Exhibit 10.20(b)

 

NONQUALIFIED SUPPLEMENTAL

 

DEFERRED COMPENSATION PLAN

 

ADOPTION AGREEMENT

 

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NONQUALIFIED SUPPLEMENTAL

DEFERRED COMPENSATION PLAN

ADOPTION AGREEMENT

 

ADOPTION OF PLAN  — [Select one]

 

o                                    Adoption - The undersigned
                             (the “Employer”) hereby adopts as a Nonqualified
Deferred Compensation Plan for the individuals identified in Item 5 herein the
form of Plan known as the Nonqualified Supplemental Deferred Compensation Plan.

 

o                                    Amendment of Previous Nonqualified Deferred
Compensation Plan —  With “Grandfathered” Amounts                    (the
“Employer”) previously has adopted a Nonqualified Deferred Compensation Plan,
known as the                           [enter name of previous plan], and the
execution of this Adoption Agreement constitutes an amendment to that Plan,
effective only for Deferrals, Contributions, earnings, gains, losses,
depreciation and appreciation vested and credited thereto or debited therefrom
on and after the Effective Date listed in Section 2 below, or, if otherwise
determined by the Employer, on and after January 1, 2005 with respect to Plan
provisions required under Section 409A of the Internal Revenue Code and the
regulations thereunder. All other amounts in the plan shall be subject to the
provisions of the previous plan document. This option is appropriate if the
previous plan contains grandfathered amounts not subject to Section 409A of the
Internal Revenue Code. Grandfathered amounts were contributed to the plan prior
to January 1, 2005 under the terms of the plan in effect prior to October 4,
2004, and those plan terms have not since been materially modified.
Grandfathered amounts and earnings will be administered under the terms of the
prior plan document.

 

x                                  Restatement of Previous Nonqualified Deferred
Compensation Plan — Affymetrix, Inc. (the “Employer”) previously has adopted a
Nonqualified Deferred Compensation Plan, known as the Affymetrix, Inc. Deferred
Compensation Plan [enter name of previous plan], and the execution of this
Adoption Agreement constitutes a restatement of that Plan, effective as of the
Effective Date listed in Section 2 below for all funds under the Plan. This
option is appropriate if the previous plan does not contain “grandfathered”
amounts (see description above), or if Employer wishes to apply Section 409A
rules to all amounts in the plan (even pre-2005 amounts), or if previous plan
has been materially modified and thus become subject to Section 409A.

 

NAME OF PLAN

 

The name of this Plan as adopted by the Employer is the  [enter name of Plan]
Affymetrix, Inc. Deferred Compensation Plan (the “Plan”).

 

INDIVIDUALIZED PLAN INFORMATION

 

With respect to the variable features contained in the Plan, the Employer hereby
makes the following selections granted under the provisions of the Plan:

 

1.                                       Adopting Entity. The Employer adopts
the Plan as:

 

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List type of business entity (corporation, partnership, controlled group of
corporations, etc.) Corporation

 

List each Employer adopting the Plan and Employer Identification Number (EIN):

 

Name of Employer:

 

Affymetrix, Inc.

 

EIN:

 

77-0319159

Name of Employer:

 

 

 

EIN:

 

 

Name of Employer:

 

 

 

EIN:

 

 

Name of Employer:

 

 

 

EIN:

 

 

Name of Employer:

 

 

 

EIN:

 

 

(attach additional lists as necessary)

 

The adopting Employers and the Employer are referred to herein collectively as
the “Employer.”

 

Select state of controlling law (see Section 10.7 of Plan Document):

 

x                                  State of incorporation;   Delaware

 

o                                    State of domicile

 

2.                                       Effective Date. The “Effective Date” of
the adoption of this Plan, this Plan amendment or this Plan restatement is
[enter date] December 31, 2008.

 

3.                                       Plan Year. The “Plan year” of the Plan
shall be [select one]:

 

x                                  the calendar year.

 

o                                    the fiscal year or other 12- month period
ending on the last day of [specify month].

 

o                                    a short Plan year beginning on    ,     and
ending on    ,    ; and thereafter the Plan year shall be as indicated in (a) or
(b) above.

 

4.                                       Plan Administrator. The “Administrator”
of the Plan is Senior Director, Compensation, Benefits and HRIS.

 

 [fill in the name(s) of the individual(s) or job title(s) or entity (such as a
committee) that is (are) responsible for administration of the Plan], and such
other person(s) or entity as the Employer shall appoint from time to time.

