<PAGE>

                                                                    Exhibit 10.7


                                 Patent License

                              Gemini Research Ltd.

                                      and

                                Affymetrix, inc.
<PAGE>

                                Table of Contents

1.    INTRODUCTION......................................................     1

2.    DEFINITIONS.......................................................     1

3.    GRANT OF LICENSE..................................................     2

4.    OBLIGATIONS OF AFFYMETRIX.........................................     3

5.    FINANCIAL PROVISIONS..............................................     3

6.    ACCOUNTS..........................................................     5

7.    INTELLECTUAL PROPERTY PROTECTION AND PROCEEDINGS..................     5

8.    DURATION AND TERMINATION..........................................     6

9.    NATURE OF AGREEMENT...............................................     7

10.   APPLICABLE LAW AND JURISDICTION...................................     8

11.   NOTICES AND SERVICE...............................................     8

12.   MISCELLANEOUS.....................................................     9
<PAGE>


This AGREEMENT is dated ___________ BETWEEN: Gemini Research Ltd. whose
registered office is at 162 Science Park, Milton Road, Cambridge, CB4 4GH,
England ("GEMINI"), and Affymetrix, Inc., a company incorporated in the State of
Delaware, USA whose principal office is at 3380 Central Expressway, Santa Clara,
California 95051, USA ("Affymetrix").

1.    INTRODUCTION

      1.1.     GEMINI is the owner of relating to certain sequences as a gene
               family known as COLA1 ("the Gene") which has potential uses in
               relation to osteoporosis, in respect of which GEMINI has applied
               to obtain patent protection in the United States and elsewhere.

      1.2.     Affymatrix wishes to obtain a License under GEMINI's patents and
               patent applications in relation to the Gene to order to include
               genetic sequences relating to the Gene which fall within the
               claims of such patents and patent applications in probe arrays,
               and GEMINI is willing to grant a License to Affymetrix to do so,
               on the terms and conditions of this Agreement.

2.    DEFINITIONS

      2.1.     "Affiliate" means, in relation to either party, a company which
               controls that party, or is controlled by that party or by a
               company which controls that party; and for these purposes a
               company controls another company if, either directly or
               indirectly through one or more other companies, it can a)
               exercise a majority of the votes attached to the shares in the
               other company; or b) appoint or remove a majority of the board of
               directors of the other company.

      2.2.     "Effective Date" means January 1, 1999.

      2.3.     "Field" *

      2.4.     "Genetic Sequence" means a DNA sequence comprising all or part
               of a gene, the allele of a gene or an Express Sequence Tag (EST).

      2.5.     "Licensed Patents" means the patent applications and/or patent
               details of which are given in the Schedule, any other patent
               application made by GEMINI at any time during the Term in any
               part of the Territory in respect of the Gene or any Genetic
               Sequence relating thereto, any patent obtained in pursuance of
               any such application, any extension, reissue, division,
               continuation or continuation-in-part of any such application or
               patent and any patent of addition, supplementary protection
               certificate or similar rights based on any such patent.

      2.6.     "Licensed Products" means any product within the Field which, but
               for the License


                                        1

               Confidential Treatment Requested and the Redacted
               Material has been separately filed with the Commission
<PAGE>

               granted under this Agreement, would infringe a Valid Claim of any
               of the Licensed Patents in the relevant country or territory.

      2.7.     "Net Sales Value" means, in relation to any of the Licensed
               Products where the Licensed Product is sold by Affymetrix or any
               of its Affiliates to a third party (other than to Affymetrix or
               any of its Affiliates) on arm's length terms, the grossed amount
               invoiced less (i) any value added tax or other sales tax, (ii)
               any packaging, packing, freight, warehousing, carriage and
               insurance charges, to the extent that any of those items are
               included in the amount so invoiced, and after deducting any
               allowances for lost or damaged merchandise or returns, but
               without deducting (or, to the extent that they have been deducted
               from the price, after adding back) any discounts or rebates
               granted to the customer on account of the quantity purchased or
               promptness of payment or otherwise. Where the Licensed Product is
               so sold otherwise than on arm's length terms, but is subsequently
               sold on arms length terms, the gross amount invoiced under the
               first such arm's length sale, calculated in accordance with sales
               on an arms length basis as described above. For purposes of
               clarity, Net Sales Value will primarily relate to sales of
               Affymetrix probe arrays not associated software license fees,
               reagent costs, or technology access fees.

