exv10w6



 







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

2900 Cork Airport Business Park

Airport Road

Cork, Ireland

Attn: Legal Director




 









 








     with copies to:


Pfizer Inc.

235 East 42nd Street

New York, NY 10017

Attn: General Counsel



Pfizer Global Research and Development

50 Pequot Avenue

New London, CT 06320

Attn: General Counsel




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



[REMAINDER OF THIS PAGE IS INTENTIONALLY LEFT BLANK]





 









 








     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/ 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.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 








	 	 	 	 	 
	 	 	MAVERICK FUND LDC
	 
	 	 	 	 
	 

	 	By:	 	/s/ John McCafferty
	 

	 	 	 	 
	 

	 	Name:	 	 
	 

	 	 	 	 
	 

	 	Title:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Maverick Capital
	 	 	300 Crescent Court, 18th Floor
	 	 	Dallas, TX 75201
	 
	 	 	 	 
	 	 	Attn: John McCafferty, General Counsel






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 	 	MAVERICK FUND USA, LTD.
	 
	 	 	 	 
	 

	 	By:	 	/s/ John McCafferty
	 

	 	 	 	 
	 

	 	Name:	 	 
	 

	 	 	 	 
	 

	 	Title:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address: Maverick Capital
	 	 	300 Crescent Court, 18th Floor
	 	 	Dallas, TX 75201
	 
	 	 	 	 
	 	 	Attn: John McCafferty, General Counsel






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 	 	MAVERICK FUND II, LTD.
	 
	 	 	 	 
	 

	 	By:	 	/s/ John McCafferty
	 

	 	 	 	 
	 

	 	Name:	 	 
	 

	 	 	 	 
	 

	 	Title:	 	 
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address Maverick Capital
	 	 	300 Crescent Court, 18th Floor
	 	 	Dallas, TX 75201
	 
	 	 	 	 
	 	 	Attn: John McCafferty, General Counsel






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 








	 	 	 	 	 
	 	 	VULCAN VENTURES INC.
	 
	 	 	 	 
	 

	 	By:	 	/s/ W. Lance Conn 
	 

	 	 	 	 
	 

	 	Name:	 	W. Lance Conn 
	 

	 	 	 	 
	 

	 	Title:	 	Executive Vice President 
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Michael Kranda
	 	 	505 5th Avenue South, Suite 900
	 	 	Seattle, WA 98104






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 	 	UNILEVER TECHNOLOGY VENTURES
	 	 	FUND B.V.
	 
	 	 	 	 
	 

	 	By:	 	/s/ Loek Helderman
	 	 	 


	 	 	Name: Loek Helderman
	 	 	Title: 
	 
	 	 	 	 
	 

	 	By:	 	/s/ W.E.M. Mulders
	 	 	 


	 	 	Name: W.E.M. Mulders
	 	 	Title: Director
	 
	 	 	 	 
	 	 	Address:
	 	 	Weena 45
	 	 	3013 Rotterdam
The
Netherlands






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 	 	BIOMEDICAL SCIENCES INVESTMENT
	 	 	FUND PTE LTD
	 
	 	 	 	 
	 

	 	By:	 	/s/ Chu Swee Yeok
	 

	 	 	 	 
	 	 	Name: Chu Swee Yeok
	 	 	Title: Director
	 
	 	 	 	 
	 	 	Address:
	 	 	20 Biopolis Way
	 	 	#09-01 Centros
	 	 	Singapore 138668
	 	 	Attention: Sim Sze Kuan






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 	 	SB LIFE SCIENCE
VENTURES I, L.P.
Mr. Kazuhiko Kasai, Director
SB Life Science
Pte. Ltd.
as general partner of
SB Life Science Partners,
L.P.
as general partner of
SB Life Science Ventures I, L.P. 
	 
	 	 	 	 
	 

	 	By:	 	/s/ Kazuhiko Kasai
	 

	 	 	 	 
	 

	 	Name:	 	Kazuhiko Kasai
	 

	 	 	 	 
	 

	 	Title:	 	Director
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	24F, Tokyo Shiodome
Building
	 	 	1-9-1 Higashi
Minato-ku
Tokyo 105-7303, Japan
	 
	 	 	 	 
	 	 	Attention: Mayo Hotta






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 








	 	 	 	 	 
	 	 	CMEA VENTURES LIFE SCIENCES 2000, L.P.
	 
