Document:

<PAGE>
                                                                     Exhibit 4.1

   NUMBER                     COMMON STOCK                      COMMON SHARES
                                ORCHID

INCORPORATED UNDER THE LAWS OF                        CUSIP 68571P100
     THE STATE OF DELAWARE                   SEE REVERSE FOR CERTAIN DEFINITIONS

                           ORCHID BIOSCIENCES, INC.

       THIS CERTIFIES THAT

    is the record holder of

             FULLY PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK,
                        $0.001 PAR VALUE PER SHARE, OF

---------------------------   ORCHID BIOSCIENCES, INC.   -----------------------

transferable on the books of the Corporation by the holder hereof or by its duly
authorized attorney upon surrender of this Certificate properly endorsed or
assigned. This Certificate and the shares represented hereby are issued and
shall be held subject to the laws of the State of Delaware and the provisions of
the Certificate of Incorporation and the By-laws of the Corporation, as amended
from time to time, to which the holder assents. This Certificate is not valid
unless countersigned and registered by the Transfer Agent and Registrar.

    WITNESS the facsimile seal of the Corporation and the facsimile signatures
of its duly authorized officers.

Dated:

    /s/ Donald R. Marvin                         /s/ Dale R. Pfost
         Secretary               Chairman, President and Chief Executive Officer

Seal 1995
                           ORCHID BIOSCIENCES, INC.

                           ORCHID BIOSCIENCES, INC.

     Orchid BioSciences, Inc. will furnish to any shareholder upon request to
its principal office, and without charge, a fully statement of the designations,
preferences, limitations and relative rights of the shares of each class
authorized, and of the variations in the relative rights and preferences between
the shares of each preferred or special class in a series, so far as the same
have been fixed and determined, and the authority of the board of directors to
fix and determine the relative rights and preferences of subsequent series.

     The following abbreviations, when used in the inscription on the face of
this certificate, shall be construed as though they were written out in full
according to applicable laws or regulations:

                TEN COM - as tenants in common

                UNIF GIFT ACT - _____________ Custodian ______________
                                   (Cust)                  (Minor)

                TEN ENT - as tenants by the entireties

                JT TEN - as joint tenants with right of survivorship and not as
                         tenants in common under Uniforms Gifts to Minors

                ACT ____________________________________
                               (State)

<PAGE>

     Additional abbreviations may also be used though not in the above list.

     For value received, ________________ hereby sell, assign and transfer unto

PLEASE INSERT SOCIAL SECURITY OR OTHER
IDENTIFYING NUMBER OF ASSIGNEE
[                            ]

________________________________________________________________________________

________________________________________________________________________________
 (PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING ZIP CODE, OF ASSIGNEE)

________________________________________________________________________________

______________________________________________________________________ Shares
of the Capital Stock represented by the within Certificate, and do hereby
irrevocably constitute and appoint

______________________________________________________________________ Attorney
to transfer the said stock on the books of the within named Corporation with
full power of substitution in the premises.

Dated, _______________________________

                            ___________________________________________________
                            NOTICE: THE SIGNATURE OF THIS ASSIGNMENT MUST
                            CORRESPOND WITH THE NAME AS WRITTEN UPON THE
                            FACE OF THIS CERTIFICATE IN EVERY PARTICULAR,
                            WITHOUT ALTERATION OR ENLARGEMENT, OR ANY CHANGE
                            WHATEVER.

Signature(s) Guaranteed:
By _________________________________________
THE SIGNATURE(S) SHOULD BE GUARANTEED BY
AN ELIGIBLE GUARANTOR INSTITUTION (BANKS,
STOCKBROKERS, SAVINGS AND LOAN
ASSOCIATIONS AND CREDIT UNIONS WITH
MEMBERSHIP IN AN APPROVED SIGNATURE
GUARANTEE MEDALLION PROGRAM), PURSUANT TO
S.E.C. RULE 17 Ad-15.<PAGE>

                                                                    EXHIBIT 10.5

                            CONFIDENTIAL TREATMENT
                            ----------------------

ORCHID BIOSCIENCES, INC. HAS REQUESTED THAT THE MARKED PORTIONS OF THIS DOCUMENT
    BE ACCORDED 406 CONFIDENTIAL TREATMENT PURSUANT TO RULE 406 UNDER THE
                      SECURITIES ACT OF 1933, AS AMENDED.

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
             EXCHANGE COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

                                                                  Execution Copy

                            COLLABORATION AGREEMENT

                                 BY AND BETWEEN

                            ORCHID BIOCOMPUTER, INC.

                                      AND

                                AFFYMETRIX, INC.

                               NOVEMBER 05, 1999

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                                                                  Execution Copy

                            COLLABORATION AGREEMENT

          This COLLABORATION AGREEMENT (this "Agreement"), effective as of
November 5, 1999 (the "Effective Date"), is by and between Orchid Biocomputer,
Inc., a Delaware corporation having a place of business at 303 College Road
East, Princeton, New Jersey 08540 (hereinafter referred to as "ORCHID") and
Affymetrix, Inc., a Delaware corporation having its principal place of business
at 3380 Central Expressway, Santa Clara, California 95051 (hereinafter referred
to as "AFFYMETRIX").

      The Parties hereby agree as follows:

1.    DEFINITIONS
      -----------
      As used in this Agreement, the following terms, whether used in the
singular or plural, shall have the following meanings:

      1.1 "AFFYMETRIX Collaboration Technology" means any Technology developed
or conceived by employees of or consultants to AFFYMETRIX alone or jointly with
Third Parties, during the Term in the conduct of the Collaboration.

      1.2 "Affiliate" of a Party means any corporation or other business entity,
which controls, is controlled by, or is under common control with, a Party. For
purposes of this Section, "control" shall mean direct or indirect ownership of
more than 50% of the voting interest or economic interest in a corporation or
more than 50% of the equity interests in the case of any other entity, or such
other relationship whereby a party controls or has the right to control the
Board of Directors or equivalent governing body of a corporation or other
entity.

      1.3 "Approved Instruments" means one or more AFFYMETRIX scanners and
associated instruments and software, as such instrumentation is then
commercially available from AFFYMETRIX.

      1.4 "Clinical Use" means any use of a Product as part of the prevention,
diagnosis or treatment of any disease or condition in a patient and all
government (i.e., FDA or equivalent foreign governmental body) regulated
diagnostic uses in which the result is used in treatment of such patient.

      1.5 "Collaboration" means the Product research, development and
commercialization program jointly conceived, planned, organized, controlled and
performed by ORCHID and AFFYMETRIX pursuant to this Agreement.

      1.6 "Combination Kit" means any Custom Kit that contains Primers more than
50% of which are identical to Primers contained in any part of any Standard Kits
existing at the time of launch of such Custom Kit, or any combination of
Standard Kits existing at the time of launch of such Custom Kit.

      1.7 "Collaboration Management Committee" or "CMC" means the committee
defined in Section 2 to aid in the joint collaborative effort to develop and
commercialize Products.

      1.8 "Commercial Probe Arrays" means TAG Arrays sold by AFFYMETRIX to Third
Parties in conjunction with (although they may be separately packaged from) an
ORCHID OEM Kit.

      1.9 "Confidential Information" means all information and materials,
patentable or otherwise, of a Party and which is disclosed by or on behalf of
such Party (the "Disclosing Party") to the other Party (the "Receiving Party")
or developed, learned or obtained by the Receiving Party in connection with the
Collaboration or otherwise under this Agreement, including, but not limited to,
business, technical or financial information, DNA sequences, vectors, cells
substances, formulations, techniques, methodology, equipment, data,

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reports, know-how, preclinical and clinical trials and the results thereof,
sources of supply, patent positioning and business plans, including any negative
developments, whether or not related to the Collaboration.

      1.10 "Contract Year" means any year during the Term of this Agreement
commencing on the Effective Date or any anniversary of the Effective Date and
ending on the anniversary thereof.

      1.11 "Control" or "Controlled" means, with respect to any Technology, the
possession by a Party of the ability to grant a license or sublicense of such
Technology as provided herein without violating the terms of any agreement or
arrangement between such Party and any Third Party.

      1.12 "Custom Kit" means a kit consisting of certain Reagents, certain
Primers that have been customized by Orchid or Orchid's subcontractors for use
in the Field of Use and an End User License, and shall not include use of or
refer to any use of TAG Arrays other than for genotyping with GBA.

      1.13 "Custom Kit Information" means all information related to Custom Kits
to be provided by ORCHID to AFFYMETRIX under this Agreement, including, without
limitation, the identity of each customer, intended uses of Custom Kits by such
customer, the Primers included in such Custom Kits, quantities ordered and
forecasted and ORCHID's sale price thereof, and such other information as more
fully described on Schedule 1.13 attached hereto, subject in each such case to
                   -------------
any confidentiality obligation ORCHID may have to any Third Party (provided that
ORCHID shall use commercially reasonable efforts to minimize such obligations)
and excluding ORCHID proprietary Primers and SNPs.

      1.14 "End User" means any Third Party licensed to use a Product pursuant
to an End User License received in connection with the purchase by such Third
Party of a Product.

      1.15 "End User License" means a limited non-transferable license in form
and substance as set forth in Schedule 1.15 hereto, granted by ORCHID to End
                              -------------
Users under ORCHID End User Technology to use only the amount of the material
included in the Product in the Field of Use.

      1.16 "Field of Use" means the use of Product to practice GBA in Tag Array
format in Approved Instruments for Research Purposes and clinical reference
laboratories where work is performed under the Clinical Laboratory Improvements
Act and explicitly excludes Products that have received marketing approval from
the FDA.

      1.17 "Generic Kit" means a kit consisting of Reagents and an End User
License.

      1.18 "Joint Technology" means any Technology (i) developed or conceived by
employees of or consultants to one Party as a result of the use by such Party of
Technology of the other Party or any Joint Technology or (ii) jointly developed
by employees of or consultants to both ORCHID and AFFYMETRIX in the conduct of
the Collaboration.

      1.19 "Net Sales" with respect to an item, means the gross amount billed by
a party to third parties in connection with the sale, use or other disposition
of such item less (i) any allowances actually made and taken for returns;
shipping and insurance costs actually paid; cash discounts and promotional
allowances actually allowed in amounts and for purposes customary in the trade;
and (ii) sales, use and excise taxes and shipping charges incurred in connection
with any such sale, use or other disposition.

      1.20 "ORCHID End User Technology" means Technology Controlled by ORCHID as
of the Effective Date that is useful to practice the End User License, as listed
or described on Schedule 1.20 attached hereto.
                -------------

      1.21 "ORCHID OEM Kits" means Standard Kits or Generic Kits.

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      1.22 "ORCHID Licensed Technology" means Technology Controlled by ORCHID
and its Affiliates as of the Effective Date that is useful in the Field of Use,
as listed or described on Schedule 1.22 attached hereto. ORCHID represents and
                          -------------
warrants that the items listed on Schedule 1.22 hereto comprise all of the
                                  -------------
ORCHID Licensed Technology as of the Effective Date of this agreement. As of the
Effective Date the Orchid Licensed Technology does not require payment of
royalties to third parties. Orchid and its Affiliates will amend this Schedule
1.22 from time to time to keep it current. ORCHID and its Affiliates warrant
that all Controlled Technology for carrying out the marketing, sale, and other
disposition of Products will be included in the ORCHID Licensed Technology.

      1.23 "ORCHID Collaboration Technology" means any Technology developed or
conceived by employees of or consultants to ORCHID alone or jointly with Third
Parties, during the Term in the conduct of the Collaboration.

      1.24 "Product" means any of a Standard Kit, a Custom Kit and/or a Generic
Kit.

      1.25 "Party" means AFFYMETRIX or ORCHID; "Parties" means AFFYMETRIX and
ORCHID.

      1.26 "Primer" means GBA primers (a synthetic oligonucleotide of a sequence
known to be complementary with the oligonucleotide sequence immediately
adjacent, 5', to a SNP) or either PCR primers or information to generate PCR
primers.

      1.27 "Project Director(s)" means the senior scientists for the
Collaboration designated from time to time by AFFYMETRIX and ORCHID.

      1.28 "Reagent" means buffers, enzymes and terminators (but not Primers)
useful in GBA.

      1.29 "Research Purposes" means the detection and analysis of SNPs in
samples, such definition includes all non-government (i.e., FDA or equivalent
foreign governmental body) regulated diagnostic uses.

      1.30 "SNP" means Single Nucleotide Polymorphism.

      1.31 "Standard Kit" means a kit consisting of Reagents, CMC Approved
Primers for use in the Field of Use and an End User License.

      1.32 "Technology" means and includes all inventions, discoveries,
improvements, trade secrets and proprietary methods and materials, whether or
not patentable, including but not limited to, samples of, methods of production
or use of, and structural and functional information pertaining to, chemical
compounds, proteins or other biological substances; other data; formulations;
techniques; and know-how; including any negative results.

      1.33 "GBA" means Genetic Bit Analysis, or single nucleotide primer
extension methods designed to detect the identity of a single nucleotide at a
predetermined location in the DNA of a sample.

      1.34 "TAG Array" means a tag array GeneChip probe array. Each set of
probes consists of four probes with the following relationship to a defined
target sequence -- a perfect match to target sequence, a single base mismatch
to target sequence, a perfect match to the complement of target sequence, and, a
single base mismatch to the complement of target sequence. For the avoidance of
doubt, TAG Arrays include no license (express or implied) authorizing use for
any purpose except genotyping with GBA.

      1.35 "TAG Assay" means any assays for hybridization to a TAG Array.

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      1.36 "Term" means the period beginning on the Effective Date and ending on
the fifth anniversary thereof unless otherwise extended or terminated as
provided herein.

      1.37 "Specifications" means the specifications for ORCHID OEM Kits
established by the CMC and set forth on Schedule 1.37 attached hereto, as such
                                        -------------
specifications may be amended from time to time by the CMC.

      1.38 "Third Party" means any person or entity other than ORCHID and
AFFYMETRIX and their respective Affiliates.

      1.39 "Workplan" means any CMC-approved plan for collaborative research and
development of Products to be conducted under this Agreement. The Initial
Workplan is set forth in Schedule 1.39 to this Agreement and shall commence upon
                         -------------
approval by the newly formed CMC.

2.    THE COLLABORATION
      ------------------

      2.1 Purpose.

      The purpose of the Collaboration is to develop, manufacture, market and
sell (i) Products, and (ii) software applications for Approved Instruments all
as set forth in Schedule 1.39. The purpose of the Collaboration may be modified
and/or extended upon mutual agreement of the Parties in writing.

      2.2 Collaboration Management Committee and General Operations.

            (a) CMC. Each Party shall appoint a Project Director who shall serve
                ---
      as such Party's primary liaison with the other Party to discuss technical
      matters pertaining to the Collaboration. The Parties shall also establish
      the CMC composed of two or more representatives appointed by AFFYMETRIX
      and two or more representatives appointed by ORCHID. A Party's
      representatives shall serve at the discretion of such Party and may be
      replaced at any time by such Party. Each Party, by its representative(s),
      shall have one vote on the CMC. The CMC will coordinate the joint
      collaborative efforts to achieve the purpose of the Collaboration. The CMC
      will have general responsibility for directing both the commercial
      development of ORCHID OEM Kits developed and supplied hereunder, and the
      research effort of the Collaboration, and for monitoring the work done and
      costs incurred pursuant to the Collaboration. In addition, the CMC shall
      establish the mechanism and procedures through which each Standard Kit is
      approved for, and developed under, the Collaboration; [*] The initial
      meeting of the CMC shall occur no later then 30 days after the Effective
      Date of this Agreement, and among other things, such initial meeting shall
      consist of formal approval of the Initial Workplan (and each of the
      parties hereby agrees to cause its representatives on the CMC to vote in
      favor of such Initial Workplan, without modification.) The CMC will review
      the Workplans for the subsequent Contract Years during the Term of the
      Collaboration at least 60 days prior to the start of each subsequent
      Contract Year and make any modifications as may be required prior to
      granting its approval.

            (b) Meetings. During the Collaboration, the CMC shall meet at least
                --------
      quarterly. The site of CMC meetings shall alternate between the offices of
      AFFYMETRIX and ORCHID (or any other site or by teleconference as mutually
      agreed upon by the CMC). Whenever any action by the CMC is called for
      hereunder during a time period in which the CMC is not scheduled to meet,
      a representative of either Party may cause the CMC to take the action in
      the requested time period by calling a special meeting or written
      agreement to take such by action without a meeting. The proceedings of all
      meetings of the CMC shall be summarized in writing and sent to both
      Parties. The Party hosting the meeting shall be responsible for the
      preparation and circulation of such summaries. Draft summaries shall be
      issued in final form only upon approval by the CMC at a subsequent meeting
      or as evidenced by the signature of a majority of the representatives of
      the CMC. Each Party shall bear all expenses of their respective CMC
      representatives related to their participation on the CMC and attendance
      at CMC meetings.

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    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

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            (c) Collaboration Operations. The Collaboration shall be conducted
                ------------------------
      at and/or coordinated from the facilities of each Party under the
      supervision and direction of its Project Director. Each Party shall be
      responsible for the administrative management, fiscal control, and
      expenses incurred by it for tasks assigned to it in each Workplan. Each
      Party shall assemble a team of scientists, engineers, technical associates
      and/or assistants. So long as the Collaboration continues, any Party
      performing work under a Workplan that is funded by the other Party shall
      periodically (at least quarterly) provide to the other Party written
      progress reports summarizing the technical progress of such work, and
      associated costs relating to such work. Each Party also shall provide the
      other Party through the CMC with additional oral progress reports as
      requested from time to time by the other Party.

            (d) Generic Kit and Standard Kit Proposals. During the Term,
                --------------------------------------
      AFFYMETRIX may designate up to [*] Standard Kits that are each
      comprised of a standard assay with up to [*], and other components, all of
      which are selected by AFFYMETRIX, and the transfer price of such new
      Standard Kits. Schedule 1.39 more particularly identifies such kits
                     -------------
      including the markers and transfer price [*] and shall be deemed Standard
      Kits that have been approved by the CMC, except that such transfer prices
      shall be [*], and the parties shall use all commercially reasonable
      efforts to promptly complete development of such kits and the CMC shall
      agree on the transfer price. In addition, during the Term of the
      Collaboration, either Party may, in its sole discretion, propose that new
      Generic Kits or new Standard Kits be developed by the Collaboration by
      providing written notice thereof (including the transfer price of each
      such kit) to the CMC (such notice being referred to herein as the "New Kit
      Notice"), which notice shall include a reasonable description of the
      proposed specifications, components and the transfer price of such new
      Generic Kit or Standard Kit. If ORCHID is the Party proposing the
      development of a new Generic Kit or Standard Kit, and Affymetrix does not,
      within sixty (60) days after receipt of such New Kit Notice expressly
      agree to co-develop the new Generic Kit or Standard Kit described therein,
      then ORCHID may pursue development of the new Generic Kit or Standard Kit
      independently of AFFYMETRIX (provided that no express or implied license
      to AFFYMETRIX intellectual property is conveyed thereby.) If AFFYMETRIX is
      the Party proposing the development of a new Generic Kit or a new Standard
      Kit, and Orchid does not, within sixty (60) days after receipt of such New
      Kit Notice expressly agree to co-develop the new Generic Kit or new
      Standard Kit described therein, then AFFYMETRIX may pursue development of
      the new Generic Kit or new Standard Kit independently of ORCHID,and the
      licenses granted to AFFYMETRIX under Section 3.1 (and Section 4.1(b))
      shall include the right to directly and indirectly develop, make, use,
      market, sell and distribute such kits. In such case, AFFYMETRIX shall pay
      ORCHID a royalty of [*] of Net Sales of such kit unless the Parties agree
      in writing to a lower rate; provided, that [*] provided that reductions
      shall roll forward, if necessary, so that payments to ORCHID are not
      reduced to less than [*] of what they would have been in the absence of
      this provision.

            (e) Custom Kits. ORCHID shall provide AFFYMETRIX with quarterly
                -----------
      written reports containing Custom Kit Information relating to Custom Kits
      sold by ORCHID; subject, in each case, to any confidentiality obligations
      of ORCHID to such customers of such Custom Kits. Either Party will be free
      to use it to promote the sale of other products or services with such
      information.

                  (i) Royalties on Combination Kits. ORCHID shall pay to
                      -----------------------------
            AFFYMETRIX a per kit royalty on ORCHID's Net Sales of Combination
            Kits equal to [*] of Net Sales of each Combination Kit, reduced by
            the fraction:
            [*]

                  (ii) Conversion of Custom Kits to Standard Kits. ORCHID agrees
                       ------------------------------------------
            that, at AFFYMETRIX's option upon written notice to ORCHID at any
            time after the Conversion Date (as defined below), any Custom Kit
            sold to a given customer or group of customers for which sales in
            any Contract Year

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            exceeds [*] will, effective the first day of the first
            calendar quarter following the Contract Year in which such event
            occurred (the "Conversion Date") become a Standard Kit (each, a
            "Converted Kit"); provided that, the Parties hereby agree that (i)
                              -------------
            under no circumstances shall a Custom Kit convert to a Converted Kit
            if such conversion would violate the terms of the applicable
            agreement between ORCHID and such customer or customers or if such
            Custom Kit contains primers for the analysis of SNPs that are owned
            either by such customer or owned by ORCHID but limited to use by
            such customer, and are subject to restrictions on use by third
            parties (provided, however, ORCHID shall use commercially reasonable
            efforts to ensure that any primers contained in such Custom Kits are
            free of restrictions on use), and (ii) Custom Kits shall convert to
            Converted Kits on an individual basis, with reference to the
            Specifications of such Custom Kit. If, with respect to a Converted
            Kit, the CMC concludes that at the Conversion Date ORCHID has not
            recovered the [*] incurred by ORCHID in developing such Custom Kit,
            then the CMC may require AFFYMETRIX to pay a conversion fee in an
            amount not to exceed [*]) in an amount and payment schedule
            determined by the CMC. ORCHID may until the end of the sixth month
            following immediately after the Conversion Date sell its inventory
            of Converted Kits. Thereafter, ORCHID will cease all distribution
            activities relating to such Converted Kit, and shall transfer all
            remaining inventory of Converted Kits to AFFYMETRIX at the transfer
            price established for such Converted Kit by the CMC. Once a
            conversion occurs, the parties will negotiate reasonable commercial
            performance standards for AFFYMETRIX's sales of Converted Kits.

                  (iii) Standard Kits Analyte Specific Reagents Status. Within
                        ----------------------------------------------
            180 days after commercial release of each Standard Kit, but not
            before nine month anniversary of the Effective Date, ORCHID will use
            all commercially reasonable efforts to ensure that each Standard Kit
            shall be manufactured as an analyte specific reagent in accordance
            with 21 CFR 864. In addition, ORCHID will use all commercially
            reasonable efforts to take all steps necessary or desirable to
            ensure that the Standard Kits manufactured and sold hereunder meet
            other applicable standards, such as ISO 9000, as soon as
            practicable.

      2.3 Specific Development Duties.

      (a) Development Obligations. The Parties shall use commercially reasonable
          -----------------------
efforts to fulfill their respective obligations as set forth in each Workplan in
accordance with the time schedules set forth therein. AFFYMETRIX and ORCHID
agree to work cooperatively and expeditiously to make such modifications to the
design of Products as may be required to reduce total costs and/or improve
Product performance. Notwithstanding the foregoing, it is hereby agreed that
ORCHID shall have sole responsibility for the development of Custom Kits. With
respect to the Initial Workplan, ORCHID shall be responsible for over-all ORCHID
OEM Kit development, including, assay development and optimization,
amplification technology development, and regulatory approval, as the CMC
determines to be appropriate. Specifically ORCHID shall (1) develop generic and
standard TAG Assays with consultation from Affymetrix, (2) provide AFFYMETRIX
the GBA specific analysis algorithms as set forth in Schedule 1.39, and (3)
assist AFFYMETRIX in integrating the foregoing into the AFFYMETRIX Approved
Instrument systems. With respect to the Initial Workplan, AFFYMETRIX shall be
responsible for TAG Array design and production and Approved Instrument software
integration and analysis.

      (b) Development Costs of ORCHID OEM Kits, Custom Kits and Certain Standard
          ----------------------------------------------------------------------
Kits. As between the Parties, (i) ORCHID shall be responsible for all
----
development costs and expenses associated with the development of the ORCHID
Generic Kits (exclusive of any internal development costs and expenses incurred
by AFFYMETRIX), (ii) the Parties shall share all development costs and expenses
associated with the development of Standard Kits for which development has been
approved by the CMC in the manner and proportion agreed upon by the CMC and
(iii) AFFYMETRIX shall be responsible for all of its own development costs and
expenses associated with the development of the software for the ORCHID OEM
Kits. With respect to any Kit developed pursuant to Section 2.2(d), the Party
developing such Standard Kit shall be solely responsible for all costs and
expenses associated with developing such Standard Kit.

      (c) Training. ORCHID will provide AFFYMETRIX reasonable training in the
          --------
use of ORCHID OEM Kits at ORCHID's facility in Princeton, New Jersey. It is
anticipated that such training will take place over approximately a two- week
period and will involve two scientists from AFFYMETRIX and 2 scientists from
ORCHID. AFFYMETRIX will provide ORCHID reasonable training in the use of its TAG
Arrays at AFFYMETRIX's facility in Santa Clara, California. It is anticipated
that such training will take place over

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approximately a two-week period and will involve 2 scientists from ORCHID and
two scientists from AFFYMETRIX

      (d) Use of Instruments and TAG Arrays During Development. During
          ----------------------------------------------------
development of an ORCHID OEM Kit pursuant to a Workplan, ORCHID may purchase TAG
Arrays and Approved Instruments from AFFYMETRIX; provided, that any TAG Arrays
purchased from AFFYMETRIX may be used only to perform internally (without the
assistance of Third Party unless AFFYMETRIX gives its prior written agreement)
the development activities expressly described in the Workplan, and for no other
purpose. AFFYMETRIX agrees to sell such items to ORCHID at the list prices set
forth in Schedule 2.3(d). All payments due hereunder to AFFYMETRIX shall be paid
to AFFYMETRIX within thirty (30) days following of the date of the applicable
AFFYMETRIX invoice.

3.    DISTRIBUTION AND MARKETING
      --------------------------

      3.1 Marketing Rights and Responsibilities.

      (a) ORCHID OEM Kit License Grants. ORCHID hereby grants AFFYMETRIX, under
          -----------------------------
the ORCHID Licensed Technology and upon the terms and subject to the conditions
specified herein, an exclusive, non-transferable, worldwide, royalty-free right
and license to (a) use ORCHID OEM Kits internally for research and development
purposes, and (b) directly and indirectly offer for sale, market, distribute,
demonstrate and sell ORCHID OEM Kits.

      (b) ORCHID Information License Grant. ORCHID hereby grants AFFYMETRIX
          --------------------------------
under ORCHID's intellectual property rights, and upon the terms and subject to
the conditions specified herein, an exclusive, non-transferable, worldwide,
royalty-free right and license to use, reproduce and modify information and
materials provided by ORCHID to create marketing and related sales materials for
the Orchid OEM Kits, and to directly and indirectly distribute such information
and materials (whether in modified or unmodified form) to third parties.

      (c) The transfer price for ORCHID OEM Kits developed under the Initial
Workplan and to be paid by AFFYMETRIX to ORCHID is set forth in Schedule 2.3(d)
                                                                ---------------
attached hereto, which transfer price may be reviewed every Contract Year during
the Term by ORCHID upon sixty (60) days written notice to AFFYMETRIX. The
transfer price to be paid to ORCHID by AFFYMETRIX for ORCHID OEM Kits developed
under other Workplans shall be established and set forth in such Workplans.
AFFYMETRIX may from time to time request a discount for ORCHID OEM Kits with
respect to large volume customers or other special situations and the Parties
shall negotiate any such discount in good faith. AFFYMETRIX shall assume the
risk of payment from purchasers of ORCHID OEM Kits and AFFYMETRIX shall be free
to determine the price at which it resells ORCHID OEM Kits to such purchasers.
In the event AFFYMETRIX sells an ORCHID OEM Kit for more than [*] then
AFFYMETRIX agrees to pay ORCHID an amount equal to [*] provided, however, that
if AFFYMETRIX sells an ORCHID OEM Kit for more [*], then AFFYMETRIX agrees to
pay ORCHID an additional amount equal to [*] No employee or representative of
ORCHID shall have any authority to dictate to AFFYMETRIX or its dealers the
resale prices for ORCHID OEM Kits or in any way to inhibit their pricing
discretion with respect to ORCHID OEM Kits; provided, that, AFFYMETRIX shall
                                            --------  ----
remain liable and responsible for the performance and observance of all of its
authorized dealer's duties and obligations in accordance with the terms of this
Agreement. AFFYMETRIX shall have responsibility for marketing and providing
support directly to customers for ORCHID OEM Kits.

            (i) During the Term of this Agreement, AFFYMETRIX shall obtain
      ORCHID OEM Kits exclusively from ORCHID and may not and therefore shall
      not manufacture ORCHID OEM Kits except as otherwise permitted by this
      Agreement.

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            (ii) The Parties hereby acknowledge and agree that all sales of
      ORCHID OEM Kits to AFFYMETRIX shall be controlled by the terms contained
      in this Agreement and the terms and conditions of the respective business
      forms of the Parties shall not form part of this Agreement.

      (d) Minimum Sales Amounts. The CMC will establish minimum sales amounts
          ---------------------
for ORCHID OEM Kits at least thirty (30) days prior to the end of each Contract
Year during the Term for the following Contact Year, which minimum sales shall
be included in the Initial Workplan and in each subsequent Workplan approved by
the CMC. If AFFYMETRIX does not achieve established minimum sales amounts for
two consecutive calendar quarters, then ORCHID, in its sole discretion, may
convert the exclusive license granted pursuant to section 3.1(a) to a
non-exclusive license with respect to that certain ORCHID OEM Kit. AFFYMETRIX
may terminate its exclusive license or convert said licenses to a non-exclusive
license at any time. In the event that the license is converted to a
non-exclusive license pursuant to this section, AFFYMETRIX's minimum sales
requirements for such ORCHID OEM Kit will no longer apply.

      (e) Marketing and Distribution of Custom Kits. Except as otherwise
          -----------------------------------------
described in this Agreement, ORCHID shall be solely responsible for
manufacturing, marketing and distributing Custom Kits to customers throughout
the world.

      (f) Customer Ordering Procedure; Website. ORCHID may provide a website for
          ------------------------------------
customers to order Custom Kits. If customer indicates on such website that
customer desires to purchase an ORCHID OEM Kit, ORCHID shall transfer such
customer to AFFYMETRIX's designated website through a hyperlink in the manner
requested by AFFYMETRIX and to the location within AFFYMETRIX's website
designated by AFFYMETRIX. If a customer indicates that it desires to purchase a
Custom Kit, and ORCHID desires to sell such customer a Custom Kit, ORCHID shall
within 5 days of receipt of such order provide to AFFYMETRIX all Custom Kit
Information related to such customer's purchase (including, but not limited to
projected delivery dates) to enable AFFYMETRIX to coordinate sale of applicable
AFFYMETRIX products to such customer. At such time, ORCHID shall provide
AFFYMETRIX with the complete written specifications of such Custom Kit, subject
in each such case to any confidentiality obligation ORCHID may have to any Third
Party (and provided that ORCHID shall use commercially reasonable efforts to
minimize such obligations), which information AFFYMETRIX may use to determine
appropriate instrumentation and to promote the sale of other AFFYMETRIX
products. To the extent that such information is Confidential Information of
ORCHID, AFFYMETRIX shall not disclose such information to any third party. In
addition, to assist AFFYMETRIX with its marketing efforts with respect to the
Custom Kits, ORCHID shall on a regular basis (at least once each calendar
quarter) provide AFFYMETRIX with current marketing and sales information
relating to the Custom Kits, which may include research, analysis, customer and
distribution information and competitive analysis, to the extent not subject to
confidentiality obligations to Third Parties. All such materials shall remain
the property of ORCHID. AFFYMETRIX also shall be responsible for distributing
and selling the TAG Arrays and Approved Instruments identified in Schedule 1.39
as required for use of such Custom Kits to purchasers of Custom Kits, provided
that such customers order and pay for such items according to AFFYMETRIX's
standard terms and conditions therefor.

      (g) Joint Marketing Activities. Through the CMC, the Parties shall
          --------------------------
coordinate all marketing and promotion of Products and tag arrays distributed by
the respective Parties to potential customers of SNP analysis products.

      3.2 Product Maintenance and Support.
          -------------------------------

      (a) Generic Kit and Standard Kit. The CMC shall determine the specific
          ----------------------------
mechanics of providing maintenance and support for the products marketed and
distributed pursuant to this Agreement. However, AFFYMETRIX shall be generally
responsible for front-line customer support for all Products except the Custom
Kits, and ORCHID shall provide backline support, as and when requested by
AFFYMETRIX, for ORCHID OEM Kits. Specifically, ORCHID shall provide such support
directly to one or more designated support managers of AFFYMETRIX. With respect
to ORCHID OEM Kits, ORCHID shall provide support and maintenance services to
AFFYMETRIX as further specified by and consistent with the level of support
provided by AFFYMETRIX with respect to AFFYMETRIX instruments, and there shall
be no fee to ORCHID (other than the transfer price for the kits) for rendering
such support.

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      (b) Custom Kits. ORCHID shall have responsibility for marketing and
          -----------
supporting Custom Kits. ORCHID shall use commercially reasonable efforts to
market (including, without limitation, inclusion of the Custom Kits in ORCHID's
catalogs and other promotional materials), distribute and support the Custom
Kits (including installation, training, and agrees to provide reasonable support
for customers and AFFYMETRIX as reasonably requested by AFFYMETRIX), and shall
use commercially reasonable efforts to meet market demands for Custom Kits, and
to provide support for Custom Kits. However, AFFYMETRIX shall provide backline
support, as and when requested by ORCHID for AFFYMETRIX instruments and tag
arrays used by purchasers of Custom Kits. Specifically, AFFYMETRIX shall provide
such support directly to one or more designated support managers of ORCHID
consistent with the level of support provided by AFFYMETRIX with respect to
AFFYMETRIX Approved instruments and Tag Arrays, and there shall be no fee to
AFFYMETRIX for rendering such support. If at any time during the Term of this
Agreement, ORCHID elects to discontinue or transfer to a third party the
manufacture, sale or marketing any Custom Kit pursuant to this Agreement, ORCHID
shall notify AFFYMETRIX in writing, and AFFYMETRIX shall have 30 days to advise
ORCHID of its interest in manufacturing and/or distributing and selling such
Custom Kit during the Term. If AFFYMETRIX advises ORCHID of its interest, then
the Parties shall negotiate for 60 days in good faith to determine the
appropriate royalty or other fee (if any) that AFFYMETRIX shall pay to ORCHID.
If the parties cannot reach agreement within such period, then ORCHID may
discontinue manufacture and sale of such Custom Kit or transfer such kit to a
third party, provided that if ORCHID elects to transfer such kit to a third
party, the royalty or other fees paid by such third party must be higher than
the royalty or other fees last offered by AFFYMETRIX.

      (c) Reports. Each Party shall provide the other Party with such
          -------
information about their respective products and services as is reasonably
necessary to support the development and marketing of technical support
materials, and the training of technical support personnel for ORCHID OEM Kits.
(d) Rights to Sell Kits. ORCHID represents, warrants and covenants that the
restrictions set forth in the Security Agreement dated September 11, 1998 by and
among ORCHID and GeneScreen, Inc. ("GeneScreen Security Interest") are the only
restrictions imposed on ORCHID with respect to the manufacture, use,
distribution, modification or sale by AFFYMETRIX or use by AFFYMETRIX's end
users of ORCHID OEM Kits or the Custom Kits. In the event that the obligations
of ORCHID with respect to any such restriction is reduced, ORCHID shall promptly
notify AFFYMETRIX, and promptly provide AFFYMETRIX with any information
requested by AFFYMETRIX with respect to such restriction. If Orchid believes
that it needs to access third party intellectual property in order to avoid
encumbering its ability to sell Orchid OEM Kits to AFFYMETRIX, it will discuss
this with the CMC. If no CMC agreement is reached within 30 days, then Orchid
can enter into a license at its discretion, provided that Affymetrix's rights
under this agreement will not be limited by such license.

      (d) Rights to Sell Kits. ORCHID represents, warrants and covenants that
          -------------------
the restrictions set forth in the [*] are the only restrictions imposed on
ORCHID with respect to the manufacture, use, distribution, modification or sale
by AFFYMETRIX or use by AFFYMETRIX's end users of ORCHID OEM Kits or the Custom
Kits. In the event that the obligations of ORCHID with respect to any such
restriction is reduced, ORCHID shall promptly notify AFFYMETRIX, and promptly
provide AFFYMETRIX with any information requested by AFFYMETRIX with respect to
such restriction. If Orchid believes that it needs to access third party
intellectual property in order to avoid encumbering its ability to sell Orchid
OEM Kits to AFFYMETRIX, it will discuss this with the CMC. If no CMC agreement
is reached within 30 days, then Orchid can enter into a license at its
discretion, provided that Affymetrix's rights under this agreement will not be
limited by such license.

      (e) Covenant Not to Sue. Except for the manufacture of Orchid OEM Kits by
          -------------------
AFFYMETRIX in violation of this Agreement, ORCHID agrees that it shall not
assert in any way ORCHID Licensed Technology against AFFYMETRIX, its
subsidiaries or affiliates, for the manufacture, use, import, offer for sale or
sale of AFFYMETRIX products. If ORCHID assigns ownership of any of its ORCHID
Licensed Technology to a third party not bound by this covenant not to sue
(whether directly or by operation of law), then such assignment shall be subject
ot this covenant not to sue.

4.    MANUFACTURING
      -------------

      4.1 Forecast and Supply.
          -------------------

      (a) Forecasts. At the end of each calendar quarter during the term of this
          ---------
agreement, AFFYMETRIX shall submit to ORCHID a [*] month rolling
forecast of its then current estimates of its requirements of ORCHID OEM Kits.
AFFYMETRIX's forecasts shall reflect its good-faith expectations of customer
demand and AFFYMETRIX shall act in a commercially reasonable manner to schedule
orders to avoid creating production capacity problems for ORCHID. At the end of
each calendar quarter during the Term of this Agreement, ORCHID shall submit to
AFFYMETRIX a [*] month rolling forecast of its then current estimates of
sales of Custom Kit, which forecast shall be delineated by prospective customer,
so as to permit AFFYMETRIX to validate such customers and reasonably anticipate
the quantities of AFFYMETRIX products that

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AFFYMETRIX may make available that are associated with such Custom Kit. ORCHID's
forecasts shall reflect its good-faith expectations of customer demand.

      (b) Supply. ORCHID shall supply ORCHID OEM Kits to AFFYMETRIX in
          ------
accordance with the purchase orders submitted to ORCHID by AFFYMETRIX, including
the delivery schedules specified therein; provided, that ORCHID shall not be
required to fill any purchase orders from AFFYMETRIX requesting a delivery date
earlier than [*] after receipt of such orders by ORCHID. ORCHID will maintain
adequate production capacity to ensure delivery of ORCHID OEM Kits in accordance
with such purchase orders and shall ensure that ORCHID OEM Kits meet the
Specifications set by the CMC. ORCHID hereby grants AFFYMETRIX a, worldwide,
non-transferable, non-exclusive license under ORCHID Licensed Technology, to,
(1) develop Generic Kits and Standard Kits as authorized in Section 2.2(d), (2)
make, have made, and use (which use includes the right to modify) Orchid OEM
Kits and (3) distribute, market and sell such ORCHID OEM Kits ("OEM License")
pursuant to the license granted to AFFYMETRIX as set forth in Section 3.1 (a).
AFFYMETRIX agrees to forbear from the use and exercise of the OEM License unless
and until ORCHID fails to fill any purchase order within [*] after receipt of
such order, ORCHID has otherwise breached this Agreement, or ORCHID sells
substantially all of ORCHID's business that relates to the subject matter of
this Agreement to a third party which Affymetrix believes in good faith
materially competes with Affymetrix, or which Affymetrix believes in good faith
could not or would not satisfy its obligation hereunder. If AFFYMETRIX' use and
exercise of the OEM License is caused by ORCHID'S failure to fill a purchase
order (and no other reason), AFFYMETRIX' forbearance shall be reinstated once
ORCHID demonstrates to the reasonable satisfaction of AFFYMETRIX (which shall
not be unreasonably withheld) that ORCHID is again able to fill purchase orders
within the time limits set forth in Section 4.1. During the time that AFFYMETRIX
is not forbearing from use and exercise of the OEM License, ORCHID shall provide
promptly (at no charge) to AFFYMETRIX or an approved third party designated by
AFFYMETRIX, all technical assistance and information as reasonably required to
enable AFFYMETRIX, or said third party, to supply OEM Kits as set forth in this
Section. During the time that AFFYMETRIX is not forbearing from use and exercise
of the OEM License, AFFYMETRIX will pay ORCHID a royalty of [*] of Net Sales of
ORCHID OEM Kits which fall under the new OEM License (which royalty shall be
subject to reduction in the manner and scope described in Section 2.2(d)) unless
the Parties agree in writing to a lower rate; provided, further, however, that
if AFFYMETRIX'S use and exercise of the OEM License is caused by ORCHID'S
failure to fill a purchase order (and no other reason), and ORCHID resumes
manufacture of ORCHID OEM Kits under this Section, then the transfer price paid
by AFFYMETRIX for such ORCHID OEM Kits shall be reduced by [*] until such time
as AFFYMETRIX has recovered an amount equal to any costs and expenses incurred
to exercise the OEM License (including any royalties paid under this Section.)

      (c) Packaging; Delivery. The ORCHID OEM Kits delivered hereunder shall be
          -------------------
packaged as set forth in Schedule 4.1(c), with the names and logos of both
Parties prominently displayed on each package. ORCHID shall pack such items in
standard shipping containers in the manner requested by AFFYMETRIX. ORCHID shall
assist AFFYMETRIX in obtaining any desired insurance (in amounts that AFFYMETRIX
shall determine) and transportation, via air freight unless otherwise specified
in writing, to any destinations specified in writing from time to time by
AFFYMETRIX. [*]

      (d) Payment. ORCHID shall invoice AFFYMETRIX for all ORCHID OEM Kits on or
          -------
after the date specified for delivery in AFFYMETRIX's purchase order for such
items. AFFYMETRIX shall pay all amounts specified in such invoice not later than
thirty (30) days following the date of such invoice. Any undisputed amounts not
paid when due under this Agreement shall be subject to a late fee equal to [*]
of the outstanding amount or the maximum rate permitted by law, whichever is
less.

      (e) Audit. In keeping with established bookkeeping and accounting
          -----
practices, each Party shall maintain, for a period of [*] following
the end of the Contract Year, complete and accurate books and records fully
adequate to confirm the accuracy of the royalties, fees or commissions paid and
payable under this Agreement. Each of the Parties shall have the right, [*] per
calendar year, or more frequently if an examination determines that there has
been an underpayment of more than [*], during regular business hours and upon
[*] prior written notice, to have its independent auditors make such
examination as necessary to

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verify said records and books of account. In the event that such examination
reveals an underpayment of royalties, fees or commissions payable hereunder, all
such additional royalties, fees or commissions, as the case may be, together
with interest from the date when such additional royalties, fees or commissions
would have been due shall be paid within thirty (30) days of written notice from
the auditing party of such discrepancy. Any such audit shall be at the auditing
Party's sole expense and performed by a nationally recognized, "Big Five"
accounting firm under reasonable obligations of confidentiality. In the event
that an underpayment of more than [*] is discovered, then audited Party will
reimburse the auditing Party's reasonable costs of the audit.

      4.2  Acceptance/Rejection of Deliverables.
           ------------------------------------

      (a) Testing. AFFYMETRIX shall , in conjunction with the CMC, develop
          -------
processes for evaluation and testing of ORCHID OEM Kits to be delivered
hereunder. Such processes may from time to time be reflected or incorporated in
the applicable Specifications for ORCHID OEM Kits. Orchid shall provide
certificates of analysis certifying completion of said testing and indicating
parameters defined by the CMC.

      (b) Acceptance Procedure; Inventory Carry. Upon delivery of any shipment
          -------------------------------------
of ORCHID OEM Kits to AFFYMETRIX, AFFYMETRIX shall promptly inspect the same and
shall notify ORCHID in writing no later than [*] after receipt of each such
shipment if any such shipment is found, on reasonable inspection, to be short
against order or fails to conform to the Specifications during said [*] period.
AFFYMETRIX may reject any portion of any shipment of ORCHID OEM Kits that does
not fully conform with the Specifications. If any shipment or portion thereof is
rejected by AFFYMETRIX, ORCHID shall use diligent efforts, at AFFYMETRIX's
request, to provide replacement ORCHID OEM Kits to AFFYMETRIX or to correct any
defects in such shipment as may be reasonably requested by AFFYMETRIX. Unless
ORCHID requests the return of a rejected shipment within [*] of receipt of
AFFYMETRIX's notice of rejection, AFFYMETRIX shall destroy such shipment
promptly and provide ORCHID with a certification of such destruction. To ensure
that the Parties can supply all third party requirements with accepted ORCHID
OEM Kits, ORCHID shall at all times maintain an inventory of ORCHID OEM Kits
that is equal to at least [*] of the quantities of such products sold during the
preceding calendar quarter; if no quantities of a product have been sold in the
preceding calendar quarter, the ORCHID shall maintain an inventory level equal
to at least [*] of AFFYMETRIX's forecasted quantities of such product for the
current calendar quarter. In addition, AFFYMETRIX may upon ninety (90) days'
prior notice to ORCHID elect to terminate AFFYMETRIX's obligations to purchase,
and ORCHID's obligations to supply, any such inventoried product. Any ORCHID OEM
Kit that does not meet all of the quality control and quality assurance
requirements, and any ORCHID OEM Kit that does not conform to Specifications as
set forth in this Agreement, shall not be considered delivered.

      4.3  Governmental Approval.
           ---------------------

      (a) The Parties agree to ascertain and comply with all applicable laws and
regulations and standards of industry or professional conduct in connection with
the use, distribution or promotion of Products, including without limitation,
those applicable to exportation, importation, product claims, labeling,
approvals, registrations and notifications. In addition, ORCHID agrees to obtain
AFFYMETRIX's prior written consent to all claims, labels, instructions,
packaging or the like for ORCHID OEM Kits, which consent shall not be
unreasonably withheld.

      (b) The Parties agree to keep (and make reasonably available for the other
party's use and copying) for five years after termination of this Agreement (or
longer if required by applicable law) records of all Product sales and customers
sufficient to adequately administer a recall of any Products and to cooperate
fully in any decision by the Parties to recall, retrieve and/or replace any such
Products.

5.    OWNERSHIP; LICENSES
      -------------------

      5.1 OWNERSHIP. Subject to Section 5.2 of this Agreement, ORCHID shall have
          ---------
sole and exclusive ownership of all right, title and interest in and to all
ORCHID Collaboration Technology. AFFYMETRIX shall have sole and exclusive
ownership of all right, title and interest in and to all AFFYMETRIX
Collaboration

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Technology. ORCHID and AFFYMETRIX shall each own an undivided one-half interest
(without an obligation of accounting) in all Joint Technology.

      5.2 CERTAIN IMPROVEMENTS. Notwithstanding the foregoing, (a) if ORCHID
          --------------------
creates, invents or otherwise develops any improvements to TAG Assays (each a
"TAG Improvement"), then (i) ORCHID shall (and hereby does) assign and transfer
to AFFYMETRIX all right, title and interest in and to such TAG Improvement, and
all related intellectual property rights Controlled by ORCHID related thereto,
(ii) AFFYMETRIX shall (A) grant to ORCHID a non-exclusive, non-transferable,
royalty-free license to exploit such TAG Improvement for ORCHID's internal use,
and (B) shall include internal use rights to use such TAG Improvement within the
licenses granted to Product customers, and (iii) to the extent that AFFYMETRIX
grants any Third Party a license to exploit the TAG Improvements, AFFYMETRIX
shall pay ORCHID a royalty of [*] of the Net Sales (which royalty shall be
subject to reduction in the manner and scope described in Section 2.2(d))
received by AFFYMETRIX from (and only from) use of such TAG Improvements until
ORCHID has received an aggregate of [*], at which time no further royalties or
other fees shall be due or owing ORCHID in respect of such TAG Improvement; and
(b) if AFFYMETRIX creates, invents or otherwise develops any improvements to GBA
(each a "GBA Improvement"), then (i) AFFYMETRIX shall (and hereby does) assign
and transfer to ORCHID all right, title and interest in and to such GBA
Improvement, and all related intellectual property rights Controlled by
AFFYMETRIX related thereto, (ii) ORCHID shall (A) grant to AFFYMETRIX a non-
exclusive, non-transferable, royalty-free license to exploit such GBA
Improvement for AFFYMETRIX's internal use and (B) shall include internal use
rights to use such GBA Improvements within the licenses granted to Product
customers, and (iii) to the extent that ORCHID grants any Third Party a license
to exploit the GBA Improvements, ORCHID shall pay AFFYMETRIX a royalty of [*] of
the Net Sales (which royalty shall be subject to reduction in the manner and
scope described in Section 2.2(d)) received by ORCHID from (and only from) use
of such GBA Improvements until AFFYMETRIX has received an aggregate of [*], at
which time no further royalties or other fees shall be due or owing AFFYMETRIX
in respect of such GBA Improvement. This Section 5 does not (by implication or
otherwise) extend to either party any license to any other intellectual property
or technology such as any underlying technology in any TAG Improvement or GBA
Improvement. Notwithstanding anything to the contrary, neither party shall have
any rights, licenses or obligations, whether express or implied, except as
expressly set forth in this Agreement.

6.    CONFIDENTIAL INFORMATION
      ------------------------

      6.1 CONFIDENTIALITY. ORCHID and AFFYMETRIX each recognize that the other
          ---------------
party's Confidential Information constitutes highly valuable and proprietary
confidential information. ORCHID and AFFYMETRIX each agree that during the Term
of the Collaboration and for [*] thereafter, it will keep confidential, and will
cause its employees, consultants, Affiliates and licensees and sublicensees to
keep confidential, and shall not transfer to any Third Party, any Confidential
Information of the other Party that is disclosed or transferred to it, or to any
of its employees, consultants, Affiliates and licensees and sublicensees,
pursuant to or in connection with this Agreement, except to the extent that
disclosure, or transfer, is reasonably required in accordance with the
performance of this Agreement. Each Receiving Party's nondisclosure obligation
shall not apply to information that is (i) known to the Receiving Party at the
time of disclosure thereof (as shown by written documentation); (ii) at the time
of disclosure, or thereafter, is generally publicly available without the fault
of the Receiving Party; (iii) subsequently disclosed to the Receiving Party, its
employees, or other duly designated representatives, by any Third Party not
under a secrecy obligation to the Disclosing Party; (iv) independently developed
by the Receiving Party without reference to Confidential Information of the
Disclosing Party; (v) required, by law, regulation or action of any governmental
agency or authority, to be disclosed; or (vi) disclosed by the Receiving Party
with the prior written consent of the Disclosing Party.

