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SNPs are chosen after an iterative screening process. For the Mapping 100K Set, we selected 545,000 SNPs in silico from public and Perlegen databases. We tested SNPs for call rate, accuracy, and reproducibility across more than 54 samples and selected over 126,000 for further development. The genotypes for 120,000 of these SNPs were released to the public domain on the UCSC genome browser, and on the affymetrix.com web site. Additional studies on more than 350 samples were used to narrow the SNP list down to ~116,000 in the commercial release. SNPs were chosen for the final product based on accuracy, call rate, reproducibility, and genome coverage. |