GENOMICS SHARED RESOURCE (Core-298) ABSTRACT Overview: The Genomics Shared Resource (GSR) offers UCCC members high-quality and cost-effective services and technical support for high-throughput genomic and proteomic investigation to study cancer pathogenesis, therapeutics, genetic susceptibility and biomarker development. Equipment: The GSR houses equipment to support DNA next-generation sequencing (NGS) (Illumina HiSeq 2000, 2500 and 4000, Illumina MiSeq, and LifeTech IonPGM); DNA microarray analysis (Affymetrix GeneChip and GeneTitan systems; Illumina iScan system; and Agilent SureScan Microarray system); single-cell genomics (Fluidigm C1; Juno; Access Array and Biomark HD Systems); proteomics (Somalogic SOMAscan); and Affymetrix, Agilent and Illumina microarray and sequencing software. Services: The GSR offers methodologies for quantitative assessment of DNA/RNA/Protein including evaluation of human and murine cells harboring shRNA and CRISPR libraries UCCC members have obtained from the Functional Genomics Shared Resource (FGSR). Our capabilities include genome-wide analyses of DNA mutations and RNA expression from tissues to single cells. With these capabilities, the GSR provides: 1) Genome-wide gene variations, gene expression and transcriptome analysis, epigenetics and cytogenomics using NGS and gene microarrays; 2) Single cell genomic analysis; 3) Quantitate selected genes/panels using real time PCR and digital PCR; 4) Proteomic quantitative analysis. Consultation and Education: The GSR provides consultation for designing and analyzing reliable genomics and proteomic experiments and helps keep members up to date as technology advances through seminars and hands-on training. Management: The GSR is an institutional core managed by the UCCC, and is overseen by the Associate Director for Basic Research. Use of Services: Since July 2011, the GSR has provided services to 313 investigators. Forty-seven percent of users (148) were UCCC members, representing all 6 Programs and resulting in 155 peer reviewed publications. CCSG funding represents 5% of the annual operating budget. The remaining support comes from the University of Colorado NIH funded CTSA (Colorado Clinical and Translational Sciences Institute (CCTSI)) grant (4%), and user fees (91%). Future Directions: The GSR has three main future directions that will enhance the SR and UCCC member cancer research: 1) Optimize single cell genomics; 2) Enhance aptamer-based proteomics; 3) Adopt single molecule sequencing.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA046934-32
Application #
9867666
Study Section
Subcommittee H - Clinical Groups (NCI)
Project Start
Project End
Budget Start
2020-02-01
Budget End
2021-01-31
Support Year
32
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of Colorado Denver
Department
Type
DUNS #
041096314
City
Aurora
State
CO
Country
United States
Zip Code
80045
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Lyu, Hui; Wang, Shuiliang; Huang, Jingcao et al. (2018) Survivin-targeting miR-542-3p overcomes HER3 signaling-induced chemoresistance and enhances the antitumor activity of paclitaxel against HER2-overexpressing breast cancer. Cancer Lett 420:97-108
Noonan, Sinead A; Patil, Tejas; Gao, Dexiang et al. (2018) Baseline and On-Treatment Characteristics of Serum Tumor Markers in Stage IV Oncogene-Addicted Adenocarcinoma of the Lung. J Thorac Oncol 13:134-138
Drilon, Alexander; Laetsch, Theodore W; Kummar, Shivaani et al. (2018) Efficacy of Larotrectinib in TRK Fusion-Positive Cancers in Adults and Children. N Engl J Med 378:731-739
Radakovich, Lauren B; Marolf, Angela J; Shannon, John P et al. (2018) Development of a microcomputed tomography scoring system to characterize disease progression in the Hartley guinea pig model of spontaneous osteoarthritis. Connect Tissue Res 59:523-533

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