 

5.                                       Eligible Individuals. The following
shall be eligible to participate in the Plan:  [select all that apply – do not
list individual names]:

 

x                                  A select group of management or
highly-compensated Employees as designated by the Employer in separate
resolutions or agreements;

 

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o                                    Employee Board Members;

 

x                                  Non-Employee Board Members;

 

o                                    Other Service Providers (i.e., independent
contractors, consultants, etc.)

 

o                                    Employees or other Service Providers above
the following Compensation threshold:  [enter dollar amount]  $      ;

 

o                                    Employees with the following job titles: 
[enter job title(s); for example, “Vice President and above”]

 

o                                    Other: [enter description]

 

6.                                       Eligibility Timing. Eligibility timing
selected below shall apply uniformly to all Participant Deferrals (including
Performance-Based Bonus Deferrals), as well as Employer Matching Contributions
and Other Employer Contributions, unless otherwise indicated. If the Employer
wishes to provide for separate eligibility rules for different types of
Compensation (for example, Salary vs. Bonus), or for types of Contributions (for
example, Employer Matching Contributions vs. Participant Deferrals), mark
“Other” below and attach exhibits as necessary [select one]:

 

x                                  Eligible immediately upon properly completed
designation by the Plan administrator or Employer;

 

o                                    Eligible after the following period of
employment, Board service, etc. [enter number of days, months or years, for
example, 90 days]      ;

 

o                                    Other  [enter description]:

 

7.                                       Types and Amounts of Participant
Deferrals [select all that apply and enter minimum and maximum percentages in
increments of one percent (for example, Salary minimum 0% maximum 100%). Note
that no Deferral election can reduce a Participant’s Compensation below the
amount necessary to satisfy required withholding for FICA/Medicare/income
taxes,  required Participant Contributions into another Employer-sponsored
benefit plan such as medical insurance, 401(k) loan repayments, etc.]:

 

x                                  Salary [select one]:

 

x  percentage [enter minimum 0% and maximum 75%]

or

x  fixed dollar amount  [enter minimum $5000 annual minimum for all deferral
sources ].

 

o                                    Non-Performance-Based Bonus [select one]:

 

o  percentage [enter minimum      % and maximum       %]

or

 

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o  fixed dollar amount  [enter minimum $    ].

 

x                                  Performance-Based Bonus [select one and enter
performance period (for example, 12-month period ending each March 31 ]:
performance period from                  to                               .

 

x  percentage [enter minimum 0% and maximum 90%]

or

x  fixed dollar amount  [enter minimum $5000 annual minimum for all deferral
sources].

 

o                                    Commissions [select one]:

 

o  percentage [enter minimum   % and, maximum   %]

or

o  fixed dollar amount  [enter minimum $         ].

 

x                                  Board of Directors Fees/Retainer (note —
should not include expense reimbursements):

 

x  percentage [enter minimum 0% and, maximum 100%]

or

x  fixed dollar amount  [enter minimum $5000 annual minimum for all deferral
sources].

 

o                                    Other Service Provider Fees or other earned
income from the Employer:

 

o  percentage [enter minimum   % and, maximum   %]

or

o  fixed dollar amount  [enter minimum $  ].

 

o                                    401(k) Refund (amount deferred from
Participant’s regular Compensation equal in value to any refund paid to
Participant in that year resulting from excess deferrals in Employer’s
401(k) plan — see Subsection 2.9 of Plan document for definition.)

 

o                                    Other [enter description]:

 

8.                                       Definition of Compensation for Purposes
of Making Plan Contributions [select one]:

 

o                                    Same definition of Compensation as in
Employer’s 401(k) or other applicable qualified retirement plan, earned while
the Participant is an Eligible Individual, as determined by the Employer.

 

o                                    Participant’s total wages, salary,
commissions, overtime, bonus, etc. for a given year which the Employer is
required to report on Form W-2 or other appropriate form, (or, in the case of
Board members, Board fees and retainer only, but not including expense
reimbursements)(or, in the case of Other Service Providers,

 

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the Participant’s total remuneration from the Employer for a given year pursuant
to the agreement to provide services to the Employer), earned while the
Participant is an Eligible Individual as determined by the Employer.

