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Series GSE12032 Query DataSets for GSE12032
Status Public on Jul 02, 2009
Title Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background & Aims. The current staging system for colorectal cancer (CRC) based on TNM classification allows prediction of potential recurrence. However, it does not necessarily make reliable personalized prediction of prognosis. In this paper we describe combination of clinicopathological data and gene signature of dissected tumor specimen with stage II and III CRC patients would improve the situation.. Methods. A total of 1978 CRC were collected over 5 years, and then 371 stage II and 322 stage III of them with more than 45.9 months records were subjected to clinicopathological feature analyses. Out of this collection, 129 stage II and III CRC cases were selected for analyses of gene expression profiles with resected specimen. The gene signatures were analyzed by repeated random divisions of the samples into training and test sets to extract discriminator genes. After testing the applicability of this discriminator set, it was subjected to validation using a newly obtained set of 69 samples. Results. The pathological factors in solo or in combinations could not make personalized recurrence prediction, except for partial success with stage II patients. The gene signature, on the other hand, was capable of producing a set of discriminator genes, though the accuracy was yet to be improved. We observed that the best result was obtained when discriminators were selected from stage II CRC samples and used for prognosis of stage II CRC. When stage III cases were included in the process of discriminator extraction or in the process to validate samples, the results were poorer. Finally, we examined 31 independent stage II samples with a set of 30 such discriminators and were able to obtain results with 78 % accuracy, 90 % negative predictive value (NPV), and 55% positive predictive value (PPV). Conclusions. Independent clinicopathological variables were not able to predict prognosis of individual patient, unless the factors are combined. On the other hand, gene signatures allowed accurate prediction of prognosis for individuals, especially with stage II CRC, suggesting its potential use for selection of best treatment option for individual patients. The accuracy of discriminator prediction will be further improved when we take the evolution of CRC into consideration.
 
Overall design Of 198 samples, 129 represented the discovery phase and 69 represented the validation phase.
 
Citation(s) 21701771
Submission date Jul 08, 2008
Last update date Jul 03, 2018
Contact name masakazu miyake
E-mail(s) m.masakazu@k4.dion.ne.jp
Phone +81-6-6879-3251
Fax +81-6-6879-3259
Organization name Graduate School of Medicine, Osaka University
Department Gastroenterological Surgery
Street address Yamadaoka 2-2
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platforms (1)
GPL1291 Hitachisoft AceGene Human Oligo Chip 30K 1 Chip Version
Samples (198)
GSM304101 stageII colorectal cancer patient1 with no recurrence in discovery phase
GSM304102 stageII colorectal cancer patient2 with no recurrence in discovery phase
GSM304103 stageII colorectal cancer patient3 with no recurrence in discovery phase
Relations
BioProject PRJNA113313

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12032_RAW.tar 1.1 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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