Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

Abstract

Background: We report here the first genome-wide high-resolution polymorphism resource for non-human primate (NHP) association and linkage studies, constructed for the Caribbean-origin vervet monkey, or African green monkey (Chlorocebus aethiops sabaeus), one of the most widely used NHPs in biomedical research. We generated this resource by whole genome sequencing (WGS) of monkeys from the Vervet Research Colony (VRC), an NIH-supported research resource for which extensive phenotypic data are available.

Results: We identified genome-wide single nucleotide polymorphisms (SNPs) by WGS of 721 members of an extended pedigree from the VRC. From high-depth WGS data we identified more than 4 million polymorphic unequivocal segregating sites; by pruning these SNPs based on heterozygosity, quality control filters, and the degree of linkage disequilibrium (LD) between SNPs, we constructed genome-wide panels suitable for genetic association (about 500,000 SNPs) and linkage analysis (about 150,000 SNPs). To further enhance the utility of these resources for linkage analysis, we used a further pruned subset of the linkage panel to generate multipoint identity by descent matrices.

Conclusions: The genetic and phenotypic resources now available for the VRC and other Caribbean-origin vervets enable their use for genetic investigation of traits relevant to human diseases.

Fig. 1

Using the variant data from the WGS of the trio shown on the left, we evaluated three different down-sampling schemes, drawn on the right, to determine a pedigree-wide strategy for selecting monkeys for medium (4X) or low (1X) sequencing coverage. a The frequency of Mendelian errors in a trio increases in all three down-sampling experiments compared to the original data; however, the increase in error rate is greatest when both parents are low coverage and the child is medium coverage. b The percentage of concordant genotype calls between original data and down-sampled data is lowest when both parents are low coverage and the child is medium coverage. The percentages shown for both the rate of Mendelian inconsistency and for genotype concordance represent averages over three down-sampling experiments

Fig. 2

Boxplot of actual sequencing depth versus planned sequencing depth for the 725 monkeys in the WGS study