SNPs Set Free

A biotech company is releasing information on 120,000 gene variants, called single nucleotide polymorphisms (SNPs), to the public after studying them in dozens of volunteers. The release of so many well-characterized SNPs from a private company is a first, and researchers hope the SNPs will further efforts to link genetic variation with specific diseases.

SNPs occur when a single nucleotide in DNA is substituted for another, and many geneticists believe that individual SNPs, or broader SNP patterns, could help explain susceptibility to diseases from cancer to diabetes. But most of the nearly 6 million SNPs in public databases haven't been tested for in multiple people. This means they could be rare, and thus not useful for studying common diseases. And there's a chance that some are technical errors, says Stacey Gabriel, scientific director of the human haplotype map (HapMap) program at the Whitehead Institute/MIT Center for Genome Research in Cambridge, Massachusetts. Getting accurate SNPs is especially important for researchers working on this map, which is based on the idea that large stretches of DNA are inherited in blocks, each of which can be defined by a set of SNPs.

The new SNP information is being released by Affymetrix, the Santa Clara, California, company that has made a name for itself in the business of gene arrays. To determine how frequently certain SNPs occur among people, Affymetrix began checking out 500,000 of them. About half were from the public domain, and the other half came from a spinoff company, Mountain View, California-based Perlegen Sciences, which put together its own haplotype map last year. Almost no data from that map have been released previously; the new SNP information is available today on Affymetrix's Web site and will be posted on 17 October on the University of California, Santa Cruz, genome browser.

The company tested for the SNPs' presence in 54 volunteers--a number deemed sufficient to measure prevalence in the general population. All of the 120,000 SNPs being released appeared in at least one volunteer. Keith Jones, Affymetrix's vice president for molecular genetics, says the company is developing a chip that will allow scientists to test a DNA sample for 100,000 SNPs at once.

"It sounds like a very valuable thing for the community," says geneticist Evan Eichler of Case Western Reserve University in Cleveland, Ohio, who worked at Affymetrix years ago. But the contribution is more incremental than revolutionary, says David Altshuler, director of medical and population genetics at the Whitehead Center for Genome Research. He notes that 270,000 SNPs already in the public domain include "detailed frequency information in one or more populations"--and the public HapMap venture is regularly adding more.

Related sites
Affymetrix SNP information
University of California, Santa Cruz, Genome Bioinformatics
Perlegen Sciences
Information on the publicly funded HapMap Project
Downloads for publicly funded HapMap Project