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                                                                    EXHIBIT 10.8

                                  LICENSE AGREEMENT


     Effective as of May ____, 1998 (the "Effective Date"), TUFTS UNIVERSITY, a
body having corporate powers under the laws of the State of Massachusetts
("TUFTS"), and ILLUMINA, Inc., a California corporation having a principal place
of business at 2187 Newcastle Avenue, Suite 101, Cardiff, California 92007,
("LICENSEE") enter into this license agreement ("Agreement") and thereby agree
as follows:

1    BACKGROUND

     1.1  TUFTS is the owner of the patents and patent applications listed in
Exhibit 1 and any Licensed Patents, as hereinafter defined, which may issue
therefrom.

     1.2  TUFTS desires to have its technology developed and marketed in order
that products resulting therefrom may be available for public use and benefit.

     1.3  LICENSEE desires a worldwide, exclusive license, including the right
to sublicense, to develop, market and sell products under the Licensed Patents
and Know How (collectively, "Exclusive Technology") in all fields.

2    DEFINITIONS

     2.1  "Affiliate" means any corporation or other entity that is directly or
indirectly controlling, controlled by or under common control with LICENSEE.
For the purpose of this definition, "control" shall mean the direct or indirect
beneficial ownership of at least fifty percent (50%) in the income or stock of
such corporation or business.

     2.2  "Exclusive" means that, subject to the provision in Section 3.3, TUFTS
shall not grant further licenses to the Licensed Patents.

     2.3  "Know-How" means trade secrets, know-how, data and other information
(whether or not patentable or qualifying as a trade secret) relating to the
field of use relating to Licensed Patents discovered or developed at Tufts, or
revealed to LICENSEE pursuant to the research agreement referred to in Section 3
of the Master Agreement of even date herewith ("Research Agreement") between
Tufts and LICENSEE.  Know-How shall not include Licensed Patents.

     2.4  "Licensed Product" means any product, the manufacture or sale of which
is within a Valid Claim within the Licensed Patents in the country of
manufacture or sale.

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     2.5  "Licensed Patents" means (i) the U.S. and foreign patents and patent
applications listed on Exhibit 1 hereto, (ii) all U.S. or foreign patent
applications filed after the Effective Date owned by TUFTS or which TUFTS has
the right to license which claim one or more inventions which would be dominated
by any patent issuing on a patent application within the Licensed Patents
pending as of the Effective Date (or a division, or continuation in whole or
part of such a pending application), (iii) all divisions, and continuations in
whole or part of any of the preceding, (iv) all foreign patent applications
corresponding to or claiming priority from any of the preceding, and (v) all
U.S. and foreign patents issuing on any of the preceding, including patents of
addition, reexaminations, and reissues.

     2.6  "Licensed Territory" means worldwide.

     2.7  "LICENSEE" shall mean Illumina, Inc. and its Affiliates.

     2.8  "Net Sales" means the gross revenue actually received by LICENSEE from
sales of Licensed Products, less the following items, but only insofar as they
are included in such gross revenue and are separately stated on the invoice:

          (a)  Import, export, value-added, excise and sales taxes, and custom
               duties, all to the extent separately identified on the invoice;

          (b)  Cost of insurance, packing, and transportation from the place of
               manufacture to the customer's premises;

          (c)  normal and customary rebates, and cash and trade discounts,
               actually taken; and

          (d) Credit for returns, allowances, or trades actually allowed.

     2.9  "Valid Claim" means a claim of (i) an issued, unexpired patent which
has not been held unenforceable or invalid by a court or other governmental
entity of competent jurisdiction, and which has not been disclaimed, or
withdrawn or found invalid or unenforceable in a reissue application or re-
examination proceeding; or (ii) a patent application, provided that not more
than five (5) years have elapsed from the date the claim takes priority for
filing purposes.

3    GRANT

     3.1  Subject to Public Law 96-517 and Public Law 98-620, TUFTS hereby
grants, to the extent that it lawfully may, to LICENSEE and LICENSEE hereby
accepts an exclusive license under the Exclusive Technology to make, have made,
import, have imported, use, lease, sell and offer for sale, have sold and
otherwise commercialize and exploit Licensed Products, and to practice any
method, process, or procedure within the Exclusive Technology, in the Licensed
Territory.

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     3.2  Said license is Exclusive, including the right to sublicense pursuant
to Section 12, in the Licensed Territory for a term commencing as of the
Effective Date, and ending upon expiration of the last to expire of Licensed
Patents.

     3.3  LICENSEE agrees that TUFTS shall have the right to practice the
Exclusive Technology both on its own and/or in collaboration with third party
academic or not-for-profit research institutions, solely for non-commercial
purposes, and not for sale, license, or other distribution.