      2.8.     "Patent" means any patent application or patent, including any
               extension, reissue, division, continuation or
               continuation-in-part of any such application or patent, and any
               patent of addition, supplementary protection certificate or
               similar rights based on any patent, and the right to make any
               application for any such protection in any part of the world.

      2.9.     "Quarter" means the period of three months beginning on the
               Effective Date, each successive period of three months during the
               Term and any shorter period to the date of termination of this
               Agreement, and "Quarterly" has a corresponding meaning.

      2.10.    "Term" means the period during which this Agreement continues in
               force pursuant to Section 8.1.

      2.11.    "Territory" means all countries and territories of the world.

      2.12.    "Valid Claim" means a claim of any Patent (whether pending or
               issued) which has not expired, withdrawn, been abandoned or
               surrendered or been refused, revoked or held invalid in an
               unappealed or unappealable final decision rendered by a court of
               competent jurisdiction in the relevant country or territory.

      2.13.    "Year" means each period of four consecutive Quarters during the
               Term, and any shorter period to the termination of this
               Agreement.

3.    GRANT OF LICENSE

      3.1.     GEMINI hereby grants to Affymetrix, subject to the provisions of
               this Agreement, an exclusive, worldwide License under the
               Licensed Patents to make, have made, import, distribute, use and
               sell the Licensed Products.


                                        2
<PAGE>

      3.2.     Affymetrix shall be entitled to exercise the rights granted under
               Section 3.1 by itself or through any of its Affiliates, provided
               that Affymetrix shall at all times during the Term ensure the
               observance and performance by every such Affiliate of the
               provisions of this Agreement and indemnify GEMINI against any
               loss, damages, costs, claims or expenses which are awarded
               against or incurred by GEMINI as a result of any breach by such
               Affiliate of any of the provisions of this Agreement, as if the
               breach had been that of Affymetrix.

      3.2.     GEMINI reserves to itself all rights in respect of the Gene (or
               any Genetic Sequence relating thereto) and the Licensed Patents,
               except as expressly provided for under this Agreement.

      3.4.     Affymetrix agrees to use commercially reasonable efforts to
               commercialize Licensed Products within twenty-four (24) months
               of the Effective Date. If Affymetrix has not commercialized
               such products, Affymetrix and GEMINI shall meet and confer.
               If Affymetrix is not able to show to GEMINI reasonable
               satisfaction that such commercially reasonable efforts have been
               made, then GEMINI may, at its option, convert this license to a
               non-exclusive basis.

4.    OBLIGATIONS OF AFFYMETRIX

      4.1.     Affymetrix shall provide GEMINI with a Quarterly report as to the
               manufacture and sale of and any other dealings in the Licensed
               Products.

      4.2.     Affymetrix shall use commercially reasonable efforts at all times
               during the Term to promote and expand the sale of the Licensed
               Products in the Territory and to create and satisfy market demand
               for them.

5.    FINANCIAL PROVISIONS

      5.1.     In consideration of the rights granted under this Agreement,
               Affymetrix shall, subject to the following provisions, pay to
               GEMINI a) the non-refundable and non-creditable sum of * on
               the Effective Date; and b) * per year for each of the next
               fifteen (15) years (or for so long as the patents remain in
               force, whichever is sooner); and c) royalties in respect of
               all Licensed Products manufactured by or for Affymetrix or any
               of its Affiliates which are sold, or used or otherwise
               disposed of on a commercial basis (otherwise than to
               Affymetrix or another such Affiliate of Affymetrix) by
               Affymetrix in any country or territory at any time during the
               Term, at the rate specified in Section 5.2


