Affymetrix releases data from validated SNP database for design of custom genotyping arrays

Validated SNPs from 1000 Genomes Project and custom Axiom arrays intended to enable the next wave of genotyping studies

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SANTA CLARA, Calif. —Affymetrix Inc. recently releasedwhat it called "an unparalleled data set based on extensive validation of novelSNPs from the 1000 Genomes Project." This data is intended to give researchersaccess to more rare mutations for genome-wide association studies and reportedlyhold the promise of enabling "the rapid design of custom arrays for a varietyof applications, including the validation of sequencing results."
In an ongoing effort to screen novel, newlydiscovered single nucleotide polymorphisms (SNPs), Affymetrix has used theAxiom Genotyping Solution to screen millions of SNPs across multiplepopulations. This data set comprises approximately 500,000 SNPs from the 1000Genomes Project that have been genotyped across the 270 HapMap samples, andAffymetrix maintains that it demonstrates the comprehensiveness of its larger,highly curated database, which contains genotype calls and other usefulannotations across millions of SNPs.
A team of researchers at the University ofCalifornia, San Francisco (UCSF) and Kaiser Permanente's Division of Researchhave used the initial data set to design a custom array as part of a100,000-sample genotyping study for Kaiser Permanente's Research Program onGenes, Environment, and Health (RPGEH).
"Without this data set, we could not have easilyachieved the objectives of our initial custom array design, which includedgenomic coverage, inclusion of SNPs of interest, and coverage of genes thoughtto be highly relevant in our study," says Dr. Neil Risch, director of theInstitute for Human Genetics at UCSF. "The wealth of information thataccompanied the genotype calls was paramount to the successful design of ourarray."
By combining SNPs from this data set withAffymetrix' Axiom Custom Genotyping Arrays, which enable researchers tocustomize up to 2.6 million SNPs on a single array plate, the next wave ofgenome-wide association studies can now be realized, the parties involved withthis work maintain. They add that the information contained in the data set canalso be used in conjunction with a variety of imputation techniques that aregaining favor and seeing greater adoption.
"This groundbreaking work has taken raw data fromdiscovery projects and translated it into the first usable format," says KevinKing, president and CEO of Affymetrix. "This will enable scientists toeffectively use the 1000 Genomes Project SNP data and a host of other validatedSNPs and annotations from different sources. By combining this data with ourAxiom Custom Genotyping Arrays, researchers in need of custom arrays are nolonger constrained by information or technology limitations."

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