Bioinformatic Data Analysis Services
The 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. The CBS also provides support for data from Next Generation Sequencing (NGS) platforms for ChIP Seq, cancer variants and RNA Seq, as well data from The Cancer Genome Atlas (TCGA).
Pittsburgh Genome Resource Repository (PGRR)
The CBS is involved in developing the IT infrastructure for high-throughput data including TCGA. The CBS is an integral part of the PGRR, which has secured a single data use agreement (DUA) for over 60 named Pitt investigators for use of TCGA data. PGRR is developing the infrastructure for downloading and storing all TCGA data locally and for providing data analysis support. In these efforts, the CBS collaborates closely with the University of Pittsburgh's computing resources such as the Simulation and Modeling (SAM)'s FRANK compute clusters and also with the Pittsburgh Supercomputing Center (PSC) facilities.
Data Warehousing and Phenotyping
The CBS is tightly integrated with data informatics efforts at UPMC and UPCI to establish integration points between disparate clinical and research applications (CoPath/CaRegistry/Tissue Banks/CTMA) to provide sources for “automated annotation” and deep phenotyping for developing genotype-phenotype correlations. One example of this is a specialized data warehouse established for the UPCI Specialized Program of Research Excellence (SPORE) in Skin Cancer.