Exhibit 10.31  AGREEMENT  This Settlement and Release Agreement is made and
entered into as of the date of the last PARTY to sign the Agreement below (the Effective
Date), by and between Affymetrix, Inc., a corporation organized under the
laws of the State of Delaware having a principal place of business at 3380
Central Expressway, Santa Clara, CA 95051, (AFFYMETRIX) on behalf of itself
and its AFFILIATES, their successors and assigns, and Illumina, Inc., a
corporation organized under the laws of the State of Delaware having a
principal place of business at 9885 Towne Center Drive, San Diego, California,
92121 (ILLUMINA) on behalf of itself and its AFFILIATES, their successors and
assigns.  The signatories to this
Agreement are sometimes referred to herein jointly as the PARTIES and
individually as a PARTY.  WHEREAS, AFFYMETRIX has filed the ACTIONS in the
United States District Court for the District of Delaware, in Regional Court of
Düsseldorf (Germany), and in the High Court of Justice, Chancery Division  Patents
Court in London (United Kingdom);  WHEREAS, to avoid the necessity, expense,
inconvenience and uncertainty of additional or continued litigation, the
PARTIES wish to settle the disputes between them in the ACTIONS and to resolve
and preclude certain related and other claims as provided herein; and  WHEREAS, AFFYMETRIX and ILLUMINA wish to avoid the
uncertainties and costs associated with pursuing the ACTIONS and any
controversy or litigation relating to thereto, and they mutually desire to
resolve their differences concerning the Actions and all claims and causes of
action set forth in or contemplated thereby on the following terms and
conditions.  NOW, THEREFORE, for good and valuable consideration,
including, without limitation, the releases and mutual promises contained
herein, the receipt of which is hereby acknowledged, the Parties agree as
follows:   I.              DEFINITIONS  1.1           ACTIONS means
individually and collectively,  (i) Affymetrix, Inc.
v. Illumina, Inc.,United States District Court for the District of Delaware, Civil
Action No. 04-901-JJF filed July 26, 2004;  (ii) Affymetrix, Inc.
v. Illumina, Inc.,United States District Court for the District of Delaware Civil Action
No. 07-670-JJF filed October 24, 2007;  (iii) Affymetrix, Inc.
v. Illumina GmbH and Illumina, Inc.,in Regional Court in Düsseldorf (Germany) filed October 24,
2007; and   1


(iv) Affymetrix, Inc.
v. Illumina UK Ltd. and Illumina, Inc.,in the High Court of Justice, Chancery Division  Patents
Court in London (United Kingdom) filed October 24, 2007.  1.2           AFFILIATE
means any entity that is, directly or indirectly, controlling, controlled by or
under common control with either PARTY, but only so long as such Control
exists.  As used in this Section 1.2,
Control of an entity means the possession, directly or indirectly, of the
power to direct or cause the direction of the management and policies of such
entity, whether through the ownership of voting securities (or other ownership
interest), by contract or otherwise.  1.3           BLOCKING PATENTS
means all patents and applications therefor, anywhere in the world, currently
as of the Effective Date or at any time thereafter, owned by AFFYMETRIX (or by
an AFFYMETRIX AFFILIATE) or under which AFFYMETRIX (or an AFFYMETRIX AFFILIATE)
has the right to grant licenses or sublicenses, having a claim that covers a
CURRENT PRODUCT.  1.4           CHANGE OF CONTROL
means any transaction or series of related transactions with respect to any PARTY,
including any such transaction(s) in bankruptcy, in which, a person or
group of related persons who do not Control such PARTY prior to such
transaction or series of transactions, subsequently obtain(s) Control of
such PARTY by any means, whether by operation of law, acquisition of
securities, merger, contract, acquisition of assets, or otherwise.  As used in this Section 1.4, Control
of an entity means the possession, directly or indirectly, of the power to
direct or cause the direction of the management and policies of such entity,
whether through the ownership of voting securities (or other ownership
interest), by contract or otherwise.  1.5           CURRENT PRODUCTS
means (i) any products of ILLUMINAs (or an ILLUMINA AFFILIATEs) product
line commercialized by ILLUMINA or by an ILLUMINA AFFILIATE as of the Effective
Date, (ii) any products resulting from ILLUMINAs (or from an ILLUMINA
AFFILIATEs) research and development efforts, as of the Effective Date,
publicly announced or documented in ILLUMINAs (or in an ILLUMINA AFFILIATEs)
formal product development process, and (iii) all EVOLUTIONARY
IMPROVEMENTS to products of categories (i) and (ii).  1.6           EVOLUTIONARY IMPROVEMENTS
means modifications, revisions, additions, enhancements, changes or similar alterations
to an original product, to enhance the original product in terms of its
performance and/or functionality, and in which the original product retains its
essential character or remains identifiable.  1.6.1   For the
avoidance of doubt, EVOLUTIONARY IMPROVEMENTS do not include revolutionary
advances, i.e., advances that are different as a matter of kind in comparison
to the original product, or that fundamentally change or alter the methodology
by which the original product functions.   2


