Patent ID: 6931326

Claim:
A method of determining polymorphic sites or sub-haplotypes for a locus that correlate with an outcome of interest, comprising: (a) providing a haplotype for each allele of the locus for each subject in a cohort of subjects and an outcome value for the outcome of interest for each subject in the cohort of subjects, the locus comprising at least two polymorphic sites; (b) statistically analyzing each individual polymorphism in the haplotypes for the degree to which it correlates with the outcome of interest and calculating a numerical measure of the degree of correlation; (c) saving each individual polymorphism whose numerical measure of the degree of correlation meets a first cut-off criterion and its numerical measure of the degree of correlation; (d) generating all possible pair-wise combinations of the saved individual polymorphisms so as to provide a set of n-site sub-haplotypes where n=2; (e) statistically analyzing each newly generated n-site sub-haplotype for the degree to which it correlates with the outcome of interest and calculating the numerical measure of the degree of correlation; (f) saving each n-site sub-haplotype whose numerical measure of the degree of correlation meets the first cut-off criterion and its numerical measure of the degree of correlation; (g) generating all possible pair-wise combinations among and between the saved individual polymorphisms and saved sub-haplotypes, to produce new sub-haplotypes with increased values of n; and (h) repeating steps (e) trough (g) until either (i) no new sub-haplotypes can be generated, or (ii) no new sub-haplotypes having n less than a pre-selected limit can be generated.