Exhibit 10.1


 


May
30, 2006


 


Susan
E. Siegel


 


 


Dear
Sue:


 


This letter agreement (the “Agreement”)
sets forth our mutual agreement with respect to the change in your role with
Affymetrix, Inc. (the “Company”),
effective as of the date hereof.


 


1.                         Position with the Company. Effective April 19, 2006 (the “Transition Date”), you resigned as President of the Company.
You will remain employed with the Company, as President Emeritus, reporting to
the CEO, Stephen P.A. Fodor. You will have duties and responsibilities
commensurate with such position as are determined by the CEO and mutually
agreed with you, including those set forth on Schedule I.


 


2.                         Board Service. Effective the Transition Date, you resigned
as a member of the Board of Directors of the Company.


 


3.                         Salary, Benefits and Equity. While you remain employed with the Company,
you will receive an annual base salary of $426,315, payable in accordance with
the Company’s standard payroll practices. You will not be eligible for an
annual bonus or additional stock awards. During your employment, you will
continue to be eligible for employee benefits under the terms of the Company’s
benefit plans and for administrative and office services relating to conducting
business for the Company similar to those provided to other key employees of
the Company; your equity awards will continue to vest and remain outstanding in
accordance with their terms; and you will receive key executive services
through Right Management Consultants prior to, or immediately upon, resignation
or termination of your employment. During the term of this Agreement, the
Company will recommend and sponsor you for seminars and courses without any
obligation by the Company to pay for such courses.


 


4.                         Confidentiality Agreement. Your existing Confidentiality and Invention
Agreement with the Company (the “Confidentiality Agreement”)
remains in effect after the effective date of this Agreement and is attached
for your convenience.


 


5.                         Termination of Employment.


 


(a)                                  At-Will Employment. Your employment remains at-will, and no
special or implied conditions of employment are established unless they are
made in writing.


 


(b)                                 Termination. In the event your employment is terminated or
you resign before November 19, 2007, you will be entitled to receive the
following, subject to your signing and letting become effective the release in
the form set forth in Section 6 of this Agreement and continued compliance with
the covenants set forth in the Confidentiality Agreement and Section 8 of this
Agreement as of your termination date: 
(i) a lump sum payment equal to $675,000 less the base salary paid
to you from the Transition Date through the date of your termination of
employment; (ii) continued Company-paid health coverage through
October 19, 2007; (iii) accelerated vesting of your stock options to
the extent they would have vested if you had remained employed through
October 19, 2007; and (iv) extension of the post-termination exercise
period for your vested stock options until the period you would have had to
exercise your stock options if you had remained employed through
November 19, 2007, provided that (A) to the extent required by Code
Section 409A (as defined below), such exercise period shall be the later of the
fifteenth day of the third month following the date on which, or
December 31 of the calendar year in which, the stock options would
otherwise have expired after termination of employment under the terms of your
stock option agreements and (B) in no event shall any options be
exercisable beyond the maximum 10-year term set forth in the applicable stock
option agreement.


 

















 


Notwithstanding anything in
this Agreement to the contrary, to the extent that you and the Company in good
faith determine that any payment provided for in this Agreement constitutes a “deferral
of compensation” under Internal Revenue Code (“Code”) Section 409A, then no amount shall be payable to you
prior to the earliest of: (i) your death or “disability” (within the
meaning of Code Section 409A(a)(2) (C) following your termination date;
(ii) the date that is six months following the date of your “separation
from service” with the Company (within the meaning of Code Section 409A); or
(iii) to the extent permitted by Code Section 409A, the effective date of
a change in the ownership or effective control of the Company or in the
ownership of a substantial portion of the assets of the Company (in each case
within the meaning of Code Section 409A).


 


6.                         Release.


 


(a)                                  You acknowledge that the following release
shall extend to unknown, as well as known claims, and hereby waive the
application of any provision of law, including, without limitation,
Section 1542 of the California Civil Code, that purports to limit the
scope of a general release. Section 1542 of the California Civil Code
provides:


 


“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.”


 


(b)                                 You agree to and do fully and completely
release, discharge and waive any and all claims, complaints, causes of action
or demands of whatever kind which you have or may have against the Company, its
subsidiaries, affiliates, predecessors and successors and all its directors,
officers, employees, stockholders and other investors by reason of any event,
matter, cause or thing which has occurred prior to the date hereof (“Executive Claims”). You understand and accept that this
Agreement specifically covers, but is not limited to, any and all Executive
Claims relating in any way to compensation, to any previous agreements between
you and the Company related to your employment, or to any other terms,
conditions or circumstances of your employment with the Company, whether for severance
or based on statutory or common law claims for employment discrimination
(including discrimination on the basis of sex, age, religion or disability,
including specifically any claims under the Age Discrimination in Employment
Act (the “ADEA”), Title VII of the Civil Rights
Act of 1964, as amended, or the Americans with Disabilities Act of 1990),
wrongful discharge, breach of contract or any other theory, whether legal or
equitable. Notwithstanding the foregoing, you do not waive any rights to which
you may be entitled to seek to enforce this Agreement, or to seek
indemnification with respect to liability incurred by you as an employee,
officer or director of the Company in accordance with the Company’s bylaws and
the indemnification agreement between you and the Company (the “Indemnification Agreement”), a copy of
which is attached to this Agreement, or with respect to any claim released in
this section. The Company and you agree that the release set forth in this
section shall not release, replace, supersede or in any way materially alter or
reduce the Company’s obligations to you under the Indemnification Agreement. The
parties agree that the Indemnification Agreement shall take precedence over
this Agreement to the extent there is any conflict or inconsistency between
them. You and the Company agree that this release does not operate to release
or modify any other rights to indemnification or advancement of expenses to
which you are entitled from the Company or its insurers under the Company’s
Certificate of Incorporation, its Bylaws, any other agreement, any vote of
stockholders or disinterested directors, the General Corporation Law of the
State of Delaware, the Labor Code of the State of California, a director and
officer insurance policy (whether an existing or replacement policy), or
otherwise.


