Search

Figure S5. Flow diagram of participants in the cross-sectional study according a) to the three-gene methylation classifier and cytology results and b) to the combined three-gene methylation/cytology classifier. Abbreviations: R-PFBC, recurrent patients in follow-up for bladder cancer; NR-PFBC, non-recurrent patients in follow-up for bladder cancer; Cytol, cytology; NA, non-available; Test, combined three-gene methylation/cytology classifier. (PPTX 85Â kb)

Figure S2. Pearson correlation coefficient heat map of the percentage of methylation for every CpG dinucleotide in the seven genes. Every CpG sites are correlated (via the Pearson correlation) with all others. Correlations are scaled by the color of the corresponding cell. Parameters are represented in the same order on the x- and y-axes. (PPTX 1232Â kb)

Figure S4. Sensitivity, negative and positive predictive values of urine cytology, the three-gene methylation classifier, and the combined three-gene methylation/cytology classifier in the testing set (Nâ =â 308). Overall specificity was 94% for urine cytology, 27% for the three-gene methylation classifier, and 40% for the combined three-gene methylation/cytology classifier. Abbreviations: LG, low-grade; HG, high-grade; NMIBC nHR, non-muscle-invasive bladder cancer non-high risk; NMIBC HR, non-muscle-invasive bladder cancer high risk; NPV, negative predictive value; PPV, positive predictive value. (PPTX 189Â kb)

Table S2. Percentage of methylation for each CpG dinucleotide in the seven selected genes in control and bladder cancer urine samples. Underlined in grey the CpG site used for methylation analysis. Abbreviations: SDV; Standard Deviation. (DOCX 21Â kb)

Table S3. Diagnostic performance of the three-gene methylation classifier, cytology, and the combined methylation/cytology classifier in the training and testing subset of samples with cytology available. Abbreviations: LG, Low Grade; HG, High Grade; AUC, area under curve; MIBC, muscle invasive bladder cancer; NMIBC, Non-Muscle Invasive Bladder Cancer; NPV, Negative Predictive Value; PPV, Positive Predictive Value; SN, Sensitivity; SP, Specificity; BC, Bladder Cancer; C, Control; R-PFBC, Recurrent Patients in Follow up for Bladder Cancer; NR-PFBC, Non Recurrent Patients in Follow up for Bladder Cancer. (DOCX 20Â kb)

Table S1. Primer sequences used in PCR and pyrosequencing. (DOCX 13Â kb)

Figure S6. DNA methylation profiles for bladder cancer and control tissue samples for the three-gene classifier. Data obtained from Wanderer Web page: http://maplab.imppc.org/wanderer/ . The red arrow indicates the CpG dinucleotide analyzed in each of the three genes. (PPTX 203Â kb)

Figure S3. Representative pyrograms showing gene methylation patterns in DNA urine samples from a bladder cancer patient. Percentage of methylation is indicated above peaks (gray columns) corresponding to the CpG sites in this region. (PPTX 183Â kb)