Critical Review of Published Microarray Studies for Cancer Outcome and Guidelines on Statistical Analysis and Reporting (original) (raw)

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Affiliations of authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD (AD, RMS); Université Paris VII Denis Diderot, Paris, France (AD); Assistance Publique-Hôpitaux de Paris, Service de Dermatologie, Hôpital Saint-Louis, Paris, France (AD)

Correspondence to: Richard M. Simon, DSc, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892 (e-mail: rsimon@nih.gov ).

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Affiliations of authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD (AD, RMS); Université Paris VII Denis Diderot, Paris, France (AD); Assistance Publique-Hôpitaux de Paris, Service de Dermatologie, Hôpital Saint-Louis, Paris, France (AD)

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Revision received:

24 October 2006

Accepted:

01 December 2006

Published:

17 January 2007

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Alain Dupuy, Richard M. Simon, Critical Review of Published Microarray Studies for Cancer Outcome and Guidelines on Statistical Analysis and Reporting, JNCI: Journal of the National Cancer Institute, Volume 99, Issue 2, 17 January 2007, Pages 147–157, https://doi.org/10.1093/jnci/djk018
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Abstract

Background

Both the validity and the reproducibility of microarray-based clinical research have been challenged. There is a need for critical review of the statistical analysis and reporting in published microarray studies that focus on cancer-related clinical outcomes.

Methods

Studies published through 2004 in which microarray-based gene expression profiles were analyzed for their relation to a clinical cancer outcome were identified through a Medline search followed by hand screening of abstracts and full text articles. Studies that were eligible for our analysis addressed one or more outcomes that were either an event occurring during follow-up, such as death or relapse, or a therapeutic response. We recorded descriptive characteristics for all the selected studies. A critical review of outcome-related statistical analyses was undertaken for the articles published in 2004.

Results

Ninety studies were identified, and their descriptive characteristics are presented. Sixty-eight (76%) were published in journals of impact factor greater than 6. A detailed account of the 42 studies (47%) published in 2004 is reported. Twenty-one (50%) of them contained at least one of the following three basic flaws: 1) in outcome-related gene finding, an unstated, unclear, or inadequate control for multiple testing; 2) in class discovery, a spurious claim of correlation between clusters and clinical outcome, made after clustering samples using a selection of outcome-related differentially expressed genes; or 3) in supervised prediction, a biased estimation of the prediction accuracy through an incorrect cross-validation procedure.

Conclusions

The most common and serious mistakes and misunderstandings recorded in published studies are described and illustrated. Based on this analysis, a proposal of guidelines for statistical analysis and reporting for clinical microarray studies, presented as a checklist of “Do's and Don'ts,” is provided.

© The Author 2007. Published by Oxford University Press.

Topic:

• cancer
• follow-up
• gene expression profiling
• genes
• medline
• guidelines
• treatment outcome
• journal impact factor
• clinical research

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