Exhibit

No. 10. 1




Confidential Materials

omitted and filed separately with the




Securities and Exchange

Commission.  Asterisks denote omissions.




 




 




	

   


  	

  Worldwide

  Strategic & Operations Management


  
	

   


  	

  Pfizer

  Inc.


  
	

   


  	

  50

  Pequot Avenue  MS 6025/C5133


  
	

   


  	

  New

  London, CT 06320


  
	

   


  	

  Tel

  860 732 3735  Fax 860 732 7028


  
	

   


  	

  Email

  alan_r_proctor@groton.pfizer.com


  
	

   


  	

   


  
	

   


  	

  Global Research & Development


  
	

  Pfizer


  	

   


  
	

   


  	

  Alan R. Proctor, Ph.D.


  
	

   


  	

  Vice President, PGRD


  
	

   


  	

  Head of Strategic Alliances


  





 




May 13, 2002




 




Dr. Krishnan Nandabalan




Vice President, Alliances




Genaissance Pharmaceuticals, Inc.




5 Science Park




New Haven, CT 06511




 




Dear Dr. Nandabalan:




 




Further to our recent discussions regarding the

Agreement between Pfizer Inc. and Genaissance Pharmaceuticals, Inc. dated

August 31, 2001 (“2001 Agreement”); Pfizer Inc. (“Pfizer”) and Genaissance

Pharmaceuticals, Inc. (“Genaissance”) will amend the 2001 Agreement as follows:




 




Section 1.3   “Research Plan” shall mean the written plan

describing the research to be carried out by Genaissance.  The Research Plan is appended to and made a

part of this Agreement as Exhibit A.




 




Section 3   Term: 

The term of this Agreement is one (1) year and six months from August

31, 2001.




 




All other terms and

conditions of the 2001 Agreement shall remain unchanged and in full force.




 




Please have the

appropriate official of Genaissance Pharmaceuticals, Inc. sign both copies of

this Agreement and return one original to Kelly P. Longo at the above address.




 




Sincerely,




/s/Alan R. Proctor




Alan R. Proctor




Vice President




Strategic Alliances




 




 





























 




Agreed:




Genaissance

Pharmaceuticals, Inc.




By: /s/ Krishnan

Nandabalan
       Krishnan Nandabalan
       Vice President, Alliances




Date: 5/16/02




 





























 




PROPOSAL




Pfizer/Genaissance:  A Proposal for Comprehensive SNP

Identification in Candidate




Genes




[**]




 




 




Research

Goal:  To define comprehensive genetic variation and

haplotype information in key candidate genes of research interest to Pfizer

Global Research and Development (Pfizer, please define this acronym).




 




 




Research

Proposal




 




•                  Pfizer will provide Genaissance with an initial list of approximately

[**] candidate genes (see Appendix 1 for details) for which Genaissance will

obtain a comprehensive assessment of genetic variation.




                        Genaissance will provide genomic sequence

for the candidate genes listed in Appendix 1. 

This sequence will be generated using Genaissance’s Standard Operating

Procedure for discovering HAPTM

Markers for a gene.  This procedure

consists of sequencing, from the Index Repository, ninety-three (93) individual

samples of human genomic DNA and one sample of chimpanzee genomic DNA.  The genomic regions of each gene, which are

targeted for sequencing, are as follows.




 




(i)            “Exons” shall mean the genomic DNA

segments of a gene whose sequence information is translated into the protein

product of that gene.  The goal is to

obtain sequence information for all Exons of a gene.




 




(ii)           “Exon/Intron Junction” shall mean the

junctions between the Exons and the Introns in genomic DNA.  Beginning with the initiation codon at one

end of a gene and ending with the termination codon at the other end of a gene,

the goal is to obtain sequence information for each Exon/Intron Junction within

this genomic region.




 




(iii)          “Introns” shall mean the genomic DNA

segments of a gene, which are located between Exons.  Beginning with the initiation codon at one end of a gene and

ending with the termination codon at the other end of a gene, the goal is to

obtain a minimum of ten (10) to twenty (20) bases and a maximum of one hundred

(100) bases of sequence information from the Exon/Intron Junction into the

Intron for every Intron within this genomic region.




 




(iv)          “Promoter” shall mean the region that

is immediately upstream of the genomic segment that is found at the five-prime

end of a Messenger RNA molecule. 

(“Messenger RNA” shall mean a ribonucleic acid sequence from which the

protein product of a gene is translated). 

The goal is to obtain sequence information for up to one thousand (1000)

bases of the Promoter with the desire to obtain an additional 1KB where

possible.




 





























 




(v)           “Three-Prime Untranslated Region”

shall mean the genomic region immediately downstream from the termination codon

of a gene.  The goal is to obtain

sequence information for at least one hundred (100) bases of the Three-Prime

Untranslated Region downstream of the termination codon.  Optimally, we will have coverage to 500bases

of the 3’ UTR.




 




                Specific genomic sequence information is required to

meet the goals outlined in (i) through (v) above.  If genomic sequence information is available for a majority of

these regions, even if the available genomic sequence information is not

sufficient to meet all of the goals in (i) through (v) above, a gene will still

be queued for HAPTM Marker

discovery.




 




•                  A gene shall be considered completely sequenced if sequence information

is obtained for: (i) at least [**] of the [**]; (ii) the [**] containing the

[**]; and (iii) [**].  A specific region

targeted for sequencing within a gene shall be considered completely sequenced

if sequence information is obtained for at [**].  However, the presence of runs of guanine and cytosine, secondary

structure or errors in publicly available sequence information may prevent the

generation of sufficient sequence information for that gene to be considered

completely sequenced as defined above.




•                  The candidate genes will be interrogated using Genaissance’s SNP

Scoring and HAPTM Building

Standard Operating Procedures for identification of SNPs and inference of

haplotypes.




•                  The results of performing the above Standard Operating Procedures for

each gene will be reported [**] and will [**] in which [**]Genaissance shall

complete the forgoing Research Proposal for the initial list of [**] genes

within approximately [**] of receipt [**].




Cost structure




Payment is based [**], as set forth below.  A minimum of [**] genes will be analyzed within one calendar year

from the commencement of the collaboration.




 




Costs:




[**]




 





























 




Appendix 1 to Exhibit A




Pfizer Gene List for

comprehensive variant detection




 




 




	

  Pfizer Gene ID


  	

   


  	

  HUGO Symbol


  	

   


  	

  Gene Name


  	

   


  	

  Genbank/Ref Seq Accession  No


  	

   


  
	

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