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Affymetrix Supplying Genotyping Data to 1000 Genomes Project

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Affymetrix said today that it will contribute genotyping data for a large set of validated rare and common genomic variants to the 1000 Genomes Project.

The data the Santa Clara, Calif.-based company is supplying consists of genotyping information from more than 2 million SNPs and insertions and deletions, many of which had not been previously available from any source.

The release includes variants genotyped on the four major HapMap populations — Caucasian, Yoruba/African, Chinese, and Japanese. Other larger HapMap Phase 3 samples sets were also included, Affymetrix said. The data will be incorporated into the 1000 Genomes Project public data repository and be available freely.

Affymetrix also said that it will release a larger dataset of about 5 million variants on the company's website before the end of the year that will include 3 million human SNPs discovered by the 1000 Genomes Project that were not found in the HapMap Project or the National Center for Biotechnology Information's Single Nucleotide Polymorphism Database.

The information was generated by Affymetrix using the Axiom Genotyping Solution and will enable scientists to create customized Axiom Genotyping Arrays containing as many as 2.6 million markers, the company said in a statement. The Axiom Genomic Database provides "an extensive selection" of ready-to-use-variants for custom array design, the company said.

The dataset hosted by Affymetrix also contains comprehensive minor allele frequency information and can inform haplotype structure, which can help guide genotype studies, it said. The dataset has been genotyped in 270 HapMap reference samples. Portions have been genotyped in the HapMap Phase 3 set of 1,301 samples.