This workshop will focus on the synergies between analysis results from the PharmacoGx, Xeva and RadioGx packages and their usefulness for discovery of biomarkers of drug and/or radiation sensitivity in cancer cell lines (CCLs) and patent derived xenograft models (PDXs). We will discuss issues with data curation, consistency and reproducibility within the literature as well as illustrate the importance of unified analytical platforms, data and code sharing in bioinformatics and biomedical research. In this lab learners will be led through an analysis for each of the three packages on data provided by the download functions within them. The results of these analyses will then be explored to highlight how drug and radiation dose-response profiles in CCLs and PDXs can be used to discover potential synergistic biomarkers for drug-radiation and drug combination therapies. The resulting biomarkers will be discussed in the context of translational cancer research and clinical applications of genomic data. We will conclude with a discussion of how these biomarkers can be used to inform future in vitro and in vivo treatment screenings and ultimately provide useful insights for clinical trial design.
Participants expected to have the following required packages installed on their machines to be able to run the commands along with the instructors. PharmacoGx, Xeva, RadioGx, CoreGx and Biobase from Bioconductor The workshop will be presented as a set of analysis steps to be replicated by the learners, with instructors available to explain the why and how of applying these functions to the given datasets. Learners will write analysis scripts as well as use interactive commands to explore the generated data structures and results. Learners will then brainstorm potential applications of the analysis results in their field as well as comment on use case examples presented by the instructors on research in our lab.
For a 1-hr workshop:
|Introduction and Experimental Design||5m|
|Data Structure and Common Functions Between Packages||5m|
|Examining and Extracting data of interest||5m|
|Visualizing and modelling Sensitivity Data||14m|
|Signature Generation and Biomarker Discovery||5m|
|Integrative Analysis Across Packages and Disciplines: - 20 Minutes - Interactive Portion||20m|