Identifying IBD tracts that are tagged by rare variants

Identity by descent (IBD) between two individuals means that their alleles are identical because they were inherited from a shared common ancestor. Detection of IBD tracts is important for population genetics and association studies. IBD detection methods perform well for family studies where pedigrees are available and for common single nucleotide variants (SNVs). However, recent genotyping projects utilizing next generation sequencing comprise unrelated individuals and detect mostly rare variants. Currently, rare variants are of high interest in genetics because they are assumed to cause complex human diseases. However, their association with a disease is hard to detect as standard tests on rare variants yield low power. IBD mapping can be used to increase the power by two approaches. First, SNVs can be grouped based on IBD and subsequently their joint effect tested for disease association. Secondly, local genetic similarities between individuals can be measured by IBD and used for association tests like implemented in the sequence kernel association test (SKAT). For more see http://www.bioinf.jku.at/publications/2012/HGV2012_Povysil.pdf