Colon cancer prognosis prediction by gene expression profiling

Colon cancer prognosis prediction by gene expression profiling

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 t...

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Bibliographic Details
Published in:Oncogene Vol. 24; no. 40; pp. 6155 - 6164
Main Authors: BARRIER, Alain, LEMOINE, Antoinette, VAN DER LAAN, Mark J, SPEED, Terry, DEBUIRE, Brigitte, FLAHAULT, Antoine, DUDOIT, Sandrine, BOELLE, Pierre-Yves, TSE, Chantal, BRAULT, Didier, CHIAPPINI, Franck, BREITTSCHNEIDER, Julia, LACAINE, Francois, HOURY, Sidney, HUGUIER, Michel
Format: Journal Article
Language:English
Published: Basingstoke Nature Publishing 08-09-2005
Nature Publishing Group
Subjects:
Adenocarcinoma - genetics
Adenocarcinoma - secondary
Adult
Aged
Aged, 80 and over
Biological and medical sciences
Cancer therapies
Case-Control Studies
Cell physiology
Cell transformation and carcinogenesis. Action of oncogenes and antioncogenes
Chemotherapy
Colon cancer
Colonic Neoplasms - genetics
Colonic Neoplasms - pathology
Colorectal cancer
DNA microarrays
Female
Fundamental and applied biological sciences. Psychology
Gastroenterology. Liver. Pancreas. Abdomen
Gene expression
Gene Expression Profiling
Genetic Markers
Humans
Intestinal Mucosa
Male
Medical prognosis
Medical sciences
Middle Aged
Molecular and cellular biology
Mucosa
Neoplasm Staging
Oligonucleotide Array Sequence Analysis
Predictions
Predictive Value of Tests
Prognosis
Sensitivity and Specificity
Stomach. Duodenum. Small intestine. Colon. Rectum. Anus
Tumors
France
Paris France
Colon cancer
Prognosis
Mucosa
non-neoplastic mucosa
Prediction
Digestive diseases
Intestinal disease
cross-validation
Malignant tumor
Carcinogenesis
prognosis prediction
Functional genomics
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Summary: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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ISSN:0950-9232
1476-5594
DOI:10.1038/sj.onc.1208984