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

Yu S. Huang, Vasily Ramensky, Susan K. Service, Anna J. Jasinska, Yoon Jung, Oi Wa Choi, Rita M. Cantor, Nikoleta Juretic, Jessica Wasserscheid, Jay R. Kaplan, Matthew J. Jorgensen, Thomas D. Dyer, Ken Dewar, John Blangero, Richard K. Wilson, Wesley Warren, George M. Weinstock, Nelson B. Freimer

    Research output: Contribution to journalArticle

    13 Scopus citations

    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.

    Original languageEnglish (US)
    Article number41
    JournalBMC Biology
    Volume13
    Issue number1
    DOIs
    StatePublished - Jun 20 2015

    Keywords

    • Association
    • Linkage
    • Non-human primate
    • SNP
    • Vervet
    • Whole genome sequencing

    ASJC Scopus subject areas

    • Biotechnology
    • Structural Biology
    • Ecology, Evolution, Behavior and Systematics
    • Physiology
    • Biochemistry, Genetics and Molecular Biology(all)
    • Agricultural and Biological Sciences(all)
    • Plant Science
    • Developmental Biology
    • Cell Biology

    Fingerprint Dive into the research topics of 'Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits'. Together they form a unique fingerprint.

    Cite this