Affymetrix Genotyping Arrays Help Researchers Understand Genetic Basis of Disease

Two Plenary Sessions and Over 20 New Genetic Studies Using Affymetrix

29-Oct-2004

Santa Clara. Affymetrix, Inc. announced that researchers attending the American Society of Human genetics (ASHG) annual meeting this week will present more than 20 studies using Affymetrix GeneChip(R) DNA analysis technology to identify new genetic links to over a dozen different conditions, including prostate cancer, Alzheimer's disease and neural tube defects. In addition, two of the six major plenary presentations at ASHG will feature groundbreaking research using Affymetrix technology, enabling scientists to look at the underlying genetics of complex disease in more detail than ever before.

Presentations using Affymetrix technology at the ASHG meeting in Toronto include:

- Prostate Cancer: The GeneChip Mapping 10K Array allowed researchers to identify four regions of DNA linked to prostate cancer that were missed by a previous microsatellite scan. In a comparison between the 10K and microsatellite markers, genome scans using the 10K were faster and gave more genetic information.

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"Overall, the quality of the SNP genotypes generated using the Mapping 10K was excellent," said Daniel Schaid, Ph.D., Department of Health Sciences Research, Mayo Clinic, Rochester, who led the prostate cancer research. "We were able to complete the analytical phase of the project in a matter of months using microarray SNP-based genotyping, compared with years for microsatellite-based genotyping."

- Alzheimer's Disease: Scientists from Duke University, Vanderbilt University, and the Translational Genomics Research Institute used the Mapping 10K to identify genes that had not been previously linked to Alzheimer's Disease. Because of limitations in older technologies, the newfound disease linkages to chromosomes 2, 4, 5, and 8 had until now gone undetected. Neural Tube Defects: Researchers from Duke University used the Mapping 10K to identify the first genetic link to neural tube defects. This often fatal deformity affects 2,500 babies every year in the United States alone. The research team anticipates using these new findings to identify susceptibility genes for early screening and improved neural tube defect treatment.

- "Researchers are doing extraordinary things with the Mapping 10K and are now using the Mapping 100K to start performing whole genome association studies, research that simply wasn't possible before. Collaborators like ParAllele BioScience and Perlegen Sciences are breaking new ground in large-scale genetic analysis using Affymetrix technology, and this work will help us develop next-generation Affymetrix genotyping products," said Greg Yap, Vice President, DNA Analysis Products, Affymetrix. "Because researchers need more information to drive new discovery, we are continuing to create new easy-to-use products, including arrays to genotype up to 500,000 SNPs that will be available in 2005."

Numerous presentations made at ASHG represent the wide range of GeneChip products and technologies that customers are using to study genetic disease:

- Perlegen Sciences has pioneered advanced use of Affymetrix microarray technology for large-scale genotyping and resequencing, and was recently selected to provide approximately 70 percent of the genotype data for the International HapMap Project. Perlegen's plenary ASHG presentation (Plenary No. 4) will describe allele frequencies and correlation structure for nearly 1.6 million SNPs in each of 71 unrelated individuals who were genotyped using Affymetrix arrays.

- The Mapping 10K Array has become a definitive tool for genome-wide linkage studies. The array, featured in nearly two dozen ASHG presentations, has been used to measure changes in chromosomal copy number, compare genetics of different human populations, and find genes linked to conditions including cancer, neurological disorders, developmental disorders, and metabolic disorders.

- The Mapping 100K Array Set is the first in a family of Affymetrix products that enable genome-wide association studies. Over 75 academic, pharmaceutical and biotechnology customers are now using the 100K. At this year's ASHG meeting, customers including GlaxoSmithKline and Jurilab will present work using the 100K in pharmaceutical research. Other 100K presentations at ASHG will include reports on association studies, population genetics, and genome structure. Affymetrix scientists at the conference will also discuss the future of large-scale genotyping using more than 100,000 SNPs.

- ParAllele MegAllele(TM) Genotyping Reagents are now available in kits developed collaboratively with Affymetrix. These kits offer a powerful and cost-effective solution for customers to genotype any SNPs they choose in their own labs. ParAllele and Baylor College of Medicine will present a plenary session (Plenary No. 3) describing high-density genotyping and mapping in chromosome 12 using MegAllele reagents and Affymetrix arrays.

- CustomSeq(TM) Resequencing Arrays will also be featured in research presented at ASHG. Researchers from the University of Tuebingen and the Gregor Mendel Laboratory, Germany, will report using the array to sequence the complete CFTR gene, allowing rapid identification of the 1,000 or more mutations known to cause cystic fibrosis. Additionally, researchers from the University of Michigan and the National Institutes of Health will report using CustomSeq to identify gene mutations known to cause autosomal recessive retinitis pigmentosa.

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