Exhibits 10.29
 
AFFYMETRIX, INC.
 
A Delaware corporation
 
Change of Control Plan
 
(As Amended Through May 14, 2010)
 
This Change of Control Plan (the “Plan”) sets forth (i) the terms applicable to
equity awards of Affymetrix, Inc. (together with any successor to substantially
all of its business, stock or assets, the “Company”) in the event of a
transaction resulting in a Change of Control (as defined below) and (ii) the
receipt of severance benefits for Covered Persons of the Company in the event of
a transaction resulting in a Change of Control.
 
1.           Treatment of Equity Awards.  Upon the occurrence of a Change of
Control, or the execution by the Company of any agreement with respect to a
Change of Control, the Board shall take any one or more of the following actions
with respect to outstanding compensatory stock options, restricted stock,
restricted stock units or other equity awards (collectively, “Equity Awards”)
held by any Covered Person at such time:
 
(a) provide that outstanding Equity Awards shall be continued by the Company if
the Company is the surviving entity or shall be assumed, or equivalent Equity
Awards shall be substituted, by the acquiring or succeeding corporation (or an
affiliate thereof);
 
(b) upon written notice to the holders of Equity Awards, provide that all Equity
Awards will become vested and, if applicable, exercisable in full as of a
specified time (the “Acceleration Time”) prior to the Change of Control and will
terminate immediately prior to the consummation of such Change of Control; or
 
(c) in the event of a transaction resulting in a Change of Control, under the
terms of which holders of Common Stock, par value $0.01 per share, of the
Company (the “Common Stock”) will receive upon consummation thereof a cash
payment for each share of Common Stock surrendered pursuant to such Change of
Control (the “Acquisition Price”), provide that all outstanding Equity Awards
shall terminate upon consummation of such Change of Control and each holder of
such Equity Awards shall receive, in exchange therefor, a cash payment equal to
the amount (if any) by which the Acquisition Price multiplied by the number of
shares of Common Stock subject to such outstanding Equity Awards (whether or not
then vested), exceeds the aggregate exercise price or purchase price, if any, of
such Equity Awards.
 
Any Equity Awards held by a Non-Employee Director shall become fully vested
immediately prior to a Change of Control.
 
 
 
 

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2.           Treatment of Equity Awards Upon Triggering Event.  With respect to
any Equity Awards remaining outstanding following a Change of Control, upon a
Triggering Event, a Covered Person’s Equity Awards shall become fully vested
subject to compliance with Section 3 below.  Notwithstanding the foregoing, to
the extent that any applicable laws or regulations of the applicable
jurisdiction in which the Covered Person is employed requires certain treatment
with respect to Equity Awards upon a Triggering Event, the Covered Person shall
be entitled to the more beneficial treatment provided by either (i) the
applicable laws or regulations of the applicable jurisdiction or (ii) this Plan,
but not both.  To the extent any Equity Awards are to be settled in cash
pursuant to Section 1 or this Section 2, such Equity Awards shall be settled as
promptly as practicable but no later than two and one-half months (2-1/2) months
after the end of the taxable year of the Covered Person in which such Equity
Awards become vested.
 
3.           Enhanced Severance. 
 
(a) Upon a Triggering Event following a Change of Control, the following Covered
Persons shall receive a severance payment equal to the following amounts:
 
Covered Person Position
Severance Payment
Level 13 or above employees who are the Executive Chairman, an EVP, CEO or
President
24 months of base salary plus 200% of target bonus
Level 13 or above employees who are SVPs
15 months of base salary plus 140% of target bonus
Level 12 employees who are VPs
12 months of base salary plus 100% of target bonus
Level 10 to 11 employees who are Directors or Senior Directors
9 months of base salary plus 75% of target bonus
Level 5 to level 9 employees
6 months of base salary plus 50% of target bonus, if applicable
Level 4 or below employees
3 months of base salary plus 25% of target bonus, if applicable

 
(b)           All severance benefits under this Plan shall be conditioned on the
Covered Person signing and letting become effective a general release of claims
(the “Release”) in a form acceptable to the Company. The Covered Person shall
sign such Release within 45 days following termination.  All severance payments
under this Plan shall be made in a lump-sum within 10 days after the later of
the termination date and the date on which the Release becomes effective, and,
in any event, no later than two and one-half (2-1/2) months after the end of the
taxable year of the Covered Person in which the termination date occurs.  All
amounts paid under this Plan shall be reduced by any applicable taxes or any
other amounts required to be paid or withheld by the Company.