4    DILIGENCE

     4.1  LICENSEE will use reasonable best efforts to diligently and
continuously commercialize the Exclusive Technology.  To support the
commercialization of the Exclusive Technology, LICENSEE will raise $500,000 in
equity financing from third parties during the first year after the Effective
Date and use its best efforts to raise $2,000,000 in total financing (including
but not limited to equity or debt financing, government grant funding, sponsored
research and development funding, etc.) ("First Financing") during the second
year after the Effective Date.  If LICENSEE fails to meet any one of the
foregoing milestones within the time specified, TUFTS shall have the right to
terminate the license granted hereunder, provided that such action by TUFTS is
consistent with a determination of the arbitrators pursuant to Section 15 hereof
that LICENSEE has failed to exercise due diligence in the commercialization of
the Exclusive Technology pursuant to its obligations under this Section 4.1.

     4.2  LICENSEE shall further use its best efforts to bring one or more
Licensed Products to market through a thorough, vigorous and diligent
exploitation of Licensed Patents and to continue thereafter active, diligent
marketing of more Licensed Products throughout the life of this Agreement.

     4.3  In addition LICENSEE shall adhere to the following milestones:

          (a) LICENSEE shall deliver to TUFTS on or before the first anniversary
              of this Agreement an operating plan showing the amount of money,
              number and kind of personnel, and time budgeted and planned for
              each phase of development of the Licensed Products and shall
              provide similar reports to TUFTS on or before each subsequent
              anniversary. TUFTS agrees to keep this operating plan
              confidential.

          (b) The following expenditures shall be made by the LICENSEE, its
              Affiliates or its sublicensees on a calendar-year basis in order
              to develop and commercialize Licensed Products:

                 1999 - an expenditure of [*]

____________________
[*] CERTAIN INFORMATION ON THIS PAGE HAS BEEN OMITTED AND FILED SEPARATELY WITH
THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
OMITTED PORTIONS.

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                 2000 - an expenditure of [*]
                 2001 - an expenditure of [*]
                 2002 - an expenditure of [*]

          (c) Of the expenditures listed in Section 4.3(b), the following
              minimum expenditures shall be made by LICENSEE, its Affiliates or
              its sublicensees on a calendar-year basis in order to develop and
              commercialize a product dominated by US Patent Number 5,512,490:

                 1999 - an expenditure of [*]
                 2000 - an expenditure of [*]
                 2001 - an expenditure of [*]
                 2002 - an expenditure of [*]

          (d) LICENSEE shall permit an in-plant inspection by TUFTS on or before
              July 1, 1999 and thereafter permit in-plant inspections by TUFTS
              at regular intervals with at least six (6) months between
              inspections.

          (e) LICENSEE shall provide TUFTS with an annual report of research and
              development expenditures required under this Section 4.3.

     4.4    If LICENSEE fails to meet any of the milestones in this Section 4,
and the default has not been remedied within ninety (90) days after the date of
notice in writing of such default by TUFTS, TUFTS shall have the right to change
the license granted hereunder to a non-exclusive license.

5           PAYMENTS

     5.1    LICENSEE shall pay to TUFTS royalties equal to [*] of the Net Sales
received by LICENSEE from the sale of Licensed Products. In the event that a
Licensed Product under this Agreement is sold in a combination product
containing one or more other active ingredients or components which are or could
be separately available on a commercial basis, then Net Sales on the combination
product shall be calculated as follows:

          By multiplying the net selling price of the combination product by the
          fraction A/A+B, where A is the gross selling price, during the
          royalty-paying period being considered, of the Licensed Product sold
          separately, and B is the gross selling price, during the royalty
          period in question, of the other active ingredients or components sold
          separately.

     5.2    In the event that LICENSEE is required to take a license from any
third party in order to commercialize any Licensed Product, and LICENSEE must
make royalty payments to such third

____________________
[*] CERTAIN INFORMATION ON THIS PAGE HAS BEEN OMITTED AND FILED SEPARATELY WITH
THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
OMITTED PORTIONS.

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party ("Third Party Royalty Payment"), the royalties payable to TUFTS pursuant
to Section 5.1 above shall be reduced by an amount equal to fifty percent (50%)
of the Third Party Royalty Payment, provided, however, that such reduction shall
not reduce the royalty payment owed to Tufts in any single year to an amount
which is less than fifty per cent (50%) of that which would have been due to
TUFTS in the absence of Third Party Royalty Payments.

     5.3    LICENSEE shall pay TUFTS a sublicensing fee (the "Sublicensing Fee")
equal to [*] of the net revenue received from sublicensing of Licensed Patents
and Licensed Products covered by one or more valid claims of the Licensed
Patents in the country in which such Product is sold. The Sublicensing Fee shall
be based upon the amount actually paid to LICENSEE by a sublicensee, including
fees, royalties and milestone payments, provided that the Sublicensing Fee shall
not include research and development support payments, payments in compensation
for the grant of rights to any other intellectual property of LICENSEE, or
equity or debt financing received by LICENSEE from such sublicensee.

