Bioinformatics Core

Core Director - Paul T. Spellman, PhD

The Bay Area Breast Cancer SPORE Bioinformatics Core is responsible for supporting the SPORE in its need for information storage, retrieval, and interpretation. The Core coordinates with the UCSF Helen Diller Family Comprehensive Cancer Center Bioinformatics Core to provide support for the Projects to store molecular and biological data that they generate with an emphasis on maintaining high quality data. The Core also provides the collected data back to the Projects and Cores in formats that are designed to be easily handled and interpreted. In addition, the Core provides data from external resources (i.e. microarray experiments of breast cancer studies) to be shared to the Projects in the same formats, which allows the SPORE to leverage external resources more effectively. Finally, the Core ensures that the SPORE members have access and training to informatics tools and methods.

The Bioinformatics Core shares data through three primary modes, MAGE-TAB, versioned tab-delimited text and through the SGDI web portal. Data types served include molecular profiling (gene expression, DNA copy number, mutation status, and protein lysate arrays), drug response (GI50), and cell response (Cellomics). Data are served primarily to the Biostatistics Core for their analyses. The Bioinformatics Core itself handles specific informatics activities such as pathway network modeling, and data visualization.

The Bioinformatics Core facilitates the overall SPORE in achieving translational aims moving potential diagnostics and therapeutics forward. Specifically, large data sets that are used to predict tumor response are archived and analyzed by the Core.