Affymetrix releases SNP data

First large-scale release of SNPs from Perlegen database

Affymetrix, of Santa Clara, CA, US, has released genotype data for 120,000 validated SNPs selected from both public SNP databases and the proprietary SNP database developed by Perlegen Sciences.

The SNP data was generated using Affymetrix GeneChip brand DNA analysis technology and, the company claims, is the first significant SNP database freely available to the public that includes genotype data and allele frequencies for SNPs distributed across the entire human genome.

The 120,000 validated, genome-wide SNPs were genotyped in the same set of individuals, which will help researchers study the diversity of human variation and the genetic basis of disease and drug response. The SNP data represents a significant step forward for researchers because, while there are millions of SNPs in public databases, most have not been validated or tested in the same set of individuals.

'Half of the SNPs are from the Perlegen database and have never been released to the public before,' said Dr Stephen Fodor, chairman and ceo of Affymetrix. 'This initial release of SNP validation data will be a valuable resource freely available for all researchers, and this first release is just the beginning. Over time, we will put all of the SNPs from the Perlegen database into the public domain while also developing products that use both these and public SNPs. We believe this will aid and complement the public/private haplotype map effort led by the National Human Genome Research Institute.'

Affymetrix chose this initial release of 120,000 SNPs by testing a set of about 535,000 SNPs across 54 people using GeneChip DNA analysis arrays -- a total of about 29m genotypes in eight weeks, or about 700,000 a day. From this screening process, Affymetrix chose the SNPs that showed the best distribution across the genome and the highest accuracy and call rates.

Affymetrix is using this SNP data to develop a product that will genotype 100,000 SNPs in a single experiment. This product will leverage a novel, easy-to-use assay developed by Affymetrix that is used in Affymetrix' just-released GeneChip Mapping 10K Array.

SNP information

The SNP information is available for download at www.affymetrix.com. The information will also be available through the University of California, Santa Cruz, Genome Browser www.genome.ucsc.edu on Oct. 17. Additional information on Affymetrix DNA analysis products, including the Mapping 10K and CustomSeq resequencing arrays, can also be found on the Affymetrix web site