A major goal in diabetes research is to understand how alterafions in the epigenome and subsequent responses in gene expression impact disease phenotype and treatment regimens. The Epigenefic and Genomics Core (EGC) will provide access to microarray platforms, massively parallel sequencing instrumentafion and computafional infrastructure to advance the diabetes and metabolism research goals of DRC investigators. The EGC will provide the following services: 1. Expression microarray technology; Affymetrix, Agilent, Codelink, NimbleGen, and lllumina platforms will be provided for microarray-based mRNA expression profiling. Affymetrix, Life Technologies and Exiqon platforms will be provide for miRNA profiling. 2. Technical support will be provided for high-throughput sequencing assays on lllumina HiSeq 2000 platforms, including RNA sequencing (RNAseq), microRNA sequencing (mlRNAseq), global run-on sequencing (GRO-Seq), ribosome profiling and deep sequencing (Ribo-Seq), chromafin immunoprecipitafion linked to massively parallel sequencing (ChlP-Seq) and MethylC-sequencing. 3. Bioinformatics support will be provided for assistance with experimental design, choice of technological platform, data analysis and data quality control. Implementafion of new data management and analysis pipelines will facilitate effective data mining. 4. Training of students, postdoctoral fellows, invesfigators and technical staff in the application of highthroughput sequencing methodologies and data analysis 5. High-performance computing resources, systems administrators, and data storage/backup systems will enable users to efficiently access and analyze their data. A major emphasis in the configurafion of the ECG will be implementafion of new Core services to reduce barriers to entry to new investigators. This will be achieved by providing direct Core support at three of the crifical steps required to take advantage of sequencing-based technologies; 1) Preparafion of sequencing libraries, 2) provision of computafional resources, and 3) assistance with data analysis through both training and provision of informatics services.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Center Core Grants (P30)
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Special Emphasis Panel (ZDK1)
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University of California San Diego
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Pappas, D J; Lizee, A; Paunic, V et al. (2018) Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest. Pharmacogenomics J 18:367-376
Cardamone, Maria Dafne; Tanasa, Bogdan; Cederquist, Carly T et al. (2018) Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation. Mol Cell 69:757-772.e7
Floyd, J S; Sitlani, C M; Avery, C L et al. (2018) Large-scale pharmacogenomic study of sulfonylureas and the QT, JT and QRS intervals: CHARGE Pharmacogenomics Working Group. Pharmacogenomics J 18:127-135
Muse, Evan D; Yu, Shan; Edillor, Chantle R et al. (2018) Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. Proc Natl Acad Sci U S A 115:E4680-E4689
Hajek, Catherine; Guo, Xiuqing; Yao, Jie et al. (2018) Coronary Heart Disease Genetic Risk Score Predicts Cardiovascular Disease Risk in Men, Not Women. Circ Genom Precis Med 11:e002324
Mahajan, Anubha (see original citation for additional authors) (2018) Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes. Nat Genet 50:559-571
Kulminski, Alexander M; Huang, Jian; Loika, Yury et al. (2018) Strong impact of natural-selection-free heterogeneity in genetics of age-related phenotypes. Aging (Albany NY) 10:492-514
Malik, Rainer (see original citation for additional authors) (2018) Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. Nat Genet 50:524-537
Seyerle, A A; Sitlani, C M; Noordam, R et al. (2018) Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology. Pharmacogenomics J 18:215-226
Gao, Chuan; Tabb, Keri L; Dimitrov, Latchezar M et al. (2018) Exome Sequencing Identifies Genetic Variants Associated with Circulating Lipid Levels in Mexican Americans: The Insulin Resistance Atherosclerosis Family Study (IRASFS). Sci Rep 8:5603

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