PERLEGEN SCIENCES, INC. AMENDMENT NO. 2 TO SECOND AMENDED AND RESTATED STOCKHOLDERS? AGREEMENT

Exhibit 10.7

PERLEGEN SCIENCES, INC.

AMENDMENT NO. 2 TO

SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

     THIS AMENDMENT NO. 2 to the Second Amended and Restated Stockholders’ Agreement is made as of March 1, 2006 (the “ Effective Date ”), by and among P erlegen Sciences, Inc. a Delaware corporation (the “ Company ”), the holders of the Company’s Common Stock and Series A Preferred Stock (each an “Investor” and collectively the “ Investors ”), and the holders of the Company’s Series B Preferred Stock, Series C Preferred Stock, Series D Preferred Stock and Series D-1 Preferred Stock (each a “ Prior Purchaser ” and collectively the “ Prior Purchasers ”).

      WHEREAS, the Company is increasing the number of shares in its 2002 Equity Incentive Plan.

      WHEREAS, the Company, the Investors and the Prior Purchasers are parties to that certain Second Amended and Restated Stockholders’ Agreement, dated as of February 1, 2005 and Amendment No. 1 to the Stockholders’ Agreement dated December 22, 2005 (the “ Stockholders’ Agreement ”);

      WHEREAS, the parties to the Stockholders’ Agreement desire to amend the Stockholders’ Agreement pursuant to Section 15 of the Stockholders’ Agreement to revise Section 2.4(c) to increase the number of shares that the Company may issue without being subject to preemptive rights.

      NOW, THEREFORE , in consideration of the mutual covenants contained herein and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

     1. The Company, the Investors holding a majority of the Common Stock and Series A Preferred Stock (each as defined in the Stockholders’ Agreement), the Prior Purchasers holding a majority of the Series B Preferred Stock, Series C Preferred Stock, Series D Preferred Stock and Series D-1 Preferred Stock (each as defined in the Stockholders’ Agreement) hereby amend the Stockholders’ Agreement to increase the number of shares the Company may issue without being subject to preemptive rights.

     2. Section 2.4(c) of the Stockholders’ Agreement shall be amended in its entirety as set forth below:

     “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, Series D Stock or Series D-1 Stock, (ii) the issuance of up to 41,443,702 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-1 Stock.”

     3. The Stockholders’ Agreement as modified herein shall remain in full force and effect as so modified.

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     The Parties have executed this Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement as of the Effective Date.

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement

Signature Page to Perlegen Sciences, Inc.
Amendment No. 2 to the Second Amended and Restated Stockholders’ Agreement