 
 
 

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(c)           In the event of termination of a Covered Person with a housing
loan, such Covered Person will have one year to settle the loan with the
Company.  During such year, the Covered Person will continue to make interest
payments to the Company.
 
(d)           The Company will continue to provide health benefits (which may be
through COBRA premium reimbursement or subsidizing) to each Covered Person at
the same cost to such Covered Person as prior to the Change of Control for the
period of time set forth in Section 3(a) under “Severance Period” or, if
earlier, until such Covered Person becomes eligible for group health benefits
from another employer.
 
(e)           The Company will provide each Covered Person outplacement services
following termination of employment for a period of six months for Executive
Officers, Vice Presidents and Directors and two months for all other Covered
Persons.
 
(f)           Notwithstanding the foregoing, to the extent that any applicable
laws or regulations of the applicable jurisdiction in which the Covered Person
is employed requires certain treatment with respect to Enhanced Severance
provisions set forth in this Section 3, the Covered Person shall be entitled to
the more beneficial treatment provided by either (i) the applicable laws or
regulations of the applicable jurisdiction or (ii) this Plan, but not both.
 
4.           Definitions.  For purposes of this Plan, the following terms shall
have the following meanings:
 
(a)           “Cause” shall mean any of the following by a Covered Person:
 
(i)            willful and continued failure to substantially perform his or her
duties to the Company (other than as a result of total or partial incapacity due
to physical or mental illness);
 
(ii)            any willful act or omission constituting dishonesty, fraud or
other malfeasance against the Company;
 
(iii)            conviction of a felony under the laws of the United States or
any state thereof or any other jurisdiction in which the Company conducts
business; or
 
(iv)            breach of any of the material policies of the Company including
being under the influence of illicit drugs or alcohol at work or on the
Company’s premises.
 
 
 
 

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(b)           “Change of Control” shall mean:
 
(i)           any merger or consolidation which results in the voting securities
of the Company outstanding immediately prior thereto representing immediately
thereafter (either by remaining outstanding or by being converted into voting
securities of the surviving or acquiring entity) no more than 50% of the
combined voting power of the voting securities of the Company or such surviving
or acquiring entity outstanding immediately after such merger or consolidation;
 
(ii)           during any period of 12 consecutive calendar months, the
individuals who at the beginning of such period constitute the Company’s Board
of Directors (the “Board”), and any new directors whose election by such Board
or nomination for election by stockholders was approved or recommended by a vote
of at least a majority of the members of such Board who were either directors on
such Board at the beginning of the period or whose election or nomination for
election as directors was previously so approved or recommended, for any reason
cease to constitute at least a majority of the members thereof;
 
(iii)           any individual, entity or group (within the meaning of Section
13(d)(3) or 14(d)(2) of the Securities Exchange Act of 1934 as amended
(“Exchange Act”))(a “Person”) shall become the beneficial owner (within the
meaning of Rule 13d-3 promulgated under the Exchange Act) of at least 50% of the
total voting power represented by the Company’s then outstanding voting
securities; or
 
(iv)           any sale of all or substantially all of the assets of the
Company.
 
(c)           “Covered Person” or “Covered Persons” shall mean a full-time
employee of the Company or any of its wholly-owned subsidiaries or a member of
the Board of Directors of the Company whois employed by the Company.
 
(d)           “Non-Employee Director” shall mean a member of the Board of
Directors of the Company immediately prior to a Change of Control who is not
also an employee of the Company.
 
 
 
 

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(e)           “Triggering Event” shall mean:
 
(i)            a Covered Person’s employment is terminated by the Company (or
any successor or acquiror) without Cause in connection with, or within twelve
(12) months following, a Change of Control; provided, however, if an employee is
terminated by the Company in connection with a Change of Control but immediately
accepts employment with the Company’s successor or acquiror, such employee will
not be deemed to be covered by this subsection (i), but if such employee is
terminated without Cause by the successor or acquiror within the twelve (12)
months following the Change of Control, this subsection (i) will apply;
 
