Dr. Stephen Rich was recently awarded an NIH grant for the study of functional significance of the SNPs identified as critical to the risk of type 1 diabetes (T1D). The study “Systematic Identification of Functional T1D-associated Non-coding SNPs using Genetic, Transcriptomic and Epigenetic Methods” involves both CPHG Resident Faculty (Onengut, Farber) and Affiliated Faculty (Guertin, Adli) as well as former CPHG member Pat Concannon. The grant started 29 September 2016 and will continue through 30 June 2021. The project takes advantage of the T1D resource at UVA and the work that shows T1D-associated credible SNPs are enriched in regulatory regions in specific cell types. The grant proposes to directly examine these SNPs in T and B cells from our viably frozen PBMC collection. The team will focus on the accessible chromatin landscape at T1D risk loci, using ATAC-seq and characterize the impact of these SNPs on gene expression using RNA-seq in the same cells from the same individuals. They will test the function of the variants that impact chromatin accessibility and gene expression by perturbation experiments using CRISPR/Cas9 gene editing, followed by validation by gene expression and other functional assays.
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