Affymetrix, Inc. (NASDAQ:AFFX) today announced that it will contribute genotyping data for a large set of validated rare and common genomic variants to the 1000 Genomes Project. This powerful data consists of genotyping information from more than 2 million single nucleotide polymorphisms (SNPs), and insertions/deletions (indels), many of which were not previously available from any source. The release includes common and rare variants genotyped on the four major HapMap populations: Caucasian (CEU), Yoruba/African (YRI), Chinese (CHB), and Japanese (JPT), as well as on the larger HapMap Phase 3 sample-set. The data will be incorporated into the 1000 Genomes public data repository and will be freely available.
“The 1000 Genomes Project is pleased to have Affymetrix join the project and contribute this large data set to complement existing genotyping data in the public domain”
"The 1000 Genomes Project is pleased to have Affymetrix join the project and contribute this large data set to complement existing genotyping data in the public domain," said Dr. David Altshuler, M.D., PhD, and Co-Chair of the 1000 Genomes Project. "The genotypes that they have generated will be of interest to the project's participants, as well as to the broader research community," Dr. Altshuler noted.
In addition, Affymetrix will release a larger data set of approximately 5 million variants on its website, www.Affymetrix.com, before the end of 2010. The new data includes approximately 3 million human SNPs discovered by the 1000 Genomes Project that were not found in the HapMap Project or the NCBI's Single Nucleotide Polymorphism Database (dbSNP, release 130). This information, which was generated by Affymetrix using the Axiom™ Genotyping Solution, will allow scientists to create customized Axiom Genotyping Arrays containing 50,000 to as many as 2.6 million markers. The entire Axiom Genomic Database provides an extensive selection of ready-to-use variants for custom array designs and enables an unprecedented level of success in assay conversion.
"This vast resource is a valuable supplement to existing data sets and represents a new haplotype map which will provide further insights into human genetic diversity and population sub-structure," said Carlos Bustamante, PhD, Professor of Genetics at Stanford University. "Our ongoing work at Stanford in enabling multi- and trans-ethnic genome-wide association and medical resequencing studies will benefit greatly from this substantial data set in particular and from Affymetrix' screening capabilities in general," Dr. Bustamante added.
The Affymetrix Axiom Genome Screening Service allows researchers to screen their populations and cohorts of interest against approximately 5 million of these validated Axiom markers. For studies focused on previously underserved ethnic groups, for which public information is often limited, this service is invaluable for its ability to inform SNP selection and array design.
"The release of these data sets strengthens our longstanding tradition of partnering with the scientific community and is aimed at characterizing human genetic variation, its link to disease, and its importance in improving human health," said Affymetrix President and CEO Kevin King. "With these unprecedented data sets, the scientific community has access to new tools to design custom genotyping arrays for a wide range of studies by disease and population, as well as the support they require for meta-analysis through imputation. Moreover, the Axiom platform makes it easily accessible and flexible to use."
In addition to genotype information, the Affymetrix-hosted data set also contains comprehensive minor allele frequency information and can inform haplotype structure, which will enable more guided genotyping study designs. The data set has been genotyped in 270 HapMap reference samples and portions have also been genotyped in the HapMap Phase 3 set of 1,301 samples.
To create the data set, Affymetrix leveraged the Axiom Genotyping Solution's production-scale infrastructure to screen millions of genomic variants from phases 1 to 3 of the International HapMap Project and SNPs from pilots 1 and 2 of the 1000 Genomes Project. The database contains only those markers determined to be polymorphic in the respective population and those that meet Affymetrix' stringent data quality metrics.
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