      5.2.     The rate referred to in Section 5.1 shall be a percentage of
               the * in question calculated as the product of the following
               formula:

                   *


                                        3

               Confidential Treatment Requested and the Restated
               Material has been separately filed with the Commission
<PAGE>


      5.3      If at any time during the Term any of the Genetic Sequences
               represented on any of the Licensed Products ceases to be
               within a Valid Claim of any of the Licensed Patents (and does
               not remain within any other such Valid Claim) in the relevant
               country or territory, then that Genetic Sequence shall not be
               taken into account in the relevant country or territory for
               the purposes of calculating the * in the above formula.

      5.4.     * of the annual fee set forth in Section 5.1 shall be
               creditable against future royalties payable under Section 5.2

      5.5.     Within 30 days after each Quarter, Affymetrix shall send to
               GEMINI a written statement showing the quantity of the Licensed
               Products sold or otherwise disposed of on a commercial basis by
               Affymetrix or any of its Affiliates (showing separately any
               quantity so sold to Affymetrix or any of its Affiliates) during
               that Quarter in each country or territory; the Net Sales Value in
               respect of that quantity of Licensed Products and any further
               information necessary for the calculation of such Net Sales Value
               and/or the formula contained in Section 5.2; and the amount of
               the royalties payable under Section 5.1 in respect of that
               quantity.

      5.6.     All royalties or other sums payable under this Agreement shall be
               paid in pounds sterling or such other currency as GEMINI may
               specify in writing from time to time, and where any royalties are
               calculated in a currency other than sterling, they shall be
               converted into sterling by reference to the relevant foreign
               exchange buying rate for the currency in question of Wall Street
               Journal at the close of business in California on the last day of
               the Quarter or Year to which they relate.

      5.7.     All royalties or other sums payable under this Agreement are
               exclusive of bank charges and value added tax or other applicable
               taxes or duties, for which Affymetrix shall be additionally
               liable, and shall be paid in cleared funds to such bank account
               or in such other manner as GEMINI may specify from time to time,
               without any set off, deduction or withholding except any tax
               which Affymetrix is required by law to deduct or withhold, and if
               Affymetrix is required to make any such tax deduction or
               withholding, Affymetrix shall do all things in its power which
               may be necessary to enable or assist GEMINI to claim exemption
               from or (if that is not possible) a credit for the deduction or
               withholding under any applicable double taxation or similar
               agreement from time to time in force, and shall from time to time
               give GEMINI proper evidence as to the deduction or withholding
               and payment over of the tax, deducted or withheld.

      5.8.     If Affymetrix fails to pay in full any royalties or other sums
               payable under this Agreement on the date as within the period
               specified for payment, the amount outstanding shall be interest,
               both before and after any judgement, at the rate of 2


                                        4

               Confidential Treatment Requested and the Restated
               Material has been separately filed with the Commission
<PAGE>

               (two) per cent, per annum above the base rate of prime in the
               United States from time to time from that date or the last day of
               that period until that amount is paid in full to GEMINI.

      5.9.     The period in respect of which royalties shall be payable
               pursuant to Section 5.1 is, in respect of each country or
               territory in the Territory, the period during which any of the
               Patents remains in force in that country or territory.

6.    ACCOUNTS

      6.1.     Affymetrix shall -

         6.1.1.   keep, and procure that each of its Affiliates keeps, true and
                  accurate accounts and records in sufficient detail to enable
                  the amount of all royalties or other sums payable under this
                  Agreement to be determined;

         6.1.2.   at the reasonable request of GEMINI from time to time, allow
                  GEMINI or its agent (or procure that GEMINI or its agent is
                  allowed) to inspect those accounts and records and, to the
                  extent that they relate to the calculation of those royalties
                  or other sums, to take copies of them.

