Volume 72, Issue 4, Pages 641-649 (October 2017) Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma  Tyler J. Moss, Yuan Qi, Liu Xi, Bo Peng, Tae-Beom Kim, Nader E. Ezzedine, Maribel E. Mosqueda, Charles C. Guo, Bogdan A. Czerniak, Michael Ittmann, David A. Wheeler, Seth P. Lerner, Surena F. Matin  European Urology  Volume 72, Issue 4, Pages 641-649 (October 2017) DOI: 10.1016/j.eururo.2017.05.048 Copyright © 2017 European Association of Urology Terms and Conditions

Fig. 1 Oncoplot of genomic alterations in upper tract urothelial carcinoma (UTUC). The most frequently altered genes in 25 of 27 patients (somatic mutations in the hypermutator samples were excluded when determining top altered genes) are represented, along with the top mutated genes in UTUC in previous reports [11]. Mutations with at least ten reports in COSMIC [32] are considered recurrent (dark green and black). TERT promoter mutations were detected in two of the five samples for which we obtained sufficient sequence coverage for the TERT promoter, and are not shown here. The somatic mutation rates are represented by barplots (total number of silent and nonsilent mutations per Mb covered by ≥20 reads). Selected patient/sample clinical features are represented in top tracks. Synch BLCA=synchronous bladder cancer. European Urology 2017 72, 641-649DOI: (10.1016/j.eururo.2017.05.048) Copyright © 2017 European Association of Urology Terms and Conditions

Fig. 2 Molecular characteristics of high- and low-grade tumors. (A) Samples with mutations in genes that are components of p53 signaling (KEGG pathways) are represented by a tile plot. Pathologic grade and stage are indicated by tracks on top, along with a track indicating whether samples have a mutation in at least one gene in the pathway. (B) Copy number alterations in high- and low-grade samples. The main panel represents the chromosomal segment, with mean copy number ratios for each sample. The top panel represents the fraction of the genome with copy number gains (pink), amplification (red), losses (light blue), and deletions (blue) for each sample. The right panel represents the chromosomal segment-wise fraction of samples with copy number alterations. Mutations in DNA repair genes are indicated in the bottom panel. (C) Relative levels of proteins measured by reverse-phase protein array (RPPA). Shown are the proteins with significantly different levels (p≤0.01) between the high- and low-grade samples. European Urology 2017 72, 641-649DOI: (10.1016/j.eururo.2017.05.048) Copyright © 2017 European Association of Urology Terms and Conditions

Fig. 3 Gene expression subtypes. (A) Heatmap of unsupervised consensus clusters of RNA sequencing gene expression data. The heatmap shows the signature genes that characterize each cluster by the nearest-shrunken-centroid (PAM) method at a false discovery rate (FDR) of 0.01. The gene values shown are median-centered, variance-stabilizing transformed counts. The top tracks show the cluster ID, batch (generated in two different institutes), and important clinical variables. Tumors with pathological stage T2, T3, or T4 are considered muscle-invasive, and Ta or T1 non–muscle-invasive. Tumors with pathological stage Ta, T1, or T2 are considered organ-confined, and T3 or T4 non–organ-confined. The bottom tracks represent RNA expression of targets of immunotherapy and the five most commonly mutated genes in upper tract urothelial carcinoma. Significant association between covariate and subtypes indicated by * <0.05 and ** < 0.01. (B,C) Kaplan-Meