Imputation in families using a heuristic phasing approach

Whole genome sequencing (WGS) remains prohibitively expensive, which has encouraged the development of methods to impute WGS data into nonsequenced individuals using a framework of single nucleotide polymorphisms genotyped for genome-wide association studies (GWAS). Although successful methods have been developed for cohorts of unrelated individuals, current imputation methods in related individuals are limited by pedigree size, by the distance of relationships, or by computation time. In this article, we describe a method for imputation in arbitrarily shaped multigenerational pedigrees that can impute genotypes across distantly related individuals based on identity by descent. We evaluate this approach using GWAS data and apply this approach to WGS data distributed for Genetic Analysis Workshop 18.