         6.1.3.   If, following any inspection pursuant to Section 6.1(b),
                  GEMINI's auditors certify to GEMINI and Affymetrix that the
                  amount of the royalties paid in respect of any Quarter or Year
                  pursuant to Section 5.5 falls short of the amount of the
                  royalties which were properly payable in respect of that
                  Quarter or Year under Section 5.1, Affymetrix shall within 7
                  (seven) days of the date of certificate pay the shortfall to
                  GEMINI and, if the shortfall exceeds 10% (ten per cent) of the
                  amount properly payable, Affymetrix shall also reimburse to
                  GEMINI on demand the reasonable costs and expenses of GEMINI
                  in making the inspection.

7.    INTELLECTUAL PROPERTY PROTECTION AND PROCEEDINGS

      7.1.     GEMINI shall permit Affymetrix to have reasonable input to the
               prosecution of any applications for Patent or other forms of
               protection subsisting in the Territory in respect of the Gene, or
               any Genetic Sequence relating thereto. Gemini shall reasonably
               inform Affymetrix of all correspondence with or from the relevant
               patent offices.

      7.2.     GEMINI shall make all necessary filings and pay all requisite
               renewal fees to maintain the Licensed Patents in the Territory;
               provided that if GEMINI wishes to abandon any of the Licensed
               Patents (whether applied for or issued) in any country or
               territory, GEMINI shall give a written notice to Affymetrix
               offering to assign the same to Affymetrix at the expense of
               Affymetrix but otherwise free of charge, and if

         7.2.1.   Affymetrix accepts the offer in writing within 30 days, GEMINI
                  shall accordingly assign the Licensed Patent in question to
                  Affymetrix forthwith; or

         7.2.2.   Affymetrix does not accept the offer in writing within 30
                  days, GEMINI shall


                                        5
<PAGE>

                  have no further obligation with respect to the Licensed Patent
                  in question and shall be free to abandon the same; and

         7.2.3.   any Licensed Patent which is so assigned or abandoned shall
                  thereafter be deemed not to exist (and not to contain any
                  Valid Claim) in the relevant country or territory for the
                  purposes of Section 5.2.

      7.3.     The parties shall, at the request of either of them and at the
               expense of Affymetrix but for no further consideration, enter
               into such formal Licenses relating so the Licensed Patents as may
               be necessary or desirable in accordance with the relevant law and
               practice in each part of the Territory for the protection of
               either of the parties or the Licensed Patents.

      7.4.     Each party shall fully notify the other as soon as practicable
               after it becomes aware of -

         7.4.1.   any actual, threatened or suspected infringement of any of the
                  Licensed Patents; and

         7.4.2.   any proceedings commenced against it in which the validity or
                  GEMINI's ownership of any of the Licensed Patents is
                  challenged or it is alleged that the use of the Gene or any
                  Genetic Sequence relating thereto or the Licensed Patents
                  pursuant to the Agreement infringes the Intellectual Property
                  or other rights of any third party.

      7.5.     Each party shall do all such things and execute all such
               documents as may reasonably be required of it by the other party
               for the purpose of assisting the other party in bringing or
               defending any proceedings relating to the Licensed Patents, and
               the party receiving the assistance shall, unless otherwise agreed
               with the other party, bear the cost of providing it.

8.    DURATION AND TERMINATION

      8.1.     This Agreement shall come into force on the Effective Date and,
               unless rightfully terminated earlier for any reason, shall
               continue in force for so long as any of the Licensed Patents
               remains in force.

      8.2      GEMINI may forthwith terminate this Agreement by giving written
               notice to Affymetrix if Affymetrix commits any material breach of
               this Agreement and, if the breach is capable of remedy, fails to
               remedy it within 30 days after being giving a written notice
               containing full particulars of the breach and requiring it to be
               remedied.

      8.3.     For the purposes of Section 8.2, a breach shall be considered
               capable of remedy if the party in breach can comply with the
               provision in question in all respects other than as to the time
               of performance.