     5.4    LICENSEE hereby grants to TUFTS the right to purchase [*] shares of
LICENSEE'S common stock which represents [*] of the founding capitalization
(see Exhibit 2), at fair market value as determined by LICENSEE's Board of
Directors as of the date of purchase (such fair market value is currently $0.01
per share) pursuant to a separate stock purchase agreement ("Stock Agreement").

     5.5    The royalty on Net Sales made in currencies other than U.S. Dollars
shall be calculated using the appropriate foreign exchange rate for such
currency quoted by the Bank of America (San Francisco) foreign exchange desk, on
the close of business on the last banking day of each calendar quarter.
Royalties and payments to TUFTS shall be made in U.S. Dollars.

     5.6  Within thirty (30) days after receipt of a statement from TUFTS,
LICENSEE shall reimburse TUFTS for all costs incurred by TUFTS after the
Effective Date in connection with the preparation, filing and prosecution of all
patent applications and maintenance of Licensed Patents.

     5.7  In the event that in any country all of the valid claims within the
Licensed Patents which cover a particular Licensed Product are held invalid or
unenforceable, then LICENSEE's obligation to pay royalties on Net Sales with
respect to such Licensed Product shall terminate in such country. LICENSEE's
obligation to pay royalties on Net Sales shall terminate on a country-by-country
basis upon the expiration of the last to expire of any issued Licensed Patent in
each country.

6    ROYALTY REPORTS, PAYMENTS AND ACCOUNTING

     6.1  Beginning with the first sale of a Licensed Product, LICENSEE shall
make written reports (even if there are no further sales) of royalty payments
due, if any, to TUFTS within thirty (30) days after the end of each calendar
quarter.  This report shall state the number, description, and aggregate Net
Sales of Licensed Products during such completed calendar quarter by LICENSEE,
its

____________________
[*] CERTAIN INFORMATION ON THIS PAGE HAS BEEN OMITTED AND FILED SEPARATELY WITH
THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
OMITTED PORTIONS.

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Affiliates and Sublicensees, and resulting calculations of earned royalty
payments due TUFTS pursuant to Section 5 for such completed calendar quarter.
Each such statement shall be certified by an officer of the LICENSEE as being
true, correct and complete.  Concurrent with the submission of each such report,
LICENSEE shall pay TUFTS any royalties due for the calendar quarter covered by
such report.

     6.2  LICENSEE agrees to keep and maintain records for a period of three (3)
years showing the manufacture, sale, use and other disposition of products sold
or otherwise disposed of under the license herein granted.  Such records will
include sufficient detail to enable the royalties payable hereunder by LICENSEE
to be determined.  LICENSEE further agrees to permit its books and records to be
examined by an independent certified public accountant selected by TUFTS and
acceptable to LICENSEE once per calendar year during the term of this Agreement,
for the sole purpose of verifying the reports and royalty payments made by
LICENSEE.  Such examination shall be made at LICENSEE'S place of business during
ordinary business hours with at least thirty (30) days prior written notice.
The accountant shall report to TUFTS only whether there has been a royalty
underpayment and, if so, the amount thereof.  Such examination is to be at the
expense of TUFTS except in the event that the results of the audit reveal an
under reporting of royalties due TUFTS of five percent (5%) or more, then the
audit costs shall be paid by LICENSEE within thirty (30) days of notice by TUFTS
to LICENSEE.

7    REPRESENTATIONS AND WARRANTIES

     7.1  TUFTS Disclaimer.  TUFTS MAKES NO REPRESENTATIONS, EXTENDS NO
          ----------------
WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED (INCLUDING, WITHOUT
LIMITATION, ANY WARRANTIES OF MERCHANTABILITY OR FITNESS FOR PURPOSE), AND
ASSUMES NO RESPONSIBILITIES WHATSOEVER, WITH RESPECT TO THE LICENSED PATENTS OR
KNOW-HOW OR THE USE THEREOF, OR THE MANUFACTURE, POSSESSION, USE, MARKETING,
SALE, OR OTHER DISPOSITION BY TUFTS, LICENSEE, OR ANYONE ELSE, OF LICENSED
PRODUCT(S) OR ANY OTHER PRODUCTS OF SERVICES (INCLUDING, WITHOUT LIMITATION,
PRODUCTS MADE BY TUFTS, AND TUFTS SERVICES, THAT ARE OR WERE FURNISHED TO
LICENSEE AT ANY TIME BEFORE, ON, OR AFTER THE DATE HEREOF), EXCEPT ONLY AS
EXPRESSLY STATED HEREIN.  Without limitation of the foregoing generality,
nothing contained herein or in any disclosure of the Licensed Patents or Know-
How made by or on behalf of TUFTS shall be construed as extending any
representation or warranty with respect to the Licensed Patents or Know-How or
Licensed Products or the results to be obtained by the use of the Licensed
Patents or Know-How or any Licensed Products, or that anything made, used, or
sold by use of the Licensed Patents or Know-How or any part thereof, alone or in
combination, will be free from infringement of patents of third parties.   TUFTS
SHALL NOT BE LIABLE TO LICENSEE, ITS AFFILIATES, ITS SUBLICENSEES, OR ANY OTHER
PARTY, REGARDLESS OF THE FORM OR THEORY OF ACTION (WHETHER CONTRACT, TORT,
INCLUDING NEGLIGENCE, STRICT LIABILITY, OR OTHERWISE), FOR ANY SPECIAL,
INCIDENTAL, CONSEQUENTIAL, PUNITIVE, OR

