<PAGE>


                                                                   Exhibit 10.60


          Confidential Materials omitted and filed separately with the
        Securities and Exchange Commission. Asterisks denote omissions.


                                         Groton Laboratories
                                         Pfizer Inc.
                                         Eastern Point Road  MS 8200-30
                                         Groton, CT 06340
                                         Tel 860 441 1991  Fax 860 441 1738
                                         Email mark_dela_porta@groton.pfizer.com
[Pfizer logo]                            ---------------------------------------
                                         Global Research & Development

                                         Mark P. DellaPorta
                                         Senior Director Site Head, Groton
                                         Strategic Alliances



July 16, 2004

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:

The term of the Agreement, as defined in Section 3, will be extended by two (2)
years such that the term of the Agreement will expire on August 31, 2005.

The Research Plan, as defined in Section 1.3, will, for the extended term, be
replaced by Exhibit A appended to this letter.

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/ Mark P. DellaPorta


Mark P. DellaPorta



<PAGE>


AGREED:

GENAISSANCE PHARMACEUTICALS, INC.


By: /s/ Krishnan Nandabalan
    -----------------------

    VP, BUSINESS DEVELOPMENT
    ------------------------

Date: 7/21/2004
      ---------


<PAGE>


EXHIBIT A

                                    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

o        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 HAP(TM)
         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 gone, 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.

<PAGE>


         (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 500 bases 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
         HAP(TM) Marker discovery.

o        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.

o        The candidate genes will be interrogated using Genaissance's SNP
         Scoring and HAP(TM) Building Standard Operating Procedures for
         identification of SNPs and inference of haplotypes.

o        The results of performing the above Standard Operating Procedures for
         each gene will be reported [**] and will [**] in which [**].

o        Genaissance shall complete the forgoing Research Proposal for the
         initial list of [**] genes within approximately [**] of receipt [**].

<PAGE>


COST STRUCTURE

Payment is based [**]. Pfizer will be charged these costs as set forth below
only after Pfizer's discount of $[**] has been used.

COSTS:
[**]                                                  [**]
[**]                                                  [**]


                             APPENDIX 1 TO EXHIBIT A

              PFIZER GENE LIST FOR COMPREHENSIVE VARIANT DETECTION


<TABLE>
<CAPTION>

-------------------- ------------------- ----------------------------- -----------------------
PFIZER GENE ID       HUGO SYMBOL         GENE NAME                     GENBANK/REF SEQ
                                                                       ACCESSION NO
-------------------- ------------------- ----------------------------- -----------------------
<S>                  <C>                 <C>                           <C>
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
[**]                 [**]                [**]                          [**]
-------------------- ------------------- ----------------------------- -----------------------
</TABLE>