title: Colon cancer prognosis prediction by gene expression profiling.
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.
authors.affiliation: Service de Chirurgie Digestive, Hôpital Tenon, Université Pierre et Marie Curie, Assistance Publique, 75020 Paris, France. barrier@stat.Berkeley.edu
authors.forename: Alain
authors.initials: A
authors.lastname: Barrier
authors.forename: Antoinette
authors.initials: A
authors.lastname: Lemoine
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Boelle
authors.forename: Chantal
authors.initials: C
authors.lastname: Tse
authors.forename: Didier
authors.initials: D
authors.lastname: Brault
authors.forename: Franck
authors.initials: F
authors.lastname: Chiappini
authors.forename: Julia
authors.initials: J
authors.lastname: Breittschneider
authors.forename: François
authors.initials: F
authors.lastname: Lacaine
authors.forename: Sidney
authors.initials: S
authors.lastname: Houry
authors.forename: Michel
authors.initials: M
authors.lastname: Huguier
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Van der Laan
authors.forename: Terry
authors.initials: T
authors.lastname: Speed
authors.forename: Brigitte
authors.initials: B
authors.lastname: Debuire
authors.forename: Antoine
authors.initials: A
authors.lastname: Flahault
authors.forename: Sandrine
authors.initials: S
authors.lastname: Dudoit
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000556:secondary*; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D016022:Case-Control Studies; D003110:Colonic Neoplasms / Q000235:genetics* / Q000473:pathology*; D005260:Female; D020869:Gene Expression Profiling; D005819:Genetic Markers; D006801:Humans; D007413:Intestinal Mucosa; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D011237:Predictive Value of Tests; D011379:Prognosis; D012680:Sensitivity and Specificity
chemical_list: D005819:Genetic Markers