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OTHER EXTRAORDINARY DAMAGES ARISING OUT OF OR RELATED TO THIS AGREEMENT,
LICENSED PATENTS, THE KNOW-HOW, THE LICENSED PRODUCTS, OR ANY PRODUCTS OR
SERVICES FURNISHED OR NOT FURNISHED BY TUFTS, EVEN IF TUFTS HAS BEEN ADVISED OF
THE POSSIBILITY THEREOF.

     LICENSEE agrees that all warranties, if any, in connection with the sale or
other disposition of any Licensed Products (or any products made by TUFTS and
furnished at any time to LICENSEE) by LICENSEE, its Affiliates, or its
sublicensees will be made by them and will not directly or impliedly obligate
TUFTS.

     7.2  TUFTS Representations.  Notwithstanding the first sentence of
          ---------------------
Section 7.1, TUFTS:

               (a) Warrants to LICENSEE that TUFTS has good title to the
Exclusive Technology and any tangible personal property furnished hereunder by
TUFTS to LICENSEE, including any quantities of materials similar to the products
to be made by LICENSEE as Licensed Products (but TUFTS makes no infringement or
other representations or warranties with respect thereto).

               (b) Represents that TUFTS is a corporation organized and existing
under the laws of the Commonwealth of Massachusetts and has the power and
authority to enter into this Agreement and the right to grant all the rights
described in this Agreement, including the rights to the Licensed Patents and
Know-How described herein.

               (c) Represents that TUFTS has taken all necessary action to
authorize its execution and delivery of this Agreement by the representatives of
TUFTS who carried out such execution and delivery, and to authorize the
performance by TUFTS of its obligations hereunder.

               (d) Represents that execution and delivery of this Agreement and
its performance by TUFTS will not result in any breach or violation of, or
constitute a default under, any agreement, instrument, judgment, or order to
which TUFTS is a party or by which it is bound.

               (e) Represents that TUFTS is not aware of any other intellectual
property right owned by TUFTS for which a license is necessary to practice the
rights to the Licensed Patents as set forth herein.

     7.3  LICENSEE Representations.  LICENSEE represents and warrants to TUFTS
          ------------------------
that:

               (a) LICENSEE is a corporation organized and existing under the
laws of California and has the power and authority to enter into this Agreement.

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               (b) LICENSEE has taken all necessary action to authorize its
execution and delivery of this Agreement by the representatives of LICENSEE who
carried out such execution and delivery, and to authorize the performance by
LICENSEE of its obligations hereunder.

               (c) Execution and delivery of this Agreement and its Agreement
and its performance by LICENSEE will not result in any breach or violation of,
or constitute a default under, any agreement, instrument, judgment, or order to
which LICENSEE is a party or by which it is bound.

8  INDEMNITY

     8.1  Indemnity.  LICENSEE agrees to indemnify and hold harmless TUFTS, its
          ---------
trustees, officers and employees, from all costs, expenses (including reasonable
attorneys' fees), interest, losses, obligations, liabilities, and damages paid
or liability for which is incurred by any of said parties ("Losses"), and which
arise out of or are in connection with or are for the purpose of avoiding any
and all claims, demands, actions, causes of action, suits, appeals, and
proceedings ("Claims"), all whether groundless or not, or the settlement
thereof, based on any actual or alleged injuries, damages, or liability of any
kind whatsoever (including, without limitation, personal injury, death, property
damage, breach of warranty, or breach of contract) arising, directly or
indirectly, out of any one or more of:  any breach of LICENSEE of its
representations, warranties, or agreements hereunder; or out of any manufacture,
marketing, possession, use, sale or other disposition of Licensed Products or
products furnished by TUFTS to LICENSEE in connection herewith or in connection
with the Research Agreement (whether same occurs during or after the License or
during or after the License Period) by LICENSEE, its Affiliates, its
sublicensees, or anyone claiming by, through, or under any of them; or any
acquisition, possession, disclosure, or use of the Exclusive Technology or any
thereof, by LICENSEE, its Affiliates, its sublicensees, or anyone claiming by,
through, or under any of them; or the presence of LICENSEE's or its Affiliates'
or its sublicensees' officers, agents, employees, invitees, or property or any
thereof on TUFTS' premises, provided that the obligations of LICENSEE under this
Section 8.1 shall not apply if the Claims and any Losses resulted in whole or in
part from the intentional misconduct or gross negligence of TUFTS or any other
party indemnified under this Section.

