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.

附加文件1：表S1 本研究所用上尿路尿路上皮癌（upper-tract urothelial carcinomas，UTUC）样本的临床病理肿瘤特征。表S2 临床变量与患者无进展生存期、总生存期的相关性分析结果。表S3 对30例UTUC样本开展全外显子测序（whole-exome sequencing）所鉴定得到的体细胞突变列表（n=30）。表S4 通过MutSigCV算法鉴定出的显著突变基因列表。表S5 采用单侧Fisher精确检验对前10位最显著突变基因进行互斥性与共现性分析的结果。表S6 前10位高频显著突变的UTUC基因与肌层浸润状态的相关性分析结果。表S7 UTUC RNA无监督聚类与临床变量的相关性分析结果。表S8 基于肌层浸润性膀胱癌共识分子分类的UTUC样本亚型分型结果。表S9 前10位高频显著突变基因与UTUC样本中基于DNA甲基化的聚类簇之间的相关性分析结果。表S10 临床变量与EpiC低表达（EpiC-low）、EpiC高表达（EpiC-high）特征样本中基于DNA甲基化的UTUC聚类结果的相关性分析。表S11 相较于FGFR野生型样本，FGFR3突变型UTUC病例中低甲基化探针对应的差异甲基化区域（differentially methylated regions，DMR）列表。表S12 UTUC肿瘤样本中启动子CpG岛甲基化相关基因列表，仅报告频率高于10%的基因。表S13 TCGA膀胱癌队列中UTUC EpiC特征与临床变量的相关性分析结果。表S14 UTUC显著突变与基于TCGA DNA甲基化的监督聚类之间的相关性分析结果。表S15 突变与拷贝数变异因素及iClusters之间的相关性分析结果。