Document:

exv10w3

 

Exhibit 10.3

PERLEGEN SCIENCES, INC.

2002 EQUITY INCENTIVE PLAN

     1. Purposes of the Plan. The purposes of the Perlegen Sciences, Inc. 2002 Equity
Incentive Plan are to attract and retain the best available personnel for positions of substantial
responsibility, to provide additional incentive to Employees, Directors and Consultants and to
promote the success of the Company’s business. Options granted under the Plan may be Incentive
Stock Options or Non-Qualified Stock Options, as determined by the Administrator at the time of
grant. Stock Purchase Rights may also be granted under the Plan.

     2. Definitions. As used herein, the following definitions shall apply:

          (a) “Acquisition” means (i) any consolidation or merger of the Company with or into
any other corporation or other entity or person in which the stockholders of the Company prior to
such consolidation or merger own less than fifty percent (50%) of the Company’s voting power
immediately after such consolidation or merger, excluding any consolidation or merger effected
exclusively to change the domicile of the Company; or (ii) a sale of all or substantially all of
the assets of the Company.

          (b) “Administrator” means the Board or the Committee responsible for conducting the
general administration of the Plan, as applicable, in accordance with Section 4 hereof.

          (c) “Applicable Laws” means the requirements relating to the administration of stock
option plans under U.S. state corporate laws, U.S. federal and state securities laws, the Code, any
stock exchange or quotation system on which the Common Stock is listed or quoted and the applicable
laws of any foreign country or jurisdiction where Options or Stock Purchase Rights are granted
under the Plan.

          (d) “Board” means the Board of Directors of the Company.

          (e) “Code” means the Internal Revenue Code of 1986, as amended, or any successor
statute or statutes thereto. Reference to any particular Code section shall include any successor
section.

          (f) “Committee” means a committee appointed by the Board in accordance with Section 4
hereof.

          (g) “Common Stock” means the Common Stock of the Company, par value $0.0001 per share.

          (h) “Company” means Perlegen Sciences, Inc., a Delaware corporation.

 

 

          (i) “Consultant” means any consultant or adviser if: (i) the consultant or adviser
renders bona fide services to the Company or any Parent or Subsidiary of the Company; (ii) the
services rendered by the consultant or adviser are not in connection with the offer or sale of
securities in a capital-raising transaction and do not directly or indirectly promote or maintain a
market for the Company’s securities; and (iii) the consultant or adviser is a natural person who
has contracted directly with the Company or any Parent or Subsidiary of the Company to render such
services.

          (j) “Director” means a member of the Board.

          (k) “Employee” means any person, including an Officer or Director, who is an employee
(as defined in accordance with Section 3401(c) of the Code) of the Company or any Parent or
Subsidiary of the Company. A Service Provider shall not cease to be an Employee in the case of (i)
any leave of absence approved by the Company or (ii) transfers between locations of the Company or
between the Company, its Parent, any Subsidiary, or any successor. For purposes of Incentive Stock
Options, no such leave may exceed ninety (90) days, unless reemployment upon expiration of such
leave is guaranteed by statute or contract. Neither service as a Director nor payment of a
director’s fee by the Company shall be sufficient, by itself, to constitute “employment” by the
Company.

          (l) “Exchange Act” means the Securities Exchange Act of 1934, as amended, or any
successor statute or statutes thereto. Reference to any particular Exchange Act section shall
include any successor section.

          (m) “Fair Market Value” means, as of any date, the value of a share of Common Stock
determined as follows:

               (i) If the Common Stock is listed on any established stock exchange or a national market
system, including, without limitation, the Nasdaq National Market or The Nasdaq SmallCap Market of
The Nasdaq Stock Market, its Fair Market Value shall be the closing sales price for a share of such
stock (or the closing bid, if no sales were reported) as quoted on such exchange or system for the
last market trading day prior to the time of determination, as reported in The Wall Street Journal
or such other source as the Administrator deems reliable;

               (ii) If the Common Stock is regularly quoted by a recognized securities dealer but selling
prices are not reported, its Fair Market Value shall be the mean between the high bid and low asked
prices for a share of the Common Stock on the last market trading day prior to the day of
determination; or

               (iii) In the absence of an established market for the Common Stock, the Fair Market Value
thereof shall be determined in good faith by the Administrator.

 

 

          (n) “Holder” means a person who has been granted or awarded an Option or Stock
Purchase Right or who holds Shares acquired pursuant to the exercise of an Option or Stock Purchase
Right.

          (o) “Incentive Stock Option” means an Option intended to qualify as an incentive stock
option within the meaning of Section 422 of the Code and which is designated as an Incentive Stock
Option by the Administrator.

          (p) “Independent Director” means a Director who is not an Employee of the Company.

          (q) “Non-Qualified Stock Option” means an Option (or portion thereof) that is not
designated as an Incentive Stock Option by the Administrator, or which is designated as an
Incentive Stock Option by the Administrator but fails to qualify as an incentive stock option
within the meaning of Section 422 of the Code.

          (r) “Officer” means a person who is an officer of the Company within the meaning of
Section 16 of the Exchange Act and the rules and regulations promulgated thereunder.

          (s) “Option” means a stock option granted pursuant to the Plan.

          (t) “Option Agreement” means a written agreement between the Company and a Holder
evidencing the terms and conditions of an individual Option grant. The Option Agreement is subject
to the terms and conditions of the Plan.

          (u) “Parent” means any corporation, whether now or hereafter existing (other than the
Company), in an unbroken chain of corporations ending with the Company if each of the corporations
other than the last corporation in the unbroken chain owns stock possessing more than fifty percent
of the total combined voting power of all classes of stock in one of the other corporations in such
chain.

          (v) “Plan” means the Perlegen Sciences, Inc. 2002 Equity Incentive Plan.

          (w) “Public Trading Date” means the first date upon which Common Stock of the Company
is listed (or approved for listing) upon notice of issuance on any securities exchange or
designated (or approved for designation) upon notice of issuance as a national market security on
an interdealer quotation system.

          (x) “Restricted Stock” means Shares acquired pursuant to the exercise of an unvested
Option in accordance with Section 10(h) below or pursuant to a Stock Purchase Right granted under
Section 12 below.

          (y) “Rule 16b-3” means that certain Rule 16b-3 under the Exchange Act, as such Rule
may be amended from time to time.

 

 

          (z) “Section 16(b)” means Section 16(b) of the Exchange Act, as such Section may be
amended from time to time.

          (aa) “Securities Act” means the Securities Act of 1933, as amended, or any successor
statute or statutes thereto. Reference to any particular Securities Act section shall include any
successor section.

          (bb) “Service Provider” means an Employee, Director or Consultant.

          (cc) “Share” means a share of Common Stock, as adjusted in accordance with Section 13
below.

          (dd) “Stock Purchase Right” means a right to purchase Common Stock pursuant to Section
12 below.

          (ee) “Subsidiary” means any corporation, whether now or hereafter existing (other than
the Company), in an unbroken chain of corporations beginning with the Company if each of the
corporations other than the last corporation in the unbroken chain owns stock possessing more than
fifty percent of the total combined voting power of all classes of stock in one of the other
corporations in such chain.

     3. Stock Subject to the Plan. Subject to the provisions of Section 13 of the Plan, the
shares of stock subject to Options or Stock Purchase Rights shall be Common Stock, initially shares
of the Company’s Common Stock, par value $0.0001 per share. Subject to the provisions of Section
13 of the Plan, the maximum aggregate number of Shares which may be issued upon exercise of such
Options or Stock Purchase Rights is the sum of: (i) the number of shares of common stock of the
Company which remain available for grants of options or other awards under the Perlegen Sciences,
Inc. 2001 Stock Option Plan (the “2001 Plan”) as of the date of the Plan’s initial adoption by the
Board, plus (ii) with respect to options or other awards granted under the 2001 Plan that expire or
are canceled without having been exercised in full, the number of Shares subject to each such
option as to which such option was not exercised prior to its expiration or cancellation. Shares
issued upon exercise of Options or Stock Purchase Rights may be authorized but unissued, or
reacquired Common Stock. If an Option or Stock Purchase Right expires or becomes unexercisable
without having been exercised in full, the unpurchased Shares which were subject thereto shall
become available for future grant or sale under the Plan (unless the Plan has terminated). Shares
which are delivered by the Holder or withheld by the Company upon the exercise of an Option or
Stock Purchase Right under the Plan, in payment of the exercise price thereof or tax withholding
thereon, may again be optioned, granted or awarded hereunder, subject to the limitations of this
Section 3. If Shares of Restricted Stock are repurchased by the Company at their original purchase
price, such Shares shall become available for future grant under the Plan. Notwithstanding the
provisions of this Section 3, no Shares may again be optioned, granted or awarded if such action
would cause an Incentive Stock Option to fail to qualify as an Incentive Stock Option under Code
Section 422.

 

 

     4. Administration of the Plan.

          (a) Administrator. Unless and until the Board delegates administration to a Committee
as set forth below, the Plan shall be administered by the Board. The Board may delegate
administration of the Plan to a Committee or Committees of one or more members of the Board or one
or more Officers who are not members of the Board or any combination thereof, and the term
“Committee” shall apply to any person or persons to whom such authority has been delegated. If
administration is delegated to a Committee, except as provided in this Plan, the Committee shall
have, in connection with the administration of the Plan, the powers theretofore possessed by the
Board, including the power to delegate to a subcommittee any of the administrative powers the
Committee is authorized to exercise (and references in this Plan to the Board shall thereafter be
to the Committee or subcommittee), subject, however, to such resolutions, not inconsistent with the
provisions of the Plan, as may be adopted from time to time by the Board. Notwithstanding the
foregoing, however, from and after the Public Trading Date, a Committee of the Board shall
administer the Plan and the Committee shall consist solely of two or more Independent Directors
each of whom is both an “outside director,” within the meaning of Section 162(m) of the Code, and a
“non-employee director” within the meaning of Rule 16b-3. Within the scope of such authority, the
Board or the Committee may (i) delegate to a committee of one or more members of the Board who are
not Independent Directors or one or more Officers who are not members of the Board, or any
combination thereof, the authority to grant awards under the Plan to eligible persons who are
either (1) not then “covered employees,” within the meaning of Section 162(m) of the Code and are
not expected to be “covered employees” at the time of recognition of income resulting from such
award or (2) not persons with respect to whom the Company wishes to comply with Section 162(m) of
the Code and/or (ii) delegate to a committee of one or more members of the Board who are not
“non-employee directors,” within the meaning of Rule 16b-3 or one or more Officers who are not
members of the Board, or any combination thereof, the authority to grant awards under the Plan to
eligible persons who are not then subject to Section 16 of the Exchange Act. The Board may abolish
the Committee at any time and revest in the Board the administration of the Plan. Appointment of
Committee members shall be effective upon acceptance of appointment. Committee members may resign
at any time by delivering written notice to the Board. Vacancies in the Committee may only be
filled by the Board.

          (b) Limitation of Delegations to Officers. Notwithstanding Section 4(a) above, in the
event that Board authorizes a Committee comprised of one or more Officers who are not members of
the Board to act as Administrator, such authorization shall be in writing by resolution adopted by
the Board and shall authorize such Committee only to grant Options and Stock Purchase Rights to
Employees and to exercise such other powers under the Plan as the Board may determine; provided
that the Board shall fix the terms of the Options and Stock Purchase Rights to be granted by such
Committee (including the exercise or purchase price of such Options and Stock Purchase Rights,
which may include a formula by which the exercise or purchase price will be determined) and the
maximum number of Shares subject to Options and Stock Purchase Rights that such Committee may
grant; provided further, however, that no such Committee shall be authorized to grant Options or
Stock Purchase Rights to its members.

 

 

          (c) Powers of the Administrator. Subject to the provisions of the Plan and the
specific duties delegated by the Board to such Committee, and subject to the approval of any
relevant authorities, the Administrator shall have the authority in its sole discretion:

               (i) to determine the Fair Market Value;

               (ii) to select the Service Providers to whom Options and Stock Purchase Rights may from time
to time be granted hereunder;

               (iii) to determine the number of Shares to be covered by each such award granted hereunder;

               (iv) to approve forms of agreement for use under the Plan;

               (v) to determine the terms and conditions of any Option or Stock Purchase Right granted
hereunder (such terms and conditions include, but are not limited to, the exercise price, the time
or times when Options or Stock Purchase Rights may vest or be exercised (which may be based on
performance criteria), any vesting acceleration or waiver of forfeiture restrictions, and any
restriction or limitation regarding any Option or Stock Purchase Right or the Common Stock relating
thereto, based in each case on such factors as the Administrator, in its sole discretion, shall
determine);

               (vi) to determine whether to offer to buyout a previously granted Option as provided in
subsection 10(i) and to determine the terms and conditions of such offer and buyout (including
whether payment is to be made in cash or Shares);

               (vii) to prescribe, amend and rescind rules and regulations relating to the Plan, including
rules and regulations relating to sub-plans established for the purpose of qualifying for preferred
tax treatment under foreign tax laws;

               (viii) to allow Holders to satisfy withholding tax obligations by electing to have the Company
withhold from the Shares to be issued upon exercise of an Option or Stock Purchase Right that
number of Shares having a Fair Market Value equal to the minimum amount required to be withheld
based on the statutory withholding rates for federal and state tax purposes that apply to
supplemental taxable income. The Fair Market Value of the Shares to be withheld shall be
determined on the date that the amount of tax to be withheld is to be determined. All elections by
Holders to have Shares withheld for this purpose shall be made in such form and under such
conditions as the Administrator may deem necessary or advisable;

               (ix) to amend the Plan or any Option or Stock Purchase Right granted under the Plan as
provided in Section 15; and

               (x) to construe and interpret the terms of the Plan and awards granted pursuant to the Plan
and to exercise such powers and perform such acts as the Administrator
deems necessary or desirable to promote the best interests of the Company which are not in
conflict with the provisions of the Plan.

 

 

          (d) Effect of Administrator’s Decision. All decisions, determinations and
interpretations of the Administrator shall be final and binding on all Holders.

     5. Eligibility. Non-Qualified Stock Options and Stock Purchase Rights may be granted
to Service Providers. Incentive Stock Options may be granted only to Employees. If otherwise
eligible, a Service Provider who has been granted an Option or Stock Purchase Right may be granted
additional Options or Stock Purchase Rights.

     6. Limitations.

          (a) Each Option shall be designated by the Administrator in the Option Agreement as either an
Incentive Stock Option or a Non-Qualified Stock Option. However, notwithstanding such
designations, to the extent that the aggregate Fair Market Value of Shares subject to a Holder’s
Incentive Stock Options and other incentive stock options granted by the Company, any Parent or
Subsidiary, which become exercisable for the first time during any calendar year (under all plans
of the Company or any Parent or Subsidiary) exceeds $100,000, such excess Options or other options
shall be treated as Non-Qualified Stock Options.

          For purposes of this Section 6(a), Incentive Stock Options shall be taken into account in the
order in which they were granted, and the Fair Market Value of the Shares shall be determined as of
the time of grant.

          (b) Neither the Plan, any Option nor any Stock Purchase Right shall confer upon a Holder any
right with respect to continuing the Holder’s employment or consulting relationship with the
Company, nor shall they interfere in any way with the Holder’s right or the Company’s right to
terminate such employment or consulting relationship at any time, with or without cause.

          (c) No Service Provider shall be granted, in any calendar year, Options or Stock Purchase
Rights to purchase more than 5,000,000 Shares; provided, however, that the foregoing limitation
shall not apply prior to the Public Trading Date and, following the Public Trading Date, the
foregoing limitation shall not apply until the earliest of: (i) the first material modification of
the Plan (including any increase in the number of shares reserved for issuance under the Plan in
accordance with Section 3); (ii) the issuance of all of the shares of Common Stock reserved for
issuance under the Plan; (iii) the expiration of the Plan; (iv) the first meeting of stockholders
at which Directors of the Company are to be elected that occurs after the close of the third
calendar year following the calendar year in which occurred the first registration of an equity
security of the Company under Section 12 of the Exchange Act; or (v) such other date required by
Section 162(m) of the Code and the rules and regulations promulgated thereunder. The foregoing
limitation shall be adjusted proportionately in connection with any change in the Company’s
capitalization as described in Section 13. For purposes of this Section 6(c), if an

 

 

Option is canceled in the same calendar year it was granted (other than in connection with a
transaction described in Section 13), the canceled Option will be counted against the limit set
forth in this Section 6(c). For this purpose, if the exercise price of an Option is reduced, the
transaction shall be treated as a cancellation of the Option and the grant of a new Option.

     7. Term of Plan. The Plan shall become effective upon its initial adoption by the
Board and shall continue in effect until it is terminated under Section 15 of the Plan. No Options
or Stock Purchase Rights may be issued under the Plan after the tenth (10th) anniversary of the
earlier of (i) the date upon which the Plan is adopted by the Board or (ii) the date the Plan is
approved by the stockholders.

     8. Term of Option. The term of each Option shall be stated in the Option Agreement;
provided, however, that the term shall be no more than ten (10) years from the date of grant
thereof. In the case of an Incentive Stock Option granted to a Holder who, at the time the Option
is granted, owns (or is treated as owning under Code Section 424) stock representing more than ten
percent (10%) of the voting power of all classes of stock of the Company or any Parent or
Subsidiary, the term of the Option shall be five (5) years from the date of grant or such shorter
term as may be provided in the Option Agreement.

     9. Option Exercise Price and Consideration.

          (a) Except as provided in Section 13, the per share exercise price for the Shares to be issued
upon exercise of an Option shall be such price as is determined by the Administrator, but shall be
subject to the following:

               (i) I the case of an Incentive Stock Option

                    (A) granted to an Employee who, at the time of grant of such Option, owns (or is treated as
owning under Code Section 424) stock representing more than ten percent (10%) of the voting power
of all classes of stock of the Company or any Parent or Subsidiary, the per Share exercise price
shall be no less than one hundred ten percent (110%) of the Fair Market Value per Share on the date
of grant.

                    (B) granted to any other Employee, the per Share exercise price shall be no less than one
hundred percent (100%) of the Fair Market Value per Share on the date of grant.

               (ii) In the case of a Non-Qualified Stock Option

                    (A) granted to a Service Provider who, at the time of grant of such Option, owns stock
representing more than ten percent (10%) of the voting power of all classes of stock of the Company
or any Parent or Subsidiary, the exercise price shall be no less than one hundred ten percent
(110%) of the Fair Market Value per Share on the date of the grant.

 

 

                    (B) granted to any other Service Provider, the per Share exercise price shall be no less than
eighty-five percent (85%) of the Fair Market Value per Share on the date of grant.

               (iii) Notwithstanding the foregoing, Options may be granted with a per Share exercise price
other than as required above pursuant to a merger or other corporate transaction.

          (b) The consideration to be paid for the Shares to be issued upon exercise of an Option,
including the method of payment, shall be determined by the Administrator (and, in the case of an
Incentive Stock Option, shall be determined at the time of grant). Such consideration may consist
of (1) cash, (2) check, (3) with the consent of the Administrator, a full recourse promissory note
bearing interest (at no less than such rate as shall then preclude the imputation of interest under
the Code) and payable upon such terms as may be prescribed by the Administrator, (4) with the
consent of the Administrator, other Shares which (x) in the case of Shares acquired from the
Company, have been owned by the Holder for more than six (6) months on the date of surrender, and
(y) have a Fair Market Value on the date of surrender equal to the aggregate exercise price of the
Shares as to which such Option shall be exercised, (5) with the consent of the Administrator,
surrendered Shares then issuable upon exercise of the Option having a Fair Market Value on the date
of exercise equal to the aggregate exercise price of the Option or exercised portion thereof, (6)
property of any kind which constitutes good and valuable consideration, (7) with the consent of the
Administrator, delivery of a notice that the Holder has placed a market sell order with a broker
with respect to Shares then issuable upon exercise of the Options and that the broker has been
directed to pay a sufficient portion of the net proceeds of the sale to the Company in satisfaction
of the Option exercise price, provided, that payment of such proceeds is then made to the Company
upon settlement of such sale, or (8) with the consent of the Administrator, any combination of the
foregoing methods of payment.

     10. Exercise of Option.

          (a) Vesting; Fractional Exercises. Except as provided in Section 13, Options granted
hereunder shall be vested and exercisable according to the terms hereof at such times and under
such conditions as determined by the Administrator and set forth in the Option Agreement; provided,
however, that, except with regard to Options granted to Officers, Directors or Consultants, in no
event shall an Option granted hereunder become vested and exercisable at a rate of less than twenty
percent (20%) per year over five (5) years from the date the Option is granted, subject to
reasonable conditions, such as continuing to be a Service Provider. An Option may not be exercised
for a fraction of a Share.

          (b) Deliveries upon Exercise. All or a portion of an exercisable Option shall be
deemed exercised upon delivery of all of the following to the Secretary of the Company or his or
her office:

 

 

               (i) A written or electronic notice complying with the applicable rules established by the
Administrator stating that the Option, or a portion thereof, is exercised. The notice shall be
signed by the Holder or other person then entitled to exercise the Option or such portion of the
Option;

               (ii) Such representations and documents as the Administrator, in its sole discretion, deems
necessary or advisable to effect compliance with Applicable Laws. The Administrator may, in its
sole discretion, also take whatever additional actions it deems appropriate to effect such
compliance, including, without limitation, placing legends on share certificates and issuing stop
transfer notices to agents and registrars;

               (iii) Upon the exercise of all or a portion of an unvested Option pursuant to Section 10(h), a
Restricted Stock purchase agreement in a form determined by the Administrator and signed by the
Holder or other person then entitled to exercise the Option or such portion of the Option; and

               (iv) In the event that the Option shall be exercised pursuant to Section 10(f) by any person
or persons other than the Holder, appropriate proof of the right of such person or persons to
exercise the Option.

          (c) Conditions to Delivery of Share Certificates. The Company shall not be required
to issue or deliver any certificate or certificates for Shares purchased upon the exercise of any
Option or portion thereof prior to fulfillment of all of the following conditions:

               (i) The admission of such Shares to listing on all stock exchanges on which such class of
stock is then listed;

               (ii) The completion of any registration or other qualification of such Shares under any state
or federal law, or under the rulings or regulations of the Securities and Exchange Commission or
any other governmental regulatory body which the Administrator shall, in its sole discretion, deem
necessary or advisable;

               (iii) The obtaining of any approval or other clearance from any state or federal governmental
agency which the Administrator shall, in its sole discretion, determine to be necessary or
advisable;

               (iv) The lapse of such reasonable period of time following the exercise of the Option as the
Administrator may establish from time to time for reasons of administrative convenience; and

               (v) The receipt by the Company of full payment for such Shares, including payment of any
applicable withholding tax, which in the sole discretion of the Administrator may be in the form of
consideration used by the Holder to pay for such Shares under Section 9(b).

 

 

          (d) Termination of Relationship as a Service Provider. If a Holder ceases to be a
Service Provider other than by reason of the Holder’s disability or death, such Holder may exercise
his or her Option within such period of time as is specified in the Option Agreement to the extent
that the Option is vested on the date of termination; provided, however, that prior to the Public
Trading Date, such period of time shall not be less than thirty (30) days (but in no event later
than the expiration of the term of the Option as set forth in the Option Agreement). In the
absence of a specified time in the Option Agreement, the Option shall remain exercisable for three
(3) months following the Holder’s termination. If, on the date of termination, the Holder is not
vested as to his or her entire Option, the Shares covered by the unvested portion of the Option
immediately cease to be issuable under the Option and shall again become available for issuance
under the Plan. If, after termination, the Holder does not exercise his or her Option within the
time period specified herein, the Option shall terminate, and the Shares covered by such Option
shall again become available for issuance under the Plan.