      6.2 NON-DISCLOSURE. ORCHID and AFFYMETRIX each agree that any disclosure
          --------------
of the Confidential Information to any of its officers, employees, consultants
or agents or of any of its Affiliates and licensees and sublicensees shall be
made only if and to the extent necessary to carry out its rights and
responsibilities under this Agreement, shall be limited to the maximum extent
possible consistent with such rights and responsibilities and shall only be made
to persons who are bound by written confidentiality obligations to maintain the
confidentiality thereof and not to use such Confidential Information except as
expressly permitted by this Agreement. Each Party shall take such action, and
shall cause its Affiliates and licensees and sublicensees to take

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such action, to preserve the confidentiality of each other's Confidential
Information as it would customarily take to preserve the confidentiality of its
own Confidential Information, and in no event, less than reasonable care.

      6.3 EMPLOYEES AND CONSULTANTS. ORCHID and AFFYMETRIX each represent that
          -------------------------
all of its employees and the employees of its Affiliates, and any consultants to
such party or its Affiliates, participating in the Collaboration's activities
who shall have access to Confidential Information of the other Party are bound
by written obligations to maintain such information in confidence and not to use
such information except as expressly permitted herein. Each Party agrees to
enforce confidentiality obligations to which its employees and consultants (and
those of its Affiliates) are obligated.

      6.4 PUBLICITY. Neither Party shall disclose the existence or the terms or
          ---------
conditions of this Agreement without the express prior written consent of the
other Party, and then only pursuant to the terms authorized by such other Party;
provided, however, that either Party may make such a disclosure to the extent
required by law or by the requirements of any nationally recognized securities
exchange, quotation system or over-the-counter market on which such Party has
its securities listed or traded. The Parties, upon the execution of this
Agreement, will agree to a news release with respect to the Collaboration for
publication in general circulation and industry periodicals. Once any written
statement is approved for disclosure by both Parties, either Party may make
subsequent public disclosure of the contents of such statement without the
further approval of the other Party.

7.    TERM AND TERMINATION
      --------------------

      7.1 TERM. Unless earlier terminated in accordance with the provisions of
          ----
Section 7.2 or Section 7.3, this Agreement shall remain in effect during the
Term of this Agreement. This Agreement will renew for additional terms of one
(1) year each upon notice by either Party to the other in writing at least
ninety (90) days prior to the expiration of the Term or any extension thereof
that it wishes to renew this Agreement.

      7.2 TERMINATION FOR BREACH. Each Party shall be entitled (but not
          ----------------------
required) to terminate this Agreement by written notice to the other Party in
the event that the other Party shall be in default of any of its obligations
hereunder or if the other Party shall have breached a covenant, representation
or warranty made in this Agreement, and shall fail to remedy any such default
within thirty (30) days of receipt of notice in the case of a breach of any
payment term of this Agreement and sixty (60) days in the case of any other
breach.

      7.3 TERMINATION FOR INSOLVENCY. The Agreement may be terminated by a Party
          --------------------------
for cause immediately upon the occurrence of any of the following events: (a) If
the other Party ceases to do business, or otherwise terminates it business
operations; or (b) the other Party shall seek protection under any bankruptcy,
receivership, trust deed, creditors arrangement, composition or comparable
proceeding, or if any such proceeding is instituted against the other. All
rights and licenses granted under this Agreement are deemed to be, for purposes
of 365(n) of the United States Bankruptcy Code, license or rights to
"intellectual property" as defined by Section 101(56) of the United States
Bankruptcy Code and the parties will retain any may fully exercise all of their
rights and licenses under this Agreement, including the right to make or have
made, sell or have sold Products. The parties agree to relief from automatic
stay provisions under Section 362 of the Bankruptcy Code.

      7.4 EFFECT OF TERMINATION. Upon any termination or expiration of this
          ---------------------
Agreement, neither Party shall be relieved of any obligations incurred prior to
such termination. Notwithstanding any termination or expiration of this
Agreement, the rights and obligations of the Parties under Sections 4.1(e), 5,
6, 7, 8, 10 and 11 shall survive and continue to be enforceable. Upon any
termination of this Agreement, each Party shall promptly return to the other
Party all written Confidential Information, and all copies thereof, of the
other, except for one copy thereof that may be retained by a Party's legal
department for archival purposes or to exercise rights described above that
survive termination. Neither Party shall incur any liability or compensation
obligation whatsoever for any damage (including, without limitation, damage to
or loss of goodwill or investment), loss or expenses of any kind suffered or
incurred by the other (or for any compensation to the other) arising from or
incident to any termination of this Agreement by such Party that complies with
the terms of the Agreement whether or not such Party is aware of any such
damage, loss or expenses.

                                    Page 13
<PAGE>

                                                                  Execution Copy

8.    INDEMNIFICATION AND INSURANCE
      -----------------------------

      8.1 ORCHID INDEMNITY. ORCHID agrees to defend AFFYMETRIX and its
          ----------------
Affiliates, their agents, directors, officers and employees ("AFFYMETRIX
Indemnitees"), at ORCHID's cost and expense, and will indemnify and hold
harmless AFFYMETRIX Indemnitees from and against any and all losses, liability,
damages, costs and expenses (including, but not limited to attorneys' fees and
expenses (collectively, "Claims") (except in cases where such Claims result from
a material breach of this Agreement or willful misconduct on the part of
AFFYMETRIX) arising from or relating to (1) any alleged infringement by
AFFYMETRIX [or its customers] of any Third Party intellectual property or
proprietary rights solely attributable to AFFYMETRIX's sale or customer's use as
intended, of all or any part of the ORCHID OEM Kits or Custom Kits (including
but not limited to Reagents) or (2) any recall of any ORCHID OEM Kits or (3)
ORCHID's breach of any representation or warranty of ORCHID set forth in this
Agreement or (4) any other materials supplied by ORCHID hereunder, or (5) death
or any injury to any person or damage to property as a result of the possession
or use of any ORCHID OEM Kits or Custom Kits.

      8.2 AFFYMETRIX INDEMNITY. Subject to the obligations of ORCHID set forth
          --------------------
in 8.1 above, AFFYMETRIX agrees to defend ORCHID and its Affiliates, their
agents, directors, officers and employees ("ORCHID Indemnitees"), at
AFFYMETRIX's cost and expense, and will indemnify and hold harmless ORCHID
Indemnitees from and against any and all Claims (except in cases where such
Claims result from a material breach of this Agreement or willful misconduct on
the part of ORCHID) arising from or relating to (1) any alleged infringement
attributable to ORCHID's sales to AFFYMETRIX of ORCHID OEM Kits or sales of
Custom Kits (provided, however, that such indemnity shall be limited to Claims
of infringement caused by Approved Instruments and TAG Arrays except to the
extent that such Claim arises from or relates to any combination of the ORCHID
OEM Kits or Custom Kits with any Approved Instrument or the TAG Array) or (2)
any recall of any an Affymetrix instrument or Commercial Probe Arrays delivered
to a customer in conjunction with ORCHID OEM Kits, or (3) AFFYMETRIX's breach of
any representation or warranty of AFFYMETRIX set forth in this Agreement or (4)
any other materials supplied by AFFYMETRIX hereunder (provided, however, that
such indemnity shall not include any Claims of infringement arising from or
relating to any combination of the ORCHID OEM Kits or Custom Kits with any
Approved Instrument or the TAG Array except to the extent that such Claim would
have existed in the absence of such combination), or (5) death or any injury to
any person or damage to property as a result of the possession or use of any
Instrument or Commercial Probe Array delivered to a customer in conjunction with
ORCHID OEM Kits.

      8.3 PROCEDURE. In the event of any such claim, the Party seeking indemnity
          ---------
shall promptly notify the indemnifying Party in writing of the claim and the
indemnifying Party shall have the right, to manage and control, at its sole
expense, the defense of the claim and the settlement thereof. The indemnified
Party shall cooperate with the indemnifying Party and may, at its option and
expense, be represented in any such action or proceeding. The indemnifying Party
shall not be liable for any settlements, litigation costs or expenses incurred
by the indemnified Party without the indemnifying Party's written authorization.
Notwithstanding the foregoing, unless and until ORCHID achieves annual revenues
of [*] million, AFFYMETRIX shall have the right at their expense, but not the
obligation to defend the AFFYMETRIX Indemnitees against any claim of
infringement without tendering defense thereof to ORCHID; provided, however,
that ORCHID may participate in such defense at its own expense

      8.4 INSURANCE. Each Party agrees to use its best efforts to procure and,
          ---------
at all times during the term of this Agreement, to maintain in full force and
effect general liability insurance coverage of at least $1,000,000 per
occurrence and at least $5,000,000 aggregate (with a deductible of no more than
$50,000 aggregate per year and which policy names the other Party as a named
insured). Each Party, upon request of the other Party, will supply such other
Party with appropriate certificates of insurance evidencing the foregoing
insurance.

9.    REPRESENTATIONS AND WARRANTIES
      ------------------------------

      9.1 Each of the Parties represents and warrants to the other Party as
follows:

                                    Page 14
<PAGE>

                                                                  Execution Copy

      9.2 The execution and delivery of this Agreement and the performance of
the transactions contemplated hereby and thereby have been duly authorized by
all appropriate corporate action, and the Party has all requisite power and
authority to enter into this Agreement and to perform its obligations hereunder
and thereunder, and each representation of this Agreement constitutes a valid
and binding obligation of each Party, enforceable against each Party in
accordance with its terms.

      9.3 The performance by the Party of any of the terms and conditions of
this Agreement on its part to be performed does not and will not constitute a
breach of any other agreement or understanding, whether written or oral, to
which it or any of its affiliates is a party.

