MHC GENETIC TYPING CORE

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Abstract To enhance the Johns Hopkins University pigtail macaque colony as a research resource for studying multiple facets of HIV infection, we have concentrated on improving our understanding of pigtail macaque (Macaca nemestrina) genetics. We continue to identify and study pigtail macaque MHC class I and MHC class II alleles using state of the art next generation sequencing approaches working in collaboration with Dr. David O'Connor at the University of Wisconsin. This ongoing effort has discovered novel MHC alleles and defined MHC class I haplotypes in pigtail macaques. To broaden the scope of our efforts beyond MHC, we have worked with Dr. Michael Snyder's team at Stanford to generate a de novo assembly of the pigtail macaque genome that used long-read sequencing technology. This pigtail macaque resource will facilitate use of functional genomics approaches in SIV studies. Expanding the genetic data available for pigtail macaques will a) increase the research utility of pigtail macaques and b) assist in genetic management of the JHU colony with guidance from Dr. Sree Kanthaswamy, a long term collaborator. These goals will be accomplished through two aims under the direction of Dr. Mankowski. Specific Aim 1 is to continue to characterize pigtail macaque MHC class I and MHC class II genotypes in JHU colony-born animals using state of the art deep sequencing approaches, thereby enhancing rigor and reproducibility of SIV/macaque models of HIV. Specific Aim 2 is to improve our de novo long-read sequencing assembly of the pigtail macaque genome to increase the research value of this macaque species by enabling functional genomic approaches.