PERLEGEN SCIENCES, INC. AMENDMENT NO. 1 TO SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

Exhibit 10.6

PERLEGEN SCIENCES, INC.

AMENDMENT NO. 1 TO

SECOND AMENDED AND RESTATED STOCKHOLDERS’ AGREEMENT

THIS AMENDMENT NO. 1 to the Second Amended and Restated Stockholders’ Agreement is made as of December 22, 2005 (the “Effective Date”), between Perlegen 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, and Series D Preferred Stock (each an “Prior Purchaser” and collectively the “Prior Purchasers”).

WHEREAS, the Company is entering into the Series D-1 Preferred Stock Purchase Agreement dated as of even date herewith (the “Series D-1 Purchase Agreement”), by and among the Company and Pfizer Overseas Pharmaceuticals (the “Purchaser”), that provided for, among other things, the sale by the Company and the purchase by the Purchaser of the Series D-1 Preferred Stock.

WHEREAS, the obligations in the Series D-1 Purchase Agreement are conditioned upon the execution and delivery of this Amendment;

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 (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 add the Purchaser as a party and to provide the Purchaser with the rights and obligations thereunder.

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 (as defined in the Stockholders’ Agreement), the Prior Purchasers holding a majority of the Series B Preferred Stock, Series C Preferred Stock and Series D Preferred Stock (as defined in the Stockholders’ Agreement) hereby amend the Stockholders’ Agreement to include Pfizer Overseas Pharmaceuticals as a “Holder” thereunder and to include the Series D-1 Preferred Stock as “Preferred Stock” thereunder.

2. The definition of “Agreed Rate,” “Agreed Value,” “Certificate,” “Holders,” and “Preferred Stock” set forth in Section 1 of the Stockholders’ Agreement shall be amended in their entirety as set forth below:

“‘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 or Series D-1 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, the Original Series D Issue Price, or the Original Series D-1 Price as applicable, and (ii) the product of (a) the Original Series B Issue Price, the Original Series C Issue Price, the Original Series D Issue Price or the Original Series D-1 Price, as applicable, multiplied by (b) the Agreed Rate.”

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

“‘Holders’ shall mean the Purchasers, the Investors and Pfizer Overseas Pharmaceuticals 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.”

“‘Preferred Stock’ shall have the meaning ascribed to such term in the recitals to this Agreement and shall include the Series D-1 Preferred Stock.”

3. Two additional definitions for “Original Series D-1 Issue Price” and “Series D-1 Stock” are hereby added to Section 1:

“‘Original Series D-1 Issue Price’ shall have the meaning ascribed to such term in the Certificate.”

“‘Series D-1 Stock’ shall mean the Company’s Series D-1 Preferred Stock, par value $0.0001.”

4. Sections 2.4(c)(i) and 2.4(c)(viii) shall be amended in their entirety as set forth below:

“(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.”

“(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.”

5. Sections 4(b) and 4(c) shall be amended in their entirety as set forth below:

“4(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, Series D Stock and Series D-1 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, Series D Stock and Series D-1 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, Series D Stock and Series D-1 Stock owned by such Selling Purchaser to Affymetrix at a price per share equal to the Agreed Value.”

“4(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, Series D Stock and Series D-1 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.”

6. Section 15 shall be amended in its entirety as set forth below:

“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, Series D Stock and Series D-1 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.”

7. All notices and other communications under the Stockholder’s Agreement shall be made to Pfizer Overseas Pharmaceuticals at the address specified below and thereafter at such other address, notice of which is given in accordance with Section 11 of the Stockholders’ Agreement:

Pfizer Overseas Pharmaceuticals
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Attn: Legal Director

with copies to:

Pfizer Inc.
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Attn: General Counsel

Pfizer Global Research and Development
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Attn: General Counsel

8. 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. 1 to the Second Amended and Restated Stockholders’ Agreement as of the Effective Date.


		PERLEGEN SCIENCES, INC.

		By:		/s/ ▇▇▇▇ ▇. ▇▇▇▇▇▇

		Name: ▇▇▇▇ ▇. ▇▇▇▇▇▇
		Title: President and Chief Executive Officer

		Address:
		Perlegen Sciences, Inc.
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