**ExhibitNo. 10. 1**

Confidential Materialsomitted and filed separately with the

Securities and ExchangeCommission.  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 theAgreement between Pfizer Inc. and Genaissance Pharmaceuticals, Inc. datedAugust 31, 2001 (“2001 Agreement”); Pfizer Inc. (“Pfizer”) and GenaissancePharmaceuticals, Inc. (“Genaissance”) will amend the 2001 Agreement as follows:

 

Section 1.3   “Research Plan” shall mean the written plandescribing the research to be carried out by Genaissance.  The Research Plan is appended to and made apart of this Agreement as Exhibit A.

 

Section 3   Term: The term of this Agreement is one (1) year and six months from August31, 2001.

 

All other terms andconditions of the 2001 Agreement shall remain unchanged and in full force.

 

Please have theappropriate official of Genaissance Pharmaceuticals, Inc. sign both copies ofthis 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

 

 

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Agreed:

GenaissancePharmaceuticals, Inc.

By: /s/ KrishnanNandabalan       Krishnan Nandabalan       Vice President, Alliances

Date: 5/16/02

 

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**PROPOSAL**

**Pfizer/Genaissance:  A Proposal for Comprehensive SNPIdentification in Candidate**

**Genes**

[**]

 

 

**ResearchGoal: **To define comprehensive genetic variation andhaplotype information in key candidate genes of research interest to PfizerGlobal Research and Development (Pfizer, please define this acronym).

 

 

**ResearchProposal**

 

•                  Pfizer will provide Genaissance with an initial list of approximately[**] candidate genes (see Appendix 1 for details) for which Genaissance willobtain a comprehensive assessment of genetic variation.

                        Genaissance will provide genomic sequencefor the candidate genes listed in Appendix 1. This sequence will be generated using Genaissance’s Standard OperatingProcedure for discovering *HAPTM*Markers for a gene.  This procedureconsists of sequencing, from the Index Repository, ninety-three (93) individualsamples of human genomic DNA and one sample of chimpanzee genomic DNA.  The genomic regions of each gene, which aretargeted for sequencing, are as follows.

 

(i)            “Exons” shall mean the genomic DNAsegments of a gene whose sequence information is translated into the proteinproduct of that gene.  The goal is toobtain sequence information for all Exons of a gene.

 

(ii)           “Exon/Intron Junction” shall mean thejunctions between the Exons and the Introns in genomic DNA.  Beginning with the initiation codon at oneend 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 withinthis genomic region.

 

(iii)          “Introns” shall mean the genomic DNAsegments of a gene, which are located between Exons.  Beginning with the initiation codon at one end of a gene andending with the termination codon at the other end of a gene, the goal is toobtain 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 theIntron for every Intron within this genomic region.

 

(iv)          “Promoter” shall mean the region thatis immediately upstream of the genomic segment that is found at the five-primeend of a Messenger RNA molecule. (“Messenger RNA” shall mean a ribonucleic acid sequence from which theprotein 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 wherepossible.

 

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(v)           “Three-Prime Untranslated Region”shall mean the genomic region immediately downstream from the termination codonof a gene.  The goal is to obtainsequence information for at least one hundred (100) bases of the Three-PrimeUntranslated Region downstream of the termination codon.  Optimally, we will have coverage to 500basesof the 3’ UTR.

 

                Specific genomic sequence information is required tomeet the goals outlined in (i) through (v) above.  If genomic sequence information is available for a majority ofthese regions, even if the available genomic sequence information is notsufficient to meet all of the goals in (i) through (v) above, a gene will stillbe queued for *HAPTM* Markerdiscovery.

 

•                  A gene shall be considered completely sequenced if sequence informationis obtained for: (i) at least [**] of the [**]; (ii) the [**] containing the[**]; and (iii) [**].  A specific regiontargeted for sequencing within a gene shall be considered completely sequencedif sequence information is obtained for at [**].  However, the presence of runs of guanine and cytosine, secondarystructure or errors in publicly available sequence information may prevent thegeneration of sufficient sequence information for that gene to be consideredcompletely sequenced as defined above.

•                  The candidate genes will be interrogated using Genaissance’s SNPScoring and *HAPTM* BuildingStandard Operating Procedures for identification of SNPs and inference ofhaplotypes.

•                  The results of performing the above Standard Operating Procedures foreach gene will be reported [**] and will [**] in which [**]Genaissance shallcomplete the forgoing Research Proposal for the initial list of [**] geneswithin approximately [**] of receipt [**].

**Cost structure**

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

 

Costs:

[**]

 

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**Appendix 1 to Exhibit A**

**Pfizer Gene List forcomprehensive variant detection**

 

 
| **Pfizer Gene ID** |   | **HUGO Symbol** |   | **Gene Name** |   | **Genbank/Ref Seq Accession  No** |   |
|--------------------|--------|-----------------|--------|---------------|--------|----------------------------------------|--------|
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |
| [**]               |   | [**]            |   | [**]          |   | [**]                                   |   |

 

 

 

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