Cancer Genomics Facility (CGF) The Cancer Genomics Facility (formerly a component of the Cancer Biomarkers Facility) performs quantitative sample assessment, comprehensive genotyping, and transcriptome profiling of tumor tissues, cells and related biological fluids (blood, urine, saliva) of clinical relevance. Analysis incorporates optimized hybridization or primer driven assays for genomic capture and interrogation utilizing state of the art PCR, microarray (bead, plate, cartridge) and, since 2012, sequencing (whole genome, exome, custom targeted) technologies.
The Specific Aims of the CGF are to 1) provide ?state of the art? genomic and transcriptomic services, 2) assist with study design and provide consultation services, 3) provide integrated bioinformatics and statistical analysis support, 4) strategically develop and implement advanced technologies, and 5) provide genomics leadership, administrative, and operational excellence. The facility is located adjacent to the UPCI Tissue and Research Pathology Services shared resource to expedite processing of specimens from diverse preparations ranging from whole mounted tissues (fresh, flash frozen, formalin fixed) to individual tumor stem cells. Protocols routinely incorporate manual and laser capture microdissection to mitigate effects of tumor heterogeneity. Novel methods have been developed to capture and amplify limiting amounts of DNA and RNA (<1ng) from archival (>10 years old) formalin fixed, paraffin embedded specimens. The CGF has generated an extensive reference database of single nucleotide polymorphisms and genomic sequence (70 samples) from ?normal? tissues for patient samples lacking matched germline specimens e.g. to serve as a gene copy number control. CGF collaborates closely with TARPS and CBS to ensure that UPCI investigators have benefit from optimized workflows. The facility routinely provides services to researchers from UPCI Programs, spanning basic, population science, and translational drug discovery and disease-site programs as well as each of the 3.5 SPOREs housed at UPCI. The CGF is also an integral component of the UPCI high- risk, high-reward initiative supporting development of early stage investigators and promoting new research pathways for established investigators. During the current project period investigators in nine UPCI Research Programs used the CGF.
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