          (e) Disability of Holder. If a Holder ceases to be a Service Provider as a result of
the Holder’s disability, the Holder may exercise his or her Option within such period of time as is
specified in the Option Agreement to the extent the Option is vested on the date of termination;
provided, however, that prior to the Public Trading Date, such period of time shall not be less
than six (6) months (but in no event later than the expiration of the term of such Option as set
forth in the Option Agreement). In the absence of a specified time in the Option Agreement, the
Option shall remain exercisable for twelve (12) months following the Holder’s termination. If such
disability is not a “disability” as such term is defined in Section 22(e)(3) of the Code, in the
case of an Incentive Stock Option such Incentive Stock Option shall automatically cease to be
treated as an Incentive Stock Option and shall be treated for tax purposes as a Non-Qualified Stock
Option from and after the day which is three (3) months and one (1) day following such termination.
If, on the date of termination, the Holder is not vested as to his or her entire Option, the
Shares covered by the unvested portion of the Option shall immediately cease to be issuable under
the Option and shall again become available for issuance under the Plan. If, after termination,
the Holder does not exercise his or her Option within the time specified herein, the Option shall
terminate, and the Shares covered by such Option shall again become available for issuance under
the Plan.

          (f) Death of Holder. If a Holder dies while a Service Provider, the Option may be
exercised within such period of time as is specified in the Option Agreement provided, however,
that prior to the Public Trading Date, such period of time shall not be less than six (6) months
(but in no event later than the expiration of the term of such Option as set forth in the Notice of
Grant), by the Holder’s estate or by a person who acquires the right to exercise the Option by
bequest or inheritance, but only to the extent that the Option is vested on the date of death. In
the absence of a specified time in the Option Agreement, the Option shall remain exercisable for
twelve (12) months following the Holder’s termination. If, at the time of death, the Holder is not
vested as to his or her entire Option, the Shares covered by the unvested portion of the Option
shall immediately cease to be issuable under the Option and shall again become available for
issuance under the Plan. The Option may be exercised by the executor or administrator of the
Holder’s estate or, if none, by the person(s) entitled to exercise the Option

 

 

under the Holder’s will or the laws of descent or distribution. If the Option is not so
exercised within the time specified herein, the Option shall terminate, and the Shares covered by
such Option shall again become available for issuance under the Plan.

          (g) Regulatory Extension. A Holder’s Option Agreement may provide that if the
exercise of the Option following the termination of the Holder’s status as a Service Provider
(other than upon the Holder’s death or Disability) would be prohibited at any time solely because
the issuance of shares would violate the registration requirements under the Securities Act, then
the Option shall terminate on the earlier of (i) the expiration of the term of the Option set forth
in Section 8 or (ii) the expiration of a period of three (3) months after the termination of the
Holder’s status as a Service Provider during which the exercise of the Option would not be in
violation of such registration requirements.

          (h) Early Exercisability. The Administrator may provide in the terms of a Holder’s
Option Agreement that the Holder may, at any time before the Holder’s status as a Service Provider
terminates, exercise the Option in whole or in part prior to the full vesting of the Option;
provided, however, that subject to Section 20, Shares acquired upon exercise of an Option which has
not fully vested may be subject to any forfeiture, transfer or other restrictions as the
Administrator may determine in its sole discretion.

          (i) Buyout Provisions. The Administrator may at any time offer to buyout for a
payment in cash or Shares, an Option previously granted, based on such terms and conditions as the
Administrator shall establish and communicate to the Holder at the time that such offer is made.

     11. Transferability of Options and Stock Purchase Rights. Options and Stock Purchase
Rights may not be sold, pledged, assigned, hypothecated, transferred, or disposed of in any manner
other than by will or by the laws of descent or distribution or as permitted by Rule 701 of the
Securities Act and may be exercised, during the lifetime of the Holder, only by the Holder, unless
it has been disposed of as permitted by Rule 701 of the Securities Act .

     12. Stock Purchase Rights.

          (a) Rights to Purchase. Stock Purchase Rights may be issued either alone, in addition
to, or in tandem with Options granted under the Plan and/or cash awards made outside of the Plan.
After the Administrator determines that it will offer Stock Purchase Rights under the Plan, it
shall advise the offeree in writing of the terms, conditions and restrictions related to the offer,
including the number of Shares that such person shall be entitled to purchase, the price to be
paid, and the time within which such person must accept such offer; provided, however, that to the
extent required to comply with applicable securities laws, the purchase price of such Shares shall
not be less than the purchase price requirements set forth in Section 260.140.42 of Title 10 of the
California Code of Regulations. The offer shall be accepted by execution of a Restricted Stock
purchase agreement in the form determined by the Administrator.

 

 

          (b) Repurchase Right. Unless the Administrator determines otherwise, the Restricted
Stock purchase agreement shall grant the Company the right to repurchase Shares acquired upon
exercise of a Stock Purchase Right upon the termination of the purchaser’s status as a Service
Provider for any reason. Subject to Section 20, the purchase price for Shares repurchased by the
Company pursuant to such repurchase right and the rate at which such repurchase right shall lapse
shall be determined by the Administrator in its sole discretion, and shall be set forth in the
Restricted Stock purchase agreement.

          (c) Other Provisions. The Restricted Stock purchase agreement shall contain such
other terms, provisions and conditions not inconsistent with the Plan as may be determined by the
Administrator in its sole discretion.

          (d) Rights as a Shareholder. Once the Stock Purchase Right is exercised, the
purchaser shall have rights equivalent to those of a shareholder and shall be a shareholder when
his or her purchase is entered upon the records of the duly authorized transfer agent of the
Company. No adjustment shall be made for a dividend or other right for which the record date is
prior to the date the Stock Purchase Right is exercised, except as provided in Section 13 of the
Plan.

     13. Adjustments upon Changes in Capitalization, Merger or Asset Sale.

          (a) In the event that the Administrator determines that any dividend or other distribution
(whether in the form of cash, Common Stock, other securities, or other property), recapitalization,
reclassification, stock split, reverse stock split, reorganization, merger, consolidation,
split-up, spin-off, combination, repurchase, liquidation, dissolution, or sale, transfer, exchange
or other disposition of all or substantially all of the assets of the Company, or exchange of
Common Stock or other securities of the Company, issuance of warrants or other rights to purchase
Common Stock or other securities of the Company, or other similar corporate transaction or event,
in the Administrator’s sole discretion, affects the Common Stock such that an adjustment is
determined by the Administrator to be appropriate in order to prevent dilution or enlargement of
the benefits or potential benefits intended by the Company to be made available under the Plan or
with respect to any Option, Stock Purchase Right or Restricted Stock, then the Administrator shall,
in such manner as it may deem equitable, adjust any or all of:

               (i) the number and kind of shares of Common Stock (or other securities or property) with
respect to which Options or Stock Purchase Rights may be granted or awarded (including, but not
limited to, adjustments of the limitations in Section 3 on the maximum number and kind of shares
which may be issued and adjustments of the maximum number of Shares that may be purchased by any
Holder in any calendar year pursuant to Section 6(c));

               (ii) the number and kind of shares of Common Stock (or other securities or property) subject
to outstanding Options, Stock Purchase Rights or Restricted Stock; and

               (iii) the grant or exercise price with respect to any Option or Stock Purchase Right.

 

 

          (b) In the event of any transaction or event described in Section 13(a), the Administrator, in
its sole discretion, and on such terms and conditions as it deems appropriate, either by the terms
of the Option, Stock Purchase Right or Restricted Stock or by action taken prior to the occurrence
of such transaction or event and either automatically or upon the Holder’s request, is hereby
authorized to take any one or more of the following actions whenever the Administrator determines
that such action is appropriate in order to prevent dilution or enlargement of the benefits or
potential benefits intended by the Company to be made available under the Plan or with respect to
any Option, Stock Purchase Right or Restricted Stock granted or issued under the Plan or to
facilitate such transaction or event:

               (i) To provide for either the purchase of any such Option, Stock Purchase Right or Restricted
Stock for an amount of cash equal to the amount that could have been obtained upon the exercise of
such Option or Stock Purchase Right or realization of the Holder’s rights had such Option, Stock
Purchase Right or Restricted Stock been currently exercisable or payable or fully vested or the
replacement of such Option, Stock Purchase Right or Restricted Stock with other rights or property
selected by the Administrator in its sole discretion;

               (ii) To provide that such Option or Stock Purchase Right shall be exercisable as to all shares
covered thereby, notwithstanding anything to the contrary in the Plan or the provisions of such
Option or Stock Purchase Right;

               (iii) To provide that such Option, Stock Purchase Right or Restricted Stock be assumed by the
successor or survivor corporation, or a parent or subsidiary thereof, or shall be substituted for
by similar options, rights or awards covering the stock of the successor or survivor corporation,
or a parent or subsidiary thereof, with appropriate adjustments as to the number and kind of shares
and prices;

               (iv) To make adjustments in the number and type of shares of Common Stock (or other securities
or property) subject to outstanding Options and Stock Purchase Rights, and/or in the terms and
conditions of (including the grant or exercise price), and the criteria included in, outstanding
Options, Stock Purchase Rights or Restricted Stock or Options, Stock Purchase Rights or Restricted
Stock which may be granted in the future; and

               (v) To provide that immediately upon the consummation of such event, such Option or Stock
Purchase Right shall not be exercisable and shall terminate; provided, that for a specified period
of time prior to such event, such Option or Stock Purchase Right shall be exercisable as to all
Shares covered thereby, and the restrictions imposed under an Option Agreement or Restricted Stock
purchase agreement upon some or all Shares may be terminated and, in the case of Restricted Stock,
some or all shares of such Restricted Stock may
cease to be subject to repurchase, notwithstanding anything to the contrary in the Plan or the
provisions of such Option, Stock Purchase Right or Restricted Stock purchase agreement.

 

 

          (c) Subject to Section 3, the Administrator may, in its sole discretion, include such further
provisions and limitations in any Option, Stock Purchase Right, Restricted Stock agreement or
certificate, as it may deem equitable and in the best interests of the Company.

          (d) If the Company undergoes an Acquisition, then any surviving corporation or entity or
acquiring corporation or entity, or affiliate of such corporation or entity, may assume any
Options, Stock Purchase Rights or Restricted Stock outstanding under the Plan or may substitute
similar stock awards (including an award to acquire the same consideration paid to the stockholders
in the transaction described in this subsection 13(d)) for those outstanding under the Plan. In
the event any surviving corporation or entity or acquiring corporation or entity in an Acquisition,
or affiliate of such corporation or entity, does not assume such Options, Stock Purchase Rights or
Restricted Stock or does not substitute similar stock awards for those outstanding under the Plan,
then with respect to (i) Options, Stock Purchase Rights or Restricted Stock held by participants in
the Plan whose status as a Service Provider has not terminated prior to such event, the vesting of
such Options, Stock Purchase Rights or Restricted Stock (and, if applicable, the time during which
such awards may be exercised) shall be accelerated and made fully exercisable and all restrictions
thereon shall lapse at least ten (10) days prior to the closing of the Acquisition (and the Options
or Stock Purchase Rights terminated if not exercised prior to the closing of such Acquisition), and
(ii) any other Options or Stock Purchase Rights outstanding under the Plan, such Options or Stock
Purchase rights shall be terminated if not exercised prior to the closing of the Acquisition.

          (e) Notwithstanding the foregoing, in the event that the Company becomes a party to a
transaction that is intended to qualify for “pooling of interests” accounting treatment and, but
for one or more of the provisions of this Plan or any Option Agreement or any Restricted Stock
purchase agreement would so qualify, then this Plan and any such agreement shall be interpreted so
as to preserve such accounting treatment, and to the extent that any provision of the Plan or any
such agreement would disqualify the transaction from pooling of interests accounting treatment
(including, if applicable, an entire Option Agreement or Restricted Stock purchase agreement), then
such provision shall be null and void. All determinations to be made in connection with the
preceding sentence shall be made by the independent accounting firm whose opinion with respect to
“pooling of interests” treatment is required as a condition to the Company’s consummation of such
transaction.

          (f) The existence of the Plan, any Option Agreement or Restricted Stock purchase agreement and
the Options or Stock Purchase Rights granted hereunder shall not affect or restrict in any way the
right or power of the Company or the stockholders of the Company to make or authorize any
adjustment, recapitalization, reorganization or other change in the Company’s capital structure or
its business, any merger or consolidation of the Company, any issue of stock or of options,
warrants or rights to purchase stock or of bonds, debentures, preferred or prior preference stocks
whose rights are superior to or affect the Common Stock or

 

 

the rights thereof or which are convertible into or exchangeable for Common Stock, or the
dissolution or liquidation of the Company, or any sale or transfer of all or any part of its assets
or business, or any other corporate act or proceeding, whether of a similar character or otherwise.

     14. Time of Granting Options and Stock Purchase Rights. The date of grant of an
Option or Stock Purchase Right shall, for all purposes, be the date on which the Administrator
makes the determination granting such Option or Stock Purchase Right, or such other date as is
determined by the Administrator. Notice of the determination shall be given to each Employee or
Consultant to whom an Option or Stock Purchase Right is so granted within a reasonable time after
the date of such grant.

     15. Amendment and Termination of the Plan.

          (a) Amendment and Termination. The Board may at any time wholly or partially amend,
alter, suspend or terminate the Plan. However, without approval of the Company’s stockholders
given within twelve (12) months before or after the action by the Board, no action of the Board
may, except as provided in Section 13, increase the limits imposed in Section 3 on the maximum
number of Shares which may be issued under the Plan or extend the term of the Plan under Section 7.

          (b) Stockholder Approval. The Board shall obtain stockholder approval of any Plan
amendment to the extent necessary and desirable to comply with Applicable Laws.

          (c) Effect of Amendment or Termination. No amendment, alteration, suspension or
termination of the Plan shall impair the rights of any Holder, unless mutually agreed otherwise
between the Holder and the Administrator, which agreement must be in writing and signed by the
Holder and the Company. Termination of the Plan shall not affect the Administrator’s ability to
exercise the powers granted to it hereunder with respect to Options, Stock Purchase Rights or
Restricted Stock granted or awarded under the Plan prior to the date of such termination.

     16. Stockholder Approval. The Plan will be submitted for the approval of the
Company’s stockholders within twelve (12) months after the date of the Board’s initial adoption of
the Plan. Options, Stock Purchase Rights or Restricted Stock may be granted or awarded prior to
such stockholder approval, provided that such Options, Stock Purchase Rights and Restricted Stock
shall not be exercisable, shall not vest and the restrictions thereon shall not lapse prior to the
time when the Plan is approved by the stockholders, and provided further that if such approval has
not been obtained at the end of said twelve-month period, all Options, Stock Purchase Rights and
Restricted Stock previously granted or awarded under the Plan shall thereupon be canceled and
become null and void.

     17. Inability to Obtain Authority. The inability of the Company to obtain authority
from any regulatory body having jurisdiction, which authority is deemed by the Company’s counsel to
be necessary to the lawful issuance and sale of any Shares hereunder, shall relieve the
Company of any liability in respect of the failure to issue or sell such Shares as to which
such requisite authority shall not have been obtained.

 

 

     18. Reservation of Shares. The Company, during the term of this Plan, shall at all
times reserve and keep available such number of Shares as shall be sufficient to satisfy the
requirements of the Plan.

     19. Information to Holders and Purchasers. Prior to the Public Trading Date and to
the extent required by Section 260.140.46 of Title 10 of the California Code of Regulations, the
Company shall provide to each Holder and to each individual who acquires Shares pursuant to the
Plan, not less frequently than annually during the period such Holder or purchaser has one or more
Options or Stock Purchase Rights outstanding, and, in the case of an individual who acquires Shares
pursuant to the Plan, during the period such individual owns such Shares, copies of annual
financial statements. Notwithstanding the preceding sentence, the Company shall not be required to
provide such statements to key employees whose duties in connection with the Company assure their
access to equivalent information.

     20. Repurchase Provisions. The Administrator in its sole discretion may provide that
the Company may repurchase Shares acquired upon exercise of an Option or Stock Purchase Right upon
the occurrence of certain specified events, including, without limitation, a Holder’s termination
as a Service Provider, divorce, bankruptcy or insolvency; provided, however, that any such
repurchase right shall be set forth in the applicable Option Agreement or Restricted Stock purchase
agreement or in another agreement referred to in such agreement and, provided further, that to the
extent required by Section 260.140.41 and Section 260.140.42 of Title 10 of the California Code of
Regulations, any such repurchase right set forth in an Option or Stock Purchase Right granted prior
to the Public Trading Date to a person who is not an Officer, Director or Consultant shall be upon
the following terms: (i) if the repurchase option gives the Company the right to repurchase the
shares upon termination as a Service Provider at not less than the Fair Market Value of the shares
to be purchased on the date of termination of status as a Service Provider, then (A) the right to
repurchase shall be exercised for cash or cancellation of purchase money indebtedness for the
shares within ninety (90) days of termination of status as a Service Provider (or in the case of
shares issued upon exercise of Options or Stock Purchase Rights after such date of termination,
within ninety (90) days after the date of the exercise) or such longer period as may be agreed to
by the Administrator and the Plan participant and (B) the right terminates when the shares become
publicly traded; and (ii) if the repurchase option gives the Company the right to repurchase the
Shares upon termination as a Service Provider at the original purchase price for such Shares, then
(A) the right to repurchase at the original purchase price shall lapse at the rate of at least
twenty percent (20%) of the shares per year over five (5) years from the date the Option or Stock
Purchase Right is granted (without respect to the date the Option or Stock Purchase Right was
exercised or became exercisable) and (B) the right to repurchase shall be exercised for cash or
cancellation of purchase money indebtedness for the shares within ninety (90) days of termination
of status as a Service Provider (or, in the case of shares issued upon exercise of Options or Stock
Purchase Rights, after such date of termination,
within ninety (90) days after the date of the exercise) or such longer period as may be agreed
to by the Company and the Plan participant.

 

 

     21. Investment Intent. The Company may require a Plan participant, as a condition of
exercising or acquiring stock under any Option or Stock Purchase Right, (i) to give written
assurances satisfactory to the Company as to the participant’s knowledge and experience in
financial and business matters and/or to employ a purchaser representative reasonably satisfactory
to the Company who is knowledgeable and experienced in financial and business matters and that he
or she is capable of evaluating, alone or together with the purchaser representative, the merits
and risks of exercising the Option or Stock Purchase Right; and (ii) to give written assurances
satisfactory to the Company stating that the participant is acquiring the stock subject to the
Option or Stock Purchase Right for the participant’s own account and not with any present intention
of selling or otherwise distributing the stock. The foregoing requirements, and any assurances
given pursuant to such requirements, shall be inoperative if (A) the issuance of the shares upon
the exercise or acquisition of stock under the applicable Option or Stock Purchase Right has been
registered under a then currently effective registration statement under the Securities Act or (B)
as to any particular requirement, a determination is made by counsel for the Company that such
requirement need not be met in the circumstances under the then applicable securities laws. The
Company may, upon advice of counsel to the Company, place legends on stock certificates issued
under the Plan as such counsel deems necessary or appropriate in order to comply with applicable
securities laws, including, but not limited to, legends restricting the transfer of the stock.

     22. Governing Law. The validity and enforceability of this Plan shall be governed by
and construed in accordance with the laws of the State of Delaware without regard to otherwise
governing principles of conflicts of law.

* * * * * * *

 

 

PERLEGEN SCIENCES, INC.

2002 EQUITY INCENTIVE PLAN

STOCK OPTION AGREEMENT

     Perlegen Sciences, Inc. (the “Company”), pursuant to its 2002 Equity Incentive Plan (the
“Plan”), hereby grants to the Optionee listed below (“Optionee”), an option to purchase the number
of shares of the Company’s Common Stock set forth below, subject to the terms and conditions of the
Plan and this Stock Option Agreement. Unless otherwise defined herein, the terms defined in the
Plan shall have the same defined meanings in this Stock Option Agreement.

	I.	 	NOTICE OF STOCK OPTION GRANT

	 	 	 
	Optionee:
	 	 
	 

	 	 
	 
	 	 
	Date of Stock Option Agreement:
	 	 
	 

	 	 
	 
	 	 
	Date of Grant:
	 	 
	 

	 	 
	 
	 	 
	Vesting Commencement Date:
	 	 
	 

	 	 
	 
	 	 
	Exercise Price per Share:

	 	$                                                            
	 
	 	 
	Total Number of Shares Granted:
	 	 
	 

	 	 
	 
	 	 
	Total Exercise Price:

	 	$                                                            
	 
	 	 
	Term/Expiration Date:
	 	 
	 

	 	 

	 	 	 	 	 	 	 
	Type of Option:	 	o     Incentive Stock Option           o     Non-Qualified Stock Option
	 
	 	 	 	 	 	 
	Vesting Schedule:	 	The Shares subject to this Option shall vest according to the following schedule:
	 
	 	 	 	 	 	 
	 	 	Twenty-five percent (25%) of the Shares subject to the Option (rounded down
to the next whole number of shares) shall vest on each anniversary of the
Vesting Commencement Date, so that all of the Shares shall be vested on the
forth anniversary after the Vesting Commencement Date.
	 
	 	 	 	 	 	 
	Termination Period:	 	This Option
may be exercised, to the extent
vested, for three (3) months after
Optionee ceases to be a Service
Provider, or such longer period as
may be applicable upon the death
or disability of Optionee as
provided herein (or, if not
provided herein, then as provided
in the Plan), but in no event
later than the Term/Expiration
Date as provided above.

	II.	 	AGREEMENT

     1. Grant of Option. The Company hereby grants to the Optionee an Option to purchase
the Common Stock (the “Shares”) set forth in the Notice of Grant, at the exercise price per share
set forth in the Notice of Grant (the “Exercise Price”). Notwithstanding anything to the

 

 

contrary anywhere else in this Option Agreement, this grant of an Option is subject to the
terms, definitions and provisions of the Plan adopted by the Company, which is incorporated herein
by reference.

          If designated in the Notice of Grant as an Incentive Stock Option, this Option is intended to
qualify as an Incentive Stock Option as defined in Section 422 of the Code; provided, however, that
to the extent that the aggregate Fair Market Value of stock with respect to which Incentive Stock
Options (within the meaning of Code Section 422, but without regard to Code Section 422(d)),
including the Option, are exercisable for the first time by the Optionee during any calendar year
(under the Plan and all other incentive stock option plans of the Company or any Subsidiary)
exceeds $100,000, such options shall be treated as not qualifying under Code Section 422, but
rather shall be treated as Non-Qualified Stock Options to the extent required by Code Section 422.
The rule set forth in the preceding sentence shall be applied by taking options into account in the
order in which they were granted. For purposes of these rules, the Fair Market Value of stock
shall be determined as of the time the option with respect to such stock is granted.

     2. Exercise of Option. This Option is exercisable as follows:

          (a) Right to Exercise.

               (i) This Option shall be exercisable cumulatively according to the vesting schedule set out in
the Notice of Grant. For purposes of this Stock Option Agreement, Shares subject to this Option
shall vest based on Optionee’s continued status as a Service Provider.

               (ii) This Option may not be exercised for a fraction of a Share.

               (iii) In the event of Optionee’s death, disability or other termination of the Optionee’s
status as a Service Provider, the exercisability of the Option is governed by Sections 7, 8 and 9
below.

               (iv) In no event may this Option be exercised after the date of expiration of the term of this
Option as set forth in the Notice of Grant.

