SNP Genotyping Arrays
(Affymetrix Mapping Chips)

The Affymetrix mapping chips have the capability of interrogating up to 500,000SNPs simultaneously using their 10K, 100K, or 500K mapping chip kits, or interrogating up to 900,000 SNPs using the SNP Array 5.0 or 6.0. The SNP array 6.0 can also interrogate 950,000 markers for copy number variations.

These SNPs are defined by Affymetrix and their chromosomal positions are dependent upon the location of the SNP relative to a specific restriction enzyme site. The 100K mapping kit requires two chips, one in which the genomic DNA is digested with the restriction enzyme HindIII, the other requires digestion with XbaI; each chip interrogating 50,000 SNPs. The 500K mapping kit uses a higher density gene chip and is comprised of two chips, each interrogating 250,000 SNPs, one chip using genomic DNA digested with NspI, the other StyI.

The SNP Array 5.0 and 6.0 are single chip arrays. The SNP Array 5.0 features all of the SNPs from the two 500K mapping arrays as well as 420,000 additional non-polymorphic probes that interrogate other genetic differences such as copy number variation.

The SNP Array 6.0 contains probes for 900,000 SNPs, 480,000 from previous arrays (500K, 5.0) with 420,000 additional SNPs not previously represented. It also contains over 900,000 probes to investigate copy number variation. The overall process involves digestion of the genomic DNA with the appropriate restriction enzyme, ligating specific adaptors to the ends, PCR amplification, fragmentation of the PCR products, followed by labeling, hybridization, washing, staining, and finally scanning on the Gene Chip 3000 7G.

Investigators provide genomic DNA for the Facility staff to provide a full service, from restriction enzyme digestion through scanning. Currently, the Facility has supported a number of genome wide association scans with cohort sizes ranging from 150 to 900 samples. As with our Affymetrix Gene Expression services, investigators must provide the arrays AND the appropriate Affymetrix SNP Genotyping Kit.

*Cost is perarray, not per set.

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