     8.2  Defense; Settlement.  LICENSEE shall defend and control negotiation of
          -------------------
settlement of any Claim, as defined in Section 8.1.  TUFTS agrees to cooperate
fully in the defense of any Claim and may participate in the defense with
counsel of TUFTS' choosing, such separate counsel to be at TUFTS' expense unless
a conflict of interest exists between LICENSEE and TUFTS with respect to the
defense in which case LICENSEE shall pay the reasonable fees and expenses of
TUFTS' separate counsel.  Any settlement by which TUFTS would incur any
obligation or liability, whether for the payment of money, the taking of any
action, the refraining from any action, or otherwise, shall require the advance
written consent of TUFTS, which may be withheld in the sole discretion of TUFTS
without relieving LICENSEE of any of its indemnification or other obligations
hereunder.

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     8.3  Insurance.  Not later than thirty (30) days before the time when
          ---------
LICENSEE, any subsidiary, or any sublicensee of LICENSEE shall use in humans or
sell any Licensed Products or any products furnished to LICENSEE by TUFTS at any
time (before, on or after the date hereof) in connection herewith or in
connection with the Research Agreement, and at all times thereafter until the
expiration of all applicable statutes of limitation pertaining to any such use,
sale or other disposition of any Licensed Products or the aforesaid products
furnished by TUFTS (whether same occurs or exists before or after the Effective
Date), LICENSEE will at LICENSEE's expense, obtain and maintain in full force
and effect, comprehensive general liability insurance, including product
liability insurance, protecting TUFTS against all claims, suits, obligations,
liabilities and damages, based upon or arising out of actual or alleged bodily
injury, personal injury, death, or any other damage to or loss of persons or
property, caused by any such use, sale, or other disposition.  Such insurance
policy or policies shall be issued by companies rated by A. M. Best as A VIII or
better (or other companies acceptable to TUFTS), shall name TUFTS as an
additional named insured, shall have limits of at least one million dollars
($1,000,000) per occurrence with an aggregate of three million dollars
($3,000,000), shall be non-cancelable except upon thirty (30) days prior written
notice to TUFTS, and shall provide that as to any loss covered thereby and also
by any policies obtained by TUFTS itself, LICENSEE's policies shall provide
primary coverage for TUFTS and TUFTS' policies shall be considered excess
coverage for TUFTS.

     8.4  Certificates; Policies.  LICENSEE will forthwith after the obtaining
          ----------------------
of such insurance required by Section 8.3, obtain and deliver to TUFTS
certificates of and copies of, and at all times thereafter deliver without
further demand replacement certificates and copies of, all such insurance
policies that are in force and effect, as reasonably requested by TUFTS.

9    MARKING

     Prior to the issuance of patents under Licensed Patents, LICENSEE agrees to
mark Licensed Product(s) (or their containers or labels) made, sold, or
otherwise disposed of by it under the license granted in this Agreement with the
words "Patent Pending," and following the issuance of one or more patents, with
the numbers of any applicable Licensed Patents.

10   USE OF NAMES

     10.1  Use of Names.   LICENSEE, its Affiliates and sublicensees agrees not
           ------------
to use the name of TUFTS or any TUFTS participant in the Research, as defined in
the Research Agreement, in any form of publicity or disclosure without TUFTS'
prior written consent, which may be withheld or withdrawn in TUFTS' discretion
at any time, provided however, that no such consent will be required with regard
to: (i) any proper reference by LICENSEE to published technical publications by
such participants; (ii) disclosures to potential investors and corporate
collaborators; and (iii) TUFTS will make no objection to LICENSEE's such other
disclosures as are required as a matter of law (including disclosures made under
applicable securities regulation) and such general disclosures

                                      -9-
<PAGE>

of this Agreement as may be desired by LICENSEE for purposes of grant
solicitations from governmental authorities.

11   PATENT PROSECUTION AND INFRINGEMENT

     11.1  TUFTS shall have the primary responsibility for the prosecution,
filing and maintenance of all Licensed Patents, including the conduct of all
interference, opposition, nullity and revocation proceedings, using counsel of
its choice; provided, however, that LICENSEE shall have reasonable opportunity
to advise and consult with TUFTS on such matters and may recommend TUFTS to take
such action as LICENSEE reasonably believes necessary to protect the Licensed
Patents.  Counsel shall concurrently provide TUFTS and LICENSEE with copies of
all material correspondence related to the prosecution of the patent
applications within the Licensed Patents.  Should TUFTS elect to abandon any
patent or patent application in any country, it shall give timely notice to
LICENSEE, who may continue prosecution or maintenance, at its sole expense and
TUFTS shall have no further rights with respect to such patent application or
patent in such country.  In the event that a conflict arises with respect to
patent counsel selected by TUFTS, LICENSEE may, with just cause and after
consulting with TUFTS, select new patent counsel reasonably acceptable to TUFTS.

