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Illumina Announces Roadmap to Five Million Variants for Next-Generation Whole-Genome Genotyping

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At the 59th annual meeting of the American Society of Human Genetics, Illumina, Inc. has announced its 2010 roadmap for the Infinium whole-genome genotyping platform, offering products capable of analyzing up to five million (5M) variants per sample.

As part of this announcement, Illumina outlined an ongoing collaboration with leading researchers to select the highest-value markers from the 1000 Genomes Project for the next wave of genome-wide association studies (GWAS). This array content will facilitate testing new scientific hypotheses, including the impact of rare variants, CNVs, and other non-SNP markers on diseases and traits.

“We are at a critical point in human genetics. Next-generation sequencing in the 1000 Genomes Project and medical sequencing studies will soon create a near-complete catalogue of human DNA variants that exist at any appreciable frequency in human populations,” said David Altshuler, Ph.D., M.D., director of the program in Medical and Population Genetics at the Broad Institute. “To better understand whether and how these variants may contribute to human diseases, our collaborative group is working with Illumina to select new content for arrays that will enable ‘next-generation’ GWAS using many millions of variants in thousands of samples.”

Prior to releasing the 5M product, Illumina will release an intermediate 2.5M product that adds rare variants to the strong backbone of content currently on the HumanOmni1-Quad BeadChip. “The Infinium platform allows rapid evolution of GWAS products,” said Jay Flatley, president and CEO of Illumina. “Our genotyping product portfolio is regularly updated with the latest content to provide our customers with the most powerful analysis possible across populations and variant classes, all in one assay.”

Researchers who begin studies now using Illumina’s whole-genome genotyping products will have exclusive access to supplemental arrays that build from the Omni content to the full 5M variants. Customers on this preferred path will have the ability to incrementally interrogate novel sets of SNPs as they are released into public databases, prior to the release of the full 5M variant array.

As with Illumina’s previous whole-genome genotyping arrays, the new products will offer the high performance necessary for CNV detection, together with density of coverage enabling association of rare variants with diseases or traits.