The Experimental and Computational Genomics Core (ECGC) is a newly created Core that integrates all of the cancer genomics services in the Sidney Kimmel Comprehensive Cancer Center (SKCCC). The primary mission of the Core is to allow SKCCC investigators to harness the ongoing revolution in cancer genomics to accelerate their basic discovery and translational research. The ECGC has streamlined services that were previously offered through three separate Cores: the Microarray Core, Next-Generation Sequencing Core and Bioinformatics Core. The new joint structure recognizes that the activities of the previous three Cores are highly interdependent and formalizes a long-standing commitment to coordinate computing resources, hiring and educational activities for the common good of the SKCCC. The newly created centralized structure has streamlined access to experimental and computational genomics technologies and expertise, and enhanced opportunities for didactic and hands-on education in both the experimental and computational aspects of cancer genomics. The immense laboratory and analytical expertise brought together in the newly integrated cross-disciplinary Core are now available, in a single and clearly defined Core, to all SKCCC investigators. The services provided by this Core are not available elsewhere. An SKCCC member looking to outside resources would need to independently talk with multiple vendors and would only be able to obtain piecemeal services. This Core is led by Leslie Cope, Ph.D.; Sarah Wheelan, M.D., Ph.D.; and Srinavasan Yegnasubramanian, M.D., Ph.D., who bring together multidisciplinary expertise in genomics technologies, computational biology and biostatistics/bioinformatics. The Core provides access to, and education in, state-of-the-art, next- generation sequencing, microarray technologies and analytical workflows for probing genomic alterations (including SNVs, indels and structural alterations), cancer epigenomics (e.g., ChIP-seq and DNA methylome), transcriptomics and metagenomics. For each project, the Core uses a multidisciplinary clinic model to establish and execute an experimental and analytical plan, first meeting with each investigator and then helping them through all aspects of their genomics experiments, including experimental design, high-throughput microarray or next-generation sequencing workflows, and computational/bioinformatics data analysis. Additionally, the Core provides extensive educational resources, including short courses, workshops and a symposium, so that investigators can gain the skills they need to fully understand and utilize the data and analyses generated. The success of this Core is evidenced by the high level of usage across nearly all Programs and the cited support in a large number of impactful publications, national/international conference abstracts and successful grant applications. SKCCC Managed Core Reporting Period: Jan. 1, 2015, to Dec. 31, 2015

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA006973-57
Application #
9944488
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2020-05-01
Budget End
2021-04-30
Support Year
57
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Johns Hopkins University
Department
Type
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21205
Kaur, Harsimar B; Guedes, Liana B; Lu, Jiayun et al. (2018) Association of tumor-infiltrating T-cell density with molecular subtype, racial ancestry and clinical outcomes in prostate cancer. Mod Pathol 31:1539-1552
Connolly, Roisin M; Fackler, Mary Jo; Zhang, Zhe et al. (2018) Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008. Breast Cancer Res Treat 167:107-116
Ye, I Chae; Fertig, Elana J; DiGiacomo, Josh W et al. (2018) Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes. Mol Cancer Res 16:1889-1901
Zhu, Yezi; Sharp, Adam; Anderson, Courtney M et al. (2018) Novel Junction-specific and Quantifiable In Situ Detection of AR-V7 and its Clinical Correlates in Metastatic Castration-resistant Prostate Cancer. Eur Urol 73:727-735
Lu, Yunqi; Hu, Zhongyi; Mangala, Lingegowda S et al. (2018) MYC Targeted Long Noncoding RNA DANCR Promotes Cancer in Part by Reducing p21 Levels. Cancer Res 78:64-74
Rao, Karthik; Liang, Stella; Cardamone, Michael et al. (2018) Cost implications of PSA screening differ by age. BMC Urol 18:38
Johnson, Renee M; Fleming, Charles B; Cambron, Christopher et al. (2018) Race/Ethnicity Differences in Trends of Marijuana, Cigarette, and Alcohol Use Among 8th, 10th, and 12th Graders in Washington State, 2004-2016. Prev Sci :
Marrone, Kristen A; Zhou, Xian; Forde, Patrick M et al. (2018) A Randomized Phase II Study of Metformin plus Paclitaxel/Carboplatin/Bevacizumab in Patients with Chemotherapy-Naïve Advanced or Metastatic Nonsquamous Non-Small Cell Lung Cancer. Oncologist 23:859-865
Bar-Shir, Amnon; Alon, Lina; Korrer, Michael J et al. (2018) Quantification and tracking of genetically engineered dendritic cells for studying immunotherapy. Magn Reson Med 79:1010-1019
Altekruse, Sean F; Shiels, Meredith S; Modur, Sharada P et al. (2018) Cancer burden attributable to cigarette smoking among HIV-infected people in North America. AIDS 32:513-521

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