          (b) Method of Exercise. This Option shall be exercisable by written Notice (in the
form attached as Exhibit A). The Notice must state the number of Shares for which the
Option is being exercised, and such other representations and agreements with respect to such
shares of Common Stock as may be required by the Company pursuant to the provisions of the Plan.
The Notice must be signed by the Optionee and shall be delivered in person or by certified mail to
the Secretary of the Company. The Notice must be accompanied by payment of the Exercise Price,
including payment of any applicable withholding tax. This Option shall be deemed to be exercised
upon receipt by the Company of such written Notice accompanied by the Exercise Price and payment of
any applicable withholding tax.

2

 

          No Shares shall be issued pursuant to the exercise of an Option unless such issuance and such
exercise comply with all relevant provisions of law and the requirements of any stock exchange upon
which the Shares may then be listed. Assuming such compliance, for income tax purposes the Shares
shall be considered transferred to the Optionee on the date on which the Option is exercised with
respect to such Shares.

     3. Optionee’s Representations. If the Shares purchasable pursuant to the exercise of
this Option have not been registered under the Securities Act of 1933, as amended (the “Securities
Act”), at the time this Option is exercised, Optionee shall, if required by the Company,
concurrently with the exercise of all or any portion of this Option, deliver to the Company his or
her Investment Representation Statement in the form attached hereto as Exhibit B.

     4. Lock-Up Period. Optionee hereby agrees that if so requested by the Company or any
representative of the underwriters (the “Managing Underwriter”) in connection with any registration
of the offering of any securities of the Company under the Securities Act, Optionee shall not sell
or otherwise transfer any Shares or other securities of the Company during the 180-day period (or
such longer period as may be requested in writing by the Managing Underwriter and agreed to in
writing by the Company) (the “Market Standoff Period”) following the effective date of a
registration statement of the Company filed under the Securities Act; provided, however, that such
restriction shall apply only to the first registration statement of the Company to become effective
under the Securities Act that includes securities to be sold on behalf of the Company to the public
in an underwritten public offering under the Securities Act. The Company may impose stop-transfer
instructions with respect to securities subject to the foregoing restrictions until the end of such
Market Standoff Period.

3

 

     5. Method of Payment. Payment of the Exercise Price shall be by any of the following, or
a combination thereof, at the election of the Optionee:

          (a) cash;

          (b) check;

          (c) with the consent of the Administrator, a full recourse promissory note bearing interest
(at no less than such rate as shall then preclude the imputation of interest under the Code) and
payable upon such terms as may be prescribed by the Administrator;

          (d) with the consent of the Administrator, surrender of other shares of Common Stock of the
Company which (A) in the case of Shares acquired from the Company, have been owned by the Optionee
for more than six (6) months on the date of surrender, and (B) have a Fair Market Value on the date
of surrender equal to the Exercise Price of the Shares as to which the Option is being exercised;

          (e) with the consent of the Administrator, surrendered Shares issuable upon the exercise of
the Option having a Fair Market Value on the date of exercise equal to the aggregate Exercise Price
of the Option or exercised portion thereof;

          (f) with the consent of the Administrator, property of any kind which constitutes good and
valuable consideration; or

          (g) with the consent of the Administrator, delivery of a notice that the Optionee has placed a
market sell order with a broker with respect to Shares then issuable upon exercise of the Option
and that the broker has been directed to pay a sufficient portion of the net proceeds of the sale
to the Company in satisfaction of the aggregate Exercise Price; provided, that payment of such
proceeds is then made to the Company upon settlement of such sale.

     6. Restrictions on Exercise. This Option may not be exercised until the Plan has been
approved by the stockholders of the Company. If the issuance of Shares upon such exercise or if
the method of payment for such shares would constitute a violation of any applicable federal or
state securities or other law or regulation, then the Option may also not be exercised. The
Company may require Optionee to make any representation and warranty to the Company as may be
required by any applicable law or regulation before allowing the Option to be exercised.

     7. Termination of Relationship. If Optionee ceases to be a Service Provider (other
than by reason of the Optionee’s death or the total and permanent disability of the Optionee as
defined in Code Section 22(e)(3)), Optionee may exercise this Option during the Termination Period
set out in the Notice of Grant, to the extent the Option was vested at the date on which Optionee
ceases to be a Service Provider. To the extent that the Option is not vested at the date on which
Optionee ceases to be a Service Provider, or if Optionee does not exercise this Option within the
time specified herein, the Option shall terminate.

     8. Disability of Optionee. If Optionee ceases to be a Service Provider as a result of
his or her total and permanent disability as defined in Code Section 22(e)(3), Optionee may
exercise the Option to the extent the Option was vested at the date on which Optionee ceases to

4

 

be a Service Provider, but only within twelve (12) months from such date (and in no event
later than the expiration date of the term of this Option as set forth in the Notice of Grant). To
the extent that the Option is not vested at the date on which Optionee ceases to be a Service
Provider, or if Optionee does not exercise such Option within the time specified herein, the Option
shall terminate.

     9. Death of Optionee. If Optionee ceases to be a Service Provider as a result of the
death of Optionee, the vested portion of the Option may be exercised at any time within twelve (12)
months following the date of death (and in no event later than the expiration date of the term of
this Option as set forth in the Notice of Grant) by Optionee’s estate or by a person who acquires
the right to exercise the Option by bequest or inheritance. To the extent that the Option is not
vested at the date of death, or if the Option is not exercised within the time specified herein,
the Option shall terminate.

     10. Non-Transferability of Option. This Option may not be transferred in any manner
except by will or by the laws of descent or distribution . It may be exercised during the lifetime
of Optionee only by Optionee. The terms of this Option shall be binding upon the executors,
administrators, heirs, successors and assigns of the Optionee.

     11. Term of Option. This Option may be exercised only within the term set out in the
Notice of Grant.

[Signature page follows]

5

 

          This Agreement may be executed in two or more counterparts, each of which shall be deemed an
original and all of which shall constitute one document.

	 	 	 	 	 
	 	 	PERLEGEN SCIENCES, INC.
	 
	 	 	 	 
	 	 	By:
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Name:
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Title:
	 

	 	 	 	 

OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO THE OPTION HEREOF IS
EARNED ONLY BY CONTINUING CONSULTANCY OR EMPLOYMENT AT THE WILL OF THE COMPANY (NOT THROUGH
THE ACT OF BEING HIRED, BEING GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER). OPTIONEE
FURTHER ACKNOWLEDGES AND AGREES THAT NOTHING IN THIS AGREEMENT, NOR IN THE COMPANY’S 2002
EQUITY INCENTIVE PLAN WHICH IS INCORPORATED HEREIN BY REFERENCE, SHALL CONFER UPON OPTIONEE
ANY RIGHT WITH RESPECT TO CONTINUATION OF EMPLOYMENT OR CONSULTANCY BY THE COMPANY, NOR
SHALL IT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE
OPTIONEE’S EMPLOYMENT OR CONSULTANCY AT ANY TIME, WITH OR WITHOUT CAUSE.

     Optionee acknowledges receipt of a copy of the Plan and represents that he is familiar with
the terms and provisions thereof. Optionee hereby accepts this Option subject to all of the terms
and provisions hereof. Optionee has reviewed the Plan and this Option in their entirety, has had
an opportunity to obtain the advice of counsel prior to executing this Option and fully understands
all provisions of the Option. Optionee hereby agrees to accept as binding, conclusive and final
all decisions or interpretations of the Administrator upon any questions arising under the Plan or
this Option. Optionee further agrees to notify the Company upon any change in the residence
address indicated below.

	 	 	 	 	 	 	 
	Dated:
	 	 	 	 	 	 
	 

	 	 
	 	 	 	 
	 

	 	 	 	 	 	[OPTIONEE]
	 
	 	 	 	 	 	 
	 

	 	 	 	 	 	Residence Address:
	 
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	 	 	 

6

 

EXHIBIT A

PERLEGEN SCIENCES, INC.

2002 EQUITY INCENTIVE PLAN

EXERCISE NOTICE

Perlegen Sciences, Inc.

2021 Stierlin Court

Mountain View, CA 94043

Attention: [Title]

     1. Exercise of Option. Effective as of today,                                         ,                     , the undersigned
(“Optionee”) hereby elects to exercise Optionee’s option to purchase                     shares of the Common
Stock (the “Shares”) of Perlegen Sciences, Inc. (the “Company”) under and pursuant to the Perlegen
Sciences, Inc. 2002 Equity Incentive Plan (the “Plan”) and
the o Incentive
o Non-Qualified Stock Option
Agreement dated                                         ,                     ,(the “Option Agreement”).

	 	 	 	 	 
	Date of Grant:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Number of Shares as to which Option is
Exercised:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Exercise Price per Share:

	 	 	 	$                                        
	 
	 	 	 	 
	Total Exercise Price:

	 	 	 	$                                        
	 
	 	 	 	 
	Certificate to be issued in name of:
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	Cash Payment delivered herewith:

	 	o
	 	$                                        
	 
	 	 	 	 
	Promissory note delivered herewith:

	 	o
	 	$                                        

	 	 	Type of Option:                     o          Incentive Stock Option          o          Non-Qualified Stock Option

     2. Representations of Optionee. Optionee acknowledges that Optionee has received,
read and understood the Plan and the Option Agreement. Optionee agrees to abide by and be bound by
their terms and conditions.

     3. Rights as Stockholder. Until the stock certificate evidencing such Shares is
issued (as evidenced by the appropriate entry on the books of the Company or of a duly authorized
transfer agent of the Company), no right to vote or receive dividends or any other rights as a
stockholder shall exist with respect to Shares subject to the Option, notwithstanding the exercise
of the Option. The Company shall issue (or cause to be issued) such stock certificate promptly
after the Option is exercised. No adjustment will be made for a dividend or other right for which
the record date is prior to the date the stock certificate is issued, except as provided in Section
13 of the Plan.

 

 

          Optionee shall enjoy rights as a stockholder until such time as Optionee disposes of the
Shares or the Company and/or its assignee(s) exercises the Right of First Refusal hereunder. Upon
such exercise, Optionee shall have no further rights as a holder of the Shares so purchased except
the right to receive payment for the Shares so purchased in accordance with the provisions of this
Agreement, and Optionee shall forthwith cause the certificate(s) evidencing the Shares so purchased
to be surrendered to the Company for transfer or cancellation.

     4. Optionee’s Rights to Transfer Shares.

          (a) Company’s Right of First Refusal. Before any Shares held by Optionee or any
permitted transferee (each, a “Holder”) may be sold, pledged, assigned, hypothecated, transferred,
or otherwise disposed of (each, a “Transfer”), the Company or its assignee(s) shall have a right of
first refusal to purchase the Shares on the terms and conditions set forth in this Section (the
“Right of First Refusal”).

               (i) Notice of Proposed Transfer. The Holder of the Shares shall deliver to the
Company a written notice (the “Notice”) stating: (i) the Holder’s bona fide intention to sell or
otherwise Transfer such Shares; (ii) the name of each proposed purchaser or other transferee
(“Proposed Transferee”); (iii) the number of Shares to be Transferred to each Proposed Transferee;
and (iv) the bona fide cash price or other consideration for which the Holder proposes to Transfer
the Shares (the “Offered Price”), and the Holder shall offer the Shares at the Offered Price to the
Company or its assignee(s).

               (ii) Exercise of Right of First Refusal. Within thirty (30) days after receipt of the
Notice, the Company and/or its assignee(s) may elect in writing to purchase all, but not less than
all, of the Shares proposed to be Transferred to any one or more of the Proposed Transferees. The
purchase price will be determined in accordance with subsection (c) below.

               (iii) Purchase Price. The purchase price (“Purchase Price”) for the Shares
repurchased under this Section shall be the Offered Price. If the Offered Price includes
consideration other than cash, the cash equivalent value of the non-cash consideration shall be
determined by the Board of Directors of the Company in good faith.

               (iv) Payment. Payment of the Purchase Price shall be made, at the option of the
Company or its assignee(s), in cash (by check), by cancellation of all or a portion of any
outstanding indebtedness of the Holder to the Company (or, in the case of repurchase by an
assignee, to the assignee), or by any combination thereof within thirty (30) days after receipt of
the Notice or in the manner and at the times set forth in the Notice.

               (v) Holder’s Right to Transfer. If all of the Shares proposed in the Notice to be
transferred to a given Proposed Transferee are not purchased by the Company and/or its assignee(s)
as provided in this Section, then the Holder may sell or otherwise Transfer such Shares to that
Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other
Transfer is consummated within one hundred twenty (120) days after the date of the Notice and
provided further that any such sale or other Transfer is effected in accordance with any applicable
securities laws and the Proposed Transferee agrees in writing that the provisions of this Section
shall continue to apply to the Shares in the hands of such Proposed

2

 

Transferee. If the Shares described in the Notice are not Transferred to the Proposed
Transferee within such period, a new Notice shall be given to the Company, and the Company and/or
its assignees shall again be offered the Right of First Refusal as provided herein before any
Shares held by the Holder may be sold or otherwise Transferred.

          (b) Exception for Certain Family Transfers. Anything to the contrary contained in
this Section notwithstanding, the Transfer of any or all of the Shares during the Optionee’s
lifetime or on the Optionee’s death by will or intestacy to the Optionee’s Immediate Family or a
trust for the benefit of the Optionee’s Immediate Family shall be exempt from the Right of First
Refusal. As used herein, “Immediate Family” shall mean spouse, lineal descendant or antecedent,
father, mother, brother or sister or stepchild (whether or not adopted). In such case, the
transferee or other recipient shall receive and hold the Shares so Transferred subject to the
provisions of this Section (including the Right of First Refusal) and there shall be no further
Transfer of such Shares except in accordance with the terms of this Section.

     5. Termination of Right of First Refusal. The Right of First Refusal shall terminate
as to all Shares upon a sale of Common Stock of the Company to the general public pursuant to a
registration statement filed with and declared effective by the Securities and Exchange Commission
under the Securities Act of 1933, as amended (a “Public Offering”).

     6. Tax Consultation. Optionee understands that Optionee may suffer adverse tax
consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents
that Optionee has consulted with any tax consultants Optionee deems advisable in connection with
the purchase or disposition of the Shares and that Optionee is not relying on the Company for any
tax advice.

     7. Restrictive Legends and Stop-Transfer Orders.

          (a) Legends. Optionee understands and agrees that the Company shall cause the legends
set forth below or legends substantially equivalent thereto, to be placed upon any certificate(s)
evidencing ownership of the Shares together with any other legends that may be required by state or
federal securities laws:

THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933 (THE “ACT”) AND MAY NOT BE OFFERED, SOLD OR
OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL
REGISTERED UNDER THE ACT OR, IN THE OPINION OF COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH
OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS IN COMPLIANCE
THEREWITH.

THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN
RESTRICTIONS ON TRANSFER AND RIGHT OF FIRST REFUSAL OPTIONS HELD BY
THE

3

 

ISSUER OR ITS ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE
BETWEEN THE ISSUER AND THE ORIGINAL HOLDER OF THESE SHARES, A COPY
OF WHICH MAY BE OBTAINED AT THE PRINCIPAL OFFICE OF THE ISSUER.
SUCH TRANSFER RESTRICTIONS AND RIGHT OF FIRST REFUSAL ARE BINDING ON
TRANSFEREES OF THESE SHARES.

          (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with
the restrictions referred to herein, the Company may issue appropriate “stop transfer” instructions
to its transfer agent, if any, and that, if the Company transfers its own securities, it may make
appropriate notations to the same effect in its own records.

          (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its
books any Shares that have been sold or otherwise transferred in violation of any of the provisions
of this Agreement or (ii) to treat as owner of such Shares or to accord the right to vote or pay
dividends to any purchaser or other transferee to whom such Shares shall have been so transferred.

     8. Successors and Assigns. The Company may assign any of its rights under this
Agreement to single or multiple assignees, and this Agreement shall inure to the benefit of the
successors and assigns of the Company. Subject to the restrictions on transfer herein set forth,
this Agreement shall be binding upon Optionee and his or her heirs, executors, administrators,
successors and assigns.

     9. Interpretation. Any dispute regarding the interpretation of this Agreement shall
be submitted by Optionee or by the Company forthwith to the Company’s Board of Directors or
committee thereof that is responsible for the administration of the Plan (the “Administrator”),
which shall review such dispute at its next regular meeting. The resolution of such a dispute by
the Administrator shall be final and binding on the Company and on Optionee.

     10. Governing Law; Severability. This Agreement shall be governed by and construed in
accordance with the laws of the State of California excluding that body of law pertaining to
conflicts of law. Should any provision of this Agreement be determined by a court of law to be
illegal or unenforceable, the other provisions shall nevertheless remain effective and shall remain
enforceable.

     11. Notices. Any notice required or permitted hereunder shall be given in writing and
shall be deemed effectively given upon personal delivery or upon deposit in the United States mail
by certified mail, with postage and fees prepaid, addressed to the other party at its address as
shown below beneath its signature, or to such other address as such party may designate in writing
from time to time to the other party.

     12. Further Instruments. The parties agree to execute such further instruments and to
take such further action as may be reasonably necessary to carry out the purposes and intent of
this Agreement.

4

 

     13. Delivery of Payment. Optionee herewith delivers to the Company the full Exercise
Price for the Shares, as well as any applicable withholding tax.

     14. Entire Agreement. The Plan and Stock Option Agreement are incorporated herein by
reference. This Agreement, the Plan, the Stock Option Agreement and the Investment Representation
Statement constitute the entire agreement of the parties and supersede in their entirety all prior
undertakings and agreements of the Company and Optionee with respect to the subject matter hereof.

	 	 	 	 	 
	Accepted by:	 	Submitted by:
	 
	 	 	 	 
	PERLEGEN SCIENCES, INC.	 	OPTIONEE
	 
	 	 	 	 
	By:	 	 
	 

	 	 	 	 
	Name:	 	 
	 

	 	 
	 	 
	Its:	 	[Optionee]
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	Address:
	 
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 

5

 

EXHIBIT B

INVESTMENT REPRESENTATION STATEMENT

	 	 	 	 	 
	OPTIONEE

	 	:	 	 
	 
	 	 	 	 
	COMPANY

	 	:
	 	PERLEGEN SCIENCES, INC.
	 
	 	 	 	 
	SECURITY

	 	:
	 	COMMON STOCK
	 
	 	 	 	 
	AMOUNT

	 	:	 	 
	 
	 	 	 	 
	DATE

	 	:	 	 

     In connection with the purchase of the above-listed Securities, the undersigned Optionee
represents to the Company the following:

          (a) Optionee is aware of the Company’s business affairs and financial condition and has
acquired sufficient information about the Company to reach an informed and knowledgeable decision
to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s
own account only and not with a view to, or for resale in connection with, any “distribution”
thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”).

          (b) Optionee acknowledges and understands that the Securities constitute “restricted
securities” under the Securities Act and have not been registered under the Securities Act in
reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the
bona fide nature of Optionee’s investment intent as expressed herein. In this connection, Optionee
understands that, in the view of the Securities and Exchange Commission, the statutory basis for
such exemption may be unavailable if Optionee’s representation was predicated solely upon a present
intention to hold these Securities for the minimum capital gains period specified under tax
statutes, for a deferred sale, for or until an increase or decrease in the market price of the
Securities, or for a period of one year or any other fixed period in the future. Optionee further
understands that the Securities must be held indefinitely unless they are subsequently registered
under the Securities Act or an exemption from such registration is available. Optionee further
acknowledges and understands that the Company is under no obligation to register the Securities.

 

 

Optionee understands that the certificate evidencing the Securities will be imprinted with a
legend which prohibits the transfer of the Securities unless they are registered or such
registration is not required in the opinion of counsel satisfactory to the Company and any other
legend required under applicable state securities laws.

          (c) Optionee is familiar with the provisions of Rule 701 and Rule 144, each promulgated under
the Securities Act, which, in substance, permit limited public resale of “restricted securities”
acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to the
satisfaction of certain conditions. Rule 701 provides that if the issuer qualifies under Rule 701
at the time of the grant of the Option to the Optionee, the exercise will be exempt from
registration under the Securities Act. In the event the Company becomes subject to the reporting
requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days
thereafter (or such longer period as any market stand-off agreement may require) the Securities
exempt under Rule 701 may be resold, subject to the satisfaction of certain of the conditions
specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited
“broker’s transaction” or in transactions directly with a market maker (as said term is defined
under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability
of certain public information about the Company, (3) the amount of Securities being sold during any
three (3) month period not exceeding the limitations specified in Rule 144(e), and (4) the timely
filing of a Form 144, if applicable.

          In the event that the Company does not qualify under Rule 701 at the time of grant of the
Option, then the Securities may be resold in certain limited circumstances subject to the
provisions of Rule 144, which requires the resale to occur not less than one year after the later
of the date the Securities were sold by the Company or the date the Securities were sold by an
affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the
Securities by an affiliate, or by a non-affiliate who subsequently holds the Securities less than
two (2) years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of
the paragraph immediately above.

          (d) Optionee further understands that in the event all of the applicable requirements of Rule
701 or 144 are not satisfied, registration under the Securities Act, compliance with Regulation A,
or some other registration exemption will be required; and that, notwithstanding the fact that
Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange Commission has
expressed its opinion that persons proposing to sell private placement securities other than in a
registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden
of proof in establishing that an exemption from registration is
available for such

1

 

offers or sales, and that such persons and their respective brokers who participate in such
transactions do so at their own risk. Optionee understands that no assurances can be given that
any such other registration exemption will be available in such event.

	 	 	 
	 

	 	Signature of Optionee:
	 
	 	 
	 

	 	 
	 

	 	[Optionee]

Date:                                         ,                    

2

 

PERLEGEN SCIENCES, INC.

2002 STOCK OPTION AND INCENTIVE PLAN

NON-EMPLOYEE DIRECTOR AND SCIENTIFIC ADVISOR

NON-QUALIFIED STOCK OPTION AWARD AGREEMENT

          This Award Agreement (the “Agreement”) is entered into between Perlegen Sciences,
Inc., a Delaware corporation (the “Company”), and the Grantee whose name is set forth
below, pursuant to the Perlegen Sciences, Inc. 2002 Stock Option and Incentive Plan (the
“Plan”). Capitalized terms used in this Agreement and not defined herein are defined in
the Plan.

ARTICLE I

Grant of Option

     Section 1.1 Grant of Option

          The Company hereby grants to the Grantee a non-qualified stock option (“Option”) to
purchase shares of the Company’s common stock, par value $0.0001 per share (the “Common
Stock”), on the terms set forth below:

	 
	Grantee

	 

	Capacity in Which Granted

	 

	Grant Date

	 

	Number of Shares Subject to Option

	 

	Exercise Price per Share

	 

	Expiration Date

ARTICLE II

Vesting; Exercise; Expiration

     Section 2.1 Vesting

          The right to exercise this Option shall vest in installments as follows:

-1-

 

	 	 	 
	On or after:	 	This Option shall be exercisable as to:
	Date

	 	100% of the total shares subject to this Option

No installment of the Option shall vest after the Termination of Employment of the Grantee or
Grantee’s permanent disability or death.

     Section 2.2 Exercise

          Grantee may exercise vested Options by delivering a written notice, in such form and manner
prescribed by the Company, to the Company setting forth the number of shares of Common Stock with
respect to which the Option is exercised and delivering the aggregate Exercise Price for such
number of shares to the Company, in each case in accordance with the provisions of the Plan.
Alternatively, Grantee may exercise all (but not less than all) of Grantee’s unvested Options for
restricted Common Stock that contains vesting provisions that are the same as the vesting
provisions set forth in Article II of this Agreement by (i) delivering a written notice, in such
form and manner prescribed by the Company, to the Company, (ii) signing and delivering to the
Company the applicable restricted stock purchase agreement, in such form prescribed by the Company,
and (iii) delivering the aggregate Exercise Price for the number of shares subject to the Option to
the Company, in each case in accordance with the provisions of the Plan. An Option may be
exercised only for a whole number of shares. At the time of exercise, Grantee shall pay to the
Company, or make arrangements for payment to the satisfaction of the Company, such amount as the
Company deems necessary to satisfy its obligation to withhold Federal, state, local or other taxes
incurred by reason of such exercise.

