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

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.