     11.2  Payment of all reasonable fees and costs relating to the filing,
prosecution and maintenance of Licensed Patents which are incurred by TUFTS
after the Effective Date (including interference and/or opposition, nullity and
revocation proceedings) shall be the responsibility of LICENSEE.  TUFTS shall
periodically send LICENSEE invoices for any such patent expenses incurred by
TUFTS and LICENSEE shall pay such invoices within thirty (30) days of receipt
thereof.

     11.3  Each party shall inform the other promptly in writing of any alleged
infringement of the Licensed Patents by a third party, including all detail then
available.  TUFTS shall have the right, but shall not be obligated, to prosecute
at its own expense any such infringements, and LICENSEE agrees that TUFTS may
join LICENSEE as a plaintiff at the expense of TUFTS.  In any infringement
action commenced or defended solely by TUFTS, all expenses and all recovery for
infringement shall be those of TUFTS.

     11.4  If TUFTS has not taken legal action or been successful in obtaining
cessation of the infringement, within one hundred eighty (180) days of written
notification from LICENSEE of such infringement, or if TUFTS elects not to
continue prosecuting any legal action against an infringer, LICENSEE shall have
the right (while the LICENSEE is the exclusive licensee), but shall not be
obligated, to prosecute at its own expense any such infringement.  LICENSEE may
join TUFTS as a plaintiff in any such infringement suit at LICENSEE's expense.
No settlement, consent judgment or other voluntary final disposition of the suit
may be entered into without TUFTS' consent, which shall not be unreasonably
withheld or delayed.  In any such action by LICENSEE, after LICENSEE is first
reimbursed for LICENSEE's costs and expenses (including attorney's and expert
fees) and

                                      -10-
<PAGE>

then TUFTS is reimbursed for any credited royalties pursuant to Section 11.8,
TUFTS shall be entitled to receive an amount equal to the applicable royalties
on any recovery of profits and damages that is in excess of LICENSEE's costs and
expenses and TUFTS' royalty reimbursement. LICENSEE shall indemnify TUFTS
against any order for costs or other payments that may be made against TUFTS in
such proceedings.

     11.5  If any declaratory judgment action alleging invalidity or non-
infringement of any of the Licensed Patents shall be brought against LICENSEE,
TUFTS shall have the right at its election made within sixty (60) days after
commencement of that action, to intervene and take over the sole defense of the
action at its expense.

     11.6  In any infringement suit that either party brings to enforce the
Licensed Patents, the other party shall at the request and expense of the party
bringing the suit, cooperate in al reasonable respects, including, to the extent
possible, obtaining the testimony of its employees and making available physical
evidence in the possession of that party.

     11.7  LICENSEE, during the exclusive period of this Agreement, shall have
the exclusive right in accordance with the provisions of Section 12, to
sublicense any alleged infringer in the Licensed Territory for future use of the
Licensed Patents.

     11.8  If LICENSEE pay any amounts in fees, expenses or costs to maintain,
prosecute, bring or defend any proceeding relating to any infringement by a
third party of any Licensed Patents, any declaratory action alleging invalidity
or non-infringement of any Licensed Patents, or any interference, opposition,
nullity or revocation proceeding relating to any Licensed Patents pursuant to
this Section 11 (the "Section 11 Costs"), TUFTS agrees that 50% of the amount of
such Section 11 Costs may be credited as they are incurred by LICENSEE against
royalties due to TUFTS under Section 5 of this Agreement.

12   SUBLICENSES

     12.1  LICENSEE may grant sublicenses under the Exclusive Technology to
make, have made, import, have imported, use, lease, sell and offer for sale,
have sold and otherwise commercialize and exploit Licensed Products, and to
practice any method, process or procedure within the Exclusive Technology in the
Licensed Territory.  The terms and conditions of each sublicense shall be
consistent with the terms and conditions of this Agreement and shall contain,
among other things (by way of example but not limitation), provisions
substantially similar to and consistent with: the "Net Sales" definition;
Section 6; Section 7.1 (so that no representations or warranties inconsistent
with that Section shall be extended to or by any sublicensee); Section 10; and
Section 18.

     12.2  Any sublicense granted by LICENSEE under this Agreement shall remain
in effect in the event of any termination of this Agreement and shall provide
for the assignment of such

                                      -11-
<PAGE>

sublicense to TUFTS or its designee in the event that this Agreement is
terminated; provided, that the financial obligations of each sublicensee to
TUFTS shall be limited to the amounts such sublicensee would be obligated to pay
to LICENSEE had this Agreement not been terminated.

     12.3  Each sublicense shall provide that the obligations to TUFTS of
Sections 6, 7.1, 8.1, 10.1, 11.3, 11.4, 13.4, and 18 shall be binding on the
sublicensee and enforceable by both TUFTS and LICENSEE.

     12.4  LICENSEE shall furnish to TUFTS a true and complete copy of each
sublicense agreement and each amendment thereto, promptly after the sublicense
or amendment has been agreed upon.  TUFTS agrees that it will keep each
agreement confidential.