	 	 	 	 
	 

	 	By:	 	/s/ Tom Baruch
	 

	 	 	 	 
	 	 	Name: Tom Baruch
	 	 	Title: General Partner
	 
	 	 	 	 
	 	 	Address:
	 	 	CMEA Ventures Life Sciences 2000 Limited
	 	 	Partnership
	 	 	One Embarcadero Center, Suite 3250
	 	 	San Francisco, CA 94111-3600
	 
	 	 	 	 
	 	 	Attn: Tom Baruch






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 







	 	 	 	 	 	 
	 	 	CMEA VENTURES LIFE SCIENCES 2000,
 CIVIL LAW
PARTNERSHIP
	 
	 	 	 	 
	 

	 	By:	 	/s/ Tom Baruch
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Name: Tom Baruch
	 
	 	 	 	 
	 	 	Title: General Partner
	 
	 	 	 	 
	 	 	Address:
	 	 	CMEA Ventures Life Sciences 2000 Civil Law
	 	 	Partnership
	 	 	One Embarcadero Center, Suite 3250
	 	 	San Francisco, CA 94111-3600
	 
	 	 	 	 
	 	 	Attn: Tom Baruch






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement











 









 








	 	 	 	 	 	 
	 	 	BSI SA.
	 
	 	 	 	 
	 

	 	By:	 	/s/ Thomas Streule
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Thomas Streule
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Assistant Vice President
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	By:	 	/s/ Patricia Solari
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Patricia Solari
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Vice President
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	BSI SA
	 	 	Thomas Streule
	 	 	Assistant Vice President
	 	 	Securities Administration
	 	 	Via Magatti 2
	 	 	6901 Lugano
	 	 	Switzerland






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement







 









 








	 	 	 	 	 	 
	 	 	BSI — NEW BIOMEDICAL FRONTIER (SICAV)
	 
	 	 	 	 
	 

	 	By:	 	/s/ Raoul Paglia
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Raoul Paglia
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Manager
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address: BSI-New BioMedical Frontier
	 	 	(SICAV)
	 	 	Via Peri 23
	 	 	6900 Lugano
	 	 	Switzerland
	 
	 	 	 	 
	 	 	Attn: Francesco Badaracco






Signature
Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 






	 	 	 	 	 	 
	 	 	ZAFFARONI REVOCABLE TRUST

1/24/86
	 
	 	 	 	 
	 

	 	By:	 	/s/ Alejandro Zaffaroni
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Alejandro Zaffaroni
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Trustee
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Gonzalo M. Silveira
	 	 	c/o Technofyn Associates, LLC
	 	 	4005 Miranda Avenue, Suite 180
	 	 	Palo Alto, CA 94304-1218






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL CO., LTD.

as Investment Manager for Hitachi — CSK Internet
Business Fund
	 
	 	 	 	 
	 

	 	By:	 	/s/ Shunichi Ishimura
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Shunichi Ishimura
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	President
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	5th Floor, Reviera Minami Aoyama Bldg.
	 	 	3-3-3 Minai-Aoyama, Minato-ku
	 	 	Tokyo 107-0062
	 	 	Japan
	 
	 	 	 	 
	 	 	Attn: Makoto Kaneshiro






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL CO., LTD.

as Investment Manager CSK-4 Investment Fund
	 
	 	 	 	 
	 

	 	By:	 	/s/ Shunichi Ishimura
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Shunichi Ishimura
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	President
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	5th Floor, Reviera Minami Aoyama Bldg.
	 	 	3-3-3 Minai-Aoyama, Minato-ku
	 	 	Tokyo 107-0062
	 	 	Japan
	 	 	Attn: Makoto Kaneshiro







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	/s/
Laura L. De Surraco
	 	 	LAURA L. DE SURRACO
	 
	 	 	 	 
	 	 	Address:
	 	 	1732 West Selby Lane
	 	 	Redwood City, CA 94061





Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement







 









 