     Section 2.3 Company Repurchase Right

          If Grantee elects pursuant to Section 2.2 of this Agreement to exercise Grantee’s unvested
Options for restricted Common Stock, then, upon Grantee’s Termination of Employment, the Company
shall have the right, but not the obligation, to purchase from Grantee, within ninety (90) days of
such Termination of Employment, all of Grantee’s unvested shares of restricted Common Stock as of
the date of such Termination of Employment at the price paid by the Grantee for such shares.

     Section 2.4 Expiration

          This Agreement shall expire on, and the Option may not be exercised after, the earliest to
occur of the following:

	 	(a)	 	The expiration date set forth in Article I;

-2-

 

	 	(b)	 	Ninety days after the Termination of Employment of the Grantee
for any reason, except disability, death or by the Company for Cause;
	 
	 	(c)	 	The Termination of Employment of the Grantee by the Company for
Cause; or
	 
	 	(d)	 	One year after the date of the disability or death of the
Grantee.

     Section 2.5 “Cause”

          “Cause” shall mean the willful and continued failure by Grantee to perform
substantially his duties with Company (other than any such failure resulting from incapacity due to
physical or mental illness) after a demand for substantial performance is delivered to Grantee by
the Company which specifically identifies the manner in which Company believes Grantee has not
substantially performed his duties; conviction of a felony; habitual abuse of narcotics or alcohol;
or fraud, material dishonesty or gross misconduct in connection with the business of the Company.

ARTICLE III

     Section 3.1 Non-transferability of Option

          The Option and rights granted hereunder shall not be transferred, assigned, pledged or
exchanged in any manner whatsoever, whether voluntarily or involuntarily, by the Grantee, otherwise
than by will or the laws of descent and distribution or to an immediate family member (as defined
in the Plan), and is exercisable during the Employee’s lifetime only by the Employee or by the
Employee’s legal representative or such immediate family member.

     Section 3.2 Securities Law Matters

	(a)	 	Upon each issuance of shares of stock following proper exercise by Grantee, the
Grantee, a transferee permitted under Section 3.1 of this Agreement, or Grantee’s legal
representative, or heirs receiving the shares, shall, if requested by the Company in
order to comply with federal or state securities laws, represent in writing to the
Company that such shares are being acquired for investment and with no view to any
distribution thereof or shall make such other representations in writing to the
Company, with respect to the further transfer of such shares, as may be deemed by the
Company to be necessary or desirable under the applicable securities laws. The
Company, at its sole discretion, may take all reasonable steps, including the affixing
of a legend on certificates issued in connection with such shares of stock, or the
imposition of stop-transfer instructions, to achieve compliance.

	(b)	 	Grantee hereby agrees to subject any shares purchased pursuant to this Option
to a

-3-

 

lock-up period of up to 12 months if requested by the Company, pursuant to a
request by the underwriters, in connection with and following any underwritten
public offering of equity securities.

     Section 3.3 Incorporation of Plan by Reference; Supremacy of Plan Provisions

          The Plan is hereby incorporated into this Agreement by reference to the same extent as though
it were set forth in full herein. If there is any conflict between the provisions of the Plan and
any provision of this Agreement, this Agreement shall be construed and enforced in accordance with
the provisions of the Plan and this Agreement without regard to the conflicting provision of the
Agreement.

     Section 3.4 Merger or Sale of Company

          In the event of (i) a merger or consolidation of the Company with or into any other
corporation or entity, (ii) a sale of all or substantially all of the Company’s assets to any other
corporation or entity or (iii) any transaction by which another person, corporation or entity
(other than Affymetrix and any corporation or entity in which Affymetrix holds a controlling
interest, directly or indirectly) becomes the Beneficial Owner of more than 50% of the issued and
outstanding Shares of the Company, outstanding Options shall be treated as set forth in Section 3.7
of the Plan.

-4-

 

Executed as of the Grant Date:

	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 	 	Perlegen Sciences, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	     BradleyMargus	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	          CEO	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	 	 	 
	 

	 	 	 	          Name	 	 

-5-

 

PERLEGEN SCIENCES, INC.

2002 EQUITY INCENTIVE PLAN

EXERCISE NOTICE

Perlegen Sciences, Inc.

2021 Stierlin Court

Mountain View, CA 94043

Attention: Frank Zampella

     1. Exercise
of Option. Effective as of today,                     ,                     , the undersigned
(“Optionee”) hereby elects to exercise Optionee’s
option to purchase                      shares of the Common
Stock (the “Shares”) of Perlegen Sciences, Inc. (the “Company”) under and pursuant to the Perlegen
Sciences, Inc. 2002 Equity Incentive Plan (the “Plan”) and
the o Incentive
o Non-Qualified Stock Option
Agreement dated                     , ___, (the “Option Agreement”).

	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	Date of Grant:
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	Number of Shares as to which Option is Exercised:
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	Exercise Price per Share:

	 	 	 	$                    	 	 
	 
	 	 	 	 	 	 
	Total Exercise Price:

	 	 	 	$                    	 	 
	 
	 	 	 	 	 	 
	Certificate to be issued in name of:
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	Cash Payment delivered herewith:

	 	o
	 	$                    	 	 
	 
	 	 	 	 	 	 
	Promissory note delivered herewith:

	 	o
	 	$                    	 	 

Type of Option:          o      Incentive Stock Option           o     Non-Qualified Stock Option

     2. Representations of Optionee. Optionee acknowledges that Optionee has received,
read and understood the Plan and the Option Agreement. Optionee agrees to abide by and be bound by
their terms and conditions.

     3. Rights as Stockholder. Until the stock certificate evidencing such Shares is
issued (as evidenced by the appropriate entry on the books of the Company or of a duly authorized
transfer agent of the Company), no right to vote or receive dividends or any other rights as a
stockholder shall exist with respect to Shares subject to the Option, notwithstanding the exercise
of the Option. The Company shall issue (or cause to be issued) such stock certificate promptly
after the Option is exercised. No adjustment will be made for a dividend or other right for which
the record date is prior to the date the stock certificate is issued, except as provided in Section
13 of the Plan.

     Optionee shall enjoy rights as a stockholder until such time as Optionee disposes of the
Shares or the Company and/or its assignee(s) exercises the Right of First Refusal

 

 

hereunder. Upon such exercise, Optionee shall have no further rights as a holder of the
Shares so purchased except the right to receive payment for the Shares so purchased in accordance
with the provisions of this Agreement, and Optionee shall forthwith cause the certificate(s)
evidencing the Shares so purchased to be surrendered to the Company for transfer or cancellation.

     4. Optionee’s Rights to Transfer Shares.

          (a) Company’s Right of First Refusal. Before any Shares held by Optionee or any
permitted transferee (each, a “Holder”) may be sold, pledged, assigned, hypothecated, transferred,
or otherwise disposed of (each, a “Transfer”), the Company or its assignee(s) shall have a right of
first refusal to purchase the Shares on the terms and conditions set forth in this Section (the
“Right of First Refusal”).

               (i) Notice of Proposed Transfer. The Holder of the Shares shall deliver to the
Company a written notice (the “Notice”) stating: (i) the Holder’s bona fide intention to sell or
otherwise Transfer such Shares; (ii) the name of each proposed purchaser or other transferee
(“Proposed Transferee”); (iii) the number of Shares to be Transferred to each Proposed Transferee;
and (iv) the bona fide cash price or other consideration for which the Holder proposes to Transfer
the Shares (the “Offered Price”), and the Holder shall offer the Shares at the Offered Price to the
Company or its assignee(s).

               (ii) Exercise of Right of First Refusal. Within thirty (30) days after receipt of the
Notice, the Company and/or its assignee(s) may elect in writing to purchase all, but not less than
all, of the Shares proposed to be Transferred to any one or more of the Proposed Transferees. The
purchase price will be determined in accordance with subsection (c) below.

               (iii) Purchase Price. The purchase price (“Purchase Price”) for the Shares
repurchased under this Section shall be the Offered Price. If the Offered Price includes
consideration other than cash, the cash equivalent value of the non-cash consideration shall be
determined by the Board of Directors of the Company in good faith.

               (iv) Payment. Payment of the Purchase Price shall be made, at the option of the
Company or its assignee(s), in cash (by check), by cancellation of all or a portion of any
outstanding indebtedness of the Holder to the Company (or, in the case of repurchase by an
assignee, to the assignee), or by any combination thereof within thirty (30) days after receipt of
the Notice or in the manner and at the times set forth in the Notice.

               (v) Holder’s Right to Transfer. If all of the Shares proposed in the Notice to be
transferred to a given Proposed Transferee are not purchased by the Company and/or its assignee(s)
as provided in this Section, then the Holder may sell or otherwise Transfer such Shares to that
Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other
Transfer is consummated within one hundred twenty (120) days after the date of the Notice and
provided further that any such sale or other Transfer is effected in accordance with any applicable
securities laws and the Proposed Transferee agrees in writing that the provisions of this Section
shall continue to apply to the Shares in the hands of such Proposed Transferee. If the Shares
described in the Notice are not Transferred to the Proposed Transferee within such period, a new
Notice shall be given to the Company, and the Company and/or its

2

 

assignees shall again be offered the Right of First Refusal as provided herein before any
Shares held by the Holder may be sold or otherwise Transferred.

          (b) Exception for Certain Family Transfers. Anything to the contrary contained in
this Section notwithstanding, the Transfer of any or all of the Shares during the Optionee’s
lifetime or on the Optionee’s death by will or intestacy to the Optionee’s Immediate Family or a
trust for the benefit of the Optionee’s Immediate Family shall be exempt from the Right of First
Refusal. As used herein, “Immediate Family” shall mean spouse, lineal descendant or antecedent,
father, mother, brother or sister or stepchild (whether or not adopted). In such case, the
transferee or other recipient shall receive and hold the Shares so Transferred subject to the
provisions of this Section (including the Right of First Refusal) and there shall be no further
Transfer of such Shares except in accordance with the terms of this Section.

     5. Termination of Right of First Refusal. The Right of First Refusal shall terminate
as to all Shares upon a sale of Common Stock of the Company to the general public pursuant to a
registration statement filed with and declared effective by the Securities and Exchange Commission
under the Securities Act of 1933, as amended (a “Public Offering”).

     6. Tax Consultation. Optionee understands that Optionee may suffer adverse tax
consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents
that Optionee has consulted with any tax consultants Optionee deems advisable in connection with
the purchase or disposition of the Shares and that Optionee is not relying on the Company for any
tax advice.

     7. Restrictive Legends and Stop-Transfer Orders.

          (a) Legends. Optionee understands and agrees that the Company shall cause the legends
set forth below or legends substantially equivalent thereto, to be placed upon any certificate(s)
evidencing ownership of the Shares together with any other legends that may be required by state or
federal securities laws:

THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933 (THE “ACT”) AND MAY NOT BE OFFERED, SOLD OR
OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL
REGISTERED UNDER THE ACT OR, IN THE OPINION OF COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH
OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS IN COMPLIANCE
THEREWITH.

THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN
RESTRICTIONS ON TRANSFER AND RIGHT OF FIRST REFUSAL OPTIONS HELD BY
THE ISSUER OR ITS ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE
BETWEEN THE ISSUER AND THE

3

 

ORIGINAL HOLDER OF THESE SHARES, A COPY OF WHICH MAY BE OBTAINED AT
THE PRINCIPAL OFFICE OF THE ISSUER. SUCH TRANSFER RESTRICTIONS AND
RIGHT OF FIRST REFUSAL ARE BINDING ON TRANSFEREES OF THESE SHARES.

          (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with
the restrictions referred to herein, the Company may issue appropriate “stop transfer” instructions
to its transfer agent, if any, and that, if the Company transfers its own securities, it may make
appropriate notations to the same effect in its own records.

          (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its
books any Shares that have been sold or otherwise transferred in violation of any of the provisions
of this Agreement or (ii) to treat as owner of such Shares or to accord the right to vote or pay
dividends to any purchaser or other transferee to whom such Shares shall have been so transferred.

     8. Successors and Assigns. The Company may assign any of its rights under this
Agreement to single or multiple assignees, and this Agreement shall inure to the benefit of the
successors and assigns of the Company. Subject to the restrictions on transfer herein set forth,
this Agreement shall be binding upon Optionee and his or her heirs, executors, administrators,
successors and assigns.

     9. Interpretation. Any dispute regarding the interpretation of this Agreement shall
be submitted by Optionee or by the Company forthwith to the Company’s Board of Directors or
committee thereof that is responsible for the administration of the Plan (the “Administrator”),
which shall review such dispute at its next regular meeting. The resolution of such a dispute by
the Administrator shall be final and binding on the Company and on Optionee.

     10. Governing Law; Severability. This Agreement shall be governed by and construed in
accordance with the laws of the State of California excluding that body of law pertaining to
conflicts of law. Should any provision of this Agreement be determined by a court of law to be
illegal or unenforceable, the other provisions shall nevertheless remain effective and shall remain
enforceable.

     11. Notices. Any notice required or permitted hereunder shall be given in writing and
shall be deemed effectively given upon personal delivery or upon deposit in the United States mail
by certified mail, with postage and fees prepaid, addressed to the other party at its address as
shown below beneath its signature, or to such other address as such party may designate in writing
from time to time to the other party.

     12. Further Instruments. The parties agree to execute such further instruments and to
take such further action as may be reasonably necessary to carry out the purposes and intent of
this Agreement.

     13. Delivery of Payment. Optionee herewith delivers to the Company the full Exercise
Price for the Shares, as well as any applicable withholding tax.

4

 

     14. Entire Agreement. The Plan and Stock Option Agreement are incorporated herein by
reference. This Agreement, the Plan, the Stock Option Agreement and the Investment Representation
Statement constitute the entire agreement of the parties and supersede in their entirety all prior
undertakings and agreements of the Company and Optionee with respect to the subject matter hereof.

	 	 	 	 	 
	 

	 	 	 	 
	Accepted by:

	 	Submitted by:	 	 
	 
	 	 	 	 
	PERLEGEN SCIENCES, INC.

	 	OPTIONEE	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 
	 	 	 	 
	Name:

	 	[Optionee]	 	 
	 
	 	 	 	 
	Its:
	 	 	 	 
	 
	 	 	 	 
	 

	 	Address:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	 	 	 

5

 

EXHIBIT B

INVESTMENT REPRESENTATION STATEMENT

	 	 	 	 	 
	OPTIONEE

	 	:	 	 
	 
	 	 	 	 
	COMPANY

	 	:
	 	PERLEGEN SCIENCES, INC.
	 
	 	 	 	 
	SECURITY

	 	:
	 	COMMON STOCK
	 
	 	 	 	 
	AMOUNT

	 	:	 	 
	 
	 	 	 	 
	DATE

	 	:	 	 

     In connection with the purchase of the above-listed Securities, the undersigned Optionee
represents to the Company the following:

          (a) Optionee is aware of the Company’s business affairs and financial condition and has
acquired sufficient information about the Company to reach an informed and knowledgeable decision
to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s
own account only and not with a view to, or for resale in connection with, any “distribution”
thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”).

          (b) Optionee acknowledges and understands that the Securities constitute “restricted
securities” under the Securities Act and have not been registered under the Securities Act in
reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the
bona fide nature of Optionee’s investment intent as expressed herein. In this connection, Optionee
understands that, in the view of the Securities and Exchange Commission, the statutory basis for
such exemption may be unavailable if Optionee’s representation was predicated solely upon a present
intention to hold these Securities for the minimum capital gains period specified under tax
statutes, for a deferred sale, for or until an increase or decrease in the market price of the
Securities, or for a period of one year or any other fixed period in the future. Optionee further
understands that the Securities must be held indefinitely unless they are subsequently registered
under the Securities Act or an exemption from such registration is available. Optionee further
acknowledges and understands that the Company is under no obligation to register the Securities.
Optionee understands that the certificate evidencing the Securities will be imprinted with a legend
which prohibits the transfer of the Securities unless they are registered or such registration is
not required in the opinion of counsel satisfactory to the Company and any other legend required
under applicable state securities laws.

          (c) Optionee is familiar with the provisions of Rule 701 and Rule 144, each promulgated under
the Securities Act, which, in substance, permit limited public resale of “restricted securities”
acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to

 

 

the
satisfaction of certain conditions. Rule 701 provides that if the issuer qualifies under Rule 701
at the time of the grant of the Option to the Optionee, the exercise will be exempt from
registration under the Securities Act. In the event the Company becomes subject to the reporting
requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days
thereafter (or such longer period as any market stand-off agreement may require) the Securities
exempt under Rule 701 may be resold, subject to the satisfaction of certain of the conditions
specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited
“broker’s transaction” or in transactions directly with a market maker (as said term is defined
under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability
of certain public information about the Company, (3) the amount of Securities being sold during any
three (3) month period not exceeding the limitations specified in Rule 144(e), and (4) the timely
filing of a Form 144, if applicable.

          In the event that the Company does not qualify under Rule 701 at the time of grant of the
Option, then the Securities may be resold in certain limited circumstances subject to the
provisions of Rule 144, which requires the resale to occur not less than one year after the later
of the date the Securities were sold by the Company or the date the Securities were sold by an
affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the
Securities by an affiliate, or by a non-affiliate who subsequently holds the Securities less than
two (2) years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of
the paragraph immediately above.

          (d) Optionee further understands that in the event all of the applicable requirements of Rule
701 or 144 are not satisfied, registration under the Securities Act, compliance with Regulation A,
or some other registration exemption will be required; and that, notwithstanding the fact that
Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange Commission has
expressed its opinion that persons proposing to sell private placement securities other than in a
registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden
of proof in establishing that an exemption from registration is available for such offers or sales,
and that such persons and their respective brokers who participate in such transactions do so at
their own risk. Optionee understands that no assurances can be given that any such other
registration exemption will be available in such event.

	 	 	 	 	 	 	 
	 

	 	 	 	Signature of Optionee:
	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	[Optionee]	 	 
	 
	 	 	 	 	 	 
	Date:

	 	                                        ,                     	 	 	 	 

1

 

PERLEGEN SCIENCES, INC.

2002 EQUITY INCENTIVE PLAN

STOCK OPTION AGREEMENT

     Perlegen Sciences, Inc. (the “Company”), pursuant to its 2002 Equity Incentive Plan (the
“Plan”), hereby grants to the Optionee listed below (“Optionee”), an option to purchase the number
of shares of the Company’s Common Stock set forth below, subject to the terms and conditions of the
Plan and this Stock Option Agreement. Unless otherwise defined herein, the terms defined in the
Plan shall have the same defined meanings in this Stock Option Agreement.

I. NOTICE OF STOCK OPTION GRANT

	 	 	 	 	 
	Optionee:
	 	 	 	 
	 
	 	 	 	 
	Date of Stock Option Agreement:
	 	 	 	 
	 
	 	 	 	 
	Date of Grant:
	 	 	 	 
	 
	 	 	 	 
	Vesting Commencement Date:
	 	 	 	 
	 
	 	 	 	 
	Exercise Price per Share:

	 	 	$	 
	 
	 	 	 	 

	Total Number of Shares Granted:
	 	 	 	 
	 
	 	 	 	 
	Total Exercise Price:

	 	 	$	 
	 
	 	 	 	 

	Term/Expiration Date:
	 	 	 	 

	 	 	 
	Type of Option:

	 	þ Incentive Stock Option           o      Non-Qualified Stock Option
	 
	 	 
	Vesting Schedule:

	 	The Shares subject to this Option shall vest according to the following schedule:
	 

	 	Twenty-five percent (25%) of the Shares subject to the Option (rounded
down to the next whole number of shares) shall vest on each anniversary of
the Vesting Commencement Date, so that all of the Shares shall be vested
on the forth anniversary after the Vesting Commencement Date, subject to
Optionee continuing to be a Service Provider through each relevant vesting
date.
	 
	 	 
	Termination Period:

	 	This Option may be exercised, to the extent vested, for three (3) months after
Optionee ceases to be a Service Provider, or such longer period as may be applicable upon the
death or disability of Optionee as provided herein (or, if not provided herein, then as
provided in the Plan), but in no event later than the Term/Expiration Date as provided above.

 

 

II. AGREEMENT

     1. Grant of Option. The Company hereby grants to the Optionee an Option to purchase
the Common Stock (the “Shares”) set forth in the Notice of Grant, at the exercise price per share
set forth in the Notice of Grant (the “Exercise Price”). Notwithstanding anything to the contrary
anywhere else in this Option Agreement, this grant of an Option is subject to the terms,
definitions and provisions of the Plan adopted by the Company, which is incorporated herein by
reference.

          If designated in the Notice of Grant as an Incentive Stock Option, this Option is intended to
qualify as an Incentive Stock Option as defined in Section 422 of the Code; provided, however, that
to the extent that the aggregate Fair Market Value of stock with respect to which Incentive Stock
Options (within the meaning of Code Section 422, but without regard to Code Section 422(d)),
including the Option, are exercisable for the first time by the Optionee during any calendar year
(under the Plan and all other incentive stock option plans of the Company or any Subsidiary)
exceeds $100,000, such options shall be treated as not qualifying under Code Section 422, but
rather shall be treated as Non-Qualified Stock Options to the extent required by Code Section 422.
The rule set forth in the preceding sentence shall be applied by taking options into account in the
order in which they were granted. For purposes of these rules, the Fair Market Value of stock
shall be determined as of the time the option with respect to such stock is granted.

     2. Exercise of Option. This Option is exercisable as follows:

          (a) Right to Exercise.

               (i) This Option shall be exercisable cumulatively according to the vesting schedule set out in
the Notice of Grant. For purposes of this Stock Option Agreement, Shares subject to this Option
shall vest based on Optionee’s continued status as a Service Provider.

               (ii) This Option may not be exercised for a fraction of a Share.

               (iii) In the event of Optionee’s death, disability or other termination of the Optionee’s
status as a Service Provider, the exercisability of the Option is governed by Sections 7, 8 and 9
below.

               (iv) In no event may this Option be exercised after the date of expiration of the term of this
Option as set forth in the Notice of Grant.

          (b) Method of Exercise. This Option shall be exercisable by written Notice (in the
form attached as Exhibit A). The Notice must state the number of Shares for which the
Option is being exercised, and such other representations and agreements with respect to such
shares of Common Stock as may be required by the Company pursuant to the provisions of the Plan.
The Notice must be signed by the Optionee and shall be delivered in person or by certified mail to
the Secretary of the Company. The Notice must be accompanied by payment of the Exercise Price,
including payment of any

2

 

applicable withholding tax. This Option shall be deemed to be exercised upon receipt by the
Company of such written Notice accompanied by the Exercise Price and payment of any applicable
withholding tax.

          No Shares shall be issued pursuant to the exercise of an Option unless such issuance and such
exercise comply with all relevant provisions of law and the requirements of any stock exchange upon
which the Shares may then be listed. Assuming such compliance, for income tax purposes the Shares
shall be considered transferred to the Optionee on the date on which the Option is exercised with
respect to such Shares.

     3. Optionee’s Representations. If the Shares purchasable pursuant to the exercise of
this Option have not been registered under the Securities Act of 1933, as amended (the “Securities
Act”), at the time this Option is exercised, Optionee shall, if required by the Company,
concurrently with the exercise of all or any portion of this Option, deliver to the Company his or
her Investment Representation Statement in the form attached hereto as Exhibit B.