 

x                                  Other [enter description]:  (a) Participant’s
total annual cash compensation relating to services performed during any
calendar year, including commissions, overtime, bonus, which the Employer is
required to report on Form W-2 or other appropriate form, or, (b) in the case of
Board members, Board fees and retainer only, but not including expense
reimbursements or, (c) in the case of Other Service Providers, the Participant’s
total remuneration from the Employer for a given year pursuant to the agreement
to provide services to the Employer, earned, in each case, while the Participant
is an Eligible Individual as determined by the Employer, but in each case,
excluding distributions from nonqualified deferred compensation plans, fringe
benefits, stock options, relocation expenses, severance pay, automobile and
other allowances and non-monetary awards made to a Participant.

 

9.                                       Expiration of Participant’s Deferral
Elections [select all that apply]:

 

x                                  Renewed Each Year:  Participant’s Deferral
Elections must be renewed each year during the open enrollment period ending no
later than December 31 prior to the effective Plan year (or, in the case of
Performance-Based Bonuses, no less than 6 months prior to the end of the
applicable performance period).

 

x  For all types of Compensation Deferrals.

 

o  For Salary Deferrals only — other types of Deferrals are “evergreen”.

 

o  For Performance-Based Bonus only — other types of Deferrals are “evergreen”.

 

o  Other: [specify]

 

o                                    Evergreen:  Participant’s Deferral
Elections will be “evergreen” (i.e., will continue indefinitely until the
Participant’s Termination Date unless changed by the Participant — so each year
the Participant will be deemed to have the same election in place as the prior
year unless actively changed by the Participant during the open enrollment
period ending no later than December 31 prior to the effective Plan year or, in
the case of Performance-Based Bonuses, no less than 6 months prior to the end of
the applicable performance period).

 

o  For all types of Compensation Deferrals.

 

o  For Salary Deferrals only — other types of Deferrals are renewed each year.

 

o  For Performance-Based Bonus only — other types of Deferrals are renewed each
year.

 

o  Other: [specify]

 

10.                                 Employer Contributions [select all that
apply]:.

 

o                                    (a)                                  No
Employer Contributions.

 

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o                                    (b)                                
Matching Contributions on all Participant Compensation Deferrals [also complete
Items 11 through 14 ].

 

o                                    (c)                                 
Matching Contributions on certain types of Compensation Deferrals (for example,
Matching Contributions on Participant Performance-Based Bonus Deferrals, etc.)
[attach explanation describing which types of deferrals will be matched and also
complete Items 11 through 14]

 

x                                  (d)                                 Employer
Contributions other than Matching Contributions [complete Item 15]  (amount or
formula for determining and allocating such contributions should be documented
in writing when determined, and such writings will form part of the Plan).

 

11.                                 Amount of Matching Contribution on
Participant Compensation Deferrals. If the Employer has specified in Item
10(b) or (c) that it will make Matching Contributions on behalf of Participants
based on their Compensation Deferrals, such Matching Contributions will be in an
amount determined as follows for the applicable period selected in Item 13
below:  [Select (a), (b), (c), (d) or (e) below — if Employer has indicated in
10(c) above that Matching Contributions will be made on certain types of
Participant Compensation Deferrals and if Employer wishes for  different
Matching formulas to be used for different types of Participant Compensation
Deferrals, Employer should attach additional copies of this Item 11 completed
for each type of Participant Compensation Deferral that is matched. ]

 

o

 

(a)

 

       % of the Compensation Deferrals made by each Participant during the
applicable period.

 

 

 

 

 

o

 

(b)

 

At a percentage determined from time to time in the discretion of the Employer
of each Participant’s Compensation Deferrals for the applicable period
(percentage should be documented in writing when determined, and such writings
will form part of the plan).

 

[Optional:  If 11(a) or (b) above is selected, the Employer may also specify
here that it will not match Compensation Deferrals in excess of   $   or   % of
each Participant’s Compensation during the applicable period —specify   either a
dollar amount or a whole percentage. If no limit is entered here, the assumption
is that 100% of the Participant’s Compensation Deferrals will be matched at the
applicable percentage.]

 

o

 

(c)

 

        % of the portion of each Participant’s Compensation Deferral
Contributions during the applicable period which does not exceed    % of the
Participant’s Compensation for such period; plus    % of the portion, if any, of
each Participant’s Compensation Deferral Contributions during the applicable
period which exceeds    % but does not exceed   % of the Participant’s
Compensation for such period.

