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SNP Consortium, NHGRI to Collaborate, Help Complete Human Genome Project

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HICAGO--The SNP Consortium, in conjunction with the US National Human Genome Research Institute, is in the early stages of a sequencing project to help accelerate the Human Genome Project. The SNP Consortium has begun searching for a company to handle DNA sequencing for the collaboration, said Arthur Holden, chairman and CEO of the nonprofit entity that has pooled the resources of pharmaceutical and technology companies with the Wellcome Trust to construct a publicly available map of single-nucleotide polymorphisms in the human genome.

Holden said the consortium has been negotiating for more than a year for a partnership with NHGRI. One approach discussed called for the consortium to generate quality SNPs from incremental sequencing, Holden said. A by-product of that effort would benefit the Human Genome Project by assembling bacterial artificial chromosomes, he added.

NHGRI spokeswoman Cathy Yarborough agreed that the data generated from the sequencing project would help put the data in order.

The consortium has asked for proposals from companies to bid on the project. So far, only Incyte Pharmaceuticals has responded, but its bid was rejected by the consortium, said Holden. According to a report in the Wall Street Journal on March 14, Genome Therapeutics and Celera are considering making bids. Craig Venter, Celera’s president and chief scientific officer, couldn’t be reached for comment, and a Genome Therapeutics spokesman could not comment because of quiet period restrictions as the company has filed for a public offering of stock.

Lincoln Stein, associate professor at Cold Spring Harbor Laboratory, which is maintaining the SNP Consortium databases, said the consortium is seeking a company to help it perform plasmid-end sequencing, which the NHGRI believes will help finish the rough draft of the human genome more quickly than its projected deadline, less than two months from now.

Stein said that the consortium wants to work with the government because any source of traces that can be used for SNP calling are helpful. End sequencing information would provide orientation for unmapped BACs, he explained. "It can be used to close holes in the shotgun sequence and to detect and resolve misassemblies," he said.

The SNP Consortium uses shotgun sequencing to detect SNPs, while the Human Genome Project is relying on whole-genome sequencing. Both efforts will benefit from more information because results from one method can generally be used to check and correct results from another, commented Stein. "The more data that are available, the more parallel strategies that are pursued, the faster we’ll reach the goal," he added.

It’s not clear how funding for the sequencing project will be split between the consortium and the NHGRI. The consortium has a surplus of funds right now because its core SNP-discovery effort has been more efficient than expected. "We’re finding more SNPs for less money than we had anticipated, so there’s a little bit of extra money rattling around," said Stein.

Funding for the SNP Consortium is provided by its membership, which includes 10 pharmaceutical companies--AstraZeneca, Aventis Pharma, Bayer, Bristol-Myers Squibb, Hoffmann-La Roche, Glaxo Wellcome, Novartis Pharmaceuticals, Pfizer, Searle, SmithKline Beecham--in addition to IBM, Motorola, and its newest member Amersham Pharmacia Biotech. Aside from Cold Spring Harbor, other academic centers conducting SNP identification and analysis for the consortium are the Massachusetts Institute of Technology’s Whitehead Institute for Biomedical Research, Washington University School of Medicine in St. Louis, the Wellcome Trust’s Sanger Centre, and Stanford University’s Human Genome Center.

--Matthew Dougherty

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