title: Conditional probability methods for haplotyping in pedigrees.
abstract: Efficient haplotyping in pedigrees is important for the fine mapping of quantitative trait locus (QTL) or complex disease genes. To reconstruct haplotypes efficiently for a large pedigree with a large number of linked loci, two algorithms based on conditional probabilities and likelihood computations are presented. The first algorithm (the conditional probability method) produces a single, approximately optimal haplotype configuration, with computing time increasing linearly in the number of linked loci and the pedigree size. The other algorithm (the conditional enumeration method) identifies a set of haplotype configurations with high probabilities conditional on the observed genotype data for a pedigree. Its computing time increases less than exponentially with the size of a subset of the set of person-loci with unordered genotypes and linearly with its complement. The size of the subset is controlled by a threshold parameter. The set of identified haplotype configurations can be used to estimate the identity-by-descent (IBD) matrix at a map position for a pedigree. The algorithms have been tested on published and simulated data sets. The new haplotyping methods are much faster and provide more information than several existing stochastic and rule-based methods. The accuracies of the new methods are equivalent to or better than those of these existing methods.
authors.affiliation: Virginia Bioinformatics Institute, Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, USA.
authors.forename: Guimin
authors.initials: G
authors.lastname: Gao
authors.forename: Ina
authors.initials: I
authors.lastname: Hoeschele
authors.forename: Peter
authors.initials: P
authors.lastname: Sorensen
authors.forename: Fengxing
authors.initials: F
authors.lastname: Du
mesh_terms: D000818:Animals; D005260:Female; D005821:Genetic Techniques; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D008297:Male; D008957:Models, Genetic; D015233:Models, Statistical; D010375:Pedigree; D011336:Probability; D040641:Quantitative Trait Loci