 

 

[Note:  Example for 11(c) above — select this option if Employer wants to match
different percentages and different levels of deferral — for example, 100% of
the first 3% of compensation deferred, and 50% of the next 2%]

 

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o

 

(d)

 

         % of the Compensation of each Participant who made Compensation
Deferral Contributions during the applicable period of at least   % of
Compensation.

 

o

 

(e)

 

Other:  [describe]

 

12.                                 Applicable Period for Matching
Contributions. Employer Matching Contributions elected under Item 10(b) or
(c) shall be allocated and credited to eligible Participants’ Accounts as soon
as administratively feasible after the end of each “Applicable Period” after the
amounts have been determined by the Employer. For purposes of determining a
Participant’s share of Matching Contributions under Item 10, the Applicable
Period shall be  [Select one]:

 

o                                    the Plan Year.

 

o                                    the payroll period.

 

o                                    other (specify calendar month, Plan year
quarter, etc.)      .

 

13.                                 Employees Eligible to Receive Employer
Matching Contributions. Matching Contributions made for each Plan Year (if
applicable)  shall be allocated and credited to the Accounts of the following
Participants: [Select one if applicable]

 

o                                    Participants who were employed by the
Employer (or, in the case of non-Employee Board Members, served on the Board)
during that Plan Year, or, in the case of Other Service Providers, who provided
services to the Employer during that Plan Year.

 

o                                    Participants who were employed by the
Employer (or, in the case of non-Employee Board Members, served on the Board) on
the last day of the Plan Year, or, in the case of Other Service Providers, who
provided services to the Employer on the last day of the Plan Year.

 

o                                    Participants who were employed by the
Employer (or, in the case of non-Employee Board Members, served on the Board) on
the last day of the Plan Year or who retired, died or were Disabled during the
Plan Year, or, in the case of Other Service Providers, who provided services to
the Employer on the last day of the Plan Year or who died or were Disabled
during the Plan Year. [If this option is selected, complete Item 30 — definition
of “Disability”.]

 

14.                                 Vesting Schedule of Employer Matching
Contributions. If Matching Contributions are made to the Plan, select the rate
at which such Contributions will vest [select one]:

 

o                                    Immediate 100% vesting for all
Participants.

 

o                                    “Cliff” vesting (0%  up to cliff; 100%
after cliff) [select one]:

 

o  1 year cliff (less than 1 year 0%; 1 or more years 100%)

 

o  2 year cliff (less than 2 years 0%; 2 or more years 100%)

 

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o  Other cliff (enter number of years:  less than    years 0%;    or more years
100%)

 

o                                    “Graded” vesting  [enter vesting
percentages]:

 

1 year    %                                         6
years    %                                   11 years    %

 

2 years    %                                   7
years    %                                   12 years    %

 

3 years    %                                   8
years    %                                   13 years    %

 

4 years    %                                   9
years    %                                   14 years    %

 

5 years    %                                   10
years    %                             15 years    %

 

o                                    Other vesting schedule: [describe schedule
— subject to approval]

 

15.                                 Vesting Schedule of Employer Contributions
(Other Than Matching Contributions). If Employer Contributions (other than
Matching Contributions) are made to the Plan, select the rate at which such
Contributions will vest [select one]:

 

o                                    Immediate 100% vesting for all
Participants.

 

o                                    “Cliff” vesting (0%  up to cliff; 100%
after cliff) [select one]:

 

o  1 year cliff (less than 1 year 0%; 1 or more years 100%)

 

o  2 year cliff (less than 2 years 0%; 2 or more years 100%)

 

o  Other cliff (enter number of years:  less than    years 0%;    or more years
100%)

 

o                                    “Graded” vesting  [enter vesting
percentages]:

 

1 year    %                                         6
years    %                                   11 years    %

 

2 years    %                                   7
years    %                                   12 years    %

 

3 years    %                                   8
years    %                                   13 years    %

 

4 years    %                                   9
years    %                                   14 years    %

 

5 years    %                                   10
years    %                             15 years    %

 

x                                  Other vesting schedule: [describe schedule —
subject to approval] Employer Contribution shall vest in accordance with the
vesting schedule set forth in any agreement entered into between the Participant
and Employer. If not addressed in such agreements, Employer Contribution shall
vest in accordance with the schedule declared by a committee responsible for the
administration of the Plan.

