Patent ID: 8498825

Claim:
A method for genotyping a polymorphism in a test individual with a genotyping array, the method comprising: (a) obtaining allele specific intensity measurements for a first allele of the polymorphism and for a second allele of the polymorphism in a training set, wherein the training set comprises a plurality of individuals of known genotype for said polymorphism, and wherein the allele specific intensity measurements each represent an intensity of signal associated with one or more features on the genotyping array; (b) grouping the individuals in the training set into groups according to genotype, wherein each individual is assigned to one of the following groups: homozygous for the first allele, homozygous for the second allele, or heterozygous; (c) calculating a summary ratio of the intensity measurements for said first allele to the intensity measurements for said second allele for each group to obtain a first summary ratio for the group that are homozygous for said first allele, a second summary ratio for the group that are homozygous for said second allele and a third summary ratio for the group that are heterozygous; (d) measuring an allele specific intensity value for said first allele and for said second allele in said test individual with the genotyping array and calculating a test ratio for said test individual; (e) adjusting the allele specific intensity value for said first allele according to the third summary ratio obtained in (c) if said test ratio is closer to the third summary ratio than to the first or second summary ratios; and (f) making a genotype call for said polymorphism using the adjusted value obtained in (e) for said first allele and the intensity value obtained in (d) for the second allele.