Bioinformatic Data Analysis Services
CBS provides comprehensive bioinformatics support, from experimental design to data analysis, for high-throughput microarray-based gene expression, copy number, single nucleotide polymorphism (SNP), and methylation studies. CBS also provides support for data from Next Generation Sequencing (NGS) platforms for ChIP Seq, cancer variants and RNA Seq, integrative TCGA analysis, single cell RNA Seq, analysis of immunogenomic markers, immune/stroma cell deconvolution, neoantigen prediction, analysis of microbiota composition, taxonomy, and metabolic pathways, and integration of microbiome data with transcriptomics data.
Development of Computing Infrastructure for Genomics
CBS is involved in developing the IT infrastructure for high-throughput data including TCGA. CBS works closely with PSC and CRC in their initiatives to scale computing to meet the increasing demand from genomics. CBS has created a local regulatory compliant repository of over 2.2 PB of all raw and processed data; this repository known as the Pittsburgh Genome Resource Repository (PGRR) is available to all HCC investigators under a common Data Use Agreement (DUA).
Support for Team Science Projects
CBS supports team science projects which require broad expertise in genomics from data analysis, metadata annotation, data sharing to data hosting, such as the Breast Cancer Research Foundation’s AURORA project on metastatic breast cancer. The University of Pittsburgh and the PSC are the Data Coordination Center (DCC) for this project in which data providers include UNC for RNA Seq, Wash U for DNA Seq and Van Andel for methylation and Nationwide Children’s for biospecimens. CBS coordinates all DCC activities for this project. CBS supports multiple SPORE applications, leading the bioinformatics component for all projects which require the careful curation and analysis of large-scale, multi-dimensional cancer genomic data.