      9.4 The Party has the right to convey all technical information and
technology conveyed hereunder and that the information and technology so
conveyed does not violate the trade secret rights or copyrights of a third party
and to its knowledge, does not violate the patent or trademark rights of a third
party.

      9.5 The Party has used reasonable commercial efforts to ensure the quality
of the materials and data provided hereunder.

10.   DISPUTE RESOLUTION
      ------------------

      10.1 SENIOR OFFICIALS. In the event of any controversy or claim relating
           ----------------
to, arising out of or in any way connected to any provision of this Agreement
("Dispute"), either Party may, by notice to the other Party, have such dispute
referred to their respective senior officials designated below or their
successors, for attempted resolution by good faith negotiations within thirty
(30) days after such notice is received. Said designated employees are as
follows:

       For ORCHID:      CEO

       For AFFYMETRIX:  CEO

      10.2 MEDIATION. In the event the designated senior officials are not able
           ---------
to resolve any such dispute within the thirty (30) day period, either Party may
invoke the provisions of this Section 11.2 by initiating mediation of the
Dispute under the then correct Center for Public Resources Procedure for
Mediation of Business Disputes. Once mediation is initiated by one Party, the
other Party shall participate in and conduct the mediation procedures in good
faith. If a negotiator intends to be accompanied at a telephone conference or a
meeting by an attorney, the negotiator for the other Party shall be given at
least three (3) days notice of such intention, and may also be accompanied by an
attorney. All negotiations pursuant to this clause are confidential and shall be
treated as compromise and settlement negotiations for the purposes of the
Federal Rules of Evidence and any state rules of evidence. All applicable
statutes of limitations and defenses based on the passage of time shall be
tolled while the negotiation and mediation procedures set forth in this Section
10.2 are pending. The Parties will take such action, if any, as may be
reasonably required to effectuate such tolling.

      10.3 ARBITRATION. Any Dispute that is not resolved pursuant to Section
           -----------
10.2 shall be finally resolved by final and binding arbitration. Whenever a
Party shall decide to institute arbitration proceedings, it shall give written
notice to that effect to the other Party. The Party giving such notice shall
refrain from instituting the arbitration proceedings for a period of ten (10)
days following such notice to allow the Parties to attempt to resolve the
dispute between themselves. If the Parties are still unable to resolve the
dispute, the Party giving notice may institute the arbitration proceeding under
the rules of the American Arbitration Association ("AAA Rules"). Arbitration
shall exclusively and solely be held in San Francisco, California. The
arbitration shall be conducted before a single arbitrator mutually chosen by the
Parties, but if the parties have not agreed upon a single arbitrator within
fifteen (15) days after notice of the institution of the arbitration proceeding,
then the arbitration will be conducted by a panel of three arbitrators. In such
case, each Party shall within thirty (30) days after notice of the institution
of the arbitration proceedings appoint one arbitrator. The presiding arbitrator
shall then be appointed in accordance with AAA Rules. No arbitrator (nor the
panel of arbitrators) shall have the power to award punitive

                                    Page 15
<PAGE>

                                                                  Execution Copy

damages or any award of multiple damages under this Agreement and such awards
are expressly prohibited. Decisions of the arbitrator(s) shall be final and
binding on the Parties.

      10.4 Notwithstanding the foregoing, if within ten (10) days of the first
occasion when the Parties' representatives meet with the arbitrator(s) either
Party gives notice by written designation of any matter relating solely to the
validity or scope of any patent as being subject to the Patent Exception
referred to above, then the matter so designated shall be set aside by the
arbitrator(s) and shall not be decided by them, provided that the matter so
designated constitutes a matter of which a United States District Court would
have jurisdiction pursuant to 28 U.S.C. (S) 1338(a), whether by way of action
for declaratory judgment or otherwise, and provided further that such matter is
submitted by the designating Party for decision by such court upon a complaint
filed within thirty (30) days of such designation, to be decided as such court
may determine. The sole jurisdiction and venue for actions related to the
subject matter hereof shall be the California state and U.S. federal courts
located in San Francisco, California. In such case, the nondesignating Party may
elect (no later than the date on which it files its answer to the complaint in
the District Court) to refer the entire matter in controversy to such court, but
if such Party does not make such election the arbitrator(s) shall proceed to
decide the remaining matter before them to the extent feasible and shall take
such other action in such regard as they deem appropriate. Judgment on the award
of the arbitrator(s) may be entered in any court having jurisdiction thereof.

      10.5 Except to the extent entry of judgment and any subsequent enforcement
may require disclosure, all matters relating to the arbitration, including the
award, shall be held in confidence by the Parties.

11.   MISCELLANEOUS.
      -------------

      11.1 Except as otherwise provided in this Agreement, neither this
Agreement nor any of the rights or obligations hereunder may be assigned by
either Party without the prior written consent of the other Party, except that
either Party may assign to an Affiliate, or to a party who acquires all or
substantially all of the relevant business relating to the subject matter of
this Agreement by merger, acquisition, sale of assets or otherwise.

      11.2 This Agreement shall be governed by and interpreted in accordance
with the laws of California (without regard to its or any other jurisdiction's
choice of law principles).

      11.3 Except as expressly and unambiguously provided herein, no right,
express or implied, is granted by this Agreement to either Party to use in any
manner the name of the other or any other trade name or trademark of the other
in connection with the performance of this Agreement.

      11.4 In the event that either Party is prevented from performing or is
unable to perform any of its obligations under this Agreement due to any act of
God; fire; casualty; flood; war; strike; lockout; failure of public utilities;
injunction or any act, exercise, assertion or requirement of governmental
authority; epidemic; destruction of production facilities; riots; insurrection;
inability to procure or use materials, labor, equipment, transportation or
energy; or any other cause beyond the reasonable control of the Party invoking
this Section if such Party shall have used its best efforts to avoid such
occurrence, such Party shall give notice to the other Party in writing promptly,
and thereupon the affected Party's performance shall be excused and the time for
performance shall be extended for the period of delay or inability to perform
due to such occurrence.

      11.5 The waiver by either Party of a breach or a default of any provision
of this Agreement by the other Party shall not be construed as a waiver of any
succeeding breach of the same or any other provision, nor shall any delay or
concession on the part of either Party to exercise or avail itself of any right,
power or privilege that it has or may have hereunder operate as a waiver of any
right, power or privilege by such Party.

      11.6 Any notice or other communication in connection with this Agreement
must be in writing and if by mail, by certified mail, return receipt requested,
and shall be effective when delivered to the addressee at the address listed
below or such other address as the addressee shall have specified in a notice
actually received by the addressor.

                                    Page 16
<PAGE>

                                                                  Execution Copy

            If to AFFYMETRIX:

            Affymetrix, Inc.
            3380 Central Expressway
            Santa Clara, California 95051
            Attention:  President

            With a copy to:

            Affymetrix, Inc.
            3380 Central Expressway
            Santa Clara, California 95051
            Attention:  General Counsel

            If to ORCHID:

            303 College Road East
            Princeton, New Jersey 08540
            Attention:  President

            With a copy to:

            Mintz, Levin, Cohn, Feris, Glovsky and Popeo, D.C.
            One Financial Center
            Boston, MA
            Attention:  Jeff Wiesen, Esq.

            11.7 Unless otherwise expressly stated to be business days, all
      references to days shall mean calendar days; provided, however, that if
      the last date or the deadline for the giving of notice or performance of
      any other act or fulfillment or satisfaction of any condition set forth in
      this Agreement shall fall on a day which is not a business day, then the
      time for the giving of such notice or performance of such act or
      fulfillment or satisfaction of such condition shall be extended to the
      next business day. As used herein, the term "business days" shall mean all
      days other than Saturdays, Sundays or state or federal holidays.

            11.8 Nothing herein shall be deemed to constitute either Party as
      the agent or representative of the other Party, or both Parties as joint
      venturers or partners for any purpose. Each Party shall be an independent
      contractor, not an employee or partner of the other Party, and the manner
      in which a Party renders its services under this Agreement shall be within
      such Party's sole discretion. Neither Party shall be responsible for the
      acts or omissions of the other Party, and neither Party will have
      authority to speak for, represent or obligate the other Party in any way
      without prior written authority from the other Party.

            11.9 This Agreement and the Schedules hereto (which Schedules are
      deemed to be a part of this Agreement for all purposes) contain the full
      understanding of the Parties with respect to the subject matter hereof and
      supersede all prior understandings and writings relating thereto. No
      waiver, alteration or modification of any of the provisions hereof shall
      be binding unless made in writing and signed by the Parties by their
      respective officers thereunto duly authorized.

            11.10 The headings contained in this Agreement are for convenience
      of reference only and shall not be considered in construing this
      Agreement.

            11.11 In the event that any provision of this Agreement is held to
      be unenforceable because it is invalid or in conflict with any law of any
      relevant jurisdiction, the validity of the remaining provisions shall not
      be affected, and there shall be substituted for the provision at issue a
      valid, legal and operative provision as similar as possible to the
      provision at issue.

                                    Page 17
<PAGE>

                                                                  Execution Copy

            11.12 This Agreement shall be binding upon and inure to the benefit
      of the Parties hereto and their successors and permitted assigns.

            11.13 None of the provisions of this Agreement shall be for the
      benefit of or enforc eable by any third party.

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

            11.15 The Parties hereto acknowledge and agree that: (i) each party
      and its counsel reviewed and negotiated the terms and provisions of this
      Agreement and have contributed to its revision; (ii) the rule of
      construction to the effect that any ambiguities are resolved against the
      drafting party shall not be employed in the interpretation of this
      Agreement; and (iii) the terms and provisions of this Agreement shall be
      construed fairly as to all parties hereto and not in a favor of or against
      any party, regardless of which party was generally responsible for the
      preparation of this Agreement.

          IN WITNESS WHEREOF, the Parties hereto have caused this Agreement to
be executed in their names by their properly and duly authorized officers or
representatives as of the date first above written.

AFFYMETRIX, INC.                       ORCHID BIOCOMPUTER, INC.

By: /s/ Stephen Fodor, Ph.D            By: /s/ Dale R. Pfost, Ph.D.
    -----------------------------          -----------------------------
        Stephen Fodor, Ph.D                    Dale R. Pfost, Ph.D.