 

16.                                 Vesting Years. A “Vesting Year” described
above for purposes of determining vesting under the Plan shall be computed in
accordance with:  [select one — if this is an amendment or restatement of a
prior plan, definition from prior plan will override this definition.]

 

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o                                    Years of service (12-consecutive-month
periods) with the Employer since date of hire (or date of commencement of Board
service).

 

o                                    Years of participation in the Plan
(12-consecutive-month period between date Participant enters Plan and
anniversary of such date) (if this is an amendment or restatement of a prior
Plan, years of participation in prior plan will be included) (additional fees
will apply if this item is selected).

 

o                                    Plan Years since each Plan Year’s total
Contributions were made (“rolling vesting”) (additional fees will apply if this
item is selected). [If this option is selected, select either (a) or (b) below:]

 

o

 

(a)

 

Vesting will be credited/updated on the last day of the Plan year.

 

 

 

 

 

 

 

o

 

(b)

 

Vesting will be credited/updated on the anniversary of the date the Contribution
is credited.

 

17.                                 Full Vesting Upon Occurrence of Specific
Event. [select all that apply]

 

o                                    100% vesting upon Normal Retirement
[describe criteria such as age (can be partial year), years of service with the
Employer (must be whole years of service), or years of participation in the Plan
(must be whole years of participation)]

 

o                                    100% vesting upon Early Retirement
[describe criteria such as age (must be whole years), years of service with the
Employer (must be whole years of service), or years of participation in the Plan
(must be whole years of participation)]

 

x                                  100% vesting upon Death.

 

x                                  100% vesting upon Disability [complete Item
30 — definition of “Disability”].

 

x                                  100% vesting upon Change in Control of the
Employer [complete Items 28 and29 — definition of “Change in Control”]

 

o                                    100% vesting upon occurrence of other
event:  [describe event]

 

18.                                 Service Before Plan’s Establishment
Excluded. Years of service earned prior to establishment of the Plan shall be
disregarded for purposes of determining vesting under the Plan:

 

o                                    Yes (this may be elected only if this is
the establishment of a new Plan).

 

x                                  No.

 

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19.                                 Forfeitures for Misconduct or Violation of
Non-Compete.  Participants terminating employment prior to becoming 100% vested
will forfeit the forfeitable percentage of their Accounts as indicated in
accordance with the vesting schedule selected in Items 14 and/or 15. 
Participants may also forfeit 100% of their Matching and Employer Contribution
Accounts (if applicable) under the following circumstances:  [select any that
apply]:

 

o            Misconduct (termination for Cause). [if selected, the definition of
Misconduct or Cause should be documented in writing, and such writings will form
part of the Plan]

 

o                                    Engaging in competition with the Employer. 
[if selected, the definition of engaging in competition should be documented in
writing, and such writing will form part of the Plan]

 

20.                                 Employer Stock as Deemed Investment Option. 
If Employer stock will be a deemed investment option, indicate below how shares
are to be tracked:  [select one]

 

o                                    Partial and whole shares.

 

o                                    Unitized fund.

 

21.                                 In-Service Distributions.  If the Employer
elects below, the Plan will allow distributions of Participant Deferral
Contributions to be made to Participants while they are still employed
(“In-Service Distributions”), if they elect a fixed distribution date during the
regular election period.    [Select one — note that In-Service Distributions of
Employer Contributions is not permitted]

 

x                                  No, In-Service Distributions will not be
permitted for contributions on or after January 1, 2009.

 

o                                    Yes, In-Service Distributions will be
permitted.  [select one ].

 

o  For All Participant Deferral Contributions

 

o  For Participant Compensation Deferral Contributions (other than
Performance-Based Bonus) only.

 

o  For Participant Performance-Based Bonus Deferral Contributions.

 

Please indicate the number of years a Participant must defer payment(s) until 
In-Service Distribution(s) may begin:

 

o  2 Years after the Calendar Year for which the deferral is effective

 

o          Years after the Calendar Year for which the deferral is effective

 

Please indicate if separate In-Service Distribution Dates are allowed for each
Type of Participant Deferral selected in Item 7:

 

o  No (single distribution date allowed per Plan Year)

 

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o  Yes (requires additional tracked sources per Plan Year)

 

[Note — if “Yes” is elected above and the Plan will allow In-Service
Distributions, please indicate if Participant will be permitted to make a
“pushback” subsequent election to defer the original distribution date at least
five years in accordance with Plan provisions (see subsection 9.1 of Plan
document — note that election must be made 12 months prior to original
distribution date and election will not take effect for 12 months)    o Yes   o
No ]

 

22.                                 Unforeseeable Emergency  Distributions
Dates.  If the Employer elects below, the Plan will allow distributions to be
made to Participants while they are still employed if they meet the criteria for
an unforeseeable emergency financial hardship (“Unforeseeable Emergency
Distributions”).  Both Participant Deferral Contributions and Vested Employer
Contributions can be distributed in the event of an eligible Unforeseeable
Emergency Distribution event. [Select one]

 

o                                    No, Unforeseeable Emergency Distributions
will not be permitted.

