Patent ID: 7981609

Claim:
A method for identifying at least one single nucleotide polymorphism (SNP) useful for analyzing a genetic sample, the method comprising: (a) obtaining a population of selected genetic samples; (b) separating the population of genetic samples into a first subpopulation of genetic samples comprising a portion of the genetic samples and a second subpopulation comprising the remaining genetic samples; (c) analyzing the genotype at each SNP of a plurality of SNPs for each genetic sample in the first subpopulation of genetic samples to determine for each SNP analyzed: i) N aa , the number of genetic samples in which the SNP is homozygous for a first allele, ii) N bb , the number of genetic samples in which the SNP is homozygous for a second allele, and iii) N ab , the number of genetic samples in which the SNP is heterozygous for a first and a second allele; (d) for the genetic samples in the first subpopulation, ranking each SNP of the plurality of SNPs by how nearly the ratio N aa :N bb :N ab matches the ratio 1:1:2 to provide a ranking of SNPs; (e) analyzing the genotype at each SNP in the plurality of SNPs for each genetic sample in the second subpopulation of genetic samples to determine for each SNP: i) N′ aa , the number of genetic samples in which the SNP is homozygous for a first allele, ii) N′ bb , the number of genetic samples in which the SNP is homozygous for a second allele, and iii) N′ ab , the number of genetic samples in which the SNP is heterozygous for a first and a second allele; (f) for the genetic samples in the second subpopulation, determining how closely the ratio N′ aa :N′ bb :N′ ab matches the ratio 1:1:2 to provide a score for each SNP; (g) designating a SNP that both ranks above a pre-determined cut-off in the ranking when analyzed in the first subpopulation and has a score above a pre-determined score when analyzed in the second subpopulation as a candidate SNP; (h) repeating steps (b)-(g) at least two times, each time designating one or more SNPs as a candidate SNP to generate at least two groups of candidate SNPs; and (i) identifying a SNP designated as a candidate SNP at least two times as a SNP useful for analyzing a genetic sample.