1.7           ILLUMINA FIELD
means any technology that is not based on photolithography.  For clarity, what is carved out of the
ILLUMINA FIELD includes (i) arrays made using photolithography, and (ii) technologies
involving instruments, assays, reagents, software, and other products, methods,
or systems, in each and every case capable of being used only with arrays made
using photolithography.  By way of
example, but not by way of limitation, the technology disclosed in software
patent No. 5,795,716 asserted against ILLUMINA in the ACTIONS is within
the ILLUMINA FIELD.   II.            GRANTS  2.1           AFFYMETRIX, on its behalf and on
behalf of its AFFILIATES, hereby grants and agrees to grant to ILLUMINA and its
AFFILIATES, a fully paid-up, irrevocable, worldwide, covenant not to sue
ILLUMINA, its AFFILIATES, and their customers, under and for the lives of the
BLOCKING PATENTS, to allow ILLUMINA and its AFFILIATES to make, use and sell
(which includes, without limitation, the right to have made, offer for sale,
export, import, lease, install, service, test, repair, upgrade and otherwise
maintain, provide services using) CURRENT PRODUCTS, and to provide services
using CURRENT PRODUCTS.  For the avoidance
of doubt, the covenant not to sue granted by AFFYMETRIX under this Section 2.1
is only granted in the ILLUMINA FIELD.  2.2           For all products other than CURRENT
PRODUCTS, and for all services commercialized by ILLUMINA and its AFFILIATES
using products other than CURRENT PRODUCTS, AFFYMETRIX, on its behalf and on
behalf of its AFFILIATES, hereby grants and agrees to grant to ILLUMINA and its
AFFILIATES an irrevocable, worldwide, covenant not to sue ILLUMINA, its
AFFILIATES, and their customers, but only for a period of four (4) years
from the Effective Date, under the BLOCKING PATENTS and under any other patents
owned by AFFYMETRIX or its AFFILIATES, or regarding which AFFYMETRIX or its
AFFILIATES has the right to grant licenses or sublicenses.  The PARTIES hereby acknowledge and agree that
during such four (4)-year period no damages shall accrue as a result of
ILLUMINAs commercialization of such products and services.  The PARTIES further acknowledge and agree
that the covenant not to sue granted by AFFYMETRIX under this Section 2.2
is only granted in the ILLUMINA FIELD.  2.3           ILLUMINA, on its behalf and on behalf
of its AFFILIATES, agrees, at the request of AFFYMETRIX during the term of the
covenant of Section 2.2, to engage in good faith negotiations with
AFFYMETRIX to provide a license on usual and reasonable commercial terms to AFFYMETRIX
and its AFFILIATES with respect to any patent or patent application owned by
ILLUMINA or any of its AFFILIATES or under which ILLUMINA or any of its
AFFILIATES has the right to grant licenses or sublicenses, in any application
area but only (i) for arrays made using photolithography and/or (ii) for
technologies involving instruments, assays, reagents, software, and other
products,   3


