November 4, 2010

VICC Quantitative Sciences Seminar Series Featuring Keith Baggerly, Ph.D., and Kevin Coombes, Ph.D., Friday, Nov. 19, Noon

Vanderbilt-Ingram Cancer Center
Quantitative Sciences Seminar Series
"Reproducible Research in the Omics Era:
A Presentation and Panel Discussion"

Friday, Nov.19
noon – 2 p.m.
214 Light Hall
Keith Baggerly, PhD
Professor, Dept. of Bioinformatics and Computational Biology
M.D. Anderson Cancer Center

The Importance of Reproducible Research in High-Throughput Biology:
Case Studies in Forensic Bioinformatics

High-throughput biological assays let us ask very detailed questions about how diseases operate, promising to let us personalize therapy. Data processing, however, is often not described well enough for results to be reproduced, leading to exercises in “forensic bioinformatics” where raw data and reported results are used to infer what the methods must have been. Unfortunately, poor documentation shifts from an inconvenience to a danger when it obscures not just methods but errors.

We present some case studies involving related papers using microarray-based signatures of drug sensitivity derived from cell lines to predict patient response. Patients in clinical trials were allocated to treatment arms on the basis of these results. However, the results incorporate several simple errors that may put patients at risk. One theme that emerges is that the most common errors are simple (e.g., row or column offsets); conversely, it is our experience that the most simple errors are common.

Kevin Coombes, Ph.D.
Deputy Chair, Bioinformatics, and Professor of Bioinformatics and
Computational Biology
M.D. Anderson Cancer Center

Steps to Implement Reproducible Research
While it is relatively easy to obtain agreement in principle that reproducible research is a “good thing,” many people remain unclear about what can be done in a practical sense to improve reproducibility. In this talk, we describe recommendations for actions that journals and funding agencies can take to promote reproducible research in the area of high-throughput biology. As examples that can be adopted by individual researchers, we also discuss concrete steps that we have taken to help ensure that our own work is reproducible.

Panel Discussion at 1 p.m., following presentations:
Featuring Baggerly and Coombes, along with
Vanderbilt University School of Medicine’s
William Pao, M.D., Ph.D., Frank Harrell, Ph.D., and Yu Shyr, Ph.D.