Genomic Analysis Core

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Project Summary The Genomic Analysis Core combines the expertise and instrumentation of two NCI CCSG supported facilities, the DNA Sequencing Facility and the Genomics Facility, to provide an integrated array of services for DNA sequencing and molecular profiling. Tapan Ganguly, PhD, the Director of the DNA Sequencing Facility since 2003, has been appointed Director of the consolidated Core. The integration of the two Shared Resources provides more efficient access and clarity of technologies to Abramson Cancer Center (ACC) members. It also presents opportunities for enhancing the quality and the range of services with better coordination as well as maximizing resource utilization without duplication. A team of highly experienced and trained professionals under two Technical Directors provides a whole spectrum of genomic and molecular biological services. These services are essential to ACC members for studying the role of specific genes in normal or abnormal cellular processes found in cancer cells and tumors. Investigators are able to observe global gene expression pattern in a sample, and genetic variability in an unaffected or tumor genome. The Core offers sequencing service on two platforms, gold standard Sanger sequencing on ABI capillary sequencers, and semiconductor sequencing on Ion Torrent PGM and its upgrade, Proton. The capillary sequencers also enable microsatellite genotyping and fragment analysis. Whole genome and targeted molecular profiling are performed on multiple platforms. The Core supports quantitative RNA profiling on Affymetrix GeneChips, Luminex FlexMap 3D, Fluidigm BioMark HD, and ABI 7900 real-time PCR system while DNA profiling is available on Affymetrix SNP GeneChip, Fluidigm BioMark HD and ABI 7900. The molecular biological services include cloning, subcloning and targeting vector construction for gene targeting in mice. ACC members benefit from consultations and training available throughout their projects. The range of services along with the expertise of the Core Director facilitates gene discovery, functional characterization and other research questions to elucidate the molecular pathogenesis of human cancers. In addition, molecular profiling of DNA and RNA together with targeted sequencing of cancer genes can help ACC members in cancer diagnosis, subclassifications, risk prediction and selection of appropriate therapy. 117 ACC members used the Core in the reporting period (10/01/13- 09/30/14) representing 36% of the total Core usage. CCSG support accounts for 15% of the proposed Core budget with the remaining funding coming from chargebacks, grants/contracts and Institutional support. Additional Institutional support comes in the form of funding for equipment purchase.