     4. Lock-Up Period. Optionee hereby agrees that if so requested by the Company or any
representative of the underwriters (the “Managing Underwriter”) in connection with any registration
of the offering of any securities of the Company under the Securities Act, Optionee shall not sell
or otherwise transfer any Shares or other securities of the Company during the 180-day period (or
such longer period as may be requested in writing by the Managing Underwriter and agreed to in
writing by the Company) (the “Market Standoff Period”) following the effective date of a
registration statement of the Company filed under the Securities Act; provided, however, that such
restriction shall apply only to the first registration statement of the Company to become effective
under the Securities Act that includes securities to be sold on behalf of the Company to the public
in an underwritten public offering under the Securities Act. The Company may impose stop-transfer
instructions with respect to securities subject to the foregoing restrictions until the end of such
Market Standoff Period.

     5. Method of Payment. Payment of the Exercise Price shall be by any of the following,
or a combination thereof, at the election of the Optionee:

          (a) cash;

          (b) check;

          (c) with the consent of the Administrator, a full recourse promissory note bearing interest
(at no less than such rate as shall then preclude the imputation of interest under the Code) and
payable upon such terms as may be prescribed by the Administrator;

          (d) with the consent of the Administrator, surrender of other shares of Common Stock of the
Company which (A) in the case of Shares acquired from the Company, have been owned by the Optionee
for more than six (6) months on the date of

3

 

surrender, and (B) have a Fair Market Value on the date of surrender equal to the Exercise
Price of the Shares as to which the Option is being exercised;

          (e) with the consent of the Administrator, surrendered Shares issuable upon the exercise of
the Option having a Fair Market Value on the date of exercise equal to the aggregate Exercise Price
of the Option or exercised portion thereof;

          (f) with the consent of the Administrator, property of any kind which constitutes good and
valuable consideration; or

          (g) with the consent of the Administrator, delivery of a notice that the Optionee has placed a
market sell order with a broker with respect to Shares then issuable upon exercise of the Option
and that the broker has been directed to pay a sufficient portion of the net proceeds of the sale
to the Company in satisfaction of the aggregate Exercise Price; provided, that payment of such
proceeds is then made to the Company upon settlement of such sale.

     6. Restrictions on Exercise. This Option may not be exercised until the Plan has been
approved by the stockholders of the Company. If the issuance of Shares upon such exercise or if
the method of payment for such shares would constitute a violation of any applicable federal or
state securities or other law or regulation, then the Option may also not be exercised. The
Company may require Optionee to make any representation and warranty to the Company as may be
required by any applicable law or regulation before allowing the Option to be exercised.

     7. Termination of Relationship. If Optionee ceases to be a Service Provider (other
than by reason of the Optionee’s death or the total and permanent disability of the Optionee as
defined in Code Section 22(e)(3)), Optionee may exercise this Option during the Termination Period
set out in the Notice of Grant, to the extent the Option was vested at the date on which Optionee
ceases to be a Service Provider. To the extent that the Option is not vested at the date on which
Optionee ceases to be a Service Provider, or if Optionee does not exercise this Option within the
time specified herein, the Option shall terminate.

     8. Disability of Optionee. If Optionee ceases to be a Service Provider as a result of
his or her total and permanent disability as defined in Code Section 22(e)(3), Optionee may
exercise the Option to the extent the Option was vested at the date on which Optionee ceases to be
a Service Provider, but only within twelve (12) months from such date (and in no event later than
the expiration date of the term of this Option as set forth in the Notice of Grant). To the extent
that the Option is not vested at the date on which Optionee ceases to be a Service Provider, or if
Optionee does not exercise such Option within the time specified herein, the Option shall
terminate.

     9. Death of Optionee. If Optionee ceases to be a Service Provider as a result of the
death of Optionee, the vested portion of the Option may be exercised at any time within twelve (12)
months following the date of death (and in no event later than the expiration date of the term of
this Option as set forth in the Notice of Grant) by

4

 

Optionee’s estate or by a person who acquires the right to exercise the Option by bequest or
inheritance. To the extent that the Option is not vested at the date of death, or if the Option is
not exercised within the time specified herein, the Option shall terminate.

     10. Non-Transferability of Option. This Option may not be transferred in any manner
except by will or by the laws of descent or distribution . It may be exercised during the lifetime
of Optionee only by Optionee. The terms of this Option shall be binding upon the executors,
administrators, heirs, successors and assigns of the Optionee.

     11. Term of Option. This Option may be exercised only within the term set out in the
Notice of Grant.

     12. Tax Obligations.

          (a) Withholding. Optionee agrees to make appropriate arrangements with the Company
(or the Parent or Subsidiary employing or retaining Optionee) for the satisfaction of all Federal,
state, local and foreign income and employment tax withholding requirements as well as social
security charges applicable to the vesting of the Option, the exercise of the Option or the
disposition of any Shares acquired upon exercise. In this regard, Optionee authorizes the Company
(and/or the Parent or Subsidiary employing or retaining Optionee) to withhold all applicable taxes
legally payable by Optionee from the Optionee’s wages or other cash compensation paid to Optionee
by the Company (and/or the Parent or Subsidiary employing or retaining Optionee) or from proceeds
from the sale of Shares acquired upon exercise of the Option in an amount sufficient to cover such
tax obligations. Optionee acknowledges and agrees that the Company may refuse to honor the
exercise and refuse to deliver Shares if such withholding amounts are not delivered at the time of
exercise.

          (b) Tax Consultation. Optionee understands that he or she may suffer adverse tax
consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents
that he or she will consult with any tax advisors Optionee deems appropriate in connection with the
purchase or disposition of the Shares and that Optionee is not relying on the Company for any tax
advice.

     13. Acknowledgements.

          (a) Optionee acknowledges receipt of a copy of the Plan (including any applicable appendixes
or sub-plans thereunder) and represents that he or she is familiar with the terms and provisions
thereof, and hereby accepts this Option subject to all of the terms and provisions thereof.
Optionee has reviewed the Plan (including any applicable appendixes or sub-plans thereunder) and
this Option Agreement in their entirety, has had an opportunity to obtain the advice of counsel
prior to executing this Option and fully understands all provisions of the Option. Optionee hereby
agrees to accept as binding, conclusive and final all decisions or interpretations of the
Administrator upon any questions arising under the Plan or this Option. Optionee further agrees to
notify the Company upon any change in the residence address indicated below.

5

 

          (b) The Company (and not Optionee’s employer) is granting the Option. The Company will
administer the Plan from outside Optionee ’s country of residence and that United States of America
law will govern all Options granted under the Plan.

          (c) That benefits and rights provided under the Plan are wholly discretionary and, although
provided by the Company, do not constitute regular or periodic payments. The benefits and rights
provided under the Plan are not to be considered part of Optionee’ s salary or compensation for
purposes of calculating any severance, resignation, redundancy or other end of service payments,
vacation, bonuses, long-term service awards, indemnification, pension or retirement benefits, or
any other payments, benefits or rights of any kind. Optionee waives any and all rights to
compensation or damages as a result of the termination of employment with the Company for any
reason whatsoever insofar as those rights result or may result from:

               (i) the loss or diminution in value of such rights under the Plan, or

               (ii) Optionee ceases to have any rights under, or ceases to be entitled to any rights under
the Plan as a result of such termination.

          (d) The grant of the Option, and any future grant of Options under the Plan is entirely
voluntary, and at the complete discretion of the Company. Neither the grant of the Option nor any
future grant of an Option by the Company will be deemed to create any obligation to grant any
further Options, whether or not such a reservation is explicitly stated at the time of such a
grant. The Company has the right, at any time to amend, suspend or terminate the Plan.

          (e) The Plan will not be deemed to constitute, and will not be construed by Optionee to
constitute, part of the terms and conditions of employment, and that the Company will not incur any
liability of any kind to Optionee as a result of any change or amendment, or any cancellation, of
the Plan at any time.

          (f) Participation in the Plan will not be deemed to constitute, and will not be deemed by
Optionee to constitute, an employment or labor relationship of any kind with the Company.

          (g) By entering into this Option Agreement, and as a condition of the grant of the Option,
Optionee consents to the collection, use, and transfer of personal data as described in this
subsection to the full extent permitted by and in full compliance with Applicable Law.

               (i) Optionee understands that the Company and its Subsidiaries hold certain personal
information about the Optionee, including, but not limited to, name, home address and telephone
number, date of birth, social insurance number, salary, nationality, job title, any Shares or
directorships held in the Company, details of all Options or other entitlement to Shares awarded,
canceled, exercised, vested,

6

 

unvested, or outstanding in Optionee’s favor, for the purpose of managing and administering
the Plan (“Data”).

               (ii) Optionee further understands that the Company and/or its Subsidiaries will transfer Data
among themselves as necessary for the purposes of implementation, administration, and management of
Optionee’s participation in the Plan, and that the Company and/or its Subsidiary may each further
transfer Data to any third parties assisting the Company in the implementation, administration, and
management of the Plan (“Data Recipients” ).

               (iii) Optionee understands that these Data Recipients may be located in Optionee’s country of
residence or elsewhere, such as the United States. Optionee authorizes the Data Recipients to
receive, possess, use, retain, and transfer Data in electronic or other form, for the purposes of
implementing, administering, and managing Optionee’s participation in the Plan, including any
transfer of such Data, as may be required for the administration of the Plan and/or the subsequent
holding of Shares on Optionee’ s behalf, to a broker or third party with whom the Shares acquired
on exercise may be deposited.

               (iv) Optionee understands that Optionee may, at any time, review the Data, request that any
necessary amendments be made to it, or withdraw Optionee’s consent herein in writing by contacting
the Company. Optionee further understands that withdrawing consent may affect Optionee’s ability
to participate in the Plan.

               (h) Optionee has received the terms and conditions of this Option Agreement and any other
related communications, and Optionee consents to having received these documents in English.

     14. No Guarantee of Continued Service. Optionee acknowledges and agrees that the
vesting of Shares pursuant to the vesting schedule hereof is earned only by continuing as a Service
Provider at the will of the Company (not through the act of being hired, being granted this Option
or acquiring Shares hereunder). Optionee further acknowledges and agrees that this Option
Agreement, the transactions contemplated hereunder and the vesting schedule set forth herein do not
constitute an express or implied promise of continued engagement as a service provider for the
vesting period, for any period, or at all, and shall not interfere in any way with Optionee’s right
or the Company’s right to terminate Optionee’s relationship as a Service Provider at any time, with
or without cause.

     15. Entire Agreement; Governing Law. The Plan is incorporated herein by reference.
The Plan and this Option Agreement constitute the entire agreement of the parties with respect to
the subject matter hereof and supersede in their entirety all prior undertakings and agreements of
the Company and Optionee with respect to the subject matter hereof, and may not be modified
adversely to the Optionee’s interest except by means of a writing signed by the Company and
Optionee. This agreement is governed by the internal substantive laws but not the choice of law
rules of California.

7

 

[Signature page follows]

8

 

     This Agreement may be executed in two or more counterparts, each of which shall be deemed an
original and all of which shall constitute one document.

	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 
	 	 	PERLEGEN SCIENCES, INC.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Name:__ Brad Margus                                         	 	 
	 
	 	 	 	 	 	 
	 	 	Title:___ President
/CEO                                         	 	 

OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO THE OPTION HEREOF
IS EARNED ONLY BY CONTINUING CONSULTANCY OR EMPLOYMENT AT THE WILL OF THE COMPANY (NOT
THROUGH THE ACT OF BEING HIRED, BEING GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER).
OPTIONEE FURTHER ACKNOWLEDGES AND AGREES THAT NOTHING IN THIS AGREEMENT, NOR IN THE
COMPANY’S 2002 EQUITY INCENTIVE PLAN WHICH IS INCORPORATED HEREIN BY REFERENCE, SHALL
CONFER UPON OPTIONEE ANY RIGHT WITH RESPECT TO CONTINUATION OF EMPLOYMENT OR CONSULTANCY BY
THE COMPANY, NOR SHALL IT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT
TO TERMINATE OPTIONEE’S EMPLOYMENT OR CONSULTANCY AT ANY TIME, WITH OR WITHOUT CAUSE.

     Optionee acknowledges receipt of a copy of the Plan and represents that he is familiar with
the terms and provisions thereof. Optionee hereby accepts this Option subject to all of the terms
and provisions hereof. Optionee has reviewed the Plan and this Option in their entirety, has had
an opportunity to obtain the advice of counsel prior to executing this Option and fully understands
all provisions of the Option. Optionee hereby agrees to accept as binding, conclusive and final
all decisions or interpretations of the Administrator upon any questions arising under the Plan or
this Option. Optionee further agrees to notify the Company upon any change in the residence
address indicated below.

Dated:                                                                                                                                                                                     

9exv10w5

 

Exhibit 10.5

PERLEGEN SCIENCES, INC.

SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

February 1, 2005

 

 

SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

     This SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT (the “Agreement) is entered into as
of the 1st day of February, 2005 by and among Perlegen Sciences, Inc., a Delaware corporation (the
“Company”), the investors listed on Schedule A (each an “Investor” and collectively, the
“Investors”) and the purchasers listed on Schedule A hereto (each, a “Purchaser” and
collectively, the “Purchasers”).

WITNESSETH:

     WHEREAS, certain of the Purchasers are purchasing shares of the Company’s Series D Preferred
Stock (the “Series D Stock”), pursuant to that certain Series D Preferred Stock Purchase Agreement
(the “Purchase Agreement”) of even date herewith (the “Financing”);

     WHEREAS, the obligations in the Purchase Agreement are conditioned upon the execution and
delivery of this Agreement;

     WHEREAS, certain of the Purchasers (the “Prior Purchasers”) are holders of the Company’s
Series A Preferred Stock, Series B Preferred Stock and Series C Preferred Stock (the “Series A
Stock,” “Series B Stock” and “Series C Stock,” respectively, together with the Series D Stock, the
“Preferred Stock”);

     WHEREAS, the Prior Purchasers and the Company are parties to an Amended and Restated
Stockholders’ Agreement dated January 23, 2003 (the “Prior Agreement”);

     WHEREAS, the parties to the Prior Agreement desire to amend and restate the Prior Agreement
and accept the rights and covenants hereof in lieu of their rights and covenants under the Prior
Agreement; and

     WHEREAS, in connection with the consummation of the Financing, the Company, the Investors and
the Purchasers have agreed to the preemptive rights, bring-along rights, and other rights and
obligations as set forth below.

     NOW, THEREFORE, in consideration of these premises and for other good and valid consideration,
the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

     1. Definitions. As used in this Agreement, the following terms shall have the
meanings set forth below:

     “Affymetrix” shall mean Affymetrix, Inc., a Delaware corporation and holder of a majority of
the Series A Stock.

     “Affymetrix Agreements” shall mean the Asset Purchase Agreement, Intellectual Property
Transfer and License Agreement (Affymetrix to Perlegen), Intellectual Property Transfer and License
Agreement (Perlegen to Affymetrix), Supply Agreement, Internal Use License Agreement,
Research Agreement, Scientific Collaboration Agreement and Services Agreement, in each case
between Affymetrix and the Company.

 

 

     “Affymetrix Entity” shall mean any corporation or other entity in which Affymetrix owns more
than 50% of the outstanding voting securities of such corporation or other entity.

     “Agreed Rate” shall mean the product of (i) 0.20 multiplied by (ii) the result of (a) the
number of days in the period commencing on the day that the Series B Stock, Series C Stock or
Series D Stock, as applicable, is initially purchased by the Selling Purchaser and ending on the
day immediately preceding the Section 4 Closing divided by (b) 365.

     “Agreed Value” shall mean an amount equal to the sum of (i) the Original Series B Issue Price,
the Original Series C Issue Price or the Original Series D Issue Price, as applicable, and (ii) the
product of (a) the Original Series B Issue Price, the Original Series C Issue Price or the Original
Series D Issue Price, as applicable, multiplied by (b) the Agreed Rate.

     “Bring-Along Notice” shall have the meaning ascribed to such term in Section 3(a) of this
Agreement.

     “Bring-Along Offer” shall have the meaning ascribed to such term in Section 3(a) of this
Agreement.

     “Business Day” shall mean a day other than a Saturday or Sunday on which commercial banks in
New York, New York are not required or permitted under applicable laws or regulations to close.

     “Buyer” shall have the meaning ascribed to such term in Section 3(a) of this Agreement.

     “Certificate” shall mean the Third Amended and Restated Certificate of Incorporation of the
Company, as may be amended, modified or restated from time to time.

     “Common Stock” shall mean the common stock of the Company.

     “Controlling Group” shall have the meaning ascribed to such term in Section 3(a) of this
Agreement.

     “Custodian” shall have the meaning ascribed to such term in Section 3(b) of this Agreement.

     “Equity Securities” shall mean Common Stock and Preferred Stock.

     “Financing” shall have the meaning ascribed to such term in the recitals to this Agreement.

     “Holders” shall mean the Purchasers and the Investors, or, in each case, persons who have
acquired shares from any of such persons or their permitted transferees or assignees in each case
in accordance with the provisions of this Agreement.

2

 

     “Independent Directors” shall have the meaning ascribed to such term in Section 6(a)(iv) of
this Agreement.

     “Investor” or “Investors” shall have the meaning ascribed to such term in the recitals to this
Agreement.

     “Lien” shall mean a charge, mortgage, pledge, security interest, restriction, claim, lien,
encumbrance or adverse claim of any nature whatsoever.

     “Major Holder” shall have the meaning ascribed to such term in Section 2.4(a) of this
Agreement.

     “Major Holder’s Proportionate Share” shall mean, with respect to a Major Holder, a fraction
the numerator of which is the total number of shares of Common Stock owned and/or issued upon
conversion of Preferred Stock owned by such Major Holder, and the denominator of which is the total
number of shares of Common Stock then outstanding (assuming full conversion of outstanding
Preferred Stock and exercise of all outstanding convertible securities, rights, options and
warrants to acquire Common Stock of the Company).

     “Management Directors” shall have the meaning ascribed to such term in Section 6(a)(i) of this
Agreement.

     “Management Investor” shall mean Brad Margus, David Cox and Stephen P.A. Fodor.

     “Nominating Committee” shall have the meaning ascribed to such term in Section 6(b) of this
Agreement.

     “Original Series B Issue Price” shall have the meaning ascribed to such term in the
Certificate.

     “Original Series C Issue Price” shall have the meaning ascribed to such term in the
Certificate.

     “Original Series D Issue Price” shall have the meaning ascribed to such term in the
Certificate.

     “Permitted Transferee” shall have the meaning ascribed to such term in Section 2.3 of this
Agreement.

     “Person” shall mean an individual, partnership, corporation, trust, limited liability company
or unincorporated organization, and a government or agency or political subdivision thereof.

     “Preferred Stock” shall have the meaning ascribed to such term in the recitals to this
Agreement.

     “Prior Agreement” shall have the meaning ascribed to such term in the recitals to this
Agreement.

3

 

     “Prior Purchasers” shall have the meaning ascribed to such term in the recitals to this
Agreement.

     “Purchase Agreement” shall have the meaning ascribed to such term in the recitals to this
Agreement.

     “Purchase Event” shall mean the consummation of a purchase of Equity Securities by Affymetrix
(or one of the Affymetrix Entities) that causes Affymetrix (together with the Affymetrix Entities)
to own more than 80% of the outstanding Equity Securities.

     “Purchase Event Notice” shall have the meaning ascribed to such term in Section 4(a) of this
Agreement.

     “Purchase Event Option” shall have the meaning ascribed to such term in Section 4(b) of this
Agreement.

     “Qualified IPO” shall have the meaning ascribed to such term in the Certificate.

     “Related Person” shall mean with respect to any Person (i) any other Person that directly or
indirectly through one or more intermediaries controls or is controlled by or is under common
control with such Person, or (ii) any other Person owning or controlling 25% or more of the
outstanding voting securities of or other ownership interest in such Person or (iii) any officer,
director, general partner, managing partner or member of such Person.

     “Right” shall mean any option, warrant, security, right or other instrument convertible into
or exchangeable or exercisable for, or otherwise giving the holder thereof the right to acquire,
directly or indirectly, from the Company any Common Stock or any other such option, warrant,
security, right or instrument, including any instrument issued by the Company or any subsidiary
thereof the value of which is measured by reference to the value of the Common Stock.

     “Section 3 Closing” shall have the meaning ascribed to such term in Section 3(a) of this
Agreement.

     “Section 4 Closing” shall have the meaning ascribed to such term in Section 4(a) of this
Agreement.

     “Securities Act” shall mean the Securities Act of 1933, as amended.

     “Selling Purchaser” shall have the meaning ascribed to such term in Section 4(b) of this
Agreement.

     “Series A Director” shall have the meaning ascribed to such term in Section 6(a)(ii) of this
Agreement.

     “Series A Stock” shall have the meaning ascribed to such term in the recitals to this
Agreement.

4

 

     “Series B Stock” shall have the meaning ascribed to such term in the recitals to this
Agreement.

     “Series C Stock” shall have the meaning ascribed to such term in the recitals to the
Agreement.

     “Series D Stock” shall have the meaning ascribed to such term in the recitals to the
Agreement.

     2. Agreements Among the Company and the Holders.

          2.1 Rights of Refusal.

               (a) Transfer Notice. If at any time a Management Investor proposes to transfer Equity
Securities to one or more third parties (a “Transfer”), then the Management Investor shall give the
Company written notice of the Management Investor’s intention to make the Transfer (the “Transfer
Notice”), which Transfer Notice shall include (i) a description of the Equity Securities to be
transferred (“Offered Shares”), (ii) the identity of the prospective transferee(s) and (iii) the
consideration and the material terms and conditions upon which the proposed Transfer is to be made.
The Transfer Notice shall also include the material terms of the proposed Transfer.

               (b) Company’s Option. The Company shall have an option for a period of ten (10) days
from the Company’s receipt of the Transfer Notice to elect to purchase all but not less than all of
the Offered Shares at the same price and subject to the same material terms and conditions as
described in the Transfer Notice. The Company may exercise such purchase option and, thereby,
purchase all of the Offered Shares by notifying the Management Investor in writing before
expiration of such ten (10) day period as to the number of such shares which it wishes to purchase.
If the Company gives the Management Investor notice that it desires to purchase such shares, then
such notice shall constitute an irrevocable commitment to purchase such shares and payment for the
Offered Shares shall be by check or wire transfer, against delivery of the Offered Shares to be
purchased at a place agreed upon between the parties and at the time of the scheduled closing
therefor, which shall be no later than thirty (30) Business Days after the Company’s receipt of the
Transfer Notice, unless the Transfer Notice contemplated a later closing with the prospective third
party transferee(s) or unless the value of the purchase price has not yet been established pursuant
to Section 2.1(f) or unless antitrust or other regulatory approvals or expirations of legally
mandated waiting periods require a closing at a later date. If the Company fails to purchase all
of the Offered Shares by exercising the option granted in this Section 2.1(b) within the period
provided, the Offered Shares shall be subject to the options granted to each other Holder (each, a
“Non-Selling Holder”) pursuant to this Agreement and the Company shall provide the Non-Selling
Holders with the Additional Transfer Notice (as defined below).

               (c) Additional Transfer Notice. Subject to the Company’s right set forth in Section
2.1(b), if at any time the Management Investor proposes a Transfer, then, after the Company has
declined to purchase the Offered Shares, the Company shall give each Non-Selling Holder an
“Additional Transfer Notice” which shall include all of the information and certifications required
in a Transfer Notice and additionally shall state that the Company has declined to purchase
the Offered Shares and briefly describe the Non-Selling Holders’ rights of first refusal with
respect to the proposed Transfer.

5

 

               (d) Non-Selling Holders’ Option.