 


7.                         Acknowledgement of Waiver
of Claims Under ADEA. You
acknowledge that you are waiving and releasing any rights you may have under
the ADEA and that this waiver and release is knowing and voluntary. You and the
Company agree that this waiver and release does not apply to any rights or
claims that may arise under ADEA after the date hereof. You acknowledge that
the consideration given for this waiver and release is in addition to anything
of value to which you were already entitled. You further acknowledge that you
have been advised by this writing that:


 


(a)                                  You should consult with an attorney prior
to executing this Agreement.


 


(b)                                 You have up to 21 days within which to
consider this Agreement.


 

















 


(c)                                  You have seven days following your execution
of this Agreement to revoke the Agreement.


 


(d)                                 This Agreement shall not be effective until
the revocation period has expired.


 


8.                         Outside
Activities; Non-Solicitation; No Disparagement.


 


(a)                                  Outside Activities. During your employment with the Company,
you will not (i) engage in any other gainful employment, business or
activity without the written consent of the General Counsel; (ii) assist
any person or organization in competing with the Company or its affiliates, in
preparing to compete with the Company or its affiliates or in hiring any
employees of the Company or its affiliates; (iii) own, directly or
indirectly, any capital stock of any company which is in competition with any
line of business conducted by the Company or its affiliates; provided that (A) you may own, directly or directly, up
to 1% of the outstanding capital stock of any publicly traded corporation in a
passive investment and (B) you may serve on other corporate boards with
the consent of the General Counsel in compliance with Company policy so long as
such service does not prevent you from carrying out your duties and
responsibilities to the Company.


 


(b)                                 Non-Solicitation. You acknowledge and
recognize the highly competitive nature of the businesses of the Company and
its affiliates and accordingly agree that during your employment with the
Company and for a period of six months thereafter: (i) you will not
directly or indirectly solicit any employee of the Company or any of its
affiliates to terminate his or her employment with the Company or any of its
affiliates; and (ii) you will not directly or indirectly solicit customers
or suppliers of the Company based on confidential information of the Company or
solicit any such person to terminate his, her or its relationships with the
Company.


 


(c)                                  No Disparagement. During and after your employment with the
Company, you agree that you shall not make negative statements or
representations, or otherwise communicate negatively, directly or indirectly,
in writing, orally, or otherwise, or take any action which may, directly or
indirectly, disparage or be damaging to the Company, its subsidiaries,
affiliates, successors or their officers, directors, employees, business or
reputation, except as may be required by law or by any regulatory authority.
The Company agrees that neither it nor its officers and directors shall make
any negative statements or representations, or otherwise communicate
negatively, directly or indirectly, in writing, orally or otherwise, or take
any action which may, directly or indirectly, disparage or be damaging to you
or your reputation.


 


9.                         Remedies.


 


(a)                                  You and the Company acknowledge and agree
that the Parties’ remedies at law for a breach or threatened breach of any of
the provisions of Section 8 of
this Agreement would be inadequate and, in recognition of this fact, you agree
that, in the event of a breach or threatened breach, in addition to any
remedies at law, the Parties, without posting any bond, shall be entitled to
obtain equitable relief in the form of specific performance, temporary
restraining order, temporary or permanent injunction or any other equitable
remedy which may then be available.


 


(b)                                 It is expressly understood and agreed that
although you and the Company consider the restrictions contained in Section 8 to be reasonable, if a final judicial
determination is made by a court of competent jurisdiction that the time or
territory or any other restriction contained in Section 8 is an unenforceable restriction against you,
the provisions of Section 8
shall not be rendered void but shall be deemed amended to apply as to such
maximum time and territory and to such other maximum extent as such court may
judicially determine or indicate to be enforceable.


 


10.                   Entire Agreement; Amendment.
Except as expressly set
forth herein, and except for your stock option agreements (as amended hereby),
the Confidentiality Agreement and the Indemnification Agreement, this Agreement
shall supersede any and all existing agreements between you and the Company or
any of its affiliates relating to the terms of your employment and contains the
entire understanding of the parties with respect to your employment and the
termination thereof. This Agreement may not be altered, modified or amended
except by a written agreement signed by both parties hereto.


