M test. We then performed a multivariate logistic regression analysis to examine the prediction performance of the clinical response with other clinical variables such as patient age, debulking status, and tumor stage. We also performed Cox proportional hazard regression analyses to understand the prediction performance for patient variable survival times by the three drugs’ predictors together with other important clinical variables.Results Final Drug Biomarkers and PredictorsThe final predictor for paclitaxel was comprised of 20 biomarkers with an AUC of 0.766 for 107 patients treated with the drug in the Bonome-185 cohort (P,0.01). The predictor for cyclophosphamide consisted of 44 genes with an AUC of 0.664 for 68 cyclophosphamide-treated patients also in the Bonome-185 cohort (P = 0.024). As for topotecan, the final predictor BLU-554 chemical information included 58 genes with an AUC of 0.917 for 10 patients treated with topotecan in the TCGA-UW cohort (P = 0.143); the Topotecan predictor was not statistically significant due to the small sample size of this cohort despite a very high AUC value (see Results S1 and Figure S1 for the detailed gene lists and the ROC analyses).Predictor Evaluation with Independent EOC CohortsWe examined the prediction performance of the above predictors on independent patient sets that were not used for our biomarker discovery and model training. We first examined the stratification performance of paclitaxel predictor scores between patients with CR and NR for two independent cohorts, TCGA-448 and UVA-51, for short-term clinical response to the primary chemotherapy with paclitaxel; note that clinical response information was available only for paclitaxel, since it was used in the primary platinum-based combination chemotherapy for most EOC patients. In our univariate logistic regression analysis for each of the predictors and clinical variables, a highly significant difference was found between the two patient groups in TCGA448 (p-value = 0.003). For the UVA-51 cohort, paclitaxel predictor scores showed a marginally significant difference between 28 CR and 23 NR patients due to its relatively small sample size (pvalue = 0.075, left column in Table 2). As widely recognized, we also found that optimal vs. suboptimal debulking status was significantly associated with therapeutic response to the primary chemotherapy treatments. Adjusting for the effects of surgical outcome, age, and tumor stage, multivariate logistic regression analysis also showed that patients with higher predictor scores and optimal debulking had significantly higher chances of therapeutic response (predictor odds ratio [OR] = 3.591; 95 CI: 1.494?.85; P = 0.005, right column in Table 2). order AG-221 Therefore, the predictor showed predictive information beyond patient debulking status in this multivariate analysis. For the UVA-51 cohort, the paclitaxel predictor again showed a marginally significant association with drug response (predictor OR = 9.521; 95 CI: 0.99?25.73, P = 0.063). We next examined the prediction performance of the three drug predictors and clinical variables for long-term survival of thedoi:10.1371/journal.pone.0086532.tclinical response and survival data of EOC patients to obtain the best therapeutic predictor for each drug. For this evaluation of competing models, we used the Bonome-185 set for paclitaxel and cyclophosphamide and the TCGA-UW set for topotecan. The Bonome-185 and the TGGA-UW sets also used to pre-define predicted responders (CR) and non-r.M test. We then performed a multivariate logistic regression analysis to examine the prediction performance of the clinical response with other clinical variables such as patient age, debulking status, and tumor stage. We also performed Cox proportional hazard regression analyses to understand the prediction performance for patient variable survival times by the three drugs’ predictors together with other important clinical variables.Results Final Drug Biomarkers and PredictorsThe final predictor for paclitaxel was comprised of 20 biomarkers with an AUC of 0.766 for 107 patients treated with the drug in the Bonome-185 cohort (P,0.01). The predictor for cyclophosphamide consisted of 44 genes with an AUC of 0.664 for 68 cyclophosphamide-treated patients also in the Bonome-185 cohort (P = 0.024). As for topotecan, the final predictor included 58 genes with an AUC of 0.917 for 10 patients treated with topotecan in the TCGA-UW cohort (P = 0.143); the Topotecan predictor was not statistically significant due to the small sample size of this cohort despite a very high AUC value (see Results S1 and Figure S1 for the detailed gene lists and the ROC analyses).Predictor Evaluation with Independent EOC CohortsWe examined the prediction performance of the above predictors on independent patient sets that were not used for our biomarker discovery and model training. We first examined the stratification performance of paclitaxel predictor scores between patients with CR and NR for two independent cohorts, TCGA-448 and UVA-51, for short-term clinical response to the primary chemotherapy with paclitaxel; note that clinical response information was available only for paclitaxel, since it was used in the primary platinum-based combination chemotherapy for most EOC patients. In our univariate logistic regression analysis for each of the predictors and clinical variables, a highly significant difference was found between the two patient groups in TCGA448 (p-value = 0.003). For the UVA-51 cohort, paclitaxel predictor scores showed a marginally significant difference between 28 CR and 23 NR patients due to its relatively small sample size (pvalue = 0.075, left column in Table 2). As widely recognized, we also found that optimal vs. suboptimal debulking status was significantly associated with therapeutic response to the primary chemotherapy treatments. Adjusting for the effects of surgical outcome, age, and tumor stage, multivariate logistic regression analysis also showed that patients with higher predictor scores and optimal debulking had significantly higher chances of therapeutic response (predictor odds ratio [OR] = 3.591; 95 CI: 1.494?.85; P = 0.005, right column in Table 2). Therefore, the predictor showed predictive information beyond patient debulking status in this multivariate analysis. For the UVA-51 cohort, the paclitaxel predictor again showed a marginally significant association with drug response (predictor OR = 9.521; 95 CI: 0.99?25.73, P = 0.063). We next examined the prediction performance of the three drug predictors and clinical variables for long-term survival of thedoi:10.1371/journal.pone.0086532.tclinical response and survival data of EOC patients to obtain the best therapeutic predictor for each drug. For this evaluation of competing models, we used the Bonome-185 set for paclitaxel and cyclophosphamide and the TCGA-UW set for topotecan. The Bonome-185 and the TGGA-UW sets also used to pre-define predicted responders (CR) and non-r.