      8.4.     The rights given by this Section 8 to terminate this Agreement
               for any breach shall not prejudice any other right or remedy of
               either party in respect of the breach concerned


                                        6
<PAGE>

               any other

9.    NATURE OF AGREEMENT

      9.1.     Subject to Section 3.2, this Agreement is personal to Affymetrix
               which may not assign, mortgage, charge or sub-license any of its
               rights or sub-contract or otherwise delegate any of its
               obligations under this Agreement except in the Licensed Field.
               Affymetrix may assign this Agreement to an entity acquiring
               substantially all of the relevant business assets or stock of
               Affymetrix.

      9.2.     Nothing in this Agreement shall create, or be deemed to create, a
               partnership, or the relationship of principal and agent, between
               the parties.

      9.3.     This Agreement contains the entire agreement between the parties
               with respect to its subject matter and may not be modified except
               by an instrument in writing signed by the duly authorised
               representatives of the parties.

      9.4.     GEMINI warrants to Affymetrix that -

         9.4.1.   it has the authority to enter into this Agreement and to grant
                  the rights granted under this Agreement;

         9.4.2.   it has not granted and will not during the Term grant to any
                  third party any rights which are inconsistent with the rights
                  granted under this Agreement;

         9.4.3.   the execution by GEMINI of, and the performance of its
                  obligations under, this Agreement require no governmental or
                  other approvals or, if required, all such approvals have been
                  obtained.

      9.5.     Affymetrix warrants to GEMINI that -

         9.5.1.   it has the authority to enter into this Agreement;

         9.5.2.   the execution by Affymetrix of, and the performance of its
                  obligations under, this Agreement require no governmental or
                  other approvals or, if required, all such approvals have been
                  obtained.

      9.6.     Each party acknowledges that, in entering into this Agreement, it
               does not do so in reliance on any warranty or other provision
               except as expressly provided in this Agreement, and any
               conditions, warranties or other terms implied by statute or
               common law are excluded to the fullest extent permitted by law.

      9.7.     GEMINI does not give any warranty, representation or undertaking-

         9.7.1.   as to the efficacy or usefulness of the Gene or any Genetic
                  Sequence relating thereto or the Licensed Patents; or

         9.7.2.   as to the volumes or quality of the Licensed Products which
                  may be manufactured


                                        7
<PAGE>

                  through [ILLEGIBLE] sequence relating thereto or the Licensed
                  Patents; or

         9.7.3.   that any of the Licensed Patents is or will be valid or
                  subsisting or that any of the applications within the Licensed
                  Patents will proceed to grant; or

         9.7.4.   that the use of the Gene or any Genetic Sequence relating
                  thereto will not infringe the Intellectual Property or other
                  rights of any other person.

      9.8.     GEMINI shall not be liable to Affymetrix by reason of any
               representation (unless fraudulent) or the breach of any implied
               condition, warranty or other term or any duty at common law or
               under any statute, or under any express term of this Agreement,
               for any loss, damages, costs, expenses or other claim for
               compensation whatsoever, whether occasioned by the negligence of
               GEMINI, its servants or agents or otherwise, which arises out of
               or in connection with this Agreement, or which in any way relates
               to the Gene or any Genetic Sequence relating thereto, or the
               manufacture, use or sale of any other dealing in any of the
               Licensed Products by or for Affymetrix or any of its Affiliates,
               to the extent that the claim is for loss of profits, contracts,
               goodwill or anticipated savings or for wasted expenditure, or for
               any indirect, special or consequential loss or damages.

      9.9.     Affymetrix shall indemnify GEMINI against any loss, damages,
               costs or expenses which are awarded against or incurred by
               GEMINI as a result of any claim or threatened claim concerning
               the use by Affymetrix of the Gene or any defect in or otherwise
               in connection with the manufacture, use, sale of or any other
               dealing in any of the Licensed Products by or for Affymetrix.

      9.10.    No failure or delay by either party in exercising any of its
               rights under this Agreement shall be deemed to be a waiver of
               that right, and no waiver by either party of a breach of any
               provision of this Agreement shall be deemed to be a waiver of any
               subsequent breach of the same or any other provision.

