Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology

DOI10.1214/09-AOAS291zbMATH Open1185.92056arXiv1010.1092WikidataQ57556733 ScholiaQ57556733MaRDI QIDQ965099FDOQ965099

Authors: Keith A. Baggerly, Kevin R. Coombes 

Publication date: 21 April 2010

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1010.1092

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zbMATH Keywords

reproducibilitymicroarraysforensic bioinformatics

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50)

Cites Work

• Reproducible Research: A Bioinformatics Case Study
• Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology
• A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks

Cited In (15)

• Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology
• Integrating Ethics into the Guidelines for Assessment and Instruction in Statistics Education (GAISE)
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• Applying statistical thinking to `big data' problems
• Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies
• A practical guide to big data
• Reproducible research in statistics: a review and guidelines for the Biometrical Journal
• Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy
• Use of pretransformation to cope with extreme values in important candidate features
• Challenges and Opportunities for Statistics in the Next 25 Years
• Error statistical modeling and inference: where methodology meets ontology
• Reproducible research practices: a tool for effective and efficient leadership in collaborative statistics
• Book review of: C. Gandrud, Reproducible research with R and Rstudio.
• Statistical proof? The problem of irreproducibility
• Transparency and reproducibility in data analysis: the prostate cancer prevention trial

Uses Software

• R
• Sweave

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