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

BACKGROUND: 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. RESULTS: In this paper, we examined four family-specific low-density marker selection strategies and evaluated their performance in the context of a real pig breeding dataset. We found that family-specific or sire-specific arrays could increase imputation accuracy by 0.11 at one marker per chromosome, by 0.027 at 25 markers per chromosome and by 0.007 at 100 markers per chromosome. CONCLUSIONS: These results suggest that there may be room to use family-specific genotyping for very-low-density arrays particularly if a given sire or sire-dam pairing have a large number of offspring.