Core C: Bioinformatics

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PROJECT SUMMARY/ABSTACT The Bioinformatics Core will provide services that are vital to many of the projects with in the SPORE in Prostate Cancer, including the application and development of statistical and computational techniques to process next-generation sequencing data from a variety of applications. The Core can apply standard processing algorithms and pipelines to a large number of samples. Additionally, the personnel of this Core have the expertise to create and deploy custom methods and applications as needed by the SPORE researchers. Members of the Core can leverage their experience in processing the large amount of genomic data at Memorial Sloan Kettering Cancer Center (MSKCC) to provide SPORE projects with state-of-the-art- applications with very little development time or effort; thus, greatly reducing the time and cost required for individual projects to develop their own analysis pipelines. The specific aims of the Bioinformatics Core are: Aim 1. To develop and provide state-of-the-art genomic analysis pipelines for: • the detection of variants in targeted-DNA assays, MSK-IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) and whole exome sequence (WES). This pipeline will detect both single nucleotide changes and small insertion deletions for both somatic- and germline-variant calling scenarios. • DNA copy number analysis, which can measure both total copy number changes and allele-specific copy number, including loss of heterozygosity (LOH). Aim 2: To facilitate the sharing of data generated in the SPORE research projects and enable collaboration of integrative analysis via the MSKCC cBioPortal by collecting, formatting, and importing data generated by these research projects into the cBioPortal.