title: Identity-by-descent-based phasing and imputation in founder populations using graphical models.
abstract: Accurate knowledge of haplotypes, the combination of alleles co-residing on a single copy of a chromosome, enables powerful gene mapping and sequence imputation methods. Since humans are diploid, haplotypes must be derived from genotypes by a phasing process. In this study, we present a new computational model for haplotype phasing based on pairwise sharing of haplotypes inferred to be Identical-By-Descent (IBD). We apply the Bayesian network based model in a new phasing algorithm, called systematic long-range phasing (SLRP), that can capitalize on the close genetic relationships in isolated founder populations, and show with simulated and real genome-wide genotype data that SLRP substantially reduces the rate of phasing errors compared to previous phasing algorithms. Furthermore, the method accurately identifies regions of IBD, enabling linkage-like studies without pedigrees, and can be used to impute most genotypes with very low error rate.
authors: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors: Kimmo
authors: K
authors: Palin
authors: Harry
authors: H
authors: Campbell
authors: Alan F
authors: AF
authors: Wright
authors: James F
authors: JF
authors: Wilson
authors: Richard
authors: R
authors: Durbin
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D003196:Computer Graphics; D003198:Computer Simulation; D005828:Genetics, Population; D006239:Haplotypes; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012606:Scotland