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WTCCC Partners with Perlegen and Affymetrix to Search for Genes

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The Wellcome Trust Case Control Consortium (WTCCC), the Wellcome Trust Sanger Institute (WTSI), Perlegen Sciences and Affymetrix Inc., have announced a collaboration to undertake one of the largest whole-genome association programs ever conducted to search for genes associated with ten complex diseases.

Perlegen Sciences will genotype 15,000 individuals and produce 10 billion individual genotypes using Affymetrix GeneChip® technology, including the Human Mapping 500K Array Set.

“We plan to genotype more than 15,000 samples across 675,000 SNPs using the Affymetrix GeneChip Human Mapping 500K Array Set plus a custom 175K SNP panel,” said Professor Peter Donnelly from the Department of Statistics at Oxford, who chairs the consortium.

“We liked the combination of the existing throughput and expertise of Perlegen with Affymetrix' 500K product that can be run in different labs.”

The WTCCC is a team of 24 human geneticists that conducts research at a number of institutes throughout the United Kingdom, including the WTSI, Leicester University, Cambridge University and Oxford University.

For the first 11,000 samples, the group will search for genes associated with coronary heart disease, hypertension, types 1 and 2 diabetes, bipolar disorder, Crohn's disease, rheumatoid arthritis and tuberculosis.

As part of this collaboration, an additional 4000 samples will be analyzed by the WTSI to study the genetic origins of common diseases, such as types 1 and 2 diabetes, obesity and malaria.

All 15,000 DNA samples are being processed and arrayed by the WTSI and Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory before shipment to Perlegen.

The Affymetrix GeneChip Human Mapping 500K Array Set is designed to provide a comprehensive and unbiased view of the entire genome, enabling scientists to analyze genetic variation across the genome in large populations.

Researchers believe that the “genetic signposts” will provide a better understanding of which people are most at risk and why.

“This groundbreaking project is possible because of the sequencing of the human genome,” said Mark Walport, Ph.D., director of the Wellcome Trust.

“It is an excellent illustration of the importance of knowing the human genome sequence and cataloguing its variations.”

“We are thrilled to work with the world-class scientists from the WTCCC in rapidly applying Affymetrix' unparalleled technology to statistically powerful studies of serious diseases that affect so many people,” said Brad Margus, Chief Executive Officer of Perlegen.

“The discovery of genetic variations that increase susceptibility to these diseases will validate new drug targets and accelerate the development of new treatments, particularly treatments aimed at causes rather than symptoms.”

“These studies by the Wellcome Trust Case Control Consortium are a great example of how Affymetrix' innovative genotyping technology is providing scientists with the ability to do experiments that simply haven't been possible before,” said Stephen P.A. Fodor, Ph.D., Founder, Chairman and Chief Executive Officer of Affymetrix.

“The GeneChip Human Mapping 500K Array Set is quickly becoming the standard in large-scale genotyping, enabling researchers to accelerate discoveries in the lab and help bring new treatments and tests to the patient's bedside.”