 

x                                  Yes, Unforeseeable Emergency Distributions
will be permitted.  [select one below].

 

x  For active Participants only.

 

o  For active Participants, terminated Participants and Beneficiaries.

 

23.                                 Form of Distributions (at Termination of
Employment or Death).  Distributions will be made to Participants upon
Termination of Employment with the Employer or Death of the Participant as
follows [select one]

 

o                                    Lump sum only.

 

x                                  Lump sum unless installments elected, but can
only receive installments if Participant meets the following criteria [select
all that apply– if item not selected below, then Participants in that category
will receive lump sum only]:

 

o  Retirement [describe criteria such as age (can be partial year), years of
service with the Employer (must be whole years of service), or years of
participation in the Plan (must be whole years of participation)]

 

o  Early Retirement [describe criteria such as age (must be whole years), years
of service with the Employer (must be whole years of service), or years of
participation in the Plan (must be whole years of participation)]

 

x  Termination (other than for Misconduct, Cause or Violation of Non-Compete)

 

x          Lump sum unless installments elected, and Participant may receive
installments regardless of reason for Termination of Employment.

 

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[Note – if Installments are elected above, please indicate if Participant will
be permitted to make a subsequent election to change the number of installments
in accordance with Plan provisions (see subsection 9.2 of Plan document)     o
Yes   x No ]

 

24.          Distribution Upon Disability.  If the Employer selects below, the
Plan will allow distributions to be made to Participants upon Disability but
while they are still employed if they meet the criteria for Disability in Item
30 below.  The form of distribution will be the same as for Termination of
Employment.

 

o                                    No, distribution upon Disability will not
be permitted.

 

x                                  Yes, distributions upon Disability will be
permitted.  [complete Item 30 – definition of “Disability”].

 

25.          Expiration of Participant’s Distribution Elections [select one]:

 

o                                    Renewed Each Year:  Participant’s
Distribution Election must be selected each year during the open enrollment
period for the following year’s contributions — if no new election is made, that
year’s contributions default to payment in the form of a lump sum.

 

x                                  Evergreen:  Participant’s Distribution
Election will be “evergreen” (i.e., will continue indefinitely for each year’s
contributions until the Participant’s Termination Date unless changed by the
Participant – so each year the Participant will be deemed to have the same
distribution election in place as the prior year unless actively changed by the
Participant at open enrollment, and the change will only be applicable to future
contributions).

 

26                                    Distributions Upon Change in Control:  If
Employer elects below, distributions will be made to Participants upon Change in
Control of the Employer (without a termination of employment of the
Participant), as follows [select one, and complete Items 28 and 29 below
(definition of “Change in Control”) ]

 

o                                    No, Distributions upon Change in Control
will not be permitted.

 

x                                  Yes, Distributions upon Change in Control
will be permitted, in a lump sum only.

 

o                                    Yes, Distributions upon Change in Control
will be permitted, in a lump sum or in installments as elected by the
Participant [complete Item 23].

 

27.                                 Length of Installments (if Installment
Distributions permitted in Item 23 and/or Item 26 above)  [indicate length
below]:

 

Annual installments over no fewer than 2 [enter minimum number of years – must
be at least 2]  and no more than 15 years at Participant’s election [enter

 

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maximum number of years].

 

28.                                 “Change in Control” – Dates of
Distribution.  Distributions upon a Change in Control shall occur upon the date
that [select all that apply – see Subsection 9.9  of the Plan document for more
details]:

 

x                                  A person or group acquires more than 50% of
the total fair market value or voting power of the stock of the corporation
(select definition of “corporation” in Item 29 below).

 

o                                    A person or group acquires ownership of
stock of the corporation with at least 35% of the total voting power of the
corporation (select definition of “corporation” in Item 29 below).

