Supplementary Figure S2. Cluster analysis of multiple cohorts combined CRC set. A-C. Principal components analysis performed on all CRC patients using the top 500 mRNAs showing the highest standard deviation across all patients. The first four principal components which explain the most of the data variation are shown. Patients are labeled with different color according to the cohort which they belong. (A) The first two principal components; (B) The third and fourth principal components; (C) Explained variances of each principal components. D. Hierarchical clustering of CRC patients using the Ward method to compute the distance between patients.
ARTICLE ABSTRACTThe current tumor staging system is insufficient for predicting the outcomes for patients with colorectal cancer because of its phenotypic and genomic heterogeneity. Integrating gene expression signatures with clinicopathologic factors may yield a predictive accuracy exceeding that of the currently available system. Twenty-seven signatures that used gene expression data to predict colorectal cancer prognosis were identified and re-analyzed using bioinformatic methods. Next, clinically annotated colorectal cancer samples (n = 1710) with the corresponding expression profiles, that predicted a patient's probability of cancer recurrence, were pooled to evaluate their prognostic values and establish a clinicopathologic–genomic nomogram. Only 2 of the 27 signatures evaluated showed a significant association with prognosis and provided a reasonable prediction accuracy in the pooled cohort (HR, 2.46; 95% CI, 1.183–5.132, P < 0.001; AUC, 60.83; HR, 2.33; 95% CI, 1.218–4.453, P < 0.001; AUC, 71.34). By integrating the above signatures with prognostic clinicopathologic features, a clinicopathologic–genomic nomogram was cautiously constructed. The nomogram successfully stratified colorectal cancer patients into three risk groups with remarkably different DFS rates and further stratified stage II and III patients into distinct risk subgroups. Importantly, among patients receiving chemotherapy, the nomogram determined that those in the intermediate- (HR, 0.98; 95% CI, 0.255–0.679, P < 0.001) and high-risk (HR, 0.67; 95% CI, 0.469–0.957, P = 0.028) groups had favorable responses.Implications: These findings offer evidence that genomic data provide independent and complementary prognostic information, and incorporation of this information refines the prognosis of colorectal cancer. Mol Cancer Res; 16(9); 1373–84. ©2018 AACR.