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.

The most important metric of a whole-genome association study is the genetic power to detect an associated allele of a given effect size.

The most important study design factor affecting power is the number of cases and controls for each phenotype (or sub-phenotype) under study. The number of samples processed is generally dictated by budget and cost effectiveness of the genotyping platform. Affymetrix provides the greatest genetic power per dollar for your whole-genome association study by increasing the number of samples you can screen during your initial scan and replication phase.



One important study design factor is the quality of the data generated by the study. Random errors dilute the statistical signals or produce false positive associations. The SNP Array 6.0 demonstrates industry-leading performance, with average call rates greater than 99 percent. Average HapMap concordance exceeds 99.7%.

For those using an LD-mapping approach, one final factor affects power: genetic coverage, or the degree to which all relevant, possible alleles in the populations under study are strongly correlated with a SNP on the panel. For the SNP Array 6.0, the genetic power in most populations is approaching completeness for alleles greater than 5 percent frequency. With these innovations, the power calculations are close to the theoretical limits that would be used if one were to directly score the causative mutations.

The Genome-Wide SNP Array 6.0 enables high-performance, low-cost genotyping and provides the greatest genetic power per dollar.

Using Affymetrix' SNP Array 6.0 for Copy Number Research in Cancer with Partek's Genomics Suite
Tom Downey, Partek and Sharoni Jacobs, Affymetrix

Identifying Copy Number Variation using the Affymetrix SNP Array 6.0 and Partek Genomics Suite
Tom Downey, President, Partek Inc.

Whole-genome Association Analysis of Type 2 Diabetes
David Altshuler, M.D., Ph.D., Broad Institute of MIT & Harvard

Genome-wide Association Study of 14,000 Cases of Seven Common Diseases and 3,000 Shared Controls
Peter Donnelly, Ph.D., University of Oxford

More than 906,600 single nucleotide polymorphisms

• Unbiased selection of 482,000 SNPs; historical SNPs from the SNP Array 5.0
• Selection of additional 424,000 SNPs
  • Tag SNPs
  • SNPs from chromosomes X and Y
  • Mitochondrial SNPs
  • New SNPs added to the dbSNP database
  • SNPs in recombination hotspots

More than 946,000 copy number probes

• 202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants
• Regions resolve into 3,182 distinct, non-overlapping segments; on average 61 probes per region
• 744,000 probes, evenly spaced along the genome

The SNP Array 6.0 drives genetics forward by enabling a new study paradigm for researchers—a whole-genome approach to replication. This new approach increases the overall statistical genetic power to detect associations, and eliminates other disadvantages tied to selecting a limited subset of markers in the replication phase.

Learn more about this new approach in the Application Note, A New Paradigm for Two-Stage Association Studies.

To learn more about the new Genome-Wide SNP Array 6.0 or other Affymetrix genotyping products please call 1-888-DNA-CHIP (888-362-2447).