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

## TL;DR

This paper presents a high-resolution genetic resource for vervet monkeys, enabling future studies on medically relevant traits through genome-wide sequencing of 721 individuals.

## Contribution

The study provides the first high-depth genome-wide polymorphism resource for vervet monkeys, optimized for association and linkage analyses.

## Key findings

- Over 4 million segregating sites were identified through whole genome sequencing of 721 vervet monkeys.
- SNP panels of about 500,000 and 150,000 SNPs were constructed for association and linkage analyses, respectively.
- Multipoint identity by descent matrices were generated to enhance linkage analysis utility.

## Abstract

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.

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.

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.

The online version of this article (doi:10.1186/s12915-015-0152-2) contains supplementary material, which is available to authorized users.