Cancer Bioinformatics Services

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Abstract: Cancer Bioinformatics Services (CBS) Cancer Bioinformatics Service (CBS) focuses on providing UPCI investigators with the analysis expertise, computational infrastructure, specialized databases and research analytics to support cancer biomarker discovery. These state-of-the-art bioinformatics capabilities involve deep collaborations between the Cancer Bioinformatics Service (CBS) and the Department of Biomedical Informatics bioinformatics faculty, the Pittsburgh Supercomputing Center, the Institute of Personalized Medicine and the University of Pittsburgh’s Simulation and Modeling Center. The aims of CBS for the next renewal period are to: 1) Provide bioinformatics analysis support for all microarray and Next Generation Sequencing (NGS) platforms. This includes experimental design, differential expression (DE) analysis, miRNA target analysis, copy number analysis, queries of public databases and advanced pathway analysis using commercial (Ingenuity Pathway analysis, GeneGo, and academic (e.g. Cytoscape) tools. 2) Perform integrative analysis of TCGA and other consortia data from all platforms including expression, methylation, somatic variants and copy number. 3) Develop and implement, under a common Data Use Agreement (DUA), the Pittsburgh Genome Resource Repository (PGRR), an infrastructure for storage, analysis and archiving of large petabyte size genomic data such as from The Cancer Genome Atlas (TCGA) project. CBS will also develop PGRR informational sessions and also develop bioinformatics services to facilitate use. 4) Develop specialized databases for programs such as UPCI Skin SPORE that integrate disparate clinical data sources, enabling integration of genomics biomarker data with clinical phenotypes using the open source Informatics for Integrating Biology to the Bedside (i2b2) platforms and related technologies. 5) Provide IT support for the Cancer Genomics Facility (CGF) high performance computing needs, 6) Prepare data for publication including submitting data to the Gene Expression Omnibus (GEO) and assist with manuscript preparation, and 7) Collaborate with the Health Sciences Library System (HSLS) to evaluate bioinformatics tools for licensing and teach quarterly bioinformatics courses to the user community. The goal of CBS is to provide cost effective and efficient bioinformatics analysis services to the UPCI CCSG community. The current proposal focuses on expanding these services as they are critical to the scientific discovery of new cancer biomarkers and therapeutic targets. During that current project period all 10 Research Programs used CBS services.