Bioinformatics Core The Bioinformatics Core will be established to support the PDX data and analysis for the Research Projects and Cores of the WU-PDTC. Large PDX research projects involve many facets of information and require formalized bioinformatic and biostatistical support to effectively collate information and translate discoveries from the preclinical setting. The 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. (1) We will use our bioinformatics pipeline to process and align raw genomic and proteomic data with specific tools to find variant SNVs, SVs, indels, CNVs, etc and will use these results to assess potential druggability in the expanded original human tumors under the noisy conditions imposed by the confounding host animal. (2) We will use a broad set of statistical analyses to draw inferences from the combination of mutation/expression data, curated information, expression outlier analysis, structural analysis, co-inhibition assessment, and larger examination of pathways members regarding the effectiveness of various treatments (vehicle/treatment, dosage-response, time course, etc.) applied in the research and pilot projects. (3) 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, passage, and therapeutic experimental data, etc.) in a dedicated relational tracking database that 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, lasting resource for future trials designs and possible repurposing of drugs across cancer types.
| Devarakonda, Siddhartha; Govindan, Ramaswamy (2018) Targeting Resistance to Targeted Therapies: Combating a Resilient Foe. Clin Cancer Res 24:6112-6114 |
