New Affymetrix Microarray Set Genotypes More Than 500,000 SNPs In A Single Experiment
GeneChip Human Mapping 500K Array Set Enables Researchers to Perform Highly Detailed Whole-Genome Association Studies for the First Time
Santa Clara, CA - Affymetrix Inc. announced recently the launch of the GeneChip Human Mapping 500K Array Set, two microarrays that genotype more than 500,000 SNPs in a single experiment for less than a quarter of a cent per SNP. Based on the same proven assay used in the GeneChip Human Mapping 10K and 100K Arrays, the 500K is the first and only product available that enables researchers to search across the entire genome in detail to find genes involved in disease or drug response.
The GeneChip 500K Array Set is the latest in a line of products from Affymetrix that the company believes will continue to set the standard in genetic analysis. The 500K Set examines more SNPs than any other available genotyping solution, giving researchers higher resolution to find the genes associated with complex disease. The 500K is also the first product to utilize the output of the International HapMap Project -- SNPs from the 500K Set are publicly available and data gathered using the 500K Set can be analyzed in the context of the emerging HapMap.
"The data from the HapMap Project suggest it is possible to select polymorphisms at high density which correlate with the majority of the common genetic variation in the genome," said Mark Daly, a statistical geneticist and assistant professor at the Massachusetts General Hospital and Harvard Medical School. "With the release of the 500K, we can for the first time design an efficient and cost-effective study of a large fraction of the common variation in the genome."
Affymetrix provides the only genotyping solution for whole-genome association studies. Researchers can use the 500K to search the entire genome and then use new targeted genotyping assays developed in collaboration with ParAllele Bioscience to follow up on their genes and SNPs of choice -- all on one platform.
"We identified several significant associations for myocardial infarction using the early access Affymetrix GeneChip Human Mapping 500K Array Set," said Professor Monika Stoll from the Leibniz Institute for Atherosclerosis Research at the University of Muenster. "The results represent a significant advancement in the field of cardiovascular disease."
The GeneChip 10K and 100K Arrays, which have been used in more than 50 customer publications during the past two years, have established Affymetrix as the genotyping market leader. Previously, whole-genome genetic association studies were impractical and unaffordable because they would have required more than a million different oligonucleotide reagents and hundreds of thousands of PCR reactions. The GeneChip 500K Array Set requires only one universal primer, 500 ng of genomic DNA and a simple protocol to genotype 500,000 SNPs.
"Affymetrix continues to set the standard for whole-genome analysis," said Greg Yap, vice president of DNA Products at Affymetrix. "The GeneChip Human Mapping 500K Array Set is the first product to enable scientists to perform high-density genome-wide scans efficiently and cost-effectively. By bringing more high quality genetic information to researchers, we are enabling scientists to better understand how genetics can affect the likelihood of developing a disease or the response to a drug."
Applications of the GeneChip 500K Set
The primary application for the 500K Set is identifying genes involved in complex disease or drug response. Scientists are now beginning whole-genome association studies in complex diseases that have been difficult to study using traditional tools and techniques. Studying hundreds or even thousands of genetic markers has generally been uninformative in these diseases, but by analyzing 500,000 markers simultaneously, researchers hope to harness enough statistical power to make meaningful genetic discoveries. Researchers using the Affymetrix 100K Array Set have demonstrated the power of this approach through significant early discoveries in diseases like macular degeneration, cardiovascular disease, inflammatory disease, and cancer. More than 50 researchers have begun using the 500K under an early technology access program, at least 25 of those studies involve at least 1,000 patients.
500K Array Design
All of the SNPs on the GeneChip Mapping 500K Array Set went through a rigorous screening and validation process to maximize genome power and discovery rate. The optimal SNPs in this group were selected and tiled on arrays based on accuracy, call rate and linkage disequilibrium analysis across the genome in three populations. The 500K Set provides approximately 80 percent genome coverage for common genetic studies.
Researchers using the 500K set will be able to analyze their data in the context of all the data in the HapMap database. All 500K SNPs have been genotyped across the 270 HapMap samples and that data will be submitted to the International HapMap Project. This data is in addition to the SNPs genotyped by Perlegen using Affymetrix arrays in Phase 2 of the HapMap project. In total, Affymetrix arrays were used to generate well over 70 percent of the data collected in the International HapMap Project.
Complete Solution for Genetic Analysis
Affymetrix 500K Array Set is built on the same proven GeneChip technology that has been the industry standard in microarray research for the past decade. The system includes:
- GeneChip Human Mapping 500K Array Set
- Optimized and validated reagents based on the proven GeneChip Mapping Assay that has been validated in more than 50 peer-reviewed customer publications
- Affymetrix GeneChip DNA Analysis Software (GTYPE), which uses an automated genotype-calling algorithm that provides a confidence score for each individual genotype
- Affymetrix GCS3000 7G Scanner, the industry-standard microarray scanner that also runs Affymetrix' market-leading RNA analysis products and other DNA analysis products for targeted genotyping or sequence variation analysis
SOURCE: Affymetrix