Hybrid method for prediction of metastasis in breast cancer patients using gene expression signals

Using primary tumor gene expression has been shown to have the ability of finding metastasis-driving gene markers for prediction of breast cancer recurrence (BCR). However, there are some difficulties associated with analysis of microarray data, which led to poor predictive power and inconsistency of previously introduced gene signatures. In this study, a hybrid method was proposed for identifying more predictive gene signatures from microarray datasets. Initially, the parameters of a Rough-Set (RS) theory based feature selection method were tuned to construct a customized gene extraction algorithm. Afterward, using RS gene selection method the most informative genes selected from six independent breast cancer datasets. Then, combined set of these six signature sets, containing 114 genes, was evaluated for prediction of BCR. In final, a meta-signature, containing 18 genes, selected from the combination of datasets and its prediction accuracy compared to the combined signature. The results of 10-fold cross-validation test showed acceptable misclassification error rate (MCR) over 1338 cases of breast cancer patients. In comparison to a recent similar work, our approach reached more than 5% reduction in MCR using a fewer number of genes for prediction. The results also demonstrated 7% improvement in average accuracy in six utilized datasets, using the combined set of 114 genes in comparison with 18-genes meta-signature. In this study, a more informative gene signature was selected for prediction of BCR using a RS based gene extraction algorithm. To conclude, combining different signatures demonstrated more stable prediction over independent datasets.