Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities

In this paper, we evaluate the performance of using family-specific low-density genotype arrays to increase the accuracy of pedigree-based imputation. Genotype imputation is a widely used tool that decreases the costs of genotyping a population by genotyping the majority of individuals on a low-density array and using statistical regularities between the low-density and high-density individuals to fill in the missing genotypes. Previous work on population-based imputation has found that it is possible to increase the accuracy of imputation by maximizing the number of informative markers on an array. In the context of pedigree-based imputation, where the informativeness of a marker depends only on the genotypes of an individual’s parents, it may be beneficial to select the markers on each low-density array on a family-by-family basis.