MHC Genetic Typing Core

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Project Summary/Abstract: Macaca nemestrina serves as a critical animal model for the study and treatment of AIDS and AIDS-related diseases. However the genomic characterization of M. nemestrina remains limited. Thus one goal of the proposed work is to expand genome analysis, enabling the update of tools used to inform the genetic management and assignment of M. nemestrina for S/HIV studies. Towards this goal, we have used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) with prevalent minor alleles among subjects in the WaNPRC breeding colony. These SNPs will be used to support the design of a 96 SNP panel for use in parentage validation. The 96 SNP array will then be evaluated by genotyping a set of 96 M. nemestrina DNAs, including 6 replicate samples to test for genotype reproducibility, and 90 DNA samples from animals with known parentage to test for accurate parentage discrimination. Once validation is complete, the SNP array will be used to re-genotype the breeding colony, enabling a smooth transition from the STR platform to SNP typing for parentage assessment. In addition, this project will expand MHC Class I allele haplotype analysis of the WaNPRC breeding colony to ensure that all SPF breeding colony animals are genetically characterized.