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Colon cancer prognosis prediction by gene expression profiling

Oncogene volume 24, pages 6155–6164 (2005)Cite this article

Abstract

This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Tumour (T) and non-neoplastic mucosa (NM) mRNA samples from 18 patients (nine with a recurrence, nine with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. The k-nearest neighbour method was used for prognosis prediction using T and NM gene expression measures. Six-fold cross-validation was applied to select the number of neighbours and the number of informative genes to include in the predictors. Based on this information, one T-based and one NM-based predictor were proposed and their accuracies were estimated by double cross-validation. In six-fold cross-validation, the lowest numbers of informative genes giving the lowest numbers of false predictions (two out of 18) were 30 and 70 with the T and NM gene expression measures, respectively. A 30-gene T-based predictor and a 70-gene NM-based predictor were then built, with estimated accuracies of 78 and 83%, respectively. This study suggests that one can build an accurate prognosis predictor for stage II and III colon cancer patients, based on gene expression measures, and one can use either tumour or non-neoplastic mucosa for this purpose.

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Acknowledgements

Alain Barrier received a grant of the Fondation de France/Fédération Nationale des Centres de Lutte Contre le Cancer for a stay in the Division of Biostatistics at UC Berkeley.

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Authors and Affiliations

  1. Service de Chirurgie Digestive, Hôpital Tenon, Université Pierre et Marie Curie, Assistance Publique, Paris, 75020, France

    Alain Barrier, François Lacaine, Sidney Houry & Michel Huguier

  2. INSERM U444, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie, Paris, 75571, Cedex, 12, France

    Alain Barrier, Pierre-Yves Boelle & Antoine Flahault

  3. Division of Biostatistics, School of Public Health, University of California, 140 Earl Warren Hall, Berkeley, 94720-7360, CA, USA

    Alain Barrier, Mark J Van der Laan & Sandrine Dudoit

  4. INSERM U602, Service de Biochimie, Hôpital Paul Brousse, Université Paris XI, Villejuif, 94800, France

    Antoinette Lemoine, Franck Chiappini & Brigitte Debuire

  5. Service de Biochimie, Hôpital Tenon, Université Pierre et Marie Curie, Assistance Publique, Paris, 75020, France

    Chantal Tse & Didier Brault

  6. Department of Statistics, University of California, Berkeley, 94720-7360, CA, USA

    Julia Breittschneider & Terry Speed

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  1. Alain Barrier
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Correspondence to Alain Barrier.

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Barrier, A., Lemoine, A., Boelle, PY. et al. Colon cancer prognosis prediction by gene expression profiling. Oncogene 24, 6155–6164 (2005). https://doi.org/10.1038/sj.onc.1208984

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