Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

TY - JOUR

T1 - Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

AU - Albrechtsen, Anders

AU - Korneliussen, Thorfinn Sand

AU - Moltke, Ida

AU - van Overseem Hansen, Thomas

AU - Nielsen, Finn Cilius

AU - Nielsen, Rasmus

N1 - Keywords identity by descent • relatedness • hidden Markov model • linkage • association • complex disease • genome-wide analysis • SNP

PY - 2009

Y1 - 2009

N2 - Estimates of relatedness have several applications such as the identification of relatives or in identifying disease related genes through identity by descent (IBD) mapping. Here we present a new method for identifying IBD tracts among individuals from genome-wide single nucleotide polymorphisms data. We use a continuous time Markov model where the hidden states are the number of alleles shared IBD between pairs of individuals at a given position. In contrast to previous methods, our method accurately accounts for linkage disequilibrium using pairwise haplotype probabilities. The method provides a map of the local relatedness along the genome. We illustrate the potential of the method for mapping disease genes on a real data set, and show that the method has the potential to map causative disease mutations using only a handful of affected individuals. The new IBD mapping method provides considerable improvement in mapping power in natural populations compared to standard association mapping methods. Genet. Epidemiol. 2008. (c) 2008 Wiley-Liss, Inc.

AB - Estimates of relatedness have several applications such as the identification of relatives or in identifying disease related genes through identity by descent (IBD) mapping. Here we present a new method for identifying IBD tracts among individuals from genome-wide single nucleotide polymorphisms data. We use a continuous time Markov model where the hidden states are the number of alleles shared IBD between pairs of individuals at a given position. In contrast to previous methods, our method accurately accounts for linkage disequilibrium using pairwise haplotype probabilities. The method provides a map of the local relatedness along the genome. We illustrate the potential of the method for mapping disease genes on a real data set, and show that the method has the potential to map causative disease mutations using only a handful of affected individuals. The new IBD mapping method provides considerable improvement in mapping power in natural populations compared to standard association mapping methods. Genet. Epidemiol. 2008. (c) 2008 Wiley-Liss, Inc.

U2 - 10.1002/gepi.20378

DO - 10.1002/gepi.20378

M3 - Journal article

C2 - 19025785

SN - 0741-0395

VL - 33

SP - 266

EP - 274

JO - Genetic Epidemiology

JF - Genetic Epidemiology

IS - 3

ER -