 

o                                    A person or group acquires assets from the
corporation having a total fair market value of at least 40% of the value of all
assets of the corporation immediately prior to such acquisition.  (select
definition of “corporation” in Item 29 below).

 

x                                  A majority of the corporation’s board of
directors is replaced during any 12-month period by directors whose appointment
or election is not endorsed by a majority of the board as constituted prior to
the appointment or election (select definition of “corporation” in Item 29
below).

 

29.                                 “Change in Control” – Which Corporation the
Change Relates.  Distributions upon a Change in Control shall be made only if
the Change in Control relates to the corporation selected below:  [select all
that apply]:

 

x                                  (a)           The corporation for whom the
Participant is performing services at the time of the Change In Control event.

 

x                                  (b)           The corporation liable for
payments from the Plan to the Participant.

 

x                                  (c)           A corporation that is a
majority shareholder of a corporation described in (a) or (b) above.

 

x                                  (d)           Any corporation in the chain of
corporations in which each corporation is a majority shareholder of another
corporation in the chain, ending in a corporation described in (a) or (b) above.

 

30.                                 Definition of “Disability.” A Participant
shall be considered “Disabled” if [select one]:

 

x                            by reason of any medically determinable physical or
mental impairment which can be expected to result in death or can be expected to
last for a continuous period of at least 12 months, the Participant is receiving
income replacement benefits for at least 3 months under accident and health
plans of the Employer;

 

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o                              the Participant is unable to engage in any
substantial gainful activity by reason of any medically determinable physical or
mental impairment that can be expected to result in death or can be expected to
last for a continuous period of not less than 12 months;

 

o                              the Participant is deemed to be totally disabled
by the Social Security Administration;

 

o                              the Participant is determined to be disabled in
accordance with a disability insurance program, provided that the definition of
disability under such disability insurance program complies with the
requirements of one of the three preceding definitions above.

 

31.                                 Distributions to “Key Employees” –
Investment.  In order to comply with Internal Revenue Code Section 409A,
distributions to “key employees” (see subsection 9.3 of the Plan Document for
definition) of publicly traded companies made due to employment termination
cannot be made within 6 months of the employment termination date.  If
distribution to a key employee must be delayed to comply with this 6-month rule,
indicate below how Account balances of such a Participant will be invested
during the period of delay [select one]:

 

o                                    Valued as of most recent Valuation Date and
held at the Employer without allocation of additional gains or losses after such
Valuation Date  until payment can be made.

 

x                                  Remain invested as if termination date had
not occurred, then valued as of most recent Valuation Date and distributed.

 

32.                                QDRO Distributions.  The Employer may elect
whether distributions from a Participant’s Account shall be permitted upon
receipt by the Plan Administrator of a Qualified Domestic Relations Order
relating to a marital dissolution or separation that provides for payment of all
or a portion of a Participant’s Accounts to an alternate payee (spouse, former
spouse, children, etc.).  [Indicate below whether QDRO distributions will be
permitted]:

 

o                                    No, QDRO Distributions will not be
permitted.

 

x                                  Yes, QDRO Distributions will be permitted.

 

33.                                 Additional Survivor Death Benefit from Life
Insurance.  In the event that life insurance is utilized as a funding vehicle
for the Plan, the Employer may wish to provide additional Survivor Benefit from
the following options :  [select one]

 

o                                    No additional Survivor Benefit offered, but
rather Participant’s vested Account balance.

 

o                                    Face value of life insurance policy of
Participant, if any.

 

o                                    Greater of (a) face value of life insurance
policy of Participant, if any, or (b) Participant’s vested Account balance.

 

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x                                  Other: [enter amount or formula] $300,000 –
the employee must have elected to defer salary and/or bonus for the current plan
year in order to be eligible to receive the additional survivor death benefit
from life insurance.

 

34.           Payment of Plan Expenses.  Plan expenses may be paid as follows:
[select one]

 

x                                  Directly by the Employer.

 

o                                    Deducted from the Participant accounts and
Plan’s trust or other custodial account (mutual fund plans only, if applicable).

 

35.           “De Minimis” Small Amount Cashouts.  If selected by the Employer,
Participant account balances that do not exceed a certain threshold amount will
be automatically cashed out upon the Participant’s Termination of Employment or
Death, as provided below [select one]

 

x                                  Yes, amounts that do not exceed a threshold
dollar amount will automatically be cashed out [enter dollar amount, not to
exceed the IRS 402(g) limit  for a given year ($15,500 for 2007 and 2008)
 [enter amount] $15,000

 

o                                    No, no “de minimis” small amounts will be
cashed out.