	 	 	 	 	 	 
	 	 	THE 1989 LEECH LIVING TRUST
	 
	 	 	 	 
	 

	 	By:	 	/s/ Ana M. Leech
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Name: Ana M. Leech
	 
	 	 	 	 
	 	 	Title: Trustee
	 
	 	 	 	 
	 	 	Address: The 1989 Leech Living Trust
	 	 	3701 Brandy Rock Way
	 	 	Redwood City, CA 94061
	 
	 	 	 	 
	 	 	Attn: Ana Leech







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	/s/
Matilda Nieri
	 	 	MATILDA NIERI
	 
	 	 	 	 
	 	 	Address: Matilda Nieri
	 	 	c/o Technofyn Associates L.L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	/s/
Alejandro A. Zaffaroni
	 	 	ALEJANDRO A. ZAFFARONI
	 	 	Address:
	 	 	Gonzalo M. Silveira
	 	 	c/o Technofyn Associates, LLC
	 	 	4005 Miranda Avenue, Suite 180
	 	 	Palo Alto, CA 94304-1218







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	ALEXANDER PETER ZAFFARONI 12/29/88 TRUST
	 
	 	 	 	 
	 

	 	By:	 	/s/ Matilda Nieri
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Matilda Nieri
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Trustee
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 
	 	 	Guillermo S. Surraco
	 	 	c/o Technofyn Associates L.L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	CHARLES ADAM ZAFFARONI 12/29/88 TRUST
	 
	 	 	 	 
	 

	 	By:	 	/s/ Matilda Nieri
	 

	 	 	 	 
	 

	 	Name:	 	Matilda Nieri
	 

	 	 	 	 
	 

	 	Title:	 	Trustee
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Guillermo S. Surraco
	 	 	c/o Technofyn Associates L.L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 







	 	 	 	 	 	 
	 	 	/s/
Elisa Zaffaroni
	 	 	ELISA ZAFFARONI
	 	 	Address:
	 	 	Guillermo S. Surraco
	 	 	c/o Technofyn Associates L.L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	/s/
Leah Zaffaroni
	 	 	LEAH ZAFFARONI
	 	 	Address:
	 	 	Guillermo S. Surraco
	 	 	c/o Technofyn Associates L.L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	/s/

Donna L. Swanson
	 	 	DONNA L. SWANSON
	 	 	Address: Donna Swanson
	 	 	c/o Technofyn Associates L.C.
	 	 	4005 Miranda Avenue
	 	 	Suite 180
	 	 	Palo Alto, CA 94304






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	AFFYMETRIX, INC.
	 
	 	 	 	 
	 

	 	By:	 	/s/ Barbara A. Caufield/mcs
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Barbara A. Caufield
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Executive Vice President &
General Counsel
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Affymetrix, Inc.
	 	 	3380 Central Expressway
	 	 	Santa Clara, CA 95051
	 	 	Attn: Greg Schiffman







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	SCHWEIZERHALL HOLDING AG
	 	 	SCHWEIZERHALI MANAGEMENT
	 
	 	 	 	 
	 

	 	By:	 	/s/ L. Von Bidder
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	L. Von Bidder
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Chief Executive Officer
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	By:	 	/s/ D. Kagi
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	D. Kagi
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Investment Analyst
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	c/o Mr. Luzi von Bidder
	 	 	Nuschelerstrasse 30
	 	 	8023 Zurich
	 	 	Switzerland







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	ZAFFARONI FAMILY PARTNERSHIP, LP
	 
	 	 	 	 
	 

	 	By:	 	/s/ Alejandro Zaffaroni
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Alejandro Zaffaroni
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	General and Limited Partner
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	Gonzalo M. Silveira
	 	 	c/o Technofyn Associates, LLC
	 	 	4005 Miranda Avenue, Suite 180
	 	 	Palo Alto, CA 94304-1218







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 






	 	 	 	 	 	 
	 	 	COLUMBIA ACORN TRUST (f.k.a. LIBERTY
ACORN TRUST
	 
	 	 	 	 
	 

	 	By:	 	/s/ Bruce H. Lauer
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	Bruce H. Lauer
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Treasurer
	 

