Additional file 1 of Comprehensive integrative profiling of upper tract urothelial carcinomas

Additional file 1: Table S1. Clinicopathological tumor features of upper-tract urothelial carcinomas samples used for the study. Table S2. Association between clinical variables and patients progression-free and overall survival. Table S3. List of somatic mutations identified in the whole-exome sequencing of upper-tract urothelial carcinomas (n = 30). Table S4. List of significantly mutated genes identified by the MutSigCV algorithm. Table S5. Mutual exclusivity and co-occurrence analysis for the 10 most significantly mutated genes using the one-side Fisher’s exact test. Table S6. Association between top 10 frequently significantly mutated UTUC genes and muscle-invasive status. Table S7. Association between UTUC RNA unsupervised clustering and clinical variables. Table S8. Subtypes of UTUC samples using consensus molecular classification of muscle-invasive bladder cancer. Table S9. Association between top 10 frequently significantly mutated genes and DNA methylation-based clusters in UTUC samples. Table S10. Association between clinical variables and DNA methylation UTUC based clustering in samples with EpiC-low and EpiC-high signatures. Table S11. List of differentially methylated regions (DMR) using hypomethylated probes in FGFR3-mutated UTUC cases as compared to FGFR-wild type samples. Table S12. List of genes with promoter CpG islands methylation in UTUC tumor samples. Only those with a frequency higher than 10% are reported. Table S13. Association between UTUC EpiC signature and clinical variables in TCGA bladder carcinomas cohort. Table S14. Association between significant mutations of UTUC and supervised TCGA DNA methylation based clustering. Table S15. Association between mutation and copy number contributors and iClusters.