Bioinformatics Core

BIOINFORMATICS CORE: SUMMARY The Bioinformatics Core will support the WU-PDTC Research Projects and Cores over the spectrum of their computational biology needs. The research program we propose involves many facets of algorithms, computation, and information management, which require formalized bioinformatics support to effectively translate results into recommendations for human clinical trials. The Bioinformatics Core will provide both the infrastructure to house the experimental data and the interpretive tools and personnel to analyze these data. These responsibilities fall into 3 basic categories. This will enable scaling the PDX-based approach into a significant resource for the cancer research community in three important ways: (1) provide uniform, high-quality, proteogenomic characterization for all WU-PDTC PDX tumor models for curation into the public domain, (2) provide therapeutic response data on PDX models (e.g., breast, colon, pancreatic, and lung) including correlation with molecular characterization and phenotypic response that may be applied to other cancer types with similar characteristics, and (3) provide informatic and biostatistical tools to support evidence-based selection of promising agents for subsequent clinical trials based on known molecular and clinical data. We will organize all of this information, as well as all PDX-associated metadata (e.g. molecular and histopathologic data for both the patient and PDX tumors, passages, and therapeutic experimental data, etc.), time series metrics representing treatment responses, etc. in an extension of our WU-PDXdb relational tracking database developed in the prior funding period. This will support both our local analysis and submission obligations and the information integration with other PDTCs and PTCCCs. These informatic and statistical tools will be integrated across the PDXNet to provide a valuable and lasting resource for future clinical and pre-clinical trial designs and possible repurposing of drugs across cancer types.