 Its: Chief Executive Officer          Its: Chief Executive Officer
      ---------------------------           ----------------------------

Date: November 16, 1999                Date: November 5, 1999
      ---------------------------            ---------------------------

                                    Page 18
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.13
-------------

TRANSFER OF CUSTOM KIT ORDER INFORMATION

For each custom kit order, Orchid will:
 . email to point of contact at AFFX
 . within 5 business days of receipt of custom order by Orchid
 . Orchid will notify customer of the obligation to notify AFFX
 . Email to include the following bill to and ship to information:
  . Customer name
  . Address
  . Phone number
  . Fax number
  . Email address
 . Size and nature of custom order (# samples, # snps, multiplex)
 . Delivery date for custom order

AS PART OF THE STANDING CMC AGENDA, ORCHID WILL PROVIDE TO AFFYMETRIX A LIST OF
SNPS ORDERED FOR CUSTOM KITS AND THE QUANTITY ORDERED FOR CONSIDERATION TO BE
INCLUDED IN FUTURE STANDARD KITS AND TO EVALUATE SIMILARITIES BETWEEN CUSTOM
KITS AND STANDARD KITS.  AFFYMETRIX MAY AUDIT ORCHID TO VERIFY THIS INFORMATION.

ORCHID's Obligations contained in this schedule are subject to any
confidentiality obligation ORCHID may have to any Third Party (provided that
ORCHID shall use commercially reasonable efforts to minimize such obligations)
and such information shall exclude ORCHID proprietary Primers and SNPs.

                                    Page 19
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.15
-------------

END USER LICENSE

The purchase price of this product includes a limited, non-transferable license
under U.S. Patent 5,888,819 and its foreign counterparts owned by Orchid
Biocomputer, Inc. of Princeton NJ to use only this amount of the product to
practice Genetic Bit Analysis(TM) primer extension technology solely for use
with Affymetrix Tag Arrays in the Affymetrix GeneChip Systems for Research
Purposes and explicitly excludes use of this product for any clinical use or in
any other instrument.  Information about purchasing licenses to practice Genetic
Bit Analysis(TM) primer extension technology for clinical use or in other
systems may be obtained by contacting the Senior Director for Business
Development at Orchid Biocomputer, Inc. at (609) 750-2200.

                                    Page 20
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.20
-------------

ORCHID END USER TECHNOLOGY

US Patent 5,888,819 (and all foreign counterparts thereof)

                                    Page 21
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.22
-------------

ORCHID LICENSED TECHNOLOGY

US Patent 5,888,819

ORCHID LICENSED TECHNOLOGY includes any continuations, continuations-in-part,
divisionals, extensions, re-exams or re-issues and any foreign counterparts
thereof

                                    Page 22
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.37
-------------

SPECIFICATIONS FOR ORCHID OEM KITS

Added to agreement as approved by CMC

                                    Page 23
<PAGE>

                                                                  Execution Copy

SCHEDULE 1.39
-------------

DEFINITION OF PRODUCTS AND WORKPLAN FOR COLLABORATION

Products from Orchid
--------------------

[*]

                                    Page 24

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

<PAGE>

                                                                  Execution Copy

[*]

                                    Page 25

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

<PAGE>

                                                                  Execution Copy

[*]

                                    Page 26

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

<PAGE>

                                                                  Execution Copy

[*]
                                    Page 27

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

<PAGE>

SCHEDULE 2.3(D)
---------------

PRICING AND TIMING

[*]

                                    Page 28

[*] CONFIDENTIAL MATERIAL OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND
    COMMISSION. ASTERISKS DENOTE SUCH OMISSIONS.

<PAGE>

                                                                  Execution Copy

SCHEDULE 4.1(C)
---------------

LABELING AND PACKAGING REQUIREMENTS

LABEL TO BE INCLUDED IN PACKAGING OF ALL ORCHID KITS

EXCEPT AS EXPRESSLY SET FORTH HEREIN, NO RIGHT TO COPY, MODIFY, DISTRIBUTE, MAKE
DERIVATIVE WORKS OF, PUBLICLY DISPLAY, MAKE, HAVE MADE, OFFER TO SELL, SELL, OR
IMPORT PROBE ARRAYS OR ANY OTHER PRODUCT PROVIDED HEREUNDER IS CONVEYED OR
IMPLIED BY THE PROBE ARRAYS, INSTRUMENTS, SOFTWARE, REAGENTS OR ANY OTHER ITEMS
PROVIDED HEREUNDER. ALL PRODUCTS (INCLUDING THE PROBE ARRAYS, INSTRUMENTS,
SOFTWARE, AND REAGENTS) DELIVERED HEREUNDER ARE LICENSED TO BUYER FOR RESEARCH
USE ONLY. THIS LIMITED LICENSE PERMITS ONLY THE USE BY BUYER OF THE PARTICULAR
PRODUCT(S) THAT BUYER PURCHASES FROM AFFYMETRIX OR ITS REPRESENTATIVE(S) AND
DOES NOT PERMIT THE USE OF SUCH PRODUCTS IN A MANNER OR IN CONNECTION WITH OTHER
PRODUCTS SUCH THAT THE INTELLECTUAL PROPERTY RIGHT(S) OF AFFYMETRIX OR ANY THIRD
PARTY ARE INFRINGED. IN PARTICULAR, NO RIGHT TO MAKE, HAVE MADE, IMPORT,
DISTRIBUTE, OR USE PROBE ARRAYS OTHER THAN THOSE OF AFFYMETRIX IS IMPLIED
THROUGH THE INSTRUMENTS OR SOFTWARE CONVEYED HEREUNDER.  BUYER AGREES NOT TO
EXCEED THE SCOPE OF THIS LIMITED LICENSE OR REUSE OR ALLOW ANYONE TO REUSE A
PROBE ARRAY.

LABEL FOR TAG ARRAY - TO BE INCLUDED IN PACKAGING.

Orchid Biocomputer, Inc. (Princeton NJ ("Orchid")) hereby notifies you that The
Genetic Bit Analysis (GBA(R)) primer extension technology is covered by patents
owned by Orchid.  Orchid has exclusive and non-exclusive licenses available for
various applications of the GBA(R) primer extension technology, and Orchid and
its licensees provide end-user licenses within their designated fields. These
licenses have different terms depending on the field, and different rules may
apply in different countries. In the US and most other nations, the user should
always have a proper license to perform GBA(R). THE PURCHASE OF THIS GENECHIP(R)
PROBE ARRAY DOES NOT EXPRESSLY OR IMPLICITLY GRANT ANY LICENSE TO THE GBA(R)
PRIMER EXTENSION TECHNOLOGY THROUGH THIS PURCHASE

A license for performing the GBA(R) primer extension technology which is covered
by U.S. Patent 5,888,819 and its foreign counterparts may be obtained directly
from Orchid or by the purchase of reagents kits from Affymetrix.

 . Labeling for Orchid Kit:  [Vern please fill in].  Add labeling for all kits
  that they can only be used with GeneChip probe arrays. Legal to define
  specific wording including limitations to RUO, patent references, etc.

 . Both company's logos on kit packaging for standard and generic kits

                                    Page 29
<PAGE>

                                                                  Execution Copy

                   AMENDMENT NO. 1 TO COLLABORATION AGREEMENT

     This Amendment No. 1 to Collaboration Agreement (this "Amendment") is made
                                                            ---------
as of this 12th day of November, 1999 (the "Amendment Effective Date"), by and
                                            ------------------------
between Orchid Biocomputer, Inc., a Delaware corporation with a principal place
of business at 101 College Road East, Princeton, New Jersey 08540 ("ORCHID") and
Affymetrix, Inc., a Delaware corporation with a principal place of business at
3380 Central Expressway, Santa Clara, California 95051  ("AFFYMETRIX").
Capitalized terms used and not otherwise defined herein shall have the
respective meanings ascribed to them in the Collaboration Agreement by and
between ORCHID and AFFYMETRIX dated as of November 5, 1999 (the "Agreement").
                                                                 ---------

     WHEREAS, the parties hereto desire to amend the Agreement as set forth
herein.

     NOW, THEREFORE, for good and valuable consideration, the receipt and
sufficiency of which is hereby acknowledged, the parties hereto hereby agree as
follows:

     1.  Amendments.
         ----------

        1.1.  The definition of "Orchid Licensed Technology" contained within
 Section 1.22 of the Agreement is hereby amended by adding the following at the
 end of the first sentence thereof:

        "including without limitation the software and associated algorithms
        necessary to assign genotype and allele calls" .

        1.2.  Schedule 1.22 of the Agreement is hereby amended by adding the
 following:

        "U.S. Patent 5,762,876*

        *ORCHID agrees that, in addition to the licenses granted in Section 3.1
        and 4.2, AFFYMETRIX will have the royalty-free, perpetual right and
        license to directly and indirectly create and modify software
        embodiments of the above patent and to directly and indirectly use,
        distribute and license such embodiments (including the right to use and
        modify such embodiments) to third party customers of its Tag Arrays."

     2. Additional Warranties  ORCHID represents, warrants and covenants that
        ---------------------
there is no technology or intellectual property that ORCHID has not described to
Affymetrix in writing prior to the Effective Date (and which Affymetrix has
acknowledged receiving) that ORCHID contemplates or anticipates may be
incorporated into the Orchid Licensed Technology or may be necessary or useful
either for development, use, distribution or sale of the basic genotype and
<PAGE>

                                                                  Execution Copy

allele calling functionality of the Products, or for use of TAG Arrays or
Approved Instruments with Products.

     3. Miscellaneous.  Except as amended hereby, the Agreement shall remain in
        -------------
full force and effect.  This Amendment may be executed in one or more
counterparts, each of which shall be deemed an original.

                  [Remainder of page intentionally left blank]

                                      31

<PAGE>

                                                                  Execution Copy

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

                              ORCHID BIOCOMPUTER, INC.

                              By:    /s/ Donald R. Marvin
                                     ----------------------------------------
                                     Donald R. Marvin

                              Title: Chief Operating Officer
                                     and Senior Vice President
                                     ----------------------------------------
                              Date:  November 12, 1999
                                     ----------------------------------------

                              AFFYMETRIX, INC.

                              By:    /s/ Stephen P.A. Fodor, Ph.D.
                                     ----------------------------------------
                                     Stephen P.A. Fodor, Ph.D.

                              Title: Vice President
                                     ----------------------------------------
                              Date:  November 18, 1999
                                     ----------------------------------------

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