Translator Disclaimer
December 2009 Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
Keith A. Baggerly, Kevin R. Coombes
Ann. Appl. Stat. 3(4): 1309-1334 (December 2009). DOI: 10.1214/09-AOAS291

Abstract

High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact reproduction of the results, leading to exercises in “forensic bioinformatics” where aspects of raw data and reported results are used to infer what methods must have been employed. Unfortunately, poor documentation can shift from an inconvenience to an active danger when it obscures not just methods but errors. In this report we examine several related papers purporting to use microarray-based signatures of drug sensitivity derived from cell lines to predict patient response. Patients in clinical trials are currently being allocated to treatment arms on the basis of these results. However, we show in five case studies that the results incorporate several simple errors that may be putting 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. We then discuss steps we are taking to avoid such errors in our own investigations.

Citation

Download Citation

Keith A. Baggerly. Kevin R. Coombes. "Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology." Ann. Appl. Stat. 3 (4) 1309 - 1334, December 2009. https://doi.org/10.1214/09-AOAS291

Information

Published: December 2009
First available in Project Euclid: 1 March 2010

zbMATH: 1185.92056
MathSciNet: MR2752136
Digital Object Identifier: 10.1214/09-AOAS291

Rights: Copyright © 2009 Institute of Mathematical Statistics

JOURNAL ARTICLE
26 PAGES


SHARE
Vol.3 • No. 4 • December 2009
Back to Top