Cross-species Microarray-based Genomic Selection: application to nonhuman primate

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DESCRIPTION (provided by applicant): Nonhuman primates offer a unique model for studying human biology, disease, and evolution. Nevertheless, 95% of nonhuman primates lack the basic genomic sequence resources required for modern genetic and comparative genetic studies of disease, including AIDS. Thus, there is a need to develop affordable and efficient methods that use the available nonhuman primate genomic resources as a springboard for population- based genomic sequencing in a greater diversity of species. The focus of this R21 proposal is to test and to demonstrate the capability of a newly developed genomic technology, microarray-based genomic selection (MGS), as such a method. We and others have shown that microarrays can be used to selectively enrich for targeted regions of a complex genome from total genomic DNA, thereby providing the templates necessary for population-based resequencing of the targeted intervals. However, if MGS could be used in a cross-species format, its utility would increase exponentially. Though the cross-species application of MGS is untested, analogous studies of cross-species hybridization between nonhuman primates using gene expression microarrays have already proved successful. The first goal of this proposal is therefore to determine the capability of cross-species MGS to enrich for orthologous targeted genomic regions of nonhuman primates at divergence levels from 1-10% (Aim 1). The second goal of this proposal is to directly demonstrate the utility of cross-species MGS for nonhuman primate and AIDS research. To do so we will apply the cross-species MGS approach toward sequencing 125-250 candidate genes for the benign nature of SIV infection in the sooty mangabey, an exceptional nonhuman primate model for AIDS research that lacks genomic resources (Aim 2). In summary, a method that can simultaneously produce both comparative and population-based sequence data from targeted regions in multiple species will be tested and applied toward the identification of genetic factors that suppress progression to AIDS. PUBLIC HEALTH RELEVANCE: As our closest living relatives, nonhuman primates are a unique genetic resource for studying disease progression to AIDS. The goal of this research project is to apply a new DNA sequencing technology toward sequencing genes in nonhuman primates, including a biomedical model for AIDS research.