MHC Genetics Core

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Abstract– Core C: MHC Genetic Typing Core The objectives of the MHC Genetic Typing Core are to support the genetic characterization and breeding strategy of the rhesus macaque 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 genome-wide approaches towards more rigorous genetic characterization of the colony. Specific aim 1: MHC Class I alleles, important to AIDS investigators, will be genotyped using high resolution sequencing in collaboration with Wisconsin NPRC Genomics Services. The genotypes on 175 animals will be obtained each year. Specific aim 2: GbS (170 animals per year), whole exome sequence (WES) (24 animals per year) and whole genome sequencing (WGS) (9 animals per year) will be generated to provide a) a more robust 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 newly identified alleles relevant for AIDS research and impacting infectious disease pathogenesis and vaccine-effectiveness, and d) genetic data to share with the broader research community. Specific 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 C will work with the SPF Oversight Committee and Core A to assemble breeding groups across our single colony using parent animals from original Colonies 1 and 2 and newly acquired animals. Our characterization of the SNPRC U42-supported SPF Indian rhesus macaque colony will provide critical genomics-based information to ensure the availability of these valuable animals for AIDS researchers for many colony generations to come. Furthermore, our genomics-based data will also be important for the planned expansion of the U42-supported colony.