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Affymetrix releases data from validated SNP database for design of custom genotyping arrays
SANTA CLARA, Calif. —Affymetrix Inc. recently released what it called "an unparalleled data set based on extensive validation of novel SNPs from the 1000 Genomes Project." This data is intended to give researchers access to more rare mutations for genome-wide association studies and reportedly hold the promise of enabling "the rapid design of custom arrays for a variety of applications, including the validation of sequencing results."
In an ongoing effort to screen novel, newly discovered single nucleotide polymorphisms (SNPs), Affymetrix has used the Axiom Genotyping Solution to screen millions of SNPs across multiple populations. This data set comprises approximately 500,000 SNPs from the 1000 Genomes Project that have been genotyped across the 270 HapMap samples, and Affymetrix maintains that it demonstrates the comprehensiveness of its larger, highly curated database, which contains genotype calls and other useful annotations across millions of SNPs.
A team of researchers at the University of California, San Francisco (UCSF) and Kaiser Permanente's Division of Research have used the initial data set to design a custom array as part of a 100,000-sample genotyping study for Kaiser Permanente's Research Program on Genes, Environment, and Health (RPGEH).
"Without this data set, we could not have easily achieved the objectives of our initial custom array design, which included genomic coverage, inclusion of SNPs of interest, and coverage of genes thought to be highly relevant in our study," says Dr. Neil Risch, director of the Institute for Human Genetics at UCSF. "The wealth of information that accompanied the genotype calls was paramount to the successful design of our array."
By combining SNPs from this data set with Affymetrix' Axiom Custom Genotyping Arrays, which enable researchers to customize up to 2.6 million SNPs on a single array plate, the next wave of genome-wide association studies can now be realized, the parties involved with this work maintain. They add that the information contained in the data set can also be used in conjunction with a variety of imputation techniques that are gaining favor and seeing greater adoption.
"This groundbreaking work has taken raw data from discovery projects and translated it into the first usable format," says Kevin King, president and CEO of Affymetrix. "This will enable scientists to effectively use the 1000 Genomes Project SNP data and a host of other validated SNPs and annotations from different sources. By combining this data with our Axiom Custom Genotyping Arrays, researchers in need of custom arrays are no longer constrained by information or technology limitations."