GSE14333_eset.RdPURPOSE: Colorectal cancer prognosis is currently predicted from pathologic staging, providing limited discrimination for Dukes stage B and C disease. Additional markers for outcome are required to help guide therapy selection for individual patients. EXPERIMENTAL DESIGN: A multisite single-platform microarray study was done on 553 colorectal cancers. Gene expression changes were identified between stage A and D tumors (three training sets) and assessed as a prognosis signature in stage B and C tumors (independent test and external validation sets). RESULTS: One hundred twenty-eight genes showed reproducible expression changes between three sets of stage A and D cancers. Using consistent genes, stage B and C cancers clustered into two groups resembling early-stage and metastatic tumors. A Prediction Analysis of Microarray algorithm was developed to classify individual intermediate-stage cancers into stage A-like/good prognosis or stage D-like/poor prognosis types. For stage B patients, the treatment adjusted hazard ratio for 6-year recurrence in individuals with stage D-like cancers was 10.3 (95% confidence interval, 1.3-80.0; P = 0.011). For stage C patients, the adjusted hazard ratio was 2.9 (95% confidence interval, 1.1-7.6; P = 0.016). Similar results were obtained for an external set of stage B and C patients. The prognosis signature was enriched for downregulated immune response genes and upregulated cell signaling and extracellular matrix genes. Accordingly, sparse tumor infiltration with mononuclear chronic inflammatory cells was associated with poor outcome in independent patients. CONCLUSIONS: Metastasis-associated gene expression changes can be used to refine traditional outcome prediction, providing a rational approach for tailoring treatments to subsets of patients. (Clin Cancer Res 2009;15(24):7642-51).
data( GSE14333_eset )
experimentData(eset):
Experiment data
Experimenter name: Jorissen RN, Gibbs P, Christie M, Prakash S et al.??Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.??Clin Cancer Res??2009 Dec 15
Laboratory: Jorissen and Sieber 2008
Contact information:
Title: Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer.
URL:
PMIDs: 19996206
Abstract: A 257 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
platform_shorttitle:
Affymetrix HG-U133Plus2
platform_summary:
hgu133plus2
platform_manufacturer:
Affymetrix
platform_distribution:
commercial
platform_accession:
GPL570
platform_technology:
in situ oligonucleotide
warnings:
No warnings yet
Preprocessing: frma
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: A1BG A1BG-AS1 ... ZZZ3 (19320 total)
varLabels: probeset gene
varMetadata: labelDescription
assayData: 19320 features, 290 samples
Platform type: hgu133plus2
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Available sample meta-data:
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alt_sample_name:
Length Class Mode
290 character character
sample_type:
tumor
290
primarysite:
co re NA's
250 39 1
summarystage:
early late NA's
44 152 94
N:
0 NA's
138 152
M:
0 1
229 61
Dstage:
A B C D
44 94 91 61
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.00 58.00 67.00 65.96 75.00 92.00
summarylocation:
l r NA's
161 125 4
gender:
f m
126 164
stageall:
1 3 4 NA's
44 91 61 94
dfs_status:
deceased_or_recurrence living_norecurrence NA's
50 176 64
days_to_recurrence_or_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
27.6 668.5 1154.0 1306.0 1785.0 4276.0 64
batch:
Length Class Mode
290 character character
drug_treatment:
n y NA's
172 117 1
preop_drug_treatment:
n
290
chemotherapy:
n y NA's
172 117 1
uncurated_author_metadata:
Length Class Mode
290 character character