SNP DISCOVERY AND LD ANALYSIS IN RHESUS MACAQUES

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project aims to identify single nucleotide polymorphisms (SNPs) in 300 rhesus macaque genes and to use those SNPs to assess the extent of linkage disequilibrium (LD) across the genes. Specifically, 300 genes with significant relevance to non-human primate research will be analyzed in 24 unrelated Chinese and Indian rhesus macaques. Three distinct regions per gene (5', 3' and one intermediate region) will be PCR amplified, sequenced and compared to identify sequence variants. The compiled SNP data will be analyzed to identify allele frequencies in both Indian and Chinese populations. The SNP alleles will also be used to estimate the rate of LD decay with physical distance. The results will be reported in the public databases dbSNP and MonkeySNP.