 

















 


11.                   No Waiver. The failure of a party to insist upon
strict adherence to any term of this Agreement on any occasion shall not be
considered a waiver of such party’s rights or deprive such party of the right
thereafter to insist upon strict adherence to that term or any other term of
this Agreement.


 


12.                   Severability. In the event that any one or more of the
provisions of this Agreement shall be or become invalid, illegal or
unenforceable in any respect, the validity, legality or enforceability of the
remaining provisions of this Agreement shall not be affected thereby.


 


13.                   Assignment. This Agreement shall inure to the benefit
of and be binding upon the parties hereto and their respective heirs, representatives,
successors and assigns. This Agreement shall not be assignable by you and shall
be assignable by the Company only to an affiliate or successor thereof, which
affiliate or successor shall assume all of the Company’s obligations to you
hereunder.


 


14.                   Acknowledgement. You acknowledge that you have carefully
read this Agreement, fully understand and accept all of its provisions and sign
it voluntarily of your own free will.


 


15.                   Withholding. You agree that any payments to which you
may be entitled pursuant to this Agreement are subject to withholding by the
Company of any applicable federal, state or local taxes; provided
that you understand that you remain ultimately responsible for any tax
consequences hereunder.


 


16.                   Governing Law. This Agreement shall be governed by and
construed in accordance with the laws of the State of California, without
regard for the conflicts of law principles thereof.


 


17.                   Arbitration.


 


(a)                                  Any dispute or controversy arising out of,
relating to, or in connection with this letter agreement, or the
interpretation, validity, construction, performance, breach, or termination
thereof, shall be settled by binding and confidential arbitration to be held in
Santa Clara County, California, in accordance with the National Rules for the
Resolution of Employment Disputes then in effect of the American Arbitration
Association (the “Rules”). The
arbitrator may grant injunctions or other relief in such dispute or controversy.
The decision of the arbitrator shall be final, conclusive and binding on the
parties to the arbitration. Judgment may be entered on the arbitrator’s
decision in any court having jurisdiction.


 


(b)                                 The arbitrator(s) shall apply California law
to the merits of any dispute or claim, without reference to conflicts of law
rules. The arbitration proceedings shall be governed by federal arbitration law
and by the Rules, without reference to state arbitration law. You hereby
consent to the personal jurisdiction of the state and federal courts located in
California for any action or proceeding arising from or relating to this letter
agreement or relating to any arbitration in which the parties are participants.


 


(c)                                  The Company and you shall each pay one-half
of the costs and expenses of the arbitration, and each party shall bear its own
respective attorneys’ fees and all other costs, unless otherwise required or
allowed by law and awarded by the arbitrator.


 


18.                   Notices. Except as otherwise explicitly provided in
this Agreement, any notice provided hereunder will be deemed to be given when
delivered in writing by hand, by facsimile or sent by overnight courier. All
notices to the Company will be marked confidential and addressed to the Company’s
General Counsel. All notices to you will be addressed to your most recent
address as reflected on the Company’s payroll and sent to such other address as
you may provide from time to time by notice to the Company, or any other
persons or addresses as you may request from time to time by notice to the
Company.


 


19.                   Reimbursement of Fees and Expenses. The Company shall reimburse you for fees
and expenses of your legal counsel and personal tax advisors incurred by you in
connection with the execution of this Agreement. You will provide the Company
with reasonable evidence of such fees and expenses in the form of a summary
bill prior to receiving reimbursement.


 

















 


20.                   Counterparts. This Agreement may be signed in
counterparts, each of which shall be an original, with the same effect as if
the signatures thereto and hereto were upon the same instrument.


 


 


Please acknowledge your
acceptance of the foregoing by signing where indicated below.


 


	
   

  	
  AFFYMETRIX,
  INC.

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Barbara A. Caulfield

  
	
   

  	
   

  	
  Name:

  	
  Barbara
  A. Caulfield

  
	
   

  	
   

  	
  Title:

  	
  Executive
  Vice President and General Counsel

  



 


Attachments


 


Accepted
and Agreed:


 


 


	
  /s/ Susan E. Siegel

  	
   

  
	
  Susan
  E. Siegel

  
	
   

  
	
   

  
	
  May 31, 2006

  	
   

  
	
  Date

  



 

















 


Schedule
I


 


1.                                       Review strategic marketing plans as
requested.


 


2.                                       Analyze sales and marketing plans and
strategies with the Senior Vice President of Marketing and Sales.


 


3.                                       Visit, contact and work with high-level
business opportunities and key large accounts as requested.


 


4.                                       Review implementation plans for global
customer segments with focus in sales and sales support organization.


 


5.                                       Review market attack plans for key customer
segments, including priority targets.


 


6.                                       Mentor and assist key employees.


 


7.                                       Work with the General Counsel to develop
litigation and licensing goal for identified companies.


 


8.                                       Special Projects as developed by the CEO.


 


9.                                       Monthly reports of Company business
activities shall be provided to the General Counsel.