      9.11.    If any provision of this Agreement is held by any court or other
               competent authority to be invalid or unenforceable in whole or in
               part, the other provisions of this Agreement and the remainder of
               the affected provision shall continue to be valid.

10.   APPLICABLE LAW AND JURISDICTION

      10.1.    Except as provided in Section 10.2, California law shall apply to
               the whole of this Agreement, and each party agrees to submit to
               the exclusive jurisdiction of the California courts.

      10.2.    Any question arising out of this Agreement as to the construction
               or effect of any of the Licensed Patents shall be decided in
               accordance with the laws of the country in which the Licensed
               Patent in question has been granted or filed.

11.   NOTICES AND SERVICE


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<PAGE>

                  [ILLEGIBLE] authorised by this Agreement to be given by either
                  party to the other shall be given by -

         11.1.1.  delivering it by hand; or

         11.1.2.  sending it by pre-paid air-mail; or

         11.1.3.  sending it by facsimile transmission or similar means of
                  communication; to the other party at the address shown in the
                  introduction.

      11.2.    For this Agreement, any notice or other information sent by post
               in the manner provided by Section 11.1 which is not returned to
               the sender as undelivered shall be deemed to have been given on
               the tenth day after the envelope containing it was so posted; and
               proof that the envelope containing any such notice or other
               information was properly addressed, pre-paid, registered and
               posted, and that it has not been so returned to the sender, shall
               be sufficient evidence that the notice or other information has
               been duly given.

      11.3.    Any notice or other information sent by facsimile transmission or
               similar means of communication shall be deemed to have been duly
               given on the date of transmission, provided that a confirming
               copy of it is sent as provided in Section 11.1 to the other party
               at the address given in Section 11.4 within 24 hours after
               transmission.

      11.4.    Service of any legal proceedings concerning or arising out of
               this Agreement shall be effected by either party by causing the
               document in question to be delivered to the other party at its
               registered or principal office, or any other address which is
               notified in writing from time to time to the party serving the
               proceedings.

12.   MISCELLANEOUS

      12.1.    Each party shall from time to time do all such acts and execute
               all such documents as may be reasonably necessary in order to
               give effect to the provisions of this Agreement.

      12.2.    Except as otherwise provided in this Agreement, the parties shall
               bear their own costs of and incidental to the preparation,
               execution and implementation of this Agreement.

      12.3.    Neither party shall use the name of the other or make any press
               or other public announcement concerning any aspect of this
               Agreement without first obtaining the agreement of the other
               party to the text of that announcement.

      12.4.    This Agreement may be executed in more than one counterpart and
               shall come into force once each party has executed such a
               counterpart in identical form and exchanged it with the other
               party.


                                        9
<PAGE>

GEMINI RESEARCH LTD.                          AFFYMETRIX, INC.


By: /s/ [ILLEGIBLE]                           By: /s/ [ILLEGIBLE]
    ----------------------------                  ----------------------------

Title: Chief Executive Officer                Title: President and CEO
      --------------------------                    --------------------------

Date: 11 - 6 - 99                             Date: 16 [ILLEGIBLE] 99
     ---------------------------                   ---------------------------


                                              Approved for signature |_|
                                              by AFFX Legal Dept.    [ILLEGIBLE]


                                       10
<PAGE>

                                LICENSED PATENTS

Title: Determination of collagen genotype

Country         Application No.     Filing Date  Patent/Pub No.    Status
UK              9604305.4           29 Feb 1996                    Priority Only
World           PCT/GB97/00569      28 Feb 1997  WO 97/32041       See nat.phase
Australia       22235/97            28 Feb 1997                    Pending
Canada          2 247 171           28 Feb 1997                    Pending
European        97905309.7          28 Feb 1997  0 883 694         Pending
Mexico          987040              28 Feb 1997                    Pending
New Zealand     331489              28 Feb 1997                    Pending
USA             08/808 158          28 Feb 1997                    Allowed


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