Classification of colon cancer patients into consensus molecular subtypes using support vector machines.

Abstract

The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the consensus molecular subtypes (CMS), developed by the Colorectal Cancer Subtyping Consortium. CMS-specific RNA-Seq-dependent classification approaches are recent, with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using their RNA-seq profiles. We first identified subtype-specific and survival-associated genes using the Fuzzy C-Means algorithm and log-rank test. We then classified patients using support vector machines with backward elimination methodology. We optimized RNA-seq-based classification using 25 genes with a minimum classification error rate. In this study, we reported the classification performance using precision, sensitivity, specificity, false discovery rate, and balanced accuracy metrics. We present a gene list for colon cancer classification with minimum classification error rates and observed the lowest sensitivity but the highest specificity with CMS3-associated genes, which significantly differed due to the low number of patients in the clinic for this group.