Cancer Genomics

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PROJECT SUMMARY (See instructions): The goal of the Kimmel Cancer Center (KCC) - Cancer Genomics Shared Resource (CGSR) is to provide genomics and bioinformatics leadership to KCC members to facilitate projects in basic, translational and clinical research thus assisting investigators to achieve their overall goals. By serving as a centralized resource with a variety of platforms, a significant computational infrastructure for data analysis and storage, and experienced professionals in genomics-based methods, the CGSR offers a wide spectrum of services and high quality control at cost-effective prices to investigators for DNA and RNA analysis. Services include: 1) nucleic acid isolation and purification, and related molecular biological services including PCR, cloning, sub-cloning and site-directed mutagenesis; 2) cost-effective, reliable, long-read, automated Sanger sequencing with fast turnaround; 3) microsatellite-based genotyping and fragment analysis; 4) high-quality genome-wide SNP genotyping, copy number variation, aCGH and DNA methylation profiling analysis; 5) genome-wide mRNA and microRNA expression profiling on Affymetrix microarrays as well as custom made disease- and/or pathway-targeted arrays; 6) independent validation of candidate loci/genes by quantitative PCR analysis; 7) assisting investigators with experimental design and analyzing results providing web-based pathway analysis software; and, 8) archiving of both Sanger sequencing and Affymetrix array data. Recently added services based on Applied Biosystems SOLID 4 and 5500x1 and lon Torrent PGM include: 1) whole genome sequencing as well as targeted resequencing of human and model organisms; 2) chromatin-IP sample sequencing; 3) measuring RNA expression with both digital gene expression and RNA-sequencing (whole transcriptome) including short and long non-coding RNA; and, 4) genome-wide DNA methylation sequencing. In addition, CLIA certification was received recently to facilitate molecular profiling for clinical research-oriented studies. The range of services mentioned above coupled with the expertise of the resource director, enables the CGSR to provide full support to KCC investigators to facilitate gene discovery, functional characterization and other basic research efforts to elucidate the molecular pathogenesis of human cancers. 63 KCC members have used this Shared Resource in the last year. KCC members' usage represents 90% of the total Shared Resource usage and KCC support represents 91% of the proposed operating budget with the remaining funding coming from charge-backs and institutional support.