Integrated reference panel of Macaca mulatta haplotypes for genotype imputation in populations of mixed origin

Abstract

Genotype imputation makes it possible to considerably reduce the cost of whole-genome data acquisition preserving the information value, but its accuracy depends directly on the availability of a high-quality phased reference panel of haplotypes. The existing panels for Macaca mulatta cover mostly the Indian species lineage and do not reflect the genetic structure of laboratory populations of mixed origin. This retrospective bioinformatics study aimed to produce and validate a phased reference panel based on the consolidation of publicly available whole-genome datasets from 618 M. mulatta individuals of both geographic lineages processed in accordance with the common standardized protocol. The resulting panel includes 33,457,491 SNP markers. Validation on samples of Indian and Chinese origin with ultra-low coverage (0.1x–0.9x) confirmed high imputation accuracy, which was highest for the Indian lineage dominant in the panel. Testing on 10 independent samples with the 0.6x coverage showed a high average imputation reliability score (INFO = 0.898). The created resource opens the prospects for cost-effective genotyping of large M. mulatta cohorts and provides the basis for whole-genome association and population genetic studies in domestic and foreign primate research centers.