Genotyping the 270 HapMap samples for GAIN by Perlegen. Genotyping the 270 HapMap samples for GAIN by Perlegen

For the GAIN studies, Perlegen Sciences uses a high-density oligonucleotide array-based platform to analyze ~600,000 SNPs in large numbers of individuals. The SNP set was selected on the basis of linkage disequilibrium analysis of the HapMap data, and includes tag SNPs for all CEU bins. The arrays consist of DNA probes (short segments of DNA) that are synthesized in pre-determined positions on glass surfaces, and are designed to differentially hybridize to reference and alternate SNP alleles. Samples are prepared by amplifying regions containing SNPs across the whole genome, labeling the amplicons, and hybridizing them to the arrays. After hybridization, the arrays are washed, stained, and scanned, and the resulting fluorescence intensities are used to determine the genotype of each SNP.