Patent ID: 7058517

Claim:
A method of inferring a pair of haplotypes present in an individual for a locus having at least m polymorphic sites, comprising (a) providing a database comprising (i) haplotypes of the locus for a set of m polymorphic sites present in a reference population and (ii) a frequency of occurrence in the reference population of each haplotype; (b) constructing a list of all genotypes that could result from all possible pairs of the haplotypes in the database for the reference population; (c) calculating a frequency for each genotype on the list, wherein the frequency of a given genotype is a function of a frequency for a pair of haplotypes from which the given genotype results, calculated assuming Hardy-Weinberg equilibrium; (d) generating a set of all possible masks for the m polymorphic sites, wherein each mask blocks the identity of the nucleotides present at m-n of the polymorphic sites and admits the identity of nucleotides present at the other n polymorphic sites; (e) for each mask, calculating the ambiguity resulting from genotyping only the n polymorphic sites at which nucleotide identity is admitted by the mask; (f) from among those masks having zero ambiguity, selecting a mask which has the lowest value of n; (g) determining the genotype of the individual at the n polymorphic sites at which nucleotide identity is admitted by the selected mask; and (h) assigning to the individual a pair of m polymorphic site haplotypes in the database for the reference population by matching the individual's determined genotype to a genotype on the list of genotypes, at the n polymorphic sites at which nucleotide identity is admitted by the selected mask.