Identification of Small and Discriminative Gene Signatures for Chemosensitivity Prediction in Breast Cancer

Various gene signatures of chemosensitivity in breast cancer have been discovered. One previous study employed t-test to find a signature of 31 probe sets (27 genes) from a group of patients who received weekly preoperative chemotherapy. Based on this signature, a 30-probe set diagonal linear discriminant analysis (DLDA-30) classifier of pathologic complete response (pCR) was constructed. In this study, we sought to uncover a signature that is much smaller than the 31 probe sets and yet has enhanced predictive performance. A signature of this nature could inform us what genes are essential in response prediction. Genetic algorithms (GAs) and sparse logistic regression (SLR) were employed to identify two such small signatures. The first had 13 probe sets (10 genes) selected from the 31 probe sets and was used to build a SLR predictor of pCR (SLR-13), and the second had 14 probe sets (14 genes) selected from the genes involved in Notch signaling pathway and was used to develop another SLR predictor of pCR (SLR-Notch-14). The SLR-13 and SLR-Notch-14 had a higher accuracy and a higher positive predictive value than the DLDA-30 with much lower P values, suggesting that our two signatures had their own discriminative power with high statistical significance. The SLR prediction model also suggested the dual role of gene RNUX1 in promoting residual disease (RD) or pCR in breast cancer. Our results demonstrated that the multivariable techniques such as GAs and SLR are effective in finding significant genes in chemosensitivity prediction. They have the advantage of revealing the interacting genes, which might be missed by single variable techniques such as t-test.