Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate

Laura A. Cox, Jeremy Glenn, Simon Ascher, Shifra Birnbaum, John L. VandeBerg

    Research output: Contribution to journalArticle

    7 Scopus citations

    Abstract

    We have developed an integrated approach, using genetic and genomic methods, in conjunction with resources from the Southwest National Primate Research Center (SNPRC) baboon colony, for the identification of genes and their functional variants that encode quantitative trait loci (QTL). In addition, we use comparative genomic methods to overcome the paucity of baboon specific reagents and to augment translation of our findings in a nonhuman primate (NHP) to the human population. We are using the baboon as a model to study the genetics of cardiovascular disease (CVD). A key step for understanding gene-environment interactions in cardiovascular disease is the identification of genes and gene variants that influence CVD phenotypes. We have developed a sequential methodology that takes advantage of the SNPRC pedigreed baboon colony, the annotated human genome, and current genomic and bioinformatic tools. The process of functional polymorphism identification for genes encoding QTLs involves comparison of expression profiles for genes and predicted genes in the genomic region of the QTL for individuals discordant for the phenotypic trait mapping to the QTL. After comparison, genes of interest are prioritized, and functional polymorphisms are identified in candidate genes by genotyping and quantitative trait nucleotide analysis. This approach reduces the time and labor necessary to prioritize and identify genes and their polymorphisms influencing variation in a quantitative trait compared with traditional positional cloning methods.

    Original languageEnglish (US)
    Pages (from-to)63-69
    Number of pages7
    JournalMethods
    Volume49
    Issue number1
    DOIs
    StatePublished - Sep 1 2009

    Keywords

    • Cardiovascular disease (CVD)
    • Discordant sib-pairs
    • Functional polymorphism
    • Gene array
    • Gene networks
    • Nonhuman primate (NHP)
    • Quantitative trait loci (QTL)

    ASJC Scopus subject areas

    • Molecular Biology
    • Biochemistry, Genetics and Molecular Biology(all)

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