Efficiency of whole-exome sequencing in old world and new world primates using human capture reagents

Abstract

Background: Whole-exome sequencing (WES) can expedite research on genetic variation in non-human primate (NHP) models of human diseases. However, NHP-specific reagents for exome capture are not available. This study reports the use of human-specific capture reagents in WES for olive baboons, marmosets, and vervet monkeys.

Methods: Exome capture was carried out using the SureSelect Human All Exon V6 panel from Agilent Technologies, followed by high-throughput sequencing. Capture of protein-coding genes and detection of single nucleotide variants were evaluated.

Results: Exome capture and sequencing results showed that more than 97% of old world and 93% of new world monkey protein coding genes were detected. Single nucleotide variants were detected across the genomes and missense variants were found in genes associated with human diseases.

Conclusions: A cost-effective approach based on commercial, human-specific reagents can be used to perform WES for the discovery of genetic variants in these NHP species.

Keywords: exome capture; genetic variants; marmosets; olive baboons; vervet monkeys.

Figure 1

Protein coding genes not captured in three NHP species

Figure 2

Circos plots showing SNVs for baboon (left), marmoset (middle) and vervet (right) Red bars indicate synonymous and blue bars indicate missense variants at intervals of 5 megabases in the outer track. Asterisks indicate nonsense variants in the inner track.