     12.5  No sublicense shall relieve LICENSEE of any of its obligations
hereunder, and LICENSEE shall be responsible for the acts or omissions of its
Affliliates and sublicensees and for compliance by them with their obligations,
and LICENSEE shall take all steps necessary to enforce that compliance to the
extent required to allow LICENSEE to fully comply with all of its obligations
under this Agreement.

13   TERM AND TERMINATION

     13.1  Unless sooner terminated in a manner provided herein, this Agreement
shall continue in force on a country-by-county and Licensed Product-by-Licensed
Product basis until the expiration of the last to expire of all Valid Claims in
such country included in the Licensed Patents.  Following such an expiration,
LICENSEE shall have a non-exclusive, royalty-free, irrevocable license in such
country, to the Know-How.

     13.2  LICENSEE shall have the right to terminate the Agreement at any time
following ninety (90) days written notice to TUFTS.  LICENSEE may terminate this
Agreement with respect to any country or any Licensed Patent by giving TUFTS
notice in writing at least sixty (60) days in advance of the effective date of
termination selected by LICENSEE.

     13.3  TUFTS may terminate this Agreement if LICENSEE:

          (a)  Is in default in payment of royalty;

          (b)  Is in material breach of any provision hereof;

and LICENSEE fails to remedy any such default, or breach, or fails to act
reasonably to remedy any default, or breach, within thirty (30) days after
receipt of written notice thereof by TUFTS.

                                      -12-
<PAGE>

     13.4  TUFTS may terminate this Agreement if LICENSEE fails to cure any
default on the diligence milestones in Section 4 after a twelve month period
commencing upon LICENSEE's receipt of written notification from TUFTS of
LICENSEE's default of such milestones.

     13.5  Surviving any termination are:

          (a)  LICENSEE's obligation to pay royalties accrued or accruable;

          (b)  Any cause of action or claim of LICENSEE or TUFTS, accrued or to
               accrue, because of any breach or default by the other party; and

          (c)  The provisions of Articles 8, 10, 15, 17 and Sections 7.1, 12.2
               and 13.4.

14   ASSIGNMENT

     Neither party may assign this Agreement or any part hereof without the
express written consent of the other, which consent shall not be unreasonably
withheld; provided, however, LICENSEE may assign this Agreement or any portion
hereof to an Affiliate or to a successor of all or substantially all its
business relating to the Licensed Patents or Know-How without the written
consent of TUFTS and shall provide TUFTS notice of any such assignment.
However, no assignment or other transfer by LICENSEE shall relieve LICENSEE of
any obligations hereunder and LICENSEE shall continue to be primarily and
jointly and severally liable (along with such assignee or other transferee) for
the performance of all obligations of LICENSEE and such assignee or other
transferee hereunder.

15   ARBITRATION

     15.1  Any controversy arising under or related to this Agreement, and any
disputed claim by either party against the other under this Agreement excluding
any dispute relating to patent validity or infringement arising under this
Agreement, shall be settled by arbitration in accordance with the Rules of
Commercial Arbitration of the American Arbitration Association.

     15.2  Upon request by either party, arbitration will be initiated by a
third party arbitrator mutually agreed upon in writing by LICENSEE and TUFTS
within thirty (30) days of such arbitration request.  Judgment upon the award
rendered by the arbitrator shall be final and nonappealable and may be entered
in a court having jurisdiction thereof.  The parties agree that any provision of
applicable law notwithstanding, they will not request and the arbitrators shall
have no authority to award punitive or exemplary damages against any party.  The
costs of the arbitration, including administrative fees and fees of the
arbitrators shall be shared equally by the parties.  Each party shall bear the
cost of its own attorneys' fees and expert fees.

                                      -13-
<PAGE>

     15.3  The parties shall be entitled to discovery in like manner as if the
arbitration were a civil suit in a Superior Court of the Commonwealth of
Massachusetts; provided, however, the arbitrator may limit the scope, time
and/or issues involved in discovery.

     15.4  Any arbitration shall be held at a location mutually agreed upon in
writing by LICENSEE and TUFTS.

16   NOTICES

     All notices under this Agreement shall be deemed to have been fully given
when done in writing and deposited in the United States mail, registered or
certified, or overnight deliver service (e.g., DHL, Federal Express) and
addressed as follows:
<TABLE>
<S>   <C>               <C>
     To TUFTS:          Tufts University
                        136 Harrison Avenue (75K-1520)
                        Boston, Massachusetts  02111

                        Attention: Associate Provost for Research

     with a copy to:    Massachusetts Biomedical Inititatives
                        20 Hampden Street
                        Roxbury, Massachusetts  02119

                        Attention: Director, Unified Office for Technology Transfer

     To LICENSEE:       Illumina, Inc.
                        2187 Newcastle Ave
                        Suite 101
                        Cardiff, California  92007

                        Attention: John R. Stuelpnagel
</TABLE>

Either party may change its address upon written notice to the other party.

