Patent ID: 7881875

Claim:
A computer implemented method for selecting a third pool of single nucleotide polymorphisms (SNPs) across a genome wherein said third pool of SNPs is a subset of a first pool of SNPs, comprising the steps of: (a) providing a screening array, wherein said screening array contains at least one probe that is perfectly complementary to each allele of each SNP in said first pool of SNPs; (b) genotyping a plurality of individuals to make genotype calls for the SNPs in said first pool of SNPs by hybridizing a genomic sample derived from each of said individuals to said screening array and analyzing the hybridization pattern to make genotype calls, and using the genotype calls to calculate a call rate and rate of concordance for each SNP genotyped in step (b) over the plurality of individuals; (c) evaluating the call rate and rate of concordance for each SNP using a computer to select a second pool of SNPs from said first pool of SNPs, wherein SNPs from the first pool are selected for the second pool if the SNP was genotyped in (b) with a call rate and rate of concordance that met a specified threshold; (d) identifying SNPs in the second pool that are predicted to be in exons; (e) identifying SNPs in said second pool that are not in linkage disequilibrium with another SNP in the second pool using a computer; (f) identifying SNPs in the second pool that have a minor allele frequency that is at least 1% in a selected population using a computer; (g) selecting said third pool of SNPs from the second pool of SNPs using a computer wherein the third pool comprises a plurality of SNPs that were identified in (d), (e) and (f) and has fewer SNPs than the second pool; and (h) outputting the third pool of SNPs in a computer file, a display or a printout.