methods, or systems, in
each and every case capable of being used only with arrays made using
photolithography.  2.4           All covenants of this Article II
shall become effective only upon receipt by AFFYMETRIX of the payment specified
in Section 4.1 hereof and of the required executed sets of the Agreement.  2.5           Nothing in this Agreement shall limit
or in any way affect the rights of either PARTY to engage in any administrative
or judicial proceeding to challenge, invalidate, narrow, condition, or
otherwise affect the term or scope of any patent or patent application of the
other PARTY or its AFFILIATES, or otherwise affect the course of prosecution,
maintenance, or enforcement of any patent or patent application of the other
PARTY or its AFFILIATES, including but not limited to such actions as
participating, directly or indirectly, in oppositions, interferences,
reexaminations, or similar proceeding anywhere in the World.  It is expressly understood and agreed,
however, that the payment obligations specified in Section 4.1 are
irrevocable, and such payments are to be made by ILLUMINA in accordance with
the provisions of Section 4.1 and without regard to the outcome of any
proceeding referred to in this Section 2.5 or any other event or condition
whatsoever.   III.           RELEASES, DISMISSALS AND WAIVERS  3.1           AFFYMETRIX, for itself, its
AFFILIATES, their successors and assigns, hereby irrevocably and
unconditionally (except for the payment obligations set forth in Section 4.1
hereof) releases, acquits and forever discharges ILLUMINA and its AFFILIATES,
together with their past and present directors, officers, employees, successors
and assigns, and customers (the ILLUMINA Released Parties), in each and every
case, from any and all claims and causes of action, of whatever kind or nature,
whether in law or in equity and whether known or unknown, that AFFYMETRIX or
its AFFILIATES now has, ever had, or could in the future have (but for this
release) against the ILLUMINA Released Parties, asserted in, arising out of,
resulting from, or relating in any way to the ACTIONS or that are otherwise
based on CURRENT PRODUCTS. 
Notwithstanding the preceding provisions of this Section 3.1 or any
other provision of this Agreement, all actions to enforce payment of amounts
due under Section 4.1 of this Agreement, and to enforce claims against any
future acts of patent infringement not covered by the covenants in Article II,
are expressly preserved.  3.2           ILLUMINA, for itself, its AFFILIATES,
their successors and assigns, hereby irrevocably and unconditionally (except
for the covenants specified in Sections 2.1 and 2.2) releases, acquits and
forever discharges AFFYMETRIX and its AFFILIATES, together with their past and
present directors, officers, employees, successors and assigns, and customers
(the AFFYMETRIX Released Parties), in each and every case, from any and all
claims and causes of action, of whatever kind or nature, whether in law or in
equity and whether known or unknown, that ILLUMINA or its AFFILIATES now has,
ever had, or could in the future have (but for this release) against the
AFFYMETRIX   4


Released Parties, asserted
in, arising out of, resulting from, or relating in any way to the ACTIONS.  Notwithstanding the preceding provisions of
this Section 3.2 or any other provision of this Agreement, all actions to
enforce claims against any acts of patent infringement are expressly preserved.  3.3           In consideration of the rights and
obligations hereunder, the PARTIES have agreed to discontinue the ACTIONS and
to enter appropriate orders of dismissal of such ACTIONS with prejudice and
without costs and disbursements (and to make such other filings to effectuate
the same) in a Stipulation of Dismissal agreed to by the PARTIES, and each
PARTY hereby agrees to give the other PARTY written evidence thereof.  3.4           The PARTIES assume the risk of any
mistake of fact in connection with the subject matter of the Agreement, the
ACTIONS, and with respect to any fact that is now unknown to the PARTIES or to
their officers, directors, employees, agents or representatives.  Accordingly, as applicable, the PARTIES
expressly waive all rights under Section 1542 of the Civil Code of
California which reads as follows:  A general release does
not extend to claims which
the creditor does not know or suspect to exist in his
favor at the time of executing the release, which if
known by him must have materially affected his
settlement with the debtor.   IV.           PAYMENTS  4.1           In complete consideration of the
irrevocable and unconditional releases, waivers and covenants granted
hereunder, ILLUMINA shall pay to AFFYMETRIX the sum of Ninety Million U.S.
Dollars ($90,000,000.00 U.S.D.) payable within five (5) business days of
the receipt by the PARTIES of written evidence that the ACTIONS have been
dismissed as required under Section 3.3.  4.2           All payments to AFFYMETRIX hereunder
shall be made by wire transfer to ,
Account Number .  4.3           The PARTIES agree that each and all
payments due by ILLUMINA to AFFYMETRIX under Section 4.1 are
non-refundable, non-creditable against any other payments that may now be due
or will ever be due from ILLUMINA to AFFYMETRIX, fixed, determined, and are not
contingent on any future event or condition whatsoever on the part of
AFFYMETRIX or any other entity.   V.            THIRD PARTY BENEFICIARIES  The PARTIES acknowledge
and agree that customers of ILLUMINA and of ILLUMINAs AFFILIATES are third
party beneficiaries to this Agreement, and that the   5


