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Method and system for determining haplotypes from a collection of polymorphisms

  • US 20030211501A1
  • Filed: 10/18/2002
  • Published: 11/13/2003
  • Est. Priority Date: 04/18/2001
  • Status: Abandoned Application
First Claim
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1. A method for assigning haplotype pairs for a polymorphic genomic region to a plurality of individuals, comprising:

  • (a) obtaining a genotype for the polymorphic genomic region from each of the individuals;

    (b) enumerating all possible haplotypes hi that are consistent with each genotype;

    (c) assigning an evidence score si to each of the enumerated haplotypes hi;

    (d) calculating an initial haplotype frequency fi for each haplotype among the possible haplotypes, wherein the initial haplotype frequency fi is a function of the evidence score si;

    (e) determining for each genotype obtained in step (a) a pair score Fk for each pair of haplotypes that is consistent with that genotype, wherein Fk is a function of the frequency fi for each of the haplotypes in the pair;

    (f) calculating, for each genotype and consistent haplotype pair whose pair score Fk meets a pair score criterion, a probability pk that assignment of that haplotype pair to the genotype would be correct;

    (g) generating a revised haplotype frequency fi for each haplotype, wherein the revised haplotype frequency fi is a function of the probability pk for each consistent haplotype pair which contains the haplotype; and

    (h) repeating steps (e) through (g) until an end condition is reached, with the proviso that for each repetition the frequency fi employed in step (e) is replaced by the revised frequency fi determined in step (g).

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