Core B: Bioinformatics and Functional Genomics Core

University Of Wisconsin-Madison, Madison WI

Investigators

Abstract

PROJECT SUMMARY/ABSTRACT – BIOINFORMATICS AND FUNCTIONAL GENOMICS CORE The Bioinformatics and Functional Genomics (BFG) Core forms a foundation for the P01 application by providing critical resources including functional genomics and biostatistical capacity to all three projects, to support the overarching goals of identifying the molecular drivers of prostate cancer (PC) and biomarker development. The performance of translational research mandates that investigators have ready access to advanced experimental approaches, clinical genomics analysis, and biostatistical support and analytical capacity. To accomplish the objectives of the Core, to support the P01 projects, we designed three Specific Aims: Specific Aim 1: To provide support and expertise for clinical genomics analysis, integrating rapid autopsy data with mCRPC tumor and liquid biopsy data to enable efficient data sharing and management. The BFG core will integrate clinical genomics data from metastatic prostate tumor biopsies including but not limited to transcriptomic, methylation, and chromatin conformation assays. The core will perform analysis on these assays to assist project teams in target analysis and development of mechanistic hypotheses for individual projects. Specific Aim 2: To provide support and expertise for bioinformatics studies across the P01 projects, including the execution and analysis of functional genomic screen experiments employed in all P01 projects. The BFG core will execute and perform bioinformatic analysis on high-throughput perturb-seq CRISPR screens that will identify transcriptional modulators of ARPC, DNPC, and NEPC subtypes of prostate cancer. Specific Aim 3: To provide support and expertise in biostatistical design, analysis, and dissemination of results from P01 biomarker studies. The core will be a resource for all three projects in project aims that involve the design and development of prognostic and predictive biomarkers derived from liquid biopsy studies performed on clinical trial samples. The core will also serve as a consultant for the design and interpretation of in vivo animal studies. The Bioinformatics and Functional Genomics Core is highly integrated with all three Projects and all Projects will rely significantly on the Core resources and expertise.