Additional file 1: Table S1. of Using gene expression from urine sediment to diagnose prostate cancer: development of a new multiplex mRNA urine test and validation of current biomarkers

Commercial Gene Expression Assays from Life Technologies used in this study. Target exons for transcript detection as well as amplicon length for each trasncrip are shown. (DOCX 18 kb

Additional file 1: of Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples

Figure S1. Somatic mutational prevalence in MuSiCa web app. Figure S2. Mutational profile representation in MuSiCa web app. Figure S3. Reconstruction of mutational profile in MuSiCa web app. Figure S4. Comparison with cancer signatures in MuSiCa web app. Figure S5. Principal component analysis in MuSiCa web app. (PDF 3039 kb

Additional file 9: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 203 kb

Additional file 4: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 183 kb

Additional file 8: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 85 kb

Additional file 1: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

Figure S1. Flowchart of the entire study. A total of seven hypermethylated genes, differentially expressed between BC patients and controls (n = 168), were determined in the discovery phase. With these results, a three-gene methylation classifier was developed. This three-gene classifier was tested in a cross-sectional study (validation phase; n = 458). Samples with available cytology results in each phase are indicated. Abbreviations: 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. (PPTX 75 kb

Additional file 5: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 21 kb

Additional file 2: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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

Additional file 6: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 20 kb

Additional file 7: of Urine cell-based DNA methylation classifier for monitoring bladder cancer

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 (N = 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 189 kb