               (i) The Non-Selling Holders shall have an option for a period of ten (10) days from the
Non-Selling Holder’s receipt of the Additional Transfer Notice from the Company set forth in
Section 2.1(c) to elect to purchase their respective pro rata shares of the Offered Shares at the
same price and subject to the same material terms and conditions as described in the Additional
Transfer Notice. Each Non-Selling Holder may exercise such purchase option and, thereby, purchase
all or any portion of his, her or its pro rata share (with any reallotments as provided below) of
the Offered Shares, by notifying the Management Investor and the Company in writing, before
expiration of the ten (10) day period as to the number of such shares which he, she or it wishes to
purchase. Each Non-Selling Holder’s pro rata share of the Offered Shares shall be a fraction of
the Offered Shares, of which the number of shares of Common Stock (including shares of Common Stock
issuable upon conversion of Preferred Stock) owned by such Non-Selling Holder on the date of the
Additional Transfer Notice shall be the numerator and the total number of shares of Common Stock
(including shares of Common Stock issuable upon conversion of Preferred Stock) held by all Holders
(except the Management Investor) on the date of the Additional Transfer Notice shall be the
denominator.

               (ii) Each Non-Selling Holder shall have a right of reallotment such that, if any other
Non-Selling Holder fails to exercise the right to purchase its full pro rata share of the Offered
Shares within ten (10) days from the date of receipt of the Additional Transfer Notice (as
described in Section 2(d)(i) above), the Management Investor will give the Non-Selling Holders who
exercised in full such Non-Selling Holders pro rata share of Offered Stock (as set forth above in
Section 2(d)(i)) (each, a “Fully-Exercising Investor”) notice (the “Second Notice”) of the number
of Offered Shares not subscribed for by the other Non-Selling Holders. Each Fully-Exercising
Investor shall have ten (10) days from the date of receipt of the Second Notice to agree to
exercise an additional right to purchase, on a pro rata basis equal to the proportion that the
number of shares of Common Stock (including shares of Common Stock issuable upon conversion of
Preferred Stock) owned by such Fully-Exercising Investor bears to the total number of shares of
Common Stock (including shares of Common Stock issuable upon conversion of Preferred Stock) owned
by all Fully-Exercising Investors who wish to purchase such unsubscribed Offered Stock, the Offered
Shares not previously purchased. Each participating Non-Selling Holder shall be entitled to
apportion Offered Shares to be purchased among its partners and affiliates, provided that
such participating Non-Selling Holder notifies the Management Investor of such allocation. If a
Non-Selling Holder gives the Management Investor notice that it desires to purchase its pro rata
share of the Offered Shares and, as the case may be, its reallotment, then such notice shall
constitute an irrevocable commitment to purchase such shares and payment for the Offered Shares
shall be by check or wire transfer, against delivery of the Offered Shares to be purchased at a
place agreed upon between the parties and at the time of the scheduled closing therefor, which
shall be no later than thirty (30) Business Days after the Company’s receipt of the Transfer
Notice, unless the Transfer Notice contemplated a later closing with the prospective third party
transferee(s) or unless the value of the purchase price has not yet been established pursuant to
Section 2.1(f) or unless antitrust or
other regulatory approvals or expirations of legally mandated waiting periods require a
closing at a later date.

6

 

               (e) [Intentionally Omitted]

               (f) Valuation of Property. Should the purchase price specified in the Transfer Notice
or Additional Transfer Notice be payable in property other than cash or evidences of indebtedness,
the Company (and/or the Non-Selling Holders) shall have the right to pay the purchase price in the
form of cash equal in amount to the value of such property. If the Management Investor and the
Company (and/or the Non-Selling Holders) cannot agree on such cash value within ten (10) Business
Days after the Company’s receipt of the Transfer Notice, the valuation shall be made by an
appraiser of recognized standing selected by the Management Investor and the Company (and/or the
Non-Selling Holders) or, if they cannot agree on an appraiser within twenty (20) Business Days
after the Company’s receipt of the Transfer Notice, each shall select an appraiser of recognized
standing and the two appraisers shall designate a third appraiser of recognized standing, whose
appraisal shall be determinative of such value. The cost of such appraisal shall be paid by the
Company (and/or the Non-Selling Holders). The cost borne by the Company and the Non-Selling
Holders shall be borne pro rata by each based on the number of shares such parties desire to
purchase pursuant to this Section 2. If the time for the closing of the Company’s purchase or the
Non-Selling Holders’ purchase has expired but for the determination of the value of the purchase
price offered by the prospective transferee(s), then such closing shall be held on or prior to the
fifth Business Day after such valuation shall have been made pursuant to this subsection.

          2.2 Non-Exercise of Rights. In the event that the Company and the Non-Selling Holders
have not exercised their rights to purchase the Offered Shares within the time periods specified in
Section 2.1, the Management Investor shall have a period of ninety (90) days from the expiration of
such rights (or such longer period as is necessary to comply with any applicable regulatory waiting
period or obtain any applicable regulatory approval) in which to sell the Offered Shares upon terms
and conditions (including the purchase price) no more favorable than those specified in the
Transfer Notice to the third-party transferee(s) identified in the Transfer Notice. The
third-party transferee(s) shall acquire the Offered Shares free and clear of subsequent rights of
first refusal under this Agreement. In the event the Management Investor does not consummate the
sale or disposition of the Offered Shares within the ninety (90) day period from the expiration of
these rights (or such longer period as is necessary to comply with any applicable regulatory
waiting period or obtain any applicable regulatory approval), the Company’s and the Non-Selling
Holders’ first refusal rights shall continue to be applicable to any subsequent disposition of the
Offered Shares by the Management Investor until such right lapses in accordance with the terms of
this Agreement. Furthermore, the exercise or non-exercise of the rights of the Company or the
Non-Selling Holders under this Section 2 to purchase Equity Securities from the Management Investor
shall not adversely affect their rights to make subsequent purchases from the Management Investor
of Equity Securities.

          2.3 Limitations to Rights of Refusal.

     Each Management Investor may sell or otherwise assign, with or without consideration, Equity
Securities (a) in the case of a Management Investor who is an individual, (i) to any spouse or
member of such Management Investor’s immediate family, or to a custodian, trustee (including a

7

 

trustee of a voting trust), executor, or other fiduciary for the account of such Management
Investor’s spouse or members of the Management Investor’s immediate family, or to a trust for the
Management Investor’s own self, or a charitable remainder trust, and (ii) to a family limited
partnership or family limited liability company which is controlled by the Management Investor and
in which all partners or members are members of the Management Investor’s immediate family, or (b)
in the case of a Management Investor that is not an individual, to any person or entity
controlling, controlled by or under common control with such Management Investor, provided,
however, that for any transfer effected pursuant to this Section 2.3 each such transferee or
assignee (each, a “Permitted Transferee”), prior to the completion of the sale, transfer, or
assignment shall have executed documents assuming the obligations of the Management Investor under
this Agreement with respect to the transferred securities.

     2.4 Preemptive Rights.

               (a) If the Company proposes to issue, grant or sell equity securities or Rights, the Company
shall first give to the Holders of 1,000,000 or more shares (subject to appropriate adjustments for
stock splits, stock dividends, combinations and other recapitalizations) of Common Stock, including
shares of Common Stock issuable upon conversion of the Preferred Stock in the Company (a “Major
Holder”) written notice setting forth in reasonable detail the price and other terms on which such
equity securities or Rights are proposed to be issued, granted or sold, the terms of any such
Rights and the amount thereof proposed to be issued, granted or sold. The Major Holders shall
thereafter have the preemptive right, exercisable by written notice to the Company no later than
ten (10) Business Days after the Company’s notice is deemed given (as determined pursuant to
Section 11 hereof), to purchase the number of such equity securities or Rights set forth in the
Major Holders’ notice (which may be less than, but in no event more than, the Major Holders’
Proportionate Share thereof, as of the date of the Company’s notice), at the price and on the other
terms set forth in the Company’s notice. Any notice by the Major Holders exercising the right to
purchase equity securities or Rights pursuant to this Section 2.4 shall constitute an irrevocable
commitment to purchase from the Company the equity securities or Rights specified in such notice,
subject to the maximum set forth in the preceding sentence. The closing of the purchase of equity
securities shall take place at the same time as the closing of such issuance, grant or sale
referred to in the Company’s notice.

               (b) From the expiration of the 10 Business Day period first referred to in Section 2.4(a) and
for a period of 90 days thereafter, the Company may offer, issue, grant and sell to any person or
entity equity securities or Rights having the terms set forth in the Company’s notice relating to
such equity securities or Rights at a price and on other terms no less favorable to the Company,
and including no less cash, than those set forth in such notice (without deduction for reasonable
underwriting, sales agency and similar fees payable in connection therewith); provided, however,
that the Company may not issue, grant or sell equity securities or Rights to third parties in an
amount greater than the amount set forth in such notice minus the amount purchased or committed to
be purchased by the Purchasers.

               (c) The provisions of this Section 2.4 shall not apply to the following issuances of
securities or Rights: (i) the issuance of Common Stock upon the conversion of Series A Stock,
Series B Stock, Series C Stock or Series D Stock, (ii) the issuance of up to 24,516,722 shares

8

 

of Common Stock (subject to adjustment for stock splits, reverse stock splits, subdivisions,
stock dividends, combinations, reclassifications, recapitalizations and similar events) pursuant to
restricted stock sold to, or the exercise of stock options issued to, employees, consultants,
officers or directors of the Company under a stock option plan or restricted stock issuance plan
approved by a majority of the board of directors of the Company, (iii) the issuance of Common Stock
as direct consideration for the acquisition of another business entity or business segment of any
such entity by the Company by merger, purchase of substantially all of the assets or other
reorganization whereby the Company will own substantially all the assets or more than fifty percent
(50%) of the voting power of such business entity or business segment of any such entity if such
issuance is approved by a majority of the board of directors of the Company, (iv) the issuance of
any shares of Common Stock in connection with a stock split or dividend of the Company (other than
a Deemed Liquidation Event as defined in the Certificate), (v) the issuance of Common Stock in
connection with a Qualified IPO, (vi) the issuance of Common Stock or Preferred Stock in connection
with a lease financing or other asset-based financing, whether issued to a lessor, guarantor or
other person (a “Lease Financing”), provided that such Lease Financing is approved by a
majority of the board of directors of the Company; and provided further that any such Lease
Financing which in aggregate amount exceeds $10,000,000 is approved by a majority of the board of
directors including the director designated by the holders of the Series C Stock and the director
designated by the holders of the Series D Stock, (vii) the issuance of Common Stock or Preferred
Stock in connection with a corporate partnering, alliance or similar strategic transaction approved
by a majority of the board of directors of the Company, or (viii) the issuance or deemed issuance
of Common Stock or Preferred Stock upon exercise or conversion of any options or warrants, or upon
the conversion of convertible securities outstanding as of the date of the first issuance of the
Series D Stock.

     3. Bring-Along Rights.

          (a) Bring-Along Notice. Notwithstanding anything contained in Section 2 to the
contrary, if Holders in excess of 80% of the outstanding shares of Common Stock (including shares
of Common Stock issuable upon conversion of Preferred Stock) (a “Controlling Group”), acting
jointly, intend to effect a sale to a third party (a “Buyer”) of in excess of 80% of the
outstanding shares of Common Stock (including shares of Common Stock issuable upon conversion of
Preferred Stock) and elect to exercise their rights under this Section 3, such Controlling Group
shall deliver written notice (a “Bring-Along Notice”) to the Company and the other Holders, which
notice shall (i) state (1) that the Controlling Group wishes to exercise its rights under this
Section 3 with respect to such transfer, (2) the name and address of the Buyer, (3) the per share
amount and form of consideration the Controlling Group proposes to receive for its shares of Common
Stock (including shares of Common Stock issuable upon conversion of Preferred Stock), (4) the
percentage of the shares of Common Stock (including shares of Common Stock issuable upon conversion
of Preferred Stock) held by the members of the Controlling Group being sold by the members of the
Controlling Group and (5) the terms and conditions of payment of such consideration and all other
material terms and conditions of such transfer, (ii) contain an offer (the “Bring-Along Offer”) by
the Buyer to purchase from the Holders that percentage of their shares of Common Stock (including
shares of Common Stock issuable upon conversion of Preferred Stock) as is being sold by the members
of the Controlling Group, on and subject to the same price, terms and conditions offered to the
Controlling Group and (iii) state the anticipated time and place of the closing of such transfer (a
“Section 3 Closing”), which (subject to such terms and conditions) shall occur not fewer than five
(5) Business

9

 

Days nor more than ninety (90) days after the date such Bring-Along Notice is delivered,
provided that if such Section 3 Closing shall not occur prior to the expiration of such
ninety (90) day period, the Controlling Group shall be required to deliver another Bring-Along
Notice with respect to such Bring-Along Offer. Upon request of a Controlling Group, the Company
shall provide the Controlling Group with a current list of the names and addresses of the Holders.

               (b) Conditions to Bring-Along. Upon delivery of a Bring-Along Notice, each of the
Holders shall have the obligation to transfer that percentage of its shares of Common Stock
(including shares of Common Stock issuable upon conversion of Preferred Stock) as is being sold by
the members of the Controlling Group pursuant to the Bring-Along Offer, as such offer may be
modified from time to time, provided that the members of the Controlling Group transfer the
same percentage of their shares of Common Stock (including shares of Common Stock issuable upon
conversion of Preferred Stock) to the Buyer at the Section 3 Closing and that all shares of the
Preferred Stock or Common Stock held by the Controlling Group and the Holders being so sold are
sold to the Buyer at the same price, and on the same terms and conditions. On or before the date
set for the closing in the Bring-Along Notice, each of the Holders shall deliver to a member of the
Controlling Group or such other person designated in the Bring-Along Notice (the “Custodian”)
certificates representing such Holder’s applicable percentage of shares of Common Stock (including
shares of Common Stock issuable upon conversion of Preferred Stock), duly endorsed for transfer or
accompanied by duly executed stock powers, free and clear of all Liens. On or before the date set
for the closing in the Bring-Along Notice, each Holder shall represent and warrant to and indemnify
the Buyer that (i) the agreement containing such representations, warranties and indemnities has
been duly authorized, executed and delivered by or on behalf of such Holder, (ii) such Holder has
full power, right and authority to transfer the shares to be sold by such Holder and to enter into
such agreement, (iii) immediately before the closing, such Holder will have good and valid title to
the shares to be sold by such Holder free and clear of all Liens and, upon payment for and delivery
of the shares, the Buyer will acquire all of the rights of the Holder in the shares to be sold by
the Holder and will acquire its interest in such shares free of any “adverse claim” (as defined in
Section 8-102 of the Uniform Commercial Code) and (iv) delivery of the of the shares to be sold by
such Holder to the Buyer will pass title to such shares free and clear of any Liens. The Custodian
shall hold such shares and other documents in trust for such Holder pending completion or
abandonment of such sale. If, within ninety (90) days after the Controlling Group delivers the
Bring-Along Notice, the Controlling Group has not completed the sale of the applicable percentage
of the shares of Common Stock (including shares of Common Stock issuable upon conversion of
Preferred Stock) owned by the Controlling Group and the Holders to the Buyer and another
Bring-Along Notice with respect to such Bring-Along Offer has not been sent to the Holders, the
Custodian shall return to each Holder all certificates representing the shares. Promptly after the
Section 3 Closing, the Custodian shall give notice thereof to the Holders, shall remit to each of
the Holders the total consideration for the shares of such Holder sold pursuant thereto, and shall
furnish such other evidence of the completion and time of completion of such sale and the terms
thereof as may reasonably be requested by any of the Holders.

               (c) Remedies. Each of the Holders acknowledges that the Controlling Group would be
irreparably damaged in the event of a breach or a threatened breach by such Holder of any of its
obligations under this Section 3 and each of the Holders agrees that, in the event of a breach or a
threatened breach by such Holder of any such obligation, the Controlling Group shall, in addition

10

 

to any other rights and remedies available to it in respect of such breach, be entitled to an
injunction from a court of competent jurisdiction (without any requirement to post bond) granting
it specific performance by such Holder of its obligations under this Section 3. Each of the
Holders agrees that, in the event of a breach or a threatened breach by such Holder of its
obligations under this Section 3, the Company may record the transfer of such Holders’ shares to
the Buyer on the books and records of the Company. In the event that the Controlling Group shall
file suit to enforce the covenants contained in this Section 3 (or obtain any other remedy in
respect of any breach thereof) the prevailing party in the suit shall be entitled to recover, in
addition to all other damages to which it may be entitled, the costs incurred by such party in
conducting the suit, including reasonable attorney’s fees and expenses.

     4. Purchase Rights.

          (a) Purchase Event Notice. Affymetrix shall, within 30 days following the date of the
first Purchase Event, deliver written notice (a “Purchase Event Notice’’) to the Company and each
of the Purchasers, which notice shall state (i) that a Purchase Event has occurred and (ii) the
time, date and place of the closing of the sale of any shares to be purchased by Affymetrix upon
the exercise of the Purchase Event Option (a “Section 4 Closing”), which (subject to the terms and
conditions of this Section 4) shall occur not fewer than fifteen (15) days nor more than ninety
(90) days after the date such Purchase Event Notice is delivered.

          (b) Purchase Event Option. Each Purchaser shall have an option (the “Purchase Event
Option”) for a period of ten (10) days from such Purchaser’s receipt of the Purchase Event Notice
to elect to sell all, but not less than all, of the shares of Series B Stock, Series C Stock and
Series D Stock owned by such Purchaser to Affymetrix at a price per share equal to the Agreed
Value. Each Purchaser may exercise its Purchase Event Option by notifying Affymetrix of such
exercise in writing before expiration of such ten (10) day period, which notice shall state the
number of shares of Series B Stock, Series C Stock and Series D Stock owned by such Purchaser. If
a Purchaser provides Affymetrix with such a notice (each, a “Selling Purchaser”), then such notice
shall constitute an irrevocable commitment by such Selling Purchaser to sell all of the shares of
Series B Stock, Series C Stock and Series D Stock owned by such Selling Purchaser to Affymetrix at
a price per share equal to the Agreed Value.

          (c) Purchase Event Option Closing. On or before the time set for the Section 4
Closing, each of the Selling Purchasers shall deliver to Affymetrix certificates representing such
Selling Purchaser’s Series B Stock, Series C Stock and Series D Stock, duly endorsed for transfer
or accompanied by duly executed stock powers, free and clear of all Liens. On or before the
Section 4 Closing, each Selling Purchaser shall represent and warrant to and indemnify Affymetrix
that (i) the agreement containing such representations, warranties and indemnities has been duly
authorized, executed and delivered by or on behalf of such Selling Purchaser, (ii) such Selling
Purchaser has full power, right and authority to transfer the shares to be sold by such Selling
Purchaser and to enter into such agreement, (iii) immediately before the Section 4 Closing, such
Selling Purchaser will have good and valid title to the shares to be sold by such Selling Purchaser
free and clear of all Liens and, upon payment for and delivery of the shares, Affymetrix will
acquire all of the rights of the Selling Purchaser in the shares to be sold by the Selling
Purchaser and will acquire its interest in such shares free of any “adverse claim” (as defined in
Section 8-102 of the Uniform Commercial Code) and
(iv) delivery of the of the shares to be sold by such Selling Purchaser to Affymetrix will
pass title to such shares free and clear of any Liens.

11

 

     5. Assignments and Transfers; No Third Party Beneficiaries. This Agreement and the
rights and obligations of the parties hereunder shall inure to the benefit of, and be binding upon,
their respective successors, assigns and legal representatives, but shall not otherwise be for the
benefit of any third party. The rights of the Holders hereunder are only assignable by a Holder to
an assignee that (i) is a subsidiary, affiliate, parent, partner, limited partner, retired partner
or stockholder of a Holder, (ii) is a Permitted Transferee of a Holder pursuant to Section 2.1, or
(iii) after such assignment, holds at least 100,000 shares of Common Stock (subject to appropriate
adjustment for stock splits, stock dividends, combinations and other recapitalizations) including
shares of Common Stock issued upon conversion of Preferred Stock.

     6. Board of Directors.

          (a) The Board of Directors of the Company shall consist of not more than eight members. On
all matters relating to the election of directors of the Company, each Holder agrees to vote all
shares of issued and outstanding shares of Common Stock, including shares of Common Stock issued or
issuable upon conversion of Preferred Stock, held by them (or the holders thereof shall consent
pursuant to an action by written consent of the holders of capital stock of the Company) so as to
elect members of the Company’s Board of Directors as follows:

               (i) the Chief Executive Officer of the Company (the “Management Director”), who shall
initially be Brad Margus;

               (ii) two persons that are designated by the holders of a majority of the Series A Stock (the
“Series A Directors”), who shall initially be Stephen Fodor, Ph.D. and John A. Young;

               (iii) one person elected by the holders of a majority of the Series C Stock, who shall be
designated by Maverick Fund L.D.C., and its affiliates (“Maverick”), for such time as Maverick
holds at least 4,000,000 shares of Preferred Stock (as adjusted for any stock splits, dividends,
recapitalizations or the like) who shall initially be Dr. Howard Furst;

               (iv) three persons that are independent of the holders of the Series A Stock and are
designated by the Nominating Committee (the “Independent Directors”); and

               (v) one person elected by the holders of a majority of the Series D Stock, who shall be
designated by CSK Ventures, Ltd., and its affiliates (“CSK”), for such time as CSK holds at least
4,000,000 shares of Preferred Stock (as adjusted for any stock splits, dividends, recapitalizations
or the like) who shall initially be Makoto Kaneshiro.

     If not already appointed to serve on the Board of Directors within ten (10) Business Days
following the initial issuance of the Series D Stock, the stockholders of the Company shall elect
by written consent the director designated by CSK. Makoto Kaneshiro has agreed to serve as the
initial Director designated by CSK if elected by the stockholders of the Company.

12

 

     Any vote taken to remove any director elected pursuant to this Section 6, or to fill any
vacancy created by the resignation or death of a director elected pursuant to this Section 6, shall
also be subject to the provisions of this Section 6.

     Other than the Series A Directors, no director of the Company shall also be a director or
officer of Affymetrix.

          (b) The Board of Directors of the Company shall maintain a Nominating Committee (the
“Nominating Committee”) consisting of at least two people, one of whom shall be an Independent
Director, to the extent that one or more Independent Directors are then serving on the Board of
Directors; provided, however, that in no event shall the Nominating Committee consist of two Series
A Directors. The Nominating Committee may consider recommendations for candidates to the three
Independent Director positions on the Board of Directors. The Nominating Committee shall designate
the three Independent Directors.

     7. Covenants of the Company.

          (a) Basic Financial Information and Reporting.

               (i) The Company will maintain true books and records of account in which full and correct
entries will be made of all its business transactions pursuant to a system of accounting
established and administered in accordance with generally accepted accounting principles
consistently applied.

               (ii) As soon as practicable after the end of each fiscal year of the Company, and in any event
within ninety (90) days thereafter, the Company will furnish each Major Holder a consolidated
balance sheet of the Company, as at the end of such fiscal year, and a consolidated statement of
income and a consolidated statement of cash flows of the Company, for such year, all prepared in
accordance with generally accepted accounting principles consistently applied and setting forth in
each case in comparative form the figures for the previous fiscal year, all in reasonable detail.
Such financial statements shall be accompanied by a report and opinion thereon by independent
public accountants selected by the Company’s Board of Directors.

