Family samples constitute the most intuitive setting for genotype imputation. Genotypes for a relatively modest number of genetic markers can be used to identify long stretches of haplotype shared between individuals of known relationship. These stretches of shared haplotype (or regions of “identity-by-descent”) are typically used to evaluate the evidence for linkage. Specifically, genetic linkage implies that family members who share a region of chromosome “identical-by-descent” will be more similar to each other than family members with the same degree of relatedness who do not share the region “identical-by-descent”. In the context of genotype imputation, we characterize each of these stretches in detail by genotyping additional markers in one or more individuals in the family. Genotypes for these markers can then be propagated to other family members who are only typed at a minimal set of markers.
