Second Amended and Restated Stockholders’ Agreement among Perlegen Sciences, Inc. and Investors (February 1, 2005)

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.

     “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.

     “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.

     “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.

               (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.

               (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

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

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

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.