MHC Genetic Typing Core

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PROJECT SUMMARY – Core 3: MHC Genetic Typing Core The objectives of the MHC and Genetic Typing Core are to support the genetic characterization and breeding strategy of the SPF Colony, with a focus towards optimizing the colony for AIDS-related research. The Core's three aims build upon the current strengths of the Core and incorporate new approaches towards more rigorous genetic characterization of the colony. In Aim 1, MHC Class I alleles, important to AIDS investigators, will be genotyped using high resolution sequencing in collaboration with Dr. Wiseman at the Wisconsin NPRC. The genotypes on 185 animals will be obtained each year. In Aim 2, both genotype-by-sequencing (GbS) and whole genome sequencing (WGS) will be used to provide a) a more robust Ancestry Informative Markers (AIMs) set defining Indian and Chinese ancestry information both genome-wide and at specific loci, b) parentage information to verify pedigrees and investigate colony origins, c) genotypic information to allow for the identification of animals carrying known and potentially new alleles relevant for AIDS-related research and impacting infectious disease pathogenesis and vaccine effectiveness, and d) development of a means to share the genetic data with the research community using a web-based user interface allowing access to LabKey-managed data. In Aim 3, genetic data from Aims 1 and 2 will be used to maximize genetic diversity of the colony, while maintaining sufficient numbers of animals with specific MHC Class I alleles and ancestry for SIV/HIV related studies. Core 3 will work with Core 1 and the SPF Oversight Committee to assemble breeding groups using animals derived from the both Colonies 1 and 2.