News and Events
12/9/2008
Affymetrix Technology Powers Cincinnati Children's Hospital's Innovative Test for Jaundice
12/8/2008
Affymetrix Completes Acquisition of Panomics
Plant and Animal Genome XVII Conference
1/10/2009-1/14/2009
Achieving ROI in Personalized Medicine: Barriers, Incentives, and Pathways to Commercialization
1/27/2009-1/28/2009
Scientific Publications
Genome-Wide Association
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Genome-Wide Association
Power your association study with larger sample sizes in your initial whole-genome scan and statistical replication by using the Affymetrix Genome-Wide Human SNP Array 6.0—a single array that features more than 1.8 million markers for genetic variation, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 additional probes for the detection of copy number variation.
Figure 2
Figure 1
The SNP Array 6.0 has near-saturated coverage of SNP variation. With empirically tested copy number probes with more extensive coverage of CNVs, the SNP Array 6.0 can detect 10 times the amount of copy number variation than competing products. Figure 1 and 2 demonstrates the power of the SNP 6.0 array for CNV mapping and CNV association studies. The ultra high copy number resolution of 1.8 million markers allows to fine map CNV regions and defines accurate CNV maps for CNV association studies.
Performance and Accuracy
Figure 1
Figure 2
More than 100 sites have been trained to run the Genome-Wide Human SNP Array 6.0. Across the board, it demonstrates industry-leading performance, with average call rates greater than 99 percent. The SNP Array 6.0 detects the highest proportion of de novo CNV variation than any microarray platform to date and detected approximately 10 times more than non-Affymetrix platforms. Why? One main reason is that probes on the SNP Array 6.0 were empirically selected for copy number analysis and demonstrate linear response to copy number changes.
Analysis and Throughput
Affymetrix provides highly flexible genotyping and copy number analysis solutions that include:
Figure 1
- Affymetrix® Genotyping Console™ Software, a free and easy-to-use analysis tool for determining SNP genotypes and chromosomal copy number
- Affymetrix Power Tools (APT) for cross-platform, command-line applications for high-throughput users
- A network of GeneChip-compatible™ providers for advanced statistical analysis
- GeneChip® Command Console® Software (AGCC) , an intuitive set of integrated instrument control and data management tools
Many researchers are looking for hands-off genotyping options that involve minimal user interventions, fewer laboratory technicians dedicated to genotyping production and consistent results delivered in a highly controlled environment. Affymetrix offers several automation genotyping configurations that provide up to 100 percent increased productivity and up to 50 percent savings on personnel cost. These solutions take advantage of a single kit that contains the validated and qualified reagents for the SNP 5.0/6.0 automated assay, and liquid handling-robot options from Affymetrix or our partners.
Featured Products
Genome-Wide SNP Array 6.0 for Genome-wide Association Studies
The new Affymetrix® Genome-Wide Human SNP Array 6.0 features more than 1.8 million markers for genetic variation, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 enables high-performance, high-powered and low-cost genotyping.
Genotyping Console for Genome-Wide Association Studies
Affymetrix® Genotyping Console™ Software streamlines whole-genome genotyping analysis and quality control. Genotyping Console implements robust genotyping algorithms-including Birdseed for SNP Array 6.0, BRLMM-P for the SNP Array 5.0 and BRLMM for the 500K Array-as well as cluster visualization and flexible SNP filtering capabilities.
Figure 1
Whole-genome Association Analysis of Type 2 Diabetes
David Altshuler, M.D., Ph.D., Broad Institute of MIT & Harvard
Dr. Altshuler presents results from a recent genome-wide association study of type 2 diabetes published in Science (Figure 1). In this paper, Dr. Altshuler and his team examined more than 386,000 SNPs from 1,464 type 2 diabetes patients and 1,467 matched controls and found compelling evidence of type 2 diabetes association at several novel loci and confirmed several previously identified loci.
Genome-Wide Association Study of 14,000 Cases of Seven Common Diseases and 3,000 Shared Controls
Peter Donnelly, Ph.D., University of Oxford
Copy Number Variation using the Affymetrix SNP Array 6.0 and Partek Genomics Suite
Tom Downey, President and Data Analysis Consultant at Partek®
Tom Downey demonstrates how Partek® Genomics Suite Version 6.3 can perform interactive primary and secondary copy number analyses for the SNP Arrays 6.0. He illustrates how researchers who are conducting whole-genome association studies can use the Partek® Genomics Suite to enable automatic detection of copy number changes for known and de novo CNV regions. He also discusses how it enables whole-genome copy number estimation using built-in or user-defined reference sets, including allele-specific analysis, and how it permits automatic detection of regions of LOH.