Experimental and Computational Genomics

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ABSTRACT 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