releases, waivers and
covenants granted in Articles II and III of this Agreement inure to the benefit
of all of such customers to the extent provided therein.   VI.           CONFIDENTIALITY AND PRESS RELEASES  This Agreement is
strictly confidential and the PARTIES agree not to disclose any of its terms to
third parties, except (i) to governmental entities as required by law,
regulation or subpoena or as otherwise required by law, (ii) to employees,
officers, directors, shareholders, and agents of the PARTIES with a need to
know and who are under an obligation to maintain information of this nature
confidential, (iii) to shareholders and investors but in this instance the
disclosure should be limited to the amounts paid, the timeframe of the
covenants, and the general nature of the relationship, or (iv) as required
to enforce the legal rights of a PARTY before a court or arbitrating body
having applicable jurisdiction. 
Notwithstanding the immediately preceding sentence the PARTIES agree to
issue a joint press release to be prepared by ILLUMINA and reviewed and
approved by AFFYMETRIX.   VII.         NO ADMISSION; NO WARRANTIES  7.1           The PARTIES agree that they desire to
enter into this Agreement to avoid uncertainties associated with litigation and
to reduce their litigation expenses. 
Consistent therewith, the PARTIES acknowledge and agree that by entering
into this Agreement, (a) ILLUMINA does not in any way admit, and
specifically denies, any infringement of any patents owned by AFFYMETRIX or its
AFFILIATES, and (b) the payment obligations specified in Section 4.1
are irrevocable and unconditional, and such payments are to be made by ILLUMINA
in their entirety and (without limiting the foregoing) irrespective of any
past, present or future contentions or findings regarding infringement or
otherwise regarding the AFFYMETRIX patents.  7.2.          THE PARTIES, ON THEIR OWN BEHALF AND
ON BEHALF OF THEIR RESPECTIVE AFFILIATES, HEREBY DISCLAIMS ALL REPRESENTATIONS
AND WARRANTIES, EXPRESS OR IMPLIED, ARISING BY LAW OR OTHERWISE, WITH REGARD TO
THE SUBJECT MATTER OF THIS AGREEMENT (EXCEPT AS EXPRESSLY PROVIDED BELOW IN SECTION 10.7).  WITHOUT LIMITING THE GENERALITY OF THE
FOREGOING, NO WARRANTIES OR REPRESENTATIONS ARE EXPRESSED OR IMPLIED REGARDING
THE SCOPE, COVERAGE, VALIDITY OR ENFORCEABILITY OF ANY INTELLECTUAL PROPERTY
RIGHTS, OR REGARDING THE NON-INFRINGEMENT, MERCHANTABILITY, OR FITNESS FOR A
PARTICULAR PURPOSE OR USE OF ANY PRODUCTS OR SERVICES UNDER THIS AGREEMENT.   6


VIII.        ARBITRATION  8.1           In the event of any dispute or
difference of opinion or controversy between the PARTIES arising out of or in
connection with this Agreement or with regard to performance of any obligation
hereunder by either PARTY, both PARTIES shall use their reasonable efforts to
settle such dispute or difference of opinion amicably by good-faith negotiation
for a period of fifteen business (15) days, commencing upon the receipt of
written demand for negotiation setting forth clearly and completely the nature
and basis of the dispute and the manner and extent of its proposed resolution.  After the expiration of the 15-day
negotiation period, either PARTY may commence an arbitration to resolve the
dispute set forth in the demand for negotiation as set forth below.  8.2           Subject to Section 8.1 hereof,
all disputes, differences of opinion, or controversies which may arise between
the PARTIES out of or in relation to or in connection with this Agreement or the
breach thereof, shall be finally settled by arbitration in Los Angeles,
California by a panel of three (3) arbitrators (one of whom shall be a
registered patent attorney in the field of biotechnology) selected in
accordance with the Rules of the American Arbitration Association, in the
form pertaining at the time the arbitration is initiated.  The PARTIES shall use their best efforts to
complete the arbitration proceeding within three (3) months.  The arbitration panel is hereby empowered by
the PARTIES to render whatever judgment or relief under this Agreement
(applying California and U.S. Patent laws, as applicable) is deemed appropriate
by the panel, including the power to award specific performance remedies to
enforce this Agreement.  8.3           The losing PARTY as determined by the
arbitration panel at the time it makes its award shall pay the costs of any
arbitration entered into pursuant to this Article.  However, each PARTY shall bear its own legal
costs, including attorneys fees and experts fees, incurred in connection with
such arbitration.  8.4           Judgment upon the award rendered by
the arbitrators or arbitrator, as applicable, shall be binding, final and
unappealable, and may be entered by any court having jurisdiction thereof.   IX.           CHANGE OF CONTROL, ASSIGNMENT  9.1           The provisions of this Agreement,
including the payment by ILLUMINA and receipt by AFFYMETRIX of all amounts
specified in Section 4.1, shall be binding upon and inure to the benefit
of the PARTIES and their permitted (if any) successors and assigns.  9.2.          Each PARTY may assign its rights and
obligations hereunder only in connection with the acquisition of all or
substantially all of the assets or equity interests (whether by merger,
recapitalization, reorganization or otherwise) of that PARTY, provided that the
acquiring entity agrees in writing to be fully bound by all obligations of that
PARTY under this Agreement, with a copy of such writing provided to the other
PARTY within ten (10) business days of the effective date of such assignment.   7


