By Randall Osborne

In a $45 million, two-year project to construct a map of single nucleotide polymorphisms (SNPs) that will be freely available to all, the U.K.-based Wellcome Trust and 10 pharmaceutical companies have established The SNP Consortium, a non-profit entity that will also include major academic centers.

Wellcome Trust is contributing about $14 million and the pharmaceutical firms are putting about $30 million behind the effort, said Arthur Holden, chairman and CEO of the consortium.

¿I see [the consortium] as the first byproduct of the fact that you can have a full reference sequence available,¿ said Holden, noting the Human Genome Project¿s efforts to sequence the entire human genome by 2003.

Holden, former CEO of U.K.-based Celsis International plc, spent much of his career with Baxter International Inc., of Deerfield, Ill.

The pharmaceutical companies are AstraZeneca plc, of London; Bayer AG, of Leverkusen, Germany; Bristol-Myers Squibb Co., of New York; F. Hoffman-La Roche, of Basel, Switzerland; Glaxo Wellcome plc, of London; Hoechst Marion Roussel AG, of Frankfurt, Germany; Novartis AG, of Basel, Switzerland; Pfizer Inc., of New York; G.D. Searle & Co., of Skokie, Ill.; and SmithKline Beecham plc, of London.

SNPs are common variations in DNA. Locating them is expected to help researchers find genetic differences that predispose some people to certain diseases. SNPs also underlie the variability of response to drugs.

Using DNA from a diversified, 24-member panel of anonymous volunteers obtained through the National Institutes of Health ¿ along with information from the Human Genome Project, sequencing and mapping technologies, and the resources of academic institutions ¿ the consortium expects to identify up to 300,000 and map at least 150,000 SNPs for use in further study.

¿Actually, 24 is probably more than you really need, to accurately reflect the predominance of genetic evolution across mankind,¿ Holden said. ¿The difference between 24 and 60 is not that significant, but between one or two and 10, it¿s vastly significant.¿

Academic centers taking part in the consortium are the Whitehead Institute for Biomedical Research, in Cambridge, Mass.; Washington University School of Medicine, in St. Louis; the Wellcome Trust¿s Sanger Centre, in Cambridge, U.K.; Stanford Human Genome Center, in Stanford, Calif.; and Cold Spring Harbor Laboratory, in New York.

The bioinformatics program at Cold Spring Harbor Laboratory will put together the resulting database.

About 3 billion nucleotide pairs, or ¿base pairs,¿ exist in the human genome, and 99.9 percent of them are the same. The remaining 0.1 percent is what leads to the key differences between people, and researchers believe single-base variation, or SNP, occurs every 1,000 bases.

Holden said companies that works with SNPs will be given a ¿huge stimulus¿ by the database to be created and made available through the Internet.

¿We just finished a pilot program, and we¿ll be doing scale-up over the next couple of months,¿ he said. By the start of next year, the consortium will be releasing quarterly ¿significant bundles of maps,¿ with a third of the targets finished in the first year and the remaining two-thirds finished in the second year.