 

By signing this Adoption Agreement, the Employer certifies that it has consulted
with legal counsel regarding the effects of the Plan, as applicable, on all
parties.  The Employer further certifies that it has and will limit
participation in the Plan to a select group of management or highly compensated
Employees, Board Members or Other Service Providers, as determined by the
Employer in consultation with legal counsel.  The Employer further certifies
that it is the Employer’s sole responsibility to ensure that each Participant
with the right to direct deemed investments under the Plan that are based on
securities issued by the Employer or a member of its controlled group (as
defined in Code Section 414(b) and (c)) will receive a prospectus for any such
deemed investment option based on such Employer securities.

 

The Employer is solely responsible for its compliance with applicable laws,
including Federal and state securities and other applicable laws.

 

Only those elections that are completed shall be considered as provisions
applicable to and forming a part of the Plan.

 

This Adoption Agreement may only be used in conjunction with the Plan document. 
All selections in the Adoption Agreement providing for customized or “other”
plan provisions are subject to review for administrative feasibility, and may be
subject to additional fees.

 

Terms used in this Adoption Agreement which are defined in the Plan document
shall have the meaning given them therein.

 

The Employer hereby acknowledges that it is adopting this Nonqualified
Supplemental Deferred Compensation Plan.  Federal legislation or other changes
in the law relating to

 

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nonqualified deferred compensation or other employee benefit plans may require
that the Plan be amended.

 

*      *      *

 

The undersigned duly authorized owner, or officer of the Employer hereby
executes the Plan on behalf of the Employer.

 

Dated this 6th day of November, 2008.

 

 

 

Affymetrix, Inc.

 

 

 

By

     /s/ John C. Batty

 

Its

     Chief Financial Officer

 

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ADDENDUM A
TRANSITION RULES UNDER
CODE SECTION 409A

 

Complete the following if Plan utilized any of the transition rules permitted
under Code Section 409A.  Check any that apply.

 

o                                    Deferral Election Change Prior to 3/15/05. 
[You may only elect this option if you are completing this Adoption Agreement
prior to 12/31/05].  Plan allowed Participants to elect, prior to March 15,
2005, to make new elections with respect to amounts earned in 2005 relating to
services performed on or before December 31, 2005 (provided that such amounts
were not paid or payable to the Participant prior to the election).

 

o                                    Deferral Cancellation Prior to 12/31/05. 
[You may only elect this option if you are completing this Adoption Agreement
prior to 12/31/05].  Plan allowed Participants to elect, prior to December 31,
2005, to terminate participation in the Plan and/or to cancel one or more
deferral elections previously elected with respect to amounts payable in 2005. 
Amounts subject to the termination or cancellation were included in the
Participant’s income in 2005 or, if later, in the taxable year in which the
amounts were earned and vested.

 

o                                    Change in Payment Elections or Conditions
prior to 12/31/06.  Plan allowed Participants to revoke prior payment elections
and make new payment elections with respect to amounts subject to 409A on or
before December 31, 2006.  However, Participants were not allowed to change
payment elections in 2006 with respect to payments the Participant would
otherwise receive in 2006, or to cause payments to be made in 2006.

 

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ADDENDUM B
DEFERRAL OF RESTRICTED STOCK UNITS

 

Complete the following if Employer wishes to allow for deferral of restricted
stock units. Restricted stock units (RSUs) may be deferred into the Plan, but
the election must be made by the following deadline (check any that apply):.

 

o                                    The end of the calendar year prior to the
date of grant of the RSU.

 

o                                    12 months before the payment date of the
RSU (vesting date is treated as the payment date for these purposes), but the
election will not take effect for 12 months, and the subsequent payout date must
be at least five years later than the original payment date).  Indicate
subsequent payout date:                                      .

 

o                                    Within 30 days of the date of grant (but
only if the RSU is structured so that vesting is contingent on the employee
performing services for at least an additional 12 months).

 

o                                    Within 6 months of the payment (vesting)
date, but only if the RSU is performance-based under 409A, and only if the
performance period must be at least 12 months long and either:  (i) the amount
of the compensation cannot be reasonably ascertained at the time of the
election, or (ii) the performance requirement is still not substantially certain
to be met at the time of the election.

 

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