GENE-TARGETTED SNP DISCOVERY IN RHESUS MACAQUES

Oregon Health & Science University, Portland OR

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. This project originally aimed to identify single nucleotide polymorphisms (SNPs) in 10,000 gene regions, by sequencing the 3'UTR of unrelated Chinese and Indian rhesus macaques. The compiled SNP data will be analyzed to identify SNPs and allele frequencies in both Indian and Chinese populations and to report the findings in the public databases dbSNP and MonkeySNP. In the past year we adjusted our SNP discovery strategy to include next generation sequencing technologies (Illumina short-read formats). We completed transcriptome sequencing using mRNA from the prefrontal cortex of six Indian and six Chinese rhesus macaques. Sanger re-sequencing was used to validate the candidate SNPs and to inform filtering limits to insure robust data. Over 1 million SNPs were detected in this study thus far.