               (iii) The Company will furnish each Major Holder, as soon as practicable after the end of the
first, second and third quarterly accounting periods in each fiscal year of the Company, and in any
event within forty-five (45) days thereafter, a consolidated balance sheet of the Company as of the
end of each such quarterly period, and a consolidated statement of income and a consolidated
statement of cash flows of the Company for such period and for the current fiscal year to date,
certified by an executive officer of the Company and prepared in accordance with generally accepted
accounting principles, with the exception that no notes need be attached to such statements and
normal, recurring year-end audit adjustments may not have been made.

          (b) Inspection Rights. Each Major Holder shall have the right to visit and inspect
any of the properties of the Company or any of its subsidiaries, and to discuss the affairs,
finances and accounts of the Company or any of its subsidiaries with its officers, and to review
such information as is reasonably requested all at such reasonable times and as often as may be

13

 

reasonably requested; provided, however, that the Company shall not be obligated under this
Section 7(b) with respect to a competitor of the Company or with respect to information which the
Board of Directors determines in good faith is confidential and should not, therefore, be
disclosed.

          (c) Confidentiality of Records. Each Major Holder confirms that it is aware, and that
its representatives have been advised, that the United States securities laws prohibit any person
who has material non-public information about a public company from purchasing or selling
securities of such company. Each Major Holder confirms that it is aware, and that its
representatives have been advised, that certain information that may be made available to such
Major Holder in connection with such Major Holder’s ownership of Equity Securities may constitute
material non-public information regarding Affymetrix or its securities. Each Major Holder agrees
to use, and to use its best efforts to insure that its authorized representatives use, the same
degree of care as such Major Holder uses to protect its own confidential information to keep
confidential any information furnished to it which the Company identifies as being confidential or
proprietary (so long as such information is not in the public domain, available on a
non-confidential basis from a source other than the Company, independently developed by such Major
Holder without use of such information or required to be disclosed by applicable law), except that
such Major Holder may disclose such proprietary or confidential information to any accountant,
attorney, consultant, partner, subsidiary or parent of such Major Holder for the purpose of
evaluating its investment in the Company as long as such accountant, attorney, consultant, partner,
subsidiary or parent is advised of the confidentiality and other provisions of this Section 7(c).

          (d) Directors’ Liability and Indemnification. The Company’s Certificate and Bylaws
shall provide (a) for elimination of the liability of directors to the maximum extent permitted by
Delaware General Corporation Law and (b) for indemnification of directors for acts on behalf of the
Company to the maximum extent permitted by Delaware General Corporation Law.

          (e) Reservation of Common Stock. The Company shall at all times reserve and keep
available, solely for issuance and delivery upon the conversion of the Preferred Stock, all Common
Stock issuable from time to time upon such conversion.

          (f) Day-to-Day Operations. The management of the Company shall manage the day-to-day
operations of the Company under the general supervision of the board of directors.

          (g) Assignment of Inventions and Confidentiality Agreements. Each employee and
consultant of the Company shall enter into the Company’s standard form of confidentiality,
proprietary information and invention assignment agreement.

          (h) Stock Vesting. Stock and stock equivalents issued after the Closing (as defined
in the Purchase Agreement) to officers and employees will be subject to vesting or a right of
repurchase as follows: 25% to vest at the end of the first year following such issuance, with the
remaining 75% to vest annually and equally over the next three years. The repurchase option will
provide that upon termination of the employment of the officer or employee, with or without cause,
the Company or its assignee (to the extent permissible under applicable securities law
qualification) retains the option to repurchase at cost any unvested shares held by such officer or
employee.

14

 

     8. Legends.

          (a) Each existing or replacement certificate for shares now owned or hereafter acquired by the
Holders shall bear the following legends upon its face:

“THE SALE, PLEDGE, HYPOTHECATION, ASSIGNMENT OR TRANSFER OF THE
SECURITIES REPRESENTED BY THIS CERTIFICATE IS SUBJECT TO THE TERMS AND
CONDITIONS OF A STOCKHOLDERS’ AGREEMENT BY AND BETWEEN THE STOCKHOLDER,
THE CORPORATION AND CERTAIN OTHER HOLDERS OF STOCK OF THE CORPORATION.
COPIES OF SUCH AGREEMENT MAY BE OBTAINED UPON WRITTEN REQUEST TO THE
SECRETARY OF THE CORPORATION.”

“THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER THE
UNITED STATES SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”),
AND MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED EXCEPT (A)
(1) IF REGISTERED UNDER THE SECURITIES ACT OR (2) IN A TRANSACTION EXEMPT
FROM, OR NOT SUBJECT TO, SUCH REGISTRATION (IT BEING UNDERSTOOD THAT NO
REPRESENTATION CAN BE MADE AS TO THE AVAILABILITY OF AN EXEMPTION) AND
(B) IN ACCORDANCE WITH ALL APPLICABLE SECURITIES LAWS OF THE STATES OF
THE UNITED STATES.”

     9. Further Limitations on Disposition.

          (a) Except as otherwise provided in this Agreement, each Management Investor will not sell,
assign, transfer, pledge, hypothecate, or otherwise encumber or dispose of in any way, all or any
part of or any interest in the Equity Securities now or hereafter owned or held by such Management
Investor. Any sale, assignment, transfer, pledge, hypothecation or other encumbrance or
disposition of Equity Securities not made in conformance with this Agreement shall be null and
void, shall not be recorded on the books of the Company and shall not be recognized by the Company.

          (b) Each Holder agrees not to make any disposition of all or any portion of its shares of the
Company’s capital stock or rights to acquire capital stock of the Company unless and until the
transferee has agreed in writing for the benefit of the Company to be bound by this Agreement
provided and to the extent this Agreement is then applicable, and:

               (i) There is then in effect a registration statement under the Securities Act covering such
proposed disposition and such disposition is made in accordance with such registration statement;
or

15

 

               (ii) (x) The person shall have notified the Company of the proposed disposition and shall have
furnished the Company with a detailed statement of the circumstances surrounding the proposed
disposition, and (y) if reasonably requested by the Company, such person shall have furnished the
Company with an opinion of counsel, reasonably satisfactory to the Company that such disposition
will not require registration of such shares under the Securities Act. It is agreed that the
Company will not require opinions of counsel for transactions made pursuant to Rule 144 except in
unusual circumstances.

     Notwithstanding the provisions of subsections (i) and (ii) above, no such registration
statement or opinion of counsel shall be necessary for a transfer by a Holder that is (i) a
partnership to a Permitted Transferee or a partner of such partnership or a retired partner of such
partnership who retires after the date hereof, or to the estate of any such partner or retired
partner or the transfer by gift, will or intestate succession of any partner to his or her spouse
or to the siblings, lineal descendants or ancestors of such partner or his or her spouse, (ii) a
natural person by the laws of community property or otherwise pursuant to a court order upon the
divorce of such person or (iii) that is not an individual, to any person or entity controlling,
controlled by or under common control with such Holder, in each case if the transferee agrees in
writing to be subject to the terms hereof to the same extent as if he or she were an original party
hereunder. The merger, consolidation or acquisition of a Holder or the purchase of all or
substantially all of a Holder’s assets shall not constitute a disposition of shares of the
Company’s capital stock or rights to acquire capital stock of the Company for purposes of this
Section 9.

     10. “Market Stand-Off” Agreement. Each Holder hereby agrees that he, she or it will
not, without the prior written consent of the managing underwriter, during the period commencing on
the date of the final prospectus relating to the Company’s first underwritten public offering of
its Common Stock under the Securities Act and ending on the date specified by the Company and the
managing underwriter (such period not to exceed one hundred eighty (180) days) (i) lend, offer,
pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or
contract to sell, grant any option, right or warrant to purchase, or otherwise transfer or dispose
of, directly or indirectly, any shares of Common Stock or any securities convertible into or
exercisable or exchangeable for Common Stock (whether such shares or any such securities are then
owned by such Holder or are thereafter acquired), or (ii) enter into any swap or other arrangement
that transfers to another, in whole or in part, any of the economic consequences of ownership of
the Common Stock, whether any such transaction described in clause (i) or (ii) above is to be
settled by delivery of Common Stock or such other securities, in cash or otherwise. The foregoing
provisions of this Section 10 shall (i) apply only if all directors and executive officers of the
Company and holders of at least five percent (5%) of the Company’s outstanding voting securities
have executed and delivered an agreement identical either to the provisions set forth in this
Section 10 or to that which the Holders have been requested to sign by the managing underwriter and
(ii) not apply to the sale of any shares to an underwriter pursuant to an underwriting agreement.
The underwriters in connection with a public offering of Equity Securities by the Company are
intended third party beneficiaries of this Section 10 and shall have the right, power and
authority, subject to the foregoing limitations, to enforce the provisions hereof as though they
were a party hereto.

     The standoff period shall be no longer than 180 days, provided, however, that if (1) during
the last 17 days of the standoff period the Company issues a earnings release or material news or a

16

 

material event relating to the Company occurs; or (2) prior to the expiration of the market
standoff period, the Company announces that it will release earnings results during the 16-day
period beginning on the last day of the standoff period, the restrictions imposed by this section
shall continue to apply until the expiration of the 18-day period beginning on the issuance of the
earnings release or the occurrence of the material news or material event.

     11. Notices. Any notice required or permitted by any provision of this Agreement
shall be deemed sufficiently given after three business days if sent by certified U.S. mail, return
receipt requested, or after one business day if sent by nationally recognized overnight carrier and
addressed (i) in the case of the Holders to the address as set forth in the signature pages hereto
or such other address as such party may designate in writing from to time to time; (ii) in the case
of the Company, to its principal office; and (iii) in the case of any permitted transferee of a
party to this Agreement or its transferee, to such transferee at its address as designated in
writing by such transferee to the Company from time to time.

     12. Further Instruments and Actions. The parties agree to execute such further
instruments and to take such further action as may reasonably be necessary to carry out the intent
of this Agreement. The Holders agree to cooperate affirmatively with the Company and the other
Holders to the extent reasonably requested by the Company or the other Holders, to enforce rights
and obligations pursuant hereto.

     13. Term. Sections 2, 3, 4, 5, 6, 7 and 9(a) of this Agreement shall terminate upon
the earlier of: (i) a public offering of the Company’s securities pursuant to a registration
statement filed by the Company with, and declared effective by, the Securities and Exchange
Commission under the Securities Act or (ii) the occurrence of a Deemed Liquidation Event.

     14. Entire Agreement. This Agreement contains the entire understanding of the parties
hereto with respect to the subject matter hereof, supersedes the Prior Agreement and all other
agreements between or among any of the parties with respect to the subject matter hereof and cannot
be altered or otherwise amended except pursuant to an instrument in writing signed by each of the
parties to this Agreement or as provided in Section 15 of this Agreement. Other than provisions
required to be interpreted under Delaware General Corporation Law, this Agreement shall be
interpreted under the laws of the State of California without reference to California conflicts of
law provisions.

     15. Amendments and Waivers. Any term of this Agreement may be amended and the
observance of any term of this Agreement may be waived (either generally or in a particular
instance and either retroactively or prospectively), only with the written consent of: (i) as to
the Company, the Company, (ii) as to the Investors, the written consent of the holders of a
majority of the outstanding Common Stock or the Common Stock issued or issuable upon conversion of
the Series A Stock then outstanding held by all the Investors and (iii) as to the Purchasers, the
written consent of the holders of a majority of the outstanding Common Stock or the Common Stock
issued or issuable upon conversion of the Series B Stock, Series C Stock and Series D Stock, voting
as a single class, then outstanding held by all the Purchasers; provided that each
Purchaser or Investor may waive his, her or its rights hereunder without obtaining the consent of
any other Purchaser or Investor, respectively. Any amendment or waiver effected in accordance with this Section 15 shall be binding upon the
Purchasers, the Investors and the Company and their respective successors and assigns.

17

 

     16. Severability. In case any provision of the Agreement shall be invalid, illegal or
unenforceable, the validity, legality and enforceability of the remaining provisions shall not in
any way be affected or impaired thereby.

     17. Attorney’s Fees. In the event that any dispute among the parties to this
Agreement should result in litigation, the prevailing party in such dispute shall be entitled to
recover from the losing party all fees, costs and expenses of enforcing any right of such
prevailing party under or with respect to this Agreement, including without limitation, such
reasonable fees and expenses of attorneys and accountants, which shall include, without limitation,
all fees, costs and expenses of appeals.

     18. Counterparts. This Agreement may be executed in two or more counterparts, via
facsimile or otherwise, each of which shall be deemed an original, but all of which together shall
constitute one and the same instrument. In addition, to the extent that a holder of Series A Stock,
Series B Stock or Series C Stock who is a party to the Prior Agreement is also purchasing Series D
Stock pursuant to the Series D Purchase Agreement than the execution of this Agreement by such
party shall (i) be deemed to include such party’s consent to amend and restate the Prior Agreement
and (ii) to be bound by this Agreement.

     19. Delays or Omissions. It is agreed that no delay or omission to exercise any
right, power or remedy accruing to any Holder, upon any breach, default or noncompliance of the
Company under this Agreement shall impair any such right, power or remedy, nor shall it be
construed to be a waiver of any such breach, default or noncompliance, or any acquiescence therein,
or of any similar breach, default or noncompliance thereafter occurring. It is further agreed that
any waiver, permit, consent, or approval of any kind or character on any Holder’s part of any
breach, default or noncompliance under this Agreement or any waiver on such Holder’s part of any
provisions or conditions of this Agreement must be in writing and shall be effective only to the
extent specifically set forth in such writing. All remedies, either under this Agreement, by law,
or otherwise afforded to Holders, shall be cumulative and not alternative.

     20. Aggregation of Stock. All shares of Common Stock issued or issuable upon
conversion of the Preferred Stock held or acquired by affiliated entities or persons or persons or
entities under common management or control shall be aggregated together for the purpose of
determining the availability of any rights under this Agreement.

18

 

SCHEDULE A

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Common Stock:
	 	 	 	 	 	 
	David Cox
	 	Common	 	 	1,400,000	 
	Stephen Fodor
	 	Common	 	 	1,400,000	 
	Brad Margus
	 	Common	 	 	1,400,000	 
	 
	 	 	 	 	 	 
	Series A:
	 	 	 	 	 	 
	Affymetrix, Inc.
	 	Series A Stock	 	 	34,450,000	 
	Atlantic Trust Company, FBO Robert G.
Middlebrook
	 	Series A Stock	 	 	287,000	 
	John Hans-Peter
	 	Series A Stock	 	 	50,000	 
	Margrit Kelly
	 	Series A Stock	 	 	150,000	 
	Robert G. Middlebrook Revocable Trust of
2000
	 	Series A Stock	 	 	388,000	 
	Swiss Partners
	 	Series A Stock	 	 	300,000	 
	Triaxis Trust AG
	 	Series A Stock	 	 	50,000	 
	Ursula Vollenweider
	 	Series A Stock	 	 	125,000	 
	 
	 	 	 	 	 	 
	Series B:
	 	 	 	 	 	 
	1995 Diekman Revocable Trust
	 	Series B Stock	 	 	138,889	 
	AJ Trusts Partnership
	 	Series B Stock	 	 	26,400	 
	Alexander Maxwell Djerassi Trust
	 	Series B Stock	 	 	20,000	 
	Alza Corporation Retirement Plan
	 	Series B Stock	 	 	42,000	 
	AWD LLC, Chase Manhattan Bank USA, N.A.
Trustee
	 	Series B Stock	 	 	11,111	 
	Bank Julius Baer & Co Ltd.
	 	Series B Stock	 	 	614,000	 
	Bank Julius Baer & Co. Ltd.
	 	Series B Stock	 	 	138,889	 
	Barry Ramsay Zesiger
	 	Series B Stock	 	 	42,000	 
	BioMedical Sciences Investment Fund PTE
LTD.
	 	Series B Stock	 	 	277,777	 
	Bio-X Technology Limited
	 	Series B Stock	 	 	138,889	 
	BSI SA
	 	Series B Stock	 	 	1,390,667	 
	BruschiVasco
	 	Series B Stock	 	 	1,000	 
	BSI-New BioMedical Frontier (SICAV)
	 	Series B Stock	 	 	275,000	 
	Caramia LLC
	 	Series B Stock	 	 	60,000	 
	Carissimo LLC
	 	Series B Stock	 	 	30,000	 

 

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Carl Djerassi Revocable Trust
	 	Series B Stock	 	 	20,000	 
	Carol A. Christopher
	 	Series B Stock	 	 	5,500	 
	CBG Compagnie Bancaire Geneve
	 	Series B Stock	 	 	193,055	 
	Marc Antoine-Cottet
	 	Series B Stock	 	 	1,389	 
	Chris Meyer
	 	Series B Stock	 	 	5,000	 
	City of Milford Pension & Retirement Fund
	 	Series B Stock	 	 	153,000	 
	CMEA Venture Life Sciences 2000 Civil
Law Partnership
	 	Series B Stock	 	 	78,791	 
	CMEA Venture Life Sciences 2000 Limited
Partnership
	 	Series B Stock	 	 	1,032,320	 
	Dean Witter Foundation
	 	Series B Stock	 	 	28,000	 
	Diane W. Middlebrook
	 	Series B Stock	 	 	20,000	 
	Donna Swanson
	 	Series B Stock	 	 	7,000	 
	Douglas E. Goldman 1997 Charitable Lead
Trust, Chase Manhattan Bank USA, N.A.
Trustee
	 	Series B Stock	 	 	16,667	 
	Douglas E. Goldman 2001 Trust
	 	Series B Stock	 	 	16,667	 
	Douglas E. Goldman, 1997 Long Term
Trust, Chase Manhattan Bank USA,
N.A. Trustee
	 	Series B Stock	 	 	8,333	 
	Douglas E. Goldman, Trustee, Douglas E.
Goldman Revocable Trust
	 	Series B Stock	 	 	16,667	 
	DRW Venture Partners LP
	 	Series B Stock	 	 	361,111	 
	DV Partners, L.P.
	 	Series B Stock	 	 	27,778	 
	Edward B. Rubin
	 	Series B Stock	 	 	2,100	 
	Elisa Zaffaroni
	 	Series B Stock	 	 	70,000	 
	Ernest Mario
	 	Series B Stock	 	 	138,000	 
	Fidurhone S.A.
	 	Series B Stock	 	 	69,445	 
	Francis H. M. Kelly
	 	Series B Stock	 	 	694,444	 
	Genetic Technologies
	 	Series B Stock	 	 	127,000	 
	George Rosenkranz
	 	Series B Stock	 	 	3,000	 
	GF86 LLC
	 	Series B Stock	 	 	44,445	 
	Gonzalo M. Silveira
	 	Series B Stock	 	 	34,725	 
	Guillermo S. Surraco
	 	Series B Stock	 	 	13,889	 
	Henry Weinberg
	 	Series B Stock	 	 	35,000	 
	Hilleman/Albright Family Trust
	 	Series B Stock	 	 	13,888	 
	Isy Goldwasser
	 	Series B Stock	 	 	55,556	 

2

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	J. Leighton Read
	 	Series B Stock	 	 	27,778	 
	J. Robert Coleman
	 	Series B Stock	 	 	27,778	 
	JMJ Trusts Partnership
	 	Series B Stock	 	 	30,555	 
	Joachim Herz
	 	Series B Stock	 	 	83,000	 
	John D. Goldman 1997 Charitable Lead
Trust, Chase Manhattan Bank USA,
N.A. Trustee
	 	Series B Stock	 	 	15,550	 
	John D. Goldman 1997 Long Term Trust,
Chase Manhattan Bank USA,
N.A. Trustee
	 	Series B Stock	 	 	7,789	 
	John D. Goldman 2001 Trust
	 	Series B Stock	 	 	15,550	 
	John D. Goldman and Marcia L. Goldman,
Trustees, The John & Marcia Goldman
Trust
	 	Series B Stock	 	 	23,600	 
	John J. & Catherine Kayola
	 	Series B Stock	 	 	3,000	 
	Joshua Rabinowitz
	 	Series B Stock	 	 	3,000	 
	Kenneth W. Flax
	 	Series B Stock	 	 	10,000	 
	Laura L. Lussich
	 	Series B Stock	 	 	13,889	 
	Liberty Acorn Trust
	 	Series B Stock	 	 	1,249,999	 
	Liechtensteinischee LandesBank, Vaduz
	 	Series B Stock	 	 	46,055	 
	Lombard Odier & Cie
	 	Series B Stock	 	 	3,405,555	 
	Luna Ventures LLC
	 	Series B Stock	 	 	30,000	 
	M. Lorette Viaud
	 	Series B Stock	 	 	7,000	 
	Mary C. Anderson
	 	Series B Stock	 	 	14,000	 
	Matilda Nieri
	 	Series B Stock	 	 	34,725	 
	Maverick Fund II, Ltd.
	 	Series B Stock	 	 	209,738	 
	Maverick Fund LDC
	 	Series B Stock	 	 	2,761,534	 
	Maverick Fund USA, Ltd.
	 	Series B Stock	 	 	1,195,394	 
	Maxine F. Singer
	 	Series B Stock	 	 	13,888	 
	Michael J. Donoghue
	 	Series B Stock	 	 	85,000	 
	MPM BioEquities Master Fund LP
	 	Series B Stock	 	 	1,111,112	 
	NFIB Employee Pension Trust (Booth & Co)
	 	Series B Stock	 	 	67,000	 
	NFIB SERP Assets (Booth & Co)
	 	Series B Stock	 	 	14,000	 
	Paul Joseph Cusenza
	 	Series B Stock	 	 	9,722	 
	Peter B. Coy & Judith H. Coy Trust dtd
09/12/96
	 	Series B Stock	 	 	10,000	 
	Public Employee Retirement System of
Idaho
	 	Series B Stock	 	 	373,000	 

3

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	R.A. Investment Group
	 	Series B Stock	 	 	138,889	 
	Robert D. English
	 	Series B Stock	 	 	138,890	 
	Sano Ventures IX LLC
	 	Series B Stock	 	 	833,334	 
	SB Life Science Ventures I, L.P.
	 	Series B Stock	 	 	972,222	 
	Schweizerhall Holding AG
	 	Series B Stock	 	 	2,150,000	 
	Stryer Revocable Trust
	 	Series B Stock	 	 	55,557	 
	Surinvex International Corporation
	 	Series B Stock	 	 	56,000	 
	Susan R.G. Revocable Trust, Pell Rudman
Trust Company (Atlantic), N.A. Trustee
	 	Series B Stock	 	 	44,444	 
	Terrence V. Fant
	 	Series B Stock	 	 	5,000	 
	The 1989 Leech Living Trust
	 	Series B Stock	 	 	13,889	 
	The Bay City Capital Fund II
Co-Investment Fund, LP
	 	Series B Stock	 	 	8,526	 
	The Bay City Capital Fund II, LP
	 	Series B Stock	 	 	130,363	 
	The Berg Living Trust
	 	Series B Stock	 	 	7,500	 
	The Michael L. Riodan Trust 12/11/95
	 	Series B Stock	 	 	138,888	 
	The Papageno Trust
	 	Series B Stock	 	 	30,000	 
	The RFC Trust
	 	Series B Stock	 	 	15,000	 
	The Steven and Florence Goldby Trust
	 	Series B Stock	 	 	27,800	 
	Triaxis Trust AG-1
	 	Series B Stock	 	 	34,722	 
	Triaxis Trust AG-2
	 	Series B Stock	 	 	104,166	 
	Vulcan Ventures Inc.
	 	Series B Stock	 	 	2,890,213	 
	Wells Family LLC
	 	Series B Stock	 	 	69,000	 
	White Oak Partners
	 	Series B Stock	 	 	55,556	 
	Wolfson Investment Partners LP
	 	Series B Stock	 	 	28,000	 
	Zaffaroni Family Partnership
	 	Series B Stock	 	 	278,000	 
	Zaffaroni Revocable Trust
	 	Series B Stock	 	 	2,432,438	 
	Zderic Family Trust
	 	Series B Stock	 	 	70,000	 
	 
