VMSR DNA Mapping Services

Affymetrix DNA Mapping GeneChips offer a genome-wide view of SNP genotypes for human samples. The SNPs queried by these arrays are not chosen for their functional or biological significance, but rather for their ability to provide a genome-wide picture of changes. Each array (or set) has SNPs that are somewhat uniformly distributed across the human genome, simplifying linkage analysis, association, and copy number studies.

The Genome-Wide Human SNP Array 5.0 includes nearly 500,000 SNPs from the 22 autosomes and chromosome X, as well as 420,000 non-polymorphic markers for analysis of copy-number variation (CNV). The Genome-Wide Human SNP Array 6.0 starts with the same set of SNPs as the 5.0, and includes 424,000 additional SNPs. These additional SNPs include recent additions to dbSNP, mitochondrial SNPs, SNPs from chromosome Y, SNPs in recombination hotspots, and Tag SNPs. The GWS 6.0 also includes 946,000 non-polymorphic markers for analysis of copy-number variation.

Analysis

Primary analysis of these arrays is performed with Genotyping Console. The B-RLMM algorithm has been adapted and updated for the GWS arrays, and our average call rate is higher than 99%.

Copy Number Analysis solutions are still evolving for this platform. The Genotyping Console has been updated to analyze GWS6 arrays for copy number, but does not yet support GWS5. The VMSR has one license for Partek Genomics Suite, which will handle both array types. By using the HapMap cohort as a baseline we can detect amplifications or deletions in a single sample, or we can use the Control component of a large Case-Control study

Data Format

Upon completion of the experiment, we will provide the investigator with three files for each sample completed:

Because of the size and limited utility of the Affymetrix DAT files we do not keep them after scanning, unless specially requested to by the PI.