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Principal Investigator: LOUISE C. SHOWE
Organization: WISTAR INSTITUTE
Fiscal Year: 2021
Award: $221,010
Funding agency: National Cancer Institute
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.
Terms: <Address><Animals><Antibody Repertoire><Antineoplastic Vaccine><Area><Assay><Basic Cancer Research><Bio-Informatics><Bioassay><Bioinformatics><Bioinformatics Shared Resource><Biologic Assays><Biological Assay><Blood capillaries><Budgets><CCSG><Cancer Center><Cancer Center Support Grant><Cancer Research Programs><Cancer Research Project><Cancer Vaccines><Cell Body><Cell Line><CellLine><Cells><Cellular Assay><Consultations><Corynebacterium><Cost Savings><Custom><Development><Disease><Disorder><Drug resistance><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Faculty><Formalin><Funding><Gene Expression><Gene Expression Monitoring><Gene Expression Pattern Analysis><Gene Expression Profiling><Gene Proteins><Genes><Genomics><Genomics Shared Resource><Human><Individual><Infrastructure><Institutes><Intratumoral heterogeneity><Investigators><Journals><Laboratories><Leadership><Length><Libraries><Magazine><Malignant Melanoma><Malignant Ovarian Neoplasm><Malignant Ovarian Tumor><Malignant Tumor of the Lung><Malignant Tumor of the Ovary><Malignant neoplasm of lung><Malignant neoplasm of ovary><Messenger RNA><Methylation><Mice><Mice Mammals><Micro RNA><MicroRNAs><Microarray Analysis><Microarray-Based Analysis><Microsatellite Markers><Microsatellite Repeats><Microsatellites><Mitochondria><Modern Man><Molecular><Murine><Mus><NGS Method><NGS system><Neoplasm Vaccines><Non-Polyadenylated RNA><Ovary Cancer><Paraffin Embedding><Patients><Preparation><Protein Gene Products><Proteins><Protocol><Protocols documentation><Provider><Pulmonary Cancer><Pulmonary malignant Neoplasm><RNA><RNA Gene Products><Research><Research Personnel><Researchers><Resource Sharing><Ribonucleic Acid><Sampling><Services><Site><Strains Cell Lines><System><Technology><Testing><Time><Tissue Sample><Training><Transcript Expression Analyses><Transcript Expression Analysis><Tumor Vaccines><Validation><Wing><anti-tumor vaccine><antitumor vaccine><base><bio-informatics shared resource><cancer immunology><capillary><cell assay><cell type><commercial application><cost><cultured cell line><data analysis pipeline><data processing pipeline><detection assay><developmental><digital><drug resistant><functional genomics><gene expression analysis><gene expression assay><heterogeneity in tumors><human tissue><improved><interdisciplinary approach><interest><intra-tumoral heterogeneity><intratumor heterogeneity><lung cancer><mRNA><meetings><melanoma><member><miRNA><miRNAs><microarray analyses><microarray technology><microbiome><mitochondrial><mouse model><multidisciplinary><multidisciplinary approach><murine model><nano><nano-string><nanostring><neoplasm immunology><next gen sequencing><next generation><next generation sequencing><nextgen sequencing><ovarian cancer><pathogen><promoter><promotor><protein expression><resistance to Drug><resistant to Drug><response><screening><shRNA><short hairpin RNA><single cell analysis><single cell sequencing><small hairpin RNA><targeted sequencing><transcriptional profiling><tumor heterogeneity><tumor immunology><vaccine for cancer><validation studies>