Rockefeller University to Study Genetic Roots of Obesity-Related Diseases Via Whole Genome Association Scans
High density GeneChip® research arrays to be used in comprehensive association study
Santa Clara: Affymetrix, Inc., announced that scientists at The Rockefeller University will use GeneChip® arrays to genotype more than 3,200 individuals at high density across the genome in one of the first large-scale genome-wide association studies ever undertaken. The Rockefeller research group includes Dr. Jeff Friedman, Dr. Jan Breslow, and Dr. Markus Stoffel, who will focus on discovering the genetic variations associated with obesity, high blood pressure and diabetes in virtually the entire adult population of the Micronesian island of Kosrae.
"We've been wanting to do this experiment for a long time, but simply didn't have tools with the needed power and resolution to get detailed genetic answers to define the associations between specific genes and obesity," said Dr. Friedman, Director of the Starr Center for Human Genetics and the university's Marilyn M. Simpson Professor. Dr. Friedman also is a Howard Hughes Medical Institute investigator.
Friedman has been studying obesity related-disease in Kosrae for the past ten years because of the unique population in which obesity was virtually non-existent prior to World War II. Following the arrival of US aid and food relief, the people of Kosrae changed their traditional diet of fish, fruit, and vegetables for fattier foods. Within a single generation, much of the population developed obesity, while others with the same diet habits did not. Now, Rockefeller scientists are trying to identify the exact genetic variations explaining why only some individuals developed obesity.
The source of these variations may come from the unique genetic make up of Kosrae. Kosrae was founded nearly 2,000 years ago by about 50 Polynesians, but later in the mid- to late-19th century, Caucasian whalers visited and in many cases settled on the island. The modern Caucasian/Polynesian genetic mix and the clear distribution of obesity within the population make Kosrae ideal for this kind of genetic association study.
Scientists from the Broad Institute of MIT and Harvard University will play a role in analyzing the data generated in this study. "We are delighted to collaborate in this study with Rockefeller University and Affymetrix," said David Altshuler, Director of Medical and Population Genetics at Broad. "The unique population history of Kosrae and the wonderful phenotypic data that Dr. Friedman and his colleagues have collected makes this one of the most promising opportunities in which to start doing genome-wide association studies. In addition, Affymetrix has dramatically advanced the field's ability to perform genome-wide SNP genotyping with its new 100K Set and continued innovation to higher SNP densities, making GeneChip arrays an excellent platform for these studies."
The Rockefeller scientists also are collaborating with HHMI investigator Richard P. Lifton of Yale University School of Medicine.
Previously, generating over 100,000 genotypes would have required over 100,000 PCR reactions, a hurdle that made this kind of research impractical. However, GeneChip array-based genotyping is now enabling individual scientists, like Friedman and colleagues, to perform these large-scale whole-genome studies. The collaboration plans to genotype SNPs from the new GeneChip Mapping 100K Array Set, with over 115,000 SNPs. The collaboration also plans to study 100,000 additional SNPs (up to 215,000 total) that may be relevant for the Micronesian population. About half of the SNPs are from public databases, while the other half are from the SNP database discovered by Perlegen Sciences, Inc.
"We are enthusiastic to support this unique Rockefeller University project to identify genetic causes of obesity and major related diseases like cardiovascular disease and diabetes," said Greg Yap, Sr. Marketing Director, DNA Analysis. "These genome wide association studies require high resolution, and our Mapping 100K Set is the first in a family of products to meet this need. Because of the unique genetic makeup of the Kosrae population, we have, in close collaboration with Dr. Friedman, supplemented the 100K with additional SNPs that may be informative in this population. Researchers can start generating and analyzing useful data with 100K today, and our easy, affordable genotyping assay makes it possible to add as many SNPs as desired."
The 100K Set, the first product to start enabling genome-wide association studies, is now available under an expanded technology access program and will formally launch this summer. Although the research arrays used in this collaboration are not broadly available, Affymetrix is using this collaboration to help accelerate development of next generation arrays with additional SNPs.
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