17   CONFIDENTIALITY

     TUFTS shall maintain this Agreement and the reports and any information
provided by LICENSEE to TUFTS in confidence and not disclose such information or
reports to any third party, except as required by law and disclosed after notice
to LICENSEE and after requesting confidential treatment and a protective order,
if available.  TUFTS may, however, disclose to third parties total annual
royalty payments and general statistical information regarding payments made
hereunder in

                                      -14-
<PAGE>

the context of disclosing statistical information pertaining to the performance
of the TUFTS Office of Technology Licensing.

18  COMPLIANCE WITH LAWS

     18.1  Export Controls.  The Export Control Regulations of the U.S.
           ---------------
Department of Commerce prohibit, except under special validated license, the
exportation from the United States of technical data relating to certain
commodities (listed in the Regulations), unless the exporter has received
certain written assurance from the foreign importer.  In order to facilitate the
exchange of technical information under this Agreement, LICENSEE therefore
hereby agrees and gives its assurance to TUFTS that LICENSEE will not, unless
any required prior authorization is obtained from the U.S. Office of Export
Control, re-export directly or indirectly any technical data received from TUFTS
under this Agreement and will not export directly the Licensed Products or such
technical data to any country listed on either the Commodity Control List or
Militarily-Critical Technologies List.  TUFTS makes no representation as to
whether any such license is required or, if one is required, as to whether it
will be issued by the U.S. Department of Commerce.

     18.2   Other Laws.  In addition to the foregoing export control
            ----------
requirements, LICENSEE agrees that it, its Affiliates, and its sublicensees will
comply with all applicable mandatory or permissive patent marking laws, rules,
and regulations and comply with all other laws, rules, and regulations of all
governmental authorities applicable to any of their activities contemplated by
this Agreement, and will comply with all necessary and desirable practices in
connection and compliance with safety recommendations of trade associations or
governmental authorities.

19   MISCELLANEOUS

     19.1  Governing Law.  This Agreement shall be governed by the laws of in
           -------------
the Commonwealth of Massachusetts, without reference to principles of conflicts
of laws.

     19.2  Waiver.  None of the terms of this Agreement can be waived except by
           ------
the written consent of the party waiving compliance.

     19.3  Entire Agreement.  This Agreement and any Exhibits attached hereto
           ----------------
(each of which is hereby made part hereof by this reference), and the Master
Agreement entered into by the parties on even date herewith constitute the
entire agreement between the parties concerning the subject matter hereof, and
all prior negotiations, representations, warranties, agreements, and
understandings related thereto superseded hereby.

     19.4  Force Majeure.  Neither party shall not be considered in breach of
           -------------
this Agreement to the extent any failure to perform any term or provision is
caused by any reason beyond such party's reasonable control, or by reason of any
of the following circumstances: labor or employee disturbances or disputes of
any kind; accidents; laws, rules or regulations of any government

                                      -15-
<PAGE>

(including, without limitation, export and import regulations); failure of any
government approval required; disease; failure of utilities, mechanical
breakdowns, material shortages or other similar occurrences; civil disorders or
commotions, acts of aggression, vandalism or other similar occurrences; or fire,
floods, earthquakes, or acts of God.

     19.5  Independent Contractors.  The parties hereto shall be independent
           -----------------------
contractors with respect to each other, and neither shall be deemed to be the
agent, principal, employee, servant, joint venturer, or partner of the other for
any purpose.

     19.6  Severability.  If any provision of this Agreement shall to any extent
           ------------
be found to be invalid or unenforceable, the remainder of this Agreement shall
not be affected thereby, and any such invalid or unenforceable provision shall
be reformed so as to be valid and enforceable to the fullest extent permitted by
law.

     19.7  Headings.  Headings of Articles, Sections, and subsections included
           --------
herein for convenience for reference only and shall not be used to construe this
Agreement.

     19.8  Counterparts.  This Agreement may be executed in two counterparts,
           ------------
each of which shall be deemed an original and which together shall constitute
one instrument.


     IN WITNESS WHEREOF, the parties have executed this Agreement effective as
of the Effective Date set forth above.

TUFTS UNIVERSITY                       ILLUMINA, INC.
("TUFTS")                              ("LICENSEE")



By: __________________________________  By: __________________________________

Title:________________________________  Title:________________________________

                                      -16-
<PAGE>

                                   Exhibit 1

                                      [*]
____________________
[*] CERTAIN INFORMATION ON THIS PAGE HAS BEEN OMITTED AND FILED SEPARATELY WITH
THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
OMITTED PORTIONS.

                                      -17-
<PAGE>

                                   Exhibit 2

                             Founding Capitalizaton

                                      [*]
____________________
[*] CERTAIN INFORMATION ON THIS PAGE HAS BEEN OMITTED AND FILED SEPARATELY WITH
THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
OMITTED PORTIONS.

                                      -18-