Prognostic gene expression signature associated with two molecularly distinct subtypes of colorectal cancer

Patients and gene expression data
All clinical and gene expression data are available from the
National Center for Biotechnology Information Gene Expression
Omnibus database (http://www.ncbi.nlm.nih.gov/geo). Gene
expression data from the Moffit Cancer Center (Moffit cohort,
GSE17536, n¼177) were used as the exploration data set.11 Gene
expression data from the Vanderbilt Medical Center (GSE17537,
n¼55) and Max Planck Institute (GSE12945, n¼62) were pooled
and used as the first validation data set (Vanderbilt and Max
Planck (VMP) cohort, n¼117).11 12 Gene expression data from
the Royal Melbourne Hospital that is part of GSE14333 (n¼96)
were used as the second validation data set.13 Gene expression
data of these patients were redeposited as an independent data
set to Gene Expression Omnibus (GSE29971). To test the prognostic
significance of gene expression signatures, we used only
gene expression data with available patient survival data.
Although three prognostic variables (OS, disease-specific survival
and disease-free survival (DFS)) were available for the Moffit
cohort, only OS and DFS data were available for the VMP and
Melbourne cohorts, respectively.
Adjuvant chemotherapy data were available only for the
Moffit, Vanderbilt Medical Center and Melbourne cohorts. Of
the 328 patients in the Moffit, Vanderbilt and Melbourne
cohorts, 147 (2 in AJCC stage I, 28 in stage II, 81 in stage III and
36 in stage IV) had received standard adjuvant chemotherapy
(either single-treatment 5-fluorouracil/capecitabine or a combination
of 5-fluorouracil and oxaliplatin). The remaining patients
did not receive chemotherapy (n¼168) or treatment data were
not available (n¼13).