Members or jointly by the Institute and one or
more IP Owning Consortium Members.


                                      -66-


<PAGE>   71


          Confidential Materials omitted and filed separately with the
       Securities and Exchange Commission. Asterisks denote such omission.


                                   SCHEDULE VI

                            BACKGROUND PATENT RIGHTS



         ****************************************************************
**********************************************************************
**********************************************************************
**********************************************************************
**********************************************************************
**********************************************************************
*****.


                                      -67-