	 	 	 	 
	 
	 	 	 	 
	 	 	Address:
	 	 	227 West Monroe, Suite 3000
	 	 	Chicago, IL 60606
	 
	 	 	 	 
	 	 	Attention: Geoff Wilson







Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 





	 	 	 	 	 	 	 
	 	 	CALIFORNIA EMERGING VENTURES, LLC

By: GSA Partners, LLC, its Manager	 	 
	 

	 	By: Grove Street Advisors, LLC, its Manager	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Ann. St. German	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	Ann St. German	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Member & CFO	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:

Grove Street Advisors

20 William Street, Suite 230

Wellesley, MA 024581

Attention: Ann St. German	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement




 









 








	 	 	 	 	 	 	 
	 	 	CSK FINANCE CO., LTD.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Syoji Wakita	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Syoji Wakita	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	President	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	5th Floor, Reviera Minami Aoyama Bldg.	 	 
	 	 	3-3-3 Minai-Aoyama, Minato-ku	 	 
	 	 	Tokyo 107-0062	 	 
	 	 	Japan	 	 
	 
	 	 	 	 	 	 
	 	 	Attn: Makoto Kaneshiro	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 	 	 
	 	 	CSK VENTURE CAPITAL CO., LTD.,	 	 
	 	 	As Investment Manager for CSK-VC Life Science

Investment Fund	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Shunichi Ishimura	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Shunichi Ishimura	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	President	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	5th Floor, Reviera Minami Aoyama Bldg.	 	 
	 	 	3-3-3 Minai-Aoyama, Minato-ku	 	 
	 	 	Tokyo 107-0062	 	 
	 	 	Japan	 	 
	 
	 	 	 	 	 	 
	 	 	Attn: Makoto Kaneshiro	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 
	 

	 	/s/ Guillermo Surraco
	 	 
	 

	 	 	 	 
	 

	 	GUILLERMO SURRACO
	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








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

	 	By:	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Trustee	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	Gonzalo M. Silveira	 	 
	 	 	c/o Technofyn Associates, LLC	 	 
	 	 	4005 Miranda Avenue, Suite 180	 	 
	 	 	Palo Alto, CA 94304-1218	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 








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

	 	By:	 	/s/ Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Alejandro Zaffaroni	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Trustee	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	Gonzalo M. Silveira	 	 
	 	 	c/o Technofyn Associates, LLC	 	 
	 	 	4005 Miranda Avenue, Suite 180	 	 
	 	 	Palo Alto, CA 94304-1218	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement






 









 








	 	 	 	 	 	 	 
	 	 	ALSTERTOR PRIVATE LIFE GMBH & CO. KG	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s Erich Waller / Dieter Reinhardt 	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Waller / Reinhardt	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Managing Partners	 	 
	 

	 	 	 	 	 	 





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	 	 	MPM BIOEQUITIES MASTER FUND, LP	 	 
	 	 	By: MPM BioEquities GP, LP, its General Partner	 	 
	 
	 	 	 	 	 	 
	 	 	By: MPM BioEquities GP, LLC its General Partner	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Kurt Von Emster	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Kurt Von Emster	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Manager	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	MPM Capital, LP	 	 
	 	 	601 Gateway Blvd. #350	 	 
	 	 	South San Francisco, CA 94080	 	 
	 
	 	 	 	 	 	 
	 	 	Attention: Kurt H. Von Emster	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement





 









 








	 	 	 	 	 	 	 
	 	 	PRIVATE LIFE BIOMED AG	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Marie M. Warburg / /s/ R. Gerlinger	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Warburg / R. Gerlinger	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Managing Directors	 	 
	 

	 	 	 	 	 	 
	 
	 	 	 	 	 	 
	 	 	Address:	 	 
	 	 	Katja Nehrbaß	 	 
	 	 	M.M. Warburrg & CO Schiffahrtstreuhand	 	 
	 	 	Gesellschaft mit beschränkter Haftung	 	 
	 	 	Ferdinandstraße 65-67	 	 
	 	 	D20095 Hamburg, Germany	 	 






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Amendment No. 1 to the Second Amended and Restated Stockholders’ Agreement