9.3           In the event of any assignment by ILLUMINA
as permitted hereunder, and/or in the event of any CHANGE OF CONTROL with
respect to ILLUMINA, the covenant not to sue granted by AFFYMETRIX under Article II
shall be limited in scope and shall not extend to any then-existing products or
technology of the acquiring/successor entity.  9.4           In the event of any assignment by
AFFYMETRIX as permitted hereunder, and/or in the event of any CHANGE OF CONTROL
with respect to AFFYMETRIX, the right granted by ILLUMINA under Section 2.3
shall be limited in scope and shall not extend to any then-existing products or
technology of the acquiring/successor entity.   ARTICLE
X.         MISCELLANEOUS PROVISIONS  10.1         Notice.  Any notice or request with reference to this
Agreement sent to a PARTY shall be sent by express delivery to that PARTYs
President (with copy to that PARTYs General Counsel), shall specifically refer
to this Agreement, and shall be deemed to have been sufficiently given for all purposes
on the third business day following the date of mailing.  Unless otherwise specified in writing, the
mailing addresses of the PARTIES shall be as described below:  To ILLUMINA:  ILLUMINA, INC. Attention President 9885 Towne Center Drive San Diego, CA  92121 Facsimile:  (858) 202-4599  To AFFYMETRIX:  AFFYMETRIX, INC. Attention President 3380 Central Expressway Santa Clara, CA 95051 Facsimile:  (408) 481-0422  10.2         Severability.  If any Article, Section, provision or clause
of this Agreement shall be found or held to be invalid or unenforceable by a
court or other decision-making body of competent jurisdiction, in a judgment
from which no further appeal can be taken, the remainder of the Agreement shall
remain valid and enforceable and, to the extent required in the pursuit of this
Agreement, the PARTIES shall negotiate in good faith a substitute, valid and
enforceable provision that reflects the PARTIES intent entering into the
Agreement.   8


10.3         Entire Agreement  Modification and
Waiver.  The terms and conditions
herein constitute the entire agreement between the PARTIES and supersede all
previous agreements and understandings, whether oral or written, between the
PARTIES with respect to the subject matter hereof, and no prior agreement or
understanding varying or extending the same shall be binding upon either
PARTY.  No modification or waiver of any
term of this Agreement shall be effective unless made in a writing signed by
both PARTIES.  10.4         Governing Law.  This Agreement shall be governed and interpreted
in accordance with the laws of the United States and the State of California,
without reference to conflicts of law principles.  10.5         Interpretation.  Articles, Sections, titles, and headings are
inserted for convenience of reference only and are not intended to be a part of
or to affect the meaning or interpretation hereof.  As used herein, the term business days
shall mean all days other than Saturdays, Sundays or state recognized or U.S.
federal holidays.   Ambiguities, if any, in this Agreement shall
not be construed against any PARTY, irrespective of which PARTY may be deemed
to have authored the ambiguous provision.  10.6Counterparts.  This Agreement may be executed in identical
counterparts, each of which shall constitute an original and all of which shall
constitute one and the same agreement. 
Delivery of signatures by means of facsimile or electronic mail shall be
as effective as original signatures.  10.7         Power and Authority.  Each PARTY and its undersigned representative
hereby represents and warrants that it has full power and authority to enter
into this Agreement, and to grant the covenants, releases, dismissals and
waivers set forth hereunder, on behalf of itself, and its AFFILIATES, their
successors and assigns.   IN WITNESS WHEREOF, the
PARTIES have caused their duty authorized officers to execute this Agreement on
the dates indicated below.  AFFYMETRIX, INC.
  
  ILLUMINA, INC.   By:
  /s/ Kevin M. King
  
  By:
  /s/
  Jay FlatleyName:
  Kevin M. King
  
  Name:
  Jay FlatleyTitle:
  President
  
  Title:
  CEO and PresidentDate:
  1-9-08
  
  Date:
  1/6/08Witness:
  /s/ Susanna Chau
  
  Witness:
  /s/ Chris Cabou   9