Work

Identity‐by‐descent‐based phasing and imputation in founder populations using graphical models

Year: 2011

Type: article

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.

Source: Genetic Epidemiology

DOI: 10.1002/gepi.20635

Authors: Kimmo Palin, Harry Campbell, Alan F. Wright, James F. Wilson, Richard Durbin

Institutions: Wellcome Sanger Institute, University of Edinburgh, Western General Hospital, Institute of Genetics and Cancer, MRC Human Genetics Unit

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Wellcome Trust, Scottish Government, Royal Society, European Commission

Awards: WTCCC2 core activities, G4690206792, G5808852883, The genetics of weight, BMI, adiposity and obesity