Genomics Shared Resource

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PROJECT SUMMARY – GENOMICS SHARED RESOURCE The Genomics Shared Resource (GSR) provides state-of-the-art infrastructure and support for integrated functional genomics studies of Cancer Center (CC) investigators. The highly trained staff and their efforts to maintain costs without diminishing service, provides CC members with access to the latest genomic technologies at a minimum cost. The GSR has kept pace with rapidly moving technological developments in the field and expanded its capabilities in response to CC needs. The GSR supports a large portfolio of applications for functional genomics research, including on-site Next-Generation (NG) sequencing, provided in this funding cycle by the addition of an Illumina NextSeq500 system. Other new services were added in response to input from user meetings, individual consultations and input from CC leadership. The new services included single-cell sequencing capabilities with the purchase of a Wafergen ICell8 system, and replacement of microarray-based gene expression analysis with NG 3’ end-seq. An amplification-free NanoString platform was implemented to carry out targeted gene expression using custom or commercially available panels and a NanoString RNA-Protein application was established. Gene and microRNA assays on fresh or formalin-fixed paraffin-embedded (FFPE) human tissues are routine. The GSR has established and improved protocols and yields for studies on small numbers of cells with limited RNA for the assessment of specific cell types. Lastly, the GSR implemented a qPCR-based Corynebacterium bovis detection assay that allows CC members to identify this pathogen in animal fecal and tissue samples, strengthening collaborative efforts with the Animal Shared Resource, and established mouse and human microsatellite assays for cell line verification. During the last CCSG budget cycle, the GSR moved into a newly renovated 1,733 NSF laboratory space in the west wing of the Institute with ease of access to all Cancer Center investigators. Building on a collaborative data analysis pipeline already in place with the Bioinformatics Shared Resource, the GSR successfully established an integrated research platform that includes the Molecular Screening Shared Resource to facilitate the identification of leads from shRNA screens to NG sequencing and Bioinformatics analysis in a productive, multidisciplinary scientific continuum. The GSR continues to provide critical routine services including capillary sequencing, promoter methylation studies and quantitative real-time PCR. Leveraging the rapidly increasing affordability of sequencing costs, together with the high-quality, reliable, personalized services provided, the GSR will continue to be a pivotal asset for CC investigators during the next CCSG budget cycle. The GSR plans to grow efforts in functional genomics in response to faculty expansion in the areas of epigenetics, cancer vaccines and immunology. The GSR is also critical to disease site-specific projects, particularly in ovarian cancer, lung cancer and melanoma that combine multidisciplinary approaches and require the assessment of large numbers of patient samples.