NEW YORK, Oct 6 – Affymetrix (Nasdaq: AFFX), SmithKline Beecham (NYSE: SBH), the Merck Genome Research Institute, the US National Institutes of Health, and the Wellcome Trust said Friday they have formed a consortium to speed up the DNA sequencing of the mouse genome.
The Mouse Sequencing Consortium will provide $58 million over the next six months to decipher the mouse genetic code, thought to have approximately 3 billion base pairs, roughly the same number as the human. The data generated will be freely available for the unrestricted use of biomedical researchers worldwide.
Affymetrix will contribute $3.5 million; SmithKline Beecham, $6.5 million; MGRI, $6.5 million; the Wellcome Trust, $7.75 million; and the NIH, $34 million.
The funds will support mouse DNA sequencing at the Whitehead Institute for Biomedical Research in Cambridge, Mass., Washington University School of Medicine in St. Louis, and the Sanger Centre in the UK.
The effort will use a hybrid genome sequencing strategy, combining the BAC-based method used by the Human Genome Project and the whole-genome shotgun method used by Celera Genomics (NYSE: CRA).
The Mouse Sequencing Consortium represents an emerging model—like the efforts of the SNP Consortium and the Merck-funded EST database project—in which public and private sector entities join forces to produce publicly available data sets that are crucial for basic biomedical research.
Affymetrix is interested in the mouse genome because “in the future, Affymetrix plans to download this information onto GeneChip probe arrays,” Affymetrix CEO and chairman Stephen Fodor said in a statement.
The consortium is poised to compete against Celera Genomics, which began sequencing the mouse in April. Celera is counting on its proprietary mouse sequence to add value to its database subscriptions.
Celera is sequencing 129/SvJ strain of mouse; the consortium will use a strain of mouse known as C57BL6/J, commonly called “Black 6.”
A Celera spokesperson was not immediately available to comment on the announcement.
The desire to accelerate mouse genome sequencing builds on the completion in June of a working draft of the human DNA sequence. With the working draft of the human genome sequence in hand, scientists in both industry and academia now seek to interpret its meaning.
The mouse genome sequence will provide a powerful tool to find human genes. Sequences that are highly conserved in both genomes are likely to be protein-coding regions.
In addition, mouse genome sequence will increase the value of the mouse as a model to study human disease and to develop and test new treatments in ways that cannot easily be done with humans.
The Mouse Sequencing Consortium's effort will expand and accelerate the National Human Genome Research Institute’s mouse sequencing program, begun in September 1999, which has already generated most of the data for a “fingerprint” map of the mouse genome. The NHGRI effort also has begun to sequence the mouse genome in its entirety.
By February 2001, the consortium plans to have a 2.5X to 3X coverage of about 95 percent of the unassembled mouse genome. Meanwhile the 500-base shotgun sequences will be deposited regularly in a newly-established public database operated by the National Center for Biotechnology Information and the European Bioinformatics Institute.