pap_DupuySimon_2007 - ARTICLE Critical Review of Published...

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View Full Document Right Arrow Icon JNCI | Articles 147 ARTICLE DNA microarray technology has found many applications in bio- medical research. In oncology, it is being used to better understand the biological mechanisms underlying oncogenesis, to discover new targets and new drugs, and to develop classifiers (predictors of good outcome versus poor outcome) for tailoring individualized treat- ments ( 1 – 4 ). Microarray-based clinical research is a recent and active area, with an exponentially growing number of publications. Both the reproducibility and validity of findings have been chal- lenged, however ( 5 , 6 ). In our experience, microarray-based clinical investigations have generated both unrealistic hype and excessive skepticism. We reviewed published microarray studies in which gene expression data are analyzed for relationships with cancer outcomes, and we propose guidelines for statistical analysis and reporting, based on the most common and serious problems identified. M ethods Studies were retrieved from a search of the Medline bibliographic database on the Pubmed Web site of the National Library of Medicine, followed by hand screening of abstracts and articles. The detailed process of selection is presented in Supplementary Note 1 (available online). The inclusion criteria were as follows: the work was an original clinical study on human cancer patients, published in English before December 31, 2004; it analyzed gene expression data of more than 1000 spots; and it presented statistical analyses relating the gene expression profiling to a clinical outcome. Two types of outcome were considered: 1) A relapse or death occur- ring during the course of the disease. 2) A therapeutic response. 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: [email protected] ). See “ Notes ” following “ References. ” DOI: 10.1093/jnci/djk018 © The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: [email protected] Critical Review of Published Microarray Studies for Cancer Outcome and Guidelines on Statistical Analysis and Reporting Alain Dupuy , Richard M . Simon 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.
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pap_DupuySimon_2007 - ARTICLE Critical Review of Published...

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