	 	 	 	 	 	 
	Series C:
	 	 	 	 	 	 
	1995 Diekman Revocable Trust
	 	Series C Stock	 	 	16,026	 
	AJ Trusts Partnerships
	 	Series C Stock	 	 	18,500	 
	Alejandro A. Zaffaroni
	 	Series C Stock	 	 	14,018	 
	Alexander Peter Zaffaroni 12/29/88 Trust
	 	Series C Stock	 	 	14,018	 
	Alstertor Private Life Gmbh & Co. KG
	 	Series C Stock	 	 	192,307	 
	Biofrontier Global Investment
Partnership, a Japanese Civil Partnership
	 	Series C Stock	 	 	1,282,052	 

4

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Biomedical Sciences Investment Fund PTE
Ltd.
	 	Series C Stock	 	 	1,282,051	 
	BSI S.A.
	 	Series C Stock	 	 	687,000	 
	Charles Adam Zaffaroni 12/29/88 Trust
	 	Series C Stock	 	 	14,018	 
	Charles F. Hoyng
	 	Series C Stock	 	 	4,808	 
	CMEA Ventures Life Sciences 2000 Civil
Law Partnership
	 	Series C Stock	 	 	49,731	 
	CMEA Ventures Life Sciences 2000 L.P.
	 	Series C Stock	 	 	752,640	 
	CSK Venture Capital Co., Ltd., as
Investment Manager for CSK — 4
Investment Fund
	 	Series C Stock	 	 	192,555	 
	CSK Venture Capital Co., Ltd., as
Investment Manager for Hitachi — CSK
Internet Business Fund
	 	Series C Stock	 	 	449,294	 
	Daniel S Goldman Trust
	 	Series C Stock	 	 	7,700	 
	Donna Swanson
	 	Series C Stock	 	 	5,134	 
	Douglas E. Goldman 1997 Long Term Trust
	 	Series C Stock	 	 	5,800	 
	Douglas E. Goldman 2001 Trust
	 	Series C Stock	 	 	11,500	 
	Douglas E. Goldman Charitable Lead Trust
	 	Series C Stock	 	 	11,500	 
	Douglas E. Goldman Revocable Trust
	 	Series C Stock	 	 	11,500	 
	DRW Venture Partners LP
	 	Series C Stock	 	 	176,521	 
	Eli Lilly and Company
	 	Series C Stock	 	 	641,025	 
	Elisa Zaffaroni
	 	Series C Stock	 	 	14,018	 
	Francis H. M. Kelly
	 	Series C Stock	 	 	192,591	 
	GF 86 LLC
	 	Series C Stock	 	 	23,076	 
	Gonzalo M. Silveira
	 	Series C Stock	 	 	14,018	 
	J. Leighton Read
	 	Series C Stock	 	 	12,530	 
	J. Robert Coleman, Jr.
	 	Series C Stock	 	 	20,000	 
	JMJ Trusts Partnerships
	 	Series C Stock	 	 	21,200	 
	John and Marcia Goldman Trust
	 	Series C Stock	 	 	16,000	 
	John D. Goldman 1997 Charitable Lead
Trust
	 	Series C Stock	 	 	10,800	 
	John D. Goldman 1997 Long Term Trust
	 	Series C Stock	 	 	5,400	 
	John D. Goldman 2001 Revocable Trust
	 	Series C Stock	 	 	10,800	 
	Kenneth W. Flax
	 	Series C Stock	 	 	10,013	 
	Laura L. Lussich de Surraco
	 	Series C Stock	 	 	15,019	 

5

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Leah Zaffaroni
	 	Series C Stock	 	 	14,018	 
	M. Lorette Viaud
	 	Series C Stock	 	 	3,504	 
	Mark V. Roeder
	 	Series C Stock	 	 	1,282	 
	Marta Rachetti
	 	Series C Stock	 	 	14,018	 
	Matilda Nieri
	 	Series C Stock	 	 	14,018	 
	Maverick Fund II, Ltd.
	 	Series C Stock	 	 	899,031	 
	Maverick Fund LDC
	 	Series C Stock	 	 	3,760,572	 
	Maverick Fund USA, Ltd.
	 	Series C Stock	 	 	1,750,653	 
	Michael J. Donoghue
	 	Series C Stock	 	 	128,205	 
	Nipponkoa Trust Link Investment
Enterprise Partnership
	 	Series C Stock	 	 	500,680	 
	Peter B. Coy & Judith H. Coy Trust dtd
9/12/96, Peter B. Coy & Judith H. Coy
TTEES
	 	Series C Stock	 	 	6,410	 
	Private Life Biomed AG
	 	Series C Stock	 	 	961,538	 
	Samuel E. George
	 	Series C Stock	 	 	3,205	 
	SB Life Sciences Ventures I, L. P.
	 	Series C Stock	 	 	961,756	 
	Susan R.G. Revocable Trust
	 	Series C Stock	 	 	23,076	 
	Terrance V. Fant
	 	Series C Stock	 	 	5,000	 
	The 1989 Leech Living Trust
	 	Series C Stock	 	 	14,018	 
	The Leschly Family Trust U/T/D DTD
01/14/01
	 	Series C Stock	 	 	16,025	 
	The Mendelson Family Trust
	 	Series C Stock	 	 	22,756	 
	Unilever Technology Ventures Fund B.V.
	 	Series C Stock	 	 	1,602,548	 
	VP Company Investments 2003, LLC
	 	Series C Stock	 	 	32,051	 
	Vulcan Ventures, Inc.
	 	Series C Stock	 	 	3,176,058	 
	WS Investment Company (2002A)
	 	Series C Stock	 	 	22,435	 
	WS Investment Company (2002D)
	 	Series C Stock	 	 	41,667	 
	Zaffaroni Revocable Trust 1/24/86
	 	Series C Stock	 	 	482,033	 
	 
	 	 	 	 	 	 
	Series D:
	 	 	 	 	 	 
	The 1989 Leech Living Trust
	 	Series D Stock	 	 	39,634	 
	1995 Diekman Revocable Trust
	 	Series D Stock	 	 	16,025	 
	Affymetrix, Inc.
	 	Series D Stock	 	 	1,282,051	 
	Alstertor Private Life Gmbh & Co. KG
	 	Series D Stock	 	 	65,266	 
	AquaRIMCO Biotechnology No. 3 Investment
Partnership
	 	Series D Stock	 	 	960,000	 

6

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Banco Del Gottardo
	 	Series D Stock	 	 	160,256	 
	Biofrontier Global Investment
Partnership, a Japanese Civil
Partnership
	 	Series D Stock	 	 	435,111	 
	Brookside Capital Partners Fund, L.P.
	 	Series D Stock	 	 	3,205,128	 
	BSI S.A.
	 	Series D Stock	 	 	1,148,161	 
	California Emerging Ventures
	 	Series D Stock	 	 	355,224	 
	CMEA Ventures Life Sciences 2000 Civil
Law Partnership
	 	Series D Stock	 	 	912	 
	CMEA Ventures Life Sciences 2000 L.P.
	 	Series D Stock	 	 	15,187	 
	J. Robert Coleman, Jr. & Diane Sanders
Coleman, TTEES Coleman Family Trust U/A
DTD 3/4/04
	 	Series D Stock	 	 	49,516	 
	Compagnie Bancaire Espirito Santa S.A.
	 	Series D Stock	 	 	64,800	 
	Peter B. Coy
	 	Series D Stock	 	 	9,045	 
	CSK Finance Co., Ltd.
	 	Series D Stock	 	 	6,410,257	 
	CSK Venture Capital Co., Ltd., as
Investment Manager for CSK-VC Life
Science Investment Fund
	 	Series D Stock	 	 	1,282,051	 
	Michael J. Donoghue
	 	Series D Stock	 	 	320,513	 
	Robert D. English
	 	Series D Stock	 	 	64,102	 
	Fidelity Mt.
Vernon Street Trust: Fidelity Growth Company Fund
	 	Series D Stock	 	 	12,820,512	 
	Kenneth Flax
	 	Series D Stock	 	 	13,649	 
	Glynn Emerging Opportunity
	 	Series D Stock	 	 	384,615	 
	Glynn Investment Company LLC
	 	Series D Stock	 	 	96,153	 
	Glynn Ventures IV LP
	 	Series D Stock	 	 	256,410	 
	Glynn Ventures V LP
	 	Series D Stock	 	 	448,717	 
	International Medical Technology S.A.
	 	Series D Stock	 	 	320,512	 
	Francis H. M. Kelly
	 	Series D Stock	 	 	370,512	 
	Margrit A. Kelly
	 	Series D Stock	 	 	329,487	 
	Lombard Odier Darier Hentsch & Cie
	 	Series D Stock	 	 	2,123,077	 
	Outer Islands Capital LP
	 	Series D Stock	 	 	192,307	 
	Maverick Fund LDC
	 	Series D Stock	 	 	1,460,665	 
	Maverick Fund USA, Ltd.
	 	Series D Stock	 	 	712,712	 
	Maverick Fund II Ltd.
	 	Series D Stock	 	 	1,081,751	 
	Robert G. Middlebrook Revocable Trust of
2000
	 	Series D Stock	 	 	253,000	 

7

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	Mizuho Securities Co., Ltd.
	 	Series D Stock	 	 	320,000	 
	MPM BioEquities Master Fund
	 	Series D Stock	 	 	242,152	 
	Matilda Nieri
	 	Series D Stock	 	 	61,900	 
	Karl B. Pace
	 	Series D Stock	 	 	1,000,000	 
	Private Life Biomed AG
	 	Series D Stock	 	 	326,333	 
	J. Leighton Read
	 	Series D Stock	 	 	14,317	 
	Richard Rippe & Sandra L. Rippe, As
Joint Tenants with Right of Survivorship
	 	Series D Stock	 	 	160,256	 
	Gregory Rosston
	 	Series D Stock	 	 	18,282	 
	Steven Rosston
	 	Series D Stock	 	 	36,565	 
	Sano Ventures IX LLC
	 	Series D Stock	 	 	961,540	 
	SB Life Science Ventures I, L.P.
	 	Series D Stock	 	 	320,512	 
	Gonzalo Silveira
	 	Series D Stock	 	 	73,308	 
	Surinvex International Corporation
	 	Series D Stock	 	 	141,551	 
	Guillermo Surraco
	 	Series D Stock	 	 	69,603	 
	Laura Lussich de Surraco
	 	Series D Stock	 	 	117,353	 
	Donna Swanson
	 	Series D Stock	 	 	37,811	 
	Unilever Technology Ventures Fund BV
	 	Series D Stock	 	 	320,500	 
	Maria Viaud
	 	Series D Stock	 	 	38,500	 
	WS Investment Company, LLC (2004A)
	 	Series D Stock	 	 	11,218	 
	WS Investment Company, LLC (2004D)
	 	Series D Stock	 	 	20,833	 
	Zaffaroni Family Partnership L.P.
	 	Series D Stock	 	 	1,869,264	 
	Zaffaroni Revocable Trust 1/24/86
	 	Series D Stock	 	 	155,000	 
	Zaffaroni Revocable Trust 1/24/86
	 	Series D Stock	 	 	2,000,000	 
	Zaffaroni Revocable Trust 1/24/86
	 	Series D Stock	 	 	51,767	 
	Alejandro Zaffaroni, Trustee of
Zaffaroni Retirement Trust FBO Gonzalo
M. Silveira, U/A/D 1/1/02
	 	Series D Stock	 	 	4,791	 
	Alejandro Zaffaroni, TTEE Zaffaroni
Retirement Trust FBO M. Lorette Viaud
U/A/D 1/1/02
	 	Series D Stock	 	 	5,704	 
	Alexander Peter Zaffaroni 12/29/88 Trust
	 	Series D Stock	 	 	129,441	 
	Charles Adam Zaffaroni 12/29/88 Trust
	 	Series D Stock	 	 	129,441	 
	Zesiger Capital Group, LLC:
	 	 	 	 	 	 
	Cudd & Co. FBO Asphalt
Green, Inc.
	 	Series D Stock	 	 	37,000	 
	Alexa Zesiger Carver
	 	Series D Stock	 	 	15,000	 
	City of Milford Pension & Retirement Fund
	 	Series D Stock	 	 	184,000	 

8

 

	 	 	 	 	 	 	 
	Holder	 	Class/Series of Stock	 	Number of Shares
	City of Stamford Firemen’s
Pension Fund
	 	Series D Stock	 	 	182,000	 
	Brook Dey Cosby
	 	Series D Stock	 	 	15,000	 
	Francois deMenil
	 	Series D Stock	 	 	37,000	 
	Susan Uris Halpern
	 	Series D Stock	 	 	37,000	 
	Cudd & Co. FBO Helen Hunt
	 	Series D Stock	 	 	37,000	 
	J.P. Morgan Trust Co.
(Bahamas) Ltd. As Trustee
U/A/D 11/30/93
	 	Series D Stock	 	 	145,000	 
	John J. & Catherine H. Kayola
	 	Series D Stock	 	 	4,000	 
	Peter Looram
	 	Series D Stock	 	 	30,000	 
	Meehan Foundation
	 	Series D Stock	 	 	37,000	 
	Domenic J. Mizio
	 	Series D Stock	 	 	91,000	 
	Nicola Zesiger Mullen
	 	Series D Stock	 	 	15,000	 
	Booth & Co. FBO National
Federation of Independent
Business
	 	Series D Stock	 	 	20,000	 
	Psychology Associates
	 	Series D Stock	 	 	15,000	 
	Public Employee Retirement
System of Idaho
	 	Series D Stock	 	 	964,000	 
	Theeuwes Family Trust, Felix
Theeuwes Trustee
	 	Series D Stock	 	 	37,000	 
	Albert L. Zesiger
	 	Series D Stock	 	 	91,000	 
	Barrie Ramsay Zesiger
	 	Series D Stock	 	 	43,000	 
	David Zesiger
	 	Series D Stock	 	 	15,000	 

9

 

     IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first
written above.

	 	 	 	 	 
	 	 	PERLEGEN SCIENCES, INC.
	 
	 	 	 	 
	 

	 	By:	 	/s/ Brad A. Margus
	 

	 	 	 	 
	 	 	Name: Brad A. Margus
	 	 	Title: President and Chief Executive Officer
	 
	 	 	 	 
	 	 	Address:
	 	 	Perlegen Sciences, Inc.
	 	 	2021 Stierlin Court
	 	 	Mountain View, California 94043

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	PFIZER OVERSEAS PHARMACEUTICALS	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Paul Duffy	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Name: Paul Duffy	 	 
	 

	 	 	 	Title: Director	 	 
	 
	 	 	 	 	 	 
	 	 	/s/ Ciaran Keaney	 	 
	 	 	 	 	 
	 	 	Ciaran Keaney	 	 
	 	 	Company Secretary	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	MAVERICK FUND LDC	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Michelle Perrin	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director of Fund Accounting
Maverick Capital Ltd., as
Investment Manager	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	MAVERICK FUND USA, LTD.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Michelle Perrin	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director of Fund Accounting
Maverick Capital Ltd., as
Investment Manager	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	MAVERICK FUND II, LTD.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Michelle Perrin	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director of Fund Accounting
Maverick Capital Ltd., as
Investment Manager	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	BIOFRONTIER GLOBAL INVESTMENT PARTNERSHIP, A Japanese Civil Partnership	 	 
	 
	 	 	 	 	 	 
	 	 	By: BioFrontier Partners Co., Ltd., General Partner	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Yoshihiro Ohtaki	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President	 	 

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	 	 	CMEA VENTURES LIFE SCIENCES 2000, L.P.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Tom Baruch	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     General Partner	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	CMEA VENTURES LIFE SCIENCES 2000, CIVIL LAW PARTNERSHIP	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Tom Baruch	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     General Partner	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	BSI SA.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Fulvio Bernasconi       /s/ Thomas Streule
 

	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Ass. Vice President       Ass. Vice President	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	B. Ripamonti	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Vice President	 	 

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	 	 	ZAFFARONI REVOCABLE TRUST	 	 
	 	 	1/24/86	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TRUSTEE	 	 
	 
	 	 	 	 	 	 

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	 	Title:
	 	TRUSTEE	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Francis H. M. Kelly	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Francis H. M. Kelly	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	J. ROBERT COLEMAN, JR.
& DIANE SANDERS COLEMAN TTEES COLEMAN FAMILY TRUST

U/A DTD 3/4/04	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ J. Robert Coleman /s/ Diane Sanders Coleman	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Trustees	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	     /s/ Laura L. De Surraco	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Laura L. De Surraco	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	     /s/ Matilda Nieri	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Matilda Nieri	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	     /s/ Gonzalo M. Silveira	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Gonzalo M. Silveira	 	 

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	 	 	ALEXANDER PETER ZAFFARONI 12/29/88 TRUST	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Gayle Adams	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	GAYLE ADAMS	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TRUSTEE	 	 

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	 	 	CHARLES ADAM ZAFFARONI
12/29/88

TRUST	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Gayle Adams	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	GAYLE ADAMS	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TRUSTEE	 	 

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	 	 	J. LEIGHTON READ	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ L. Leighton Read	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	 	/s/ Kenneth Flax	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Kenneth Flax	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	 	/s/ Donna Swanson	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Donna Swanson	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	 	/s/ Maria Viaud	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Maria Viaud	 	 

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	 	 	AFFYMETRIX, INC.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Greg Schiffman	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	Greg Schiffman	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Chief Financial Officer	 	 

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	 	 	BANCO DEL GOTTARDO	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ E. Ferrari	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	E. Ferrari	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Associate Director	 	 

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	 	 	 	/s/ David Cox	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	DAVID COX	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	Address:	 	 

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	 	 	THE 1989 LEECH LIVING TRUST	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Ana Leech	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Ana Leech	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Trustee	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	CALIFORNIA EMERGING VENTURES, LLC	 	 
	 
	 	 	 	 	 	 
	 	 	By: GSA Partners, LLC, its Manager	 	 
	 
	 	 	 	 	 	 
	 	 	By: Grove Street Advisors, LLC, its Manager	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Ann St. Germain	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Ann St. Germain	 	 
	 

	 	 	 	MEMBER & CFO	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	CSK FINANCE CO., LTD.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Masahiro Aozono	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Masahiro Aozono	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President & CEO	 	 
	 
	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL
CO., LTD.

as Investment Manager for CSK-VC Life Science Investment Fund	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Shunichi Ishimura	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Shunichi Ishimura	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President & CEO	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL
CO., LTD.

as Investment Manager for Hitachi — CSK Internet Business Fund	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Shunichi Ishimura	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Shunichi Ishimura	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President & CEO	 	 
	 
	 	 	 	 	 	 
	 	 	Address: 5F, Riviera Minami Aoyama Bldg.	 	 
	 	 	3-3-3 Minami-Aoyama, Minato-ku	 	 
	 	 	Tokyo 107-0062 Japan	 	 
	 
	 	 	 	 	 	 
	 

	 	Attn:
	 	Makoto Kaneshiro	 	 
	 
	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL CO., LTD.	 	 
	 	 	as Investment Manager for CSK-4 Investment Fund	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Shunichi Ishimura	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Shunichi Ishimura	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President & CEO	 	 
	 
	 	 	 	 	 	 
	 	 	Address: 5F, Riviera Minami Aoyama Bldg.	 	 
	 	 	3-3-3 Minami-Aoyama, Minato-ku	 	 
	 	 	Tokyo 107-0062 Japan	 	 
	 
	 	 	 	 	 	 
	 

	 	Attn:
	 	Makoto Kaneshiro	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Robert D. English	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Robert D. English	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Stephen P.A. Fodor	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     STEPHEN P.A. FODOR	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	Address:	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	GLYNN EMERGING OPPORTUNITY FUND	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	General Partner	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	GLYNN INVESTMENT COMPANY LLC	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Manager	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	GLYNN VENTURES IV	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	General Partner	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	INTERNATIONAL MEDICAL TECHNOLOGY S.A.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Elizabeth Cheng	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	OUTER ISLANDS CAPITAL LP	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ David H. MacCallum	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	David H. MacCallum	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Managing Member	 	 
	 
	 	 	 	 	 	 
	 	 	Address: 153 East
53rd Street	 	 
	 

	 	 	 	New York, NY 10022	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Dr. Karl Pace	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Dr. Karl Pace	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	AS JOINT TENANTS WITH RIGHT OF SURVIVORSHIP	 	 
	 
	 	 	 	 	 	 
	 	 	/s/ Richard D. Rippe	 	 
	 	 	 	 	 
	 	 	     Richard D. Rippe	 	 
	 
	 	 	 	 	 	 
	 	 	/s/ Sandra L. Rippe	 	 
	 	 	 	 	 
	 	 	     Sandra L. Rippe	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	GREGORY L. ROSSTON	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Gregory L. Rosston	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	STEVEN J. ROSSTON	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Steven J. Rosston	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Guillermo Surraco	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Guillermo Surraco	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	SURINVEX INTERNATIONAL CORPORATION
(FOREIGN CORP.)	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Juan C. Rachetti	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Juan C. Rachetti	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TREASURER	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	ALEJANDRO ZAFFARONI, TRUSTEE OF ZAFFARONI RETIREMENT TRUST FBO GONZALO M.
SILVEIRA, U/A/D 1/1/02	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TRUSTEE	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	ALEJANDRO ZAFFARONI,
TRUSTEE OF ZAFFARONI RETIREMENT TRUST FBO

M. LORETTE VIAUD, U/A/D 1/1/02	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TRUSTEE	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	Address:	 	 
	 

	 	 	 	Alejandro A. Zaffaroni	 	 
	 

	 	 	 	c/o Technofyn Associates L.L.C.	 	 
	 

	 	 	 	4005 Miranda Avenue	 	 
	 

	 	 	 	Suite 180	 	 
	 

	 	 	 	Palo Alto, CA 94304	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	ZAFFARONI FAMILY PARTNERSHIP, L.P.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	GENERAL & LIMITED PARTNER	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

 

 

	 	 	 	 	 	 	 
	 	 	Albert L. Zesiger	 	 
	 	 	Alexa Zesiger Carver	 	 
	 	 	Alza Corporation Retirement Plan	 	 
	 	 	Asphalt Green, Inc.	 	 
	 	 	Barrie Ramsay Zesiger	 	 
	 	 	Brook Dey Cosby	 	 
	 	 	City of Milford Pension & Retirement Fund	 	 
	 	 	City of Stamford Firemen’s Pension Fund	 	 
	 	 	David Zesiger	 	 
	 	 	Dean Witter Foundation	 	 
	 	 	Domenic J. Mizio	 	 
	 	 	Francois DeMenil	 	 
	 	 	Helen Hunt	 	 
	 	 	J.P. Morgan Trust Co.
(Bahamas) Ltd. As Trustee

U/A/D 11/30/93
	 	 
	 	 	John J. & Catherine H. Kayola	 	 
	 	 	Meehan Foundation	 	 
	 	 	National Federation of Independent Business	 	 
	 	 	National
Federation of Independent Business Employee

Pension Trust
	 	 
	 	 	Nicola Zesiger Mullen	 	 
	 	 	Peter Looram	 	 
	 	 	Psychology Associates	 	 
	 	 	Public Employee Retirement System of Idaho	 	 
	 	 	Susan Uris Halpern	 	 
	 	 	Theeuwes Family Trust, Felix Theeuwes Trustee	 	 
	 	 	Wells Family LLC	 	 
	 	 	Wolfson Investment Partners LP	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	ZESIGER CAPITAL GROUP LLC, as

Attorney-in-fact	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Albert L. Zesiger	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Managing Director	 	 

[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00101-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00101-of-00352.parquet"}]]