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Affymetrix releases data from
validated SNP database for design of custom genotyping arrays
07-27-2010
EDIT CONNECT
SHARING OPTIONS:
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."
Code: E07271003 Back |
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