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.
%0 Journal Article
%1 235
%A Barrier, A.
%A Lemoine, A.
%A Boelle, P.-Y.
%A Tse, C.
%A Brault, D.
%A Chiappini, F.
%A Breittschneider, J.
%A Lacaine, F.
%A Houry, S.
%A Huguier, M.
%A der Laan, M.J. Van
%A Speed, T.
%A Debuire, B.
%A Flahault, A.
%A Dudoit, S.
%D 2005
%J Oncogene
%K imported
%N 40
%P 6155--6164
%T Colon cancer prognosis prediction by gene expression profiling
%V 24
%X 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.
@article{235,
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 ${\it Affymetrix HGU133A}$
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.},
added-at = {2008-10-17T17:04:38.000+0200},
author = {Barrier, A. and Lemoine, A. and Boelle, P.-Y. and Tse, C. and Brault, D. and Chiappini, F. and Breittschneider, J. and Lacaine, F. and Houry, S. and Huguier, M. and der Laan, M.J. Van and Speed, T. and Debuire, B. and Flahault, A. and Dudoit, S.},
biburl = {https://www.bibsonomy.org/bibtex/218849d0fea318424e5ce672839c9c2b7/biobibs_matthew},
id = {info:sici/0950-9232(2005)24<6155:CCPPBG>2.0.CO;2-3,
info:doi/10.1038/sj.onc.1208984, info:pmid/16091735},
interhash = {bed34977e5054b18c3ddd507db1d9f82},
intrahash = {18849d0fea318424e5ce672839c9c2b7},
issn = {0950-9232},
journal = {Oncogene},
keywords = {imported},
number = 40,
pages = {6155--6164},
timestamp = {2008-10-17T17:04:40.000+0200},
title = {Colon cancer prognosis prediction by gene expression profiling},
volume = 24,
year = 2005
}