exv4w3



 







Exhibit 4.3



PERLEGEN SCIENCES, INC.



AMENDMENT NO. 1 TO



SECOND AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT




     THIS AMENDMENT NO. 1 to the Second Amended and Restated Registration Rights Agreement is made
as of December 22, 2005 (the “Effective Date”), between Perlegen Sciences, Inc. a Delaware
corporation (the “Company”), and the holders of the Company’s Preferred Stock (each an “Prior
Purchaser” and collectively the “Prior Purchasers”).



     WHEREAS, the Company is entering into a 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 provides 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 and the Prior Purchasers are parties to that certain Second Amended and
Restated Registration Rights Agreement, dated as of February 1, 2005 (the “Rights Agreement”);



     WHEREAS, the Company and the Prior Purchasers desire to amend the Rights Agreement pursuant to
Section 9(j) of the Rights Agreement to add the Purchaser as a party, to provide the Purchaser with
the rights and obligations thereunder and to include the Series D-1 Preferred Stock (and the Common
Stock resulting from conversion thereof) under the definition of Registrable Securities.



     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 and the Prior Purchasers holding a majority of the Registrable Securities (as
defined in the Rights Agreement) hereby amend the Rights Agreement to include Pfizer Overseas
Pharmaceuticals as a “Holder” thereunder and to include the Series D-1 Preferred Stock and the
Common Stock issuable upon conversion of the Series D-1 Preferred Stock as “Registrable Securities”
thereunder.



     2. The definition of “Holder” set forth in Section 1(e) of the Rights Agreement shall be
amended in its entirety as set forth below:




          “‘Holder’ shall mean any person owning Registrable Securities and each of its
respective successors and assigns who acquire Registrable Securities, in accordance with the
terms of this Agreement.”



     3. The definition of “Registrable Securities” set forth in Section 1(g) of the Rights
Agreement shall be amended in its entirety as set forth below:



 









 






“‘Registrable Securities’ shall mean the Common Stock issued or issuable upon
conversion of the Series A Stock, the Series B Stock, the Series C Stock, the Series
D Stock, or Series D-1 Stock; and any securities issued successively in exchange for
or in respect of any of the foregoing, whether pursuant to a merger or consolidation,
as a result of any successive stock split or reclassification of, or stock dividend
on, any of the foregoing or otherwise; provided, however, that such shares of Common
Stock or securities shall cease to be Registrable Securities when (i) a registration
statement registering such shares of Common Stock or securities, as the case may be,
under the Securities Act has been declared effective and such shares of Common Stock
or securities, as the case may be, have been sold or otherwise transferred by the
Holder thereof pursuant to such effective registration statement, (ii) such shares of
Common Stock or securities, as the case may be, are sold pursuant to Rule 144 (or any
successor provision) promulgated under the Securities Act under circumstances in
which any legend borne by such shares of Common Stock or securities relating to
restrictions on transferability thereof, under the Securities Act or otherwise, is
removed by the Company, or (iii) such shares of Common Stock or securities, as the
case may be, are eligible for sale pursuant to subparagraph (k) of Rule 144 under the
Securities Act.”



     4. All notices and other communications under the Rights 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 9(e) of the Rights 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




     5. The Rights Agreement as modified herein shall remain in full force and effect as so
modified.



[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]




 









 








     The Parties have executed this Amendment No. 1 to the Second Amended and Restated Registration
Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights Agreement






 









 









	 	 	 	 	 	 	 
	 	 	UNILEVER TECHNOLOGY VENTURES FUND B.V.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Loek Helderman	 	 
	 

	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	Loek Helderman
 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	 
 

	 	 
	 
	 	 	 	 	 	 
	 

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

	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:
	 	W. G. M. Mulders
 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Director
 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Address:	 	 
	 	 	455 Weena	 	 
	 	 	3013 AL
Rotterdam
The Netherlands	 	 






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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 Registration Rights 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 Ventures I, L.P.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Kazuhiko Kasai	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Name:	 	Kazuhiko Kasai	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	Director	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Address:	 	 
	 	 	24F, Tokyo Shiodone
Building	 	 
	 	 	1-9-1 Higashi-shimbashi
Minato-ku
Tokyo, 105-7303 Japan	 	 
	 
	 	 	 	 	 	 
	 

	 	Attention:  Mayo
Hotta
	 	 






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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 Registration Rights 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 Registration Rights Agreement







 









 








	 	 	 	 	 	 	 
	 	 	BSI SA.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Thomas Streule	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	Thomas Streule	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	Assistant Vice President	 	 
	 

	 	 	 	 

	 	 
	 

	 	By:	 	/s/ Patrizia Solari	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	Patrizia 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights 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 Registration Rights Agreement




 









 





	 	 	 	 	 
	 	 	SCHWEIZERHALL HOLDING AG

SCHWEIZERHALI MANAGEMENT
	 
	 	 	 	 
	 

	 	By:	 	/s/ L. Von Bidder
	 

	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	L. Von Bidder
	 

	 	 	 
	 
	 	 	 	 
	 

	 	Title:	 	Chief Executive Officer
	 

	 	 	 
	 
	 	 	 	 
	 

	 	By:	 	/s/ D. Kazi
	 

	 	 	 
	 
	 	 	 	 
	 

	 	Name:	 	D. Kazi
	 

	 	 	 
	 
	 	 	 	 
	 

	 	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 Registration Rights 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 Registration Rights 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 Registration Rights 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






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights Agreement




 









 





	 	 	 	 	 
	 
	 	/s/ Guillermo Surraco
	 	 	 
	 	 	GUILLERMO SURRACO





Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights 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





Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights Agreement




 









 





	 	 	 	 	 
	 
	 	 	 	 
	 	 	ALSTERTOR PRIVATE LIFE GMBH & CO.
	 	 	KG
	 
	 	 	 	 
	 

	 	By:	 	/s/ Erich Waller / Dieter Reinhardt 
	 

	 	 	 	 
	 

	 	Name: Waller/Reinhardt


	 

	 	 	 	 
	 

	 	Title: Managing Partners


	 

	 	 	 	 





Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights Agreement




 









 





	 	 	 	 	 
	 
	 	 	 	 
	 	 	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






Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights Agreement




 









 





	 	 	 	 	 
	 
	 	 	 	 
	 	 	PRIVATE LIFE BIOMED AG
	 
	 	 	 	 
	 

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

	 	 	 	 
	 

	 	Name: Marie M. Warburg/R. Gerlinger


	 

	 	 	 	 
	 

	 	Title: Managing Director


	 

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





Signature Page to Perlegen Sciences, Inc.

Amendment No. 1 to the Second Amended and Restated Registration Rights Agreement