Cancer Genomics

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CANCER GENOMICS SHARED RESOURCE In July 2006, to better meet the needs of Kimmel Cancer Center investigators, the former Nucleic Acid and Custom Microarray Facilities were restructured into the Cancer Genomics Shared Resource. The center hired a new director, manager and senior technician. This new resource provides state-of-the-art molecular assays and expertise to facilitate projects in basic, translational and clinical research. By serving as a centralized resource with a variety of platforms for genome-wide and gene-targeted services, it offers a wide spectrum of services, high quality control and low costs to investigators. This shared resource was established in response to technological advances in gene arrays and demand for high-throughput expression analysis and genome-wide analyses to investigate pathogenesis, therapeutics, genetic susceptibility and gene discovery in cancer research. For gene expression, this facility offers in-house printed slides for microRNA analysis as well as commercial arrays using the Affymetrix GeneChip platform. Differentially expressed transcripts defined by microarray-based mRNA expression profiling are confirmed by real-time RT-PCR. Since informatics is of paramount importance, the Cancer Genomics Shared Resource operates seamlessly linked to the new Biostatistic Shared Resource and has close links to the protein facility. In addition, it provides service for DNA sequence analysis, with increased throughput of DNA sequencing submission through development of a web-based program for ordering oligonucleotides, retrieving sequencing results and accounting for Shared Resource usage. Service is provided for Taqmanbased SNP typing, multiplex SNP genotyping using single-base extension (SBE) and pyrosequencing chemistry on ABI 3730, Beckman Coulter GenomeLab SNPstream and Pyrosequencing PSQ HS 96A platforms, respectively, and Affymetrix SNP Mapping GeneChips for use in genome-wide association studies, linkage analysis and copy number variation. It supports DNA sequence-based and genotyping projects ranging from single SNPs through custom multiplex to whole-genome panels. The shared resource has the flexibility to adapt, as the field of array technology changes. This shared resource will expand its services to include chromatin occupancy and epigenetic studies associated with differentiation, delineation of differences between normal and diseased states, and monitoring response to drugs. Regular microarray and novel technology seminars are provided bimonthly by major companies such as Affymetrix, Inc. (Santa Clara, CA), Agilent Technologies, Inc. (Santa Clara, CA), Luminex Corp. (Austin, TX), Beckman Coulter, Inc. (Fullerton, CA) and Applied Biosystems (Foster City, CA). In addition, presentations from users are arranged on a monthly basis for all center members and the TJU community.