exv10w5



 







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.



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     “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.



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     “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.



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     “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.



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               (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.



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               (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



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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



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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

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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



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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

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	 	 	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	 	 






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AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT]




 









 






	 	 	 	 	 	 	 
	 	 	MAVERICK FUND II, LTD.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Michelle Perrin	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

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






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	 	 	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	 	 






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	 	 	CMEA VENTURES LIFE SCIENCES 2000, CIVIL LAW PARTNERSHIP	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Tom Baruch	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     General Partner	 	 






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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	 	 






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	 	 	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	 	 






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	 	 	 	     /s/ Laura L. De Surraco	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Laura L. De Surraco	 	 




[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	 	     /s/ Matilda Nieri	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Matilda Nieri	 	 





[SIGNATURE PAGE TO PERLEGEN SCIENCES, INC. SECOND

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	 	 	 	     /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:	 	 	 	 
	 

	 	 	 	 	 	 





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	 	 	 	/s/ Kenneth Flax	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Kenneth Flax	 	 




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	 	 	 	/s/ Donna Swanson	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Donna Swanson	 	 





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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	 	 






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	 	 	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	 	 






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	 	 	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	 	 






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	 	 	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	 	 






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	 	 	 	/s/ Robert D. English	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Robert D. English	 	 




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	 	 	 	/s/ Stephen P.A. Fodor	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     STEPHEN P.A. FODOR	 	 
	 
	 	 	 	 	 	 
	 

	 	 	 	Address:	 	 





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	 	 	GLYNN EMERGING OPPORTUNITY FUND	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	General Partner	 	 






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	 	 	GLYNN INVESTMENT COMPANY LLC	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Manager	 	 






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	 	 	GLYNN VENTURES IV	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ John W. Glynn	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	General Partner	 	 






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	 	 	INTERNATIONAL MEDICAL TECHNOLOGY S.A.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Elizabeth Cheng	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director	 	 






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	 	 	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	 	 







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	 	 	 	/s/ Dr. Karl Pace	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Dr. Karl Pace	 	 





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







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	 	 	GREGORY L. ROSSTON	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Gregory L. Rosston	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 





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	 	 	STEVEN J. ROSSTON	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Steven J. Rosston	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 




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	 	 	 	/s/ Guillermo Surraco	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	Guillermo Surraco	 	 





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	 	 	SURINVEX INTERNATIONAL CORPORATION
(FOREIGN CORP.)	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Juan C. Rachetti	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	     Juan C. Rachetti	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	TREASURER	 	 






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	 	 	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	 	 





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	 	 	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	 	 






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	 	 	 	/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	 	 





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	 	 	ZAFFARONI FAMILY PARTNERSHIP, L.P.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 

	 	 	 	ALEJANDRO ZAFFARONI	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	GENERAL & LIMITED PARTNER	 	 






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	 	 	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	 	 







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