(ii)            the Covered Person, in connection with a Change of Control, is
not offered Comparable Employment.  For purposes of the foregoing, “Comparable
Employment” shall mean, (a) in the case of a Covered Person at the director
level or above, (i) employment on terms which provide the same or greater rate
of base pay or salary as in effect immediately prior to a Change of Control,
(ii) no material reduction in job duties and responsibilities as such Covered
Person had prior to a Change of Control and (iii)  equivalent or higher target
bonus opportunity to the target bonus opportunity of the Covered Person in
effect immediately prior to the Change of Control, and (b) in the case of all
Covered Persons, a principal work location that is no more than forty-five (45)
miles from the Covered Person’s principal work location immediately prior to the
Change of Control; provided, however, if such Covered Person accepts employment
that is not Comparable Employment, such employee shall not be covered by this
subsection (ii);
 
(iii)            after accepting employment with the Company (or any successor
or acquiror) after a Change of Control, the Covered Person resigns employment
within six (6) months following a Change of Control due to a Material Change in
the Covered Person’s Terms of Employment.  For purposes of the foregoing, a
“Material Change in the Covered Person’s Terms of Employment” shall occur if,
without the Covered Person’s written consent: (a) in the case of a Covered
Person at the director level or above, (i) the Covered Person’s base salary or
job duties and responsibilities are materially reduced from those in effect
immediately prior to a Change of Control or (ii) the Covered Person is subject
to a substantial reduction in target bonus opportunity from the target bonus
opportunity of that Covered Person in effect immediately prior to the Change of
Control, or (b) in the case of a Covered Person at Level 6 or above, such
Covered Person’s principal work location is to be moved more than forty-five
(45) miles from the Covered Person’s principal work location immediately prior
to a Change of Control.
 
 
 
 

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5.            Section 409A.  Notwithstanding anything to the contrary in this
Plan, if a Covered Person is a “specified employee” within the meaning of
Section 409A of the Internal Revenue Code, as amended (“Section 409A”) and the
regulations thereunder, as determined under the Company’s established
methodology for determining specified employees, as of the date of such Covered
Person’s “separation from service” as defined in Treasury Regulation Section
1.409A-1(h) (or any successor regulation), and if any payments or entitlements
provided for in this Plan constitute a “deferral of compensation” within the
meaning of Section 409A and cannot be paid or provided in the manner provided
herein without subjecting such Covered Person to additional tax, interest or
penalties under Section 409A, then any such payment and/or entitlement which is
payable during the first six months following such Covered Person’s “separation
from service” shall be paid or provided to such Covered Person in a lump sum on
the first business day immediately following the first to occur of (i) the
six-month anniversary of such Covered Person’s “separation from service” and
(ii) the date of such Covered Person’s death.  For the avoidance of doubt, any
reference to termination of employment in this Plan shal mean "separation from
service" as defined in Treasury Regulation Section 1.409A-1(h) (or any successor
regulation).
 
 6.           Amendment of Plan.  The Board shall have the power to amend this
Plan from time to time in its discretion prior to the occurrence of a Change of
Control.  Following a Change of Control, this Plan may not be terminated or
amended in a manner adversely to any Covered Person for 12 months following a
Change of Control.  The termination or amendment of the Plan at any time shall
not affect any benefits to which a Covered Person has previously become entitled
hereunder.  To the extent required by applicable law, if and when this Plan
becomes operative in connection with a Change of Control, the Company shall make
any revisions and filings necessary to the extent the Plan is determined to be a
"severance pay arrangement" within the meaning of Section 3(2)(B)(i) of ERISA.
 
7.           Mediation and Arbitration.  The parties agree that any and all
disputes, claims or controversies arising out of or relating to this Plan shall
be submitted to Judicial Arbitration and Mediation Services (“JAMS”), or its
successor, to the extent possible in the location which is the location of a
Covered Person’s principal work place, under the auspices and rules of JAMS, for
mediation, and if the matter is not resolved through mediation, then it shall be
submitted to JAMS, or its successor, for final and binding arbitration.  The
provisions of this Section may be enforced by any court of competent
jurisdiction, and the party seeking enforcement shall be entitled to an award of
all costs, fees and expenses, including attorneys’ fees, to be paid by the party
against whom enforcement is ordered.
 
8.            Superseding Plan.  This Plan (i) shall be the only plan with
respect to benefits provided to Covered Persons of the Company upon a
transaction that results in a Change of Control and (ii) shall supersede any
other plan with respect to a transaction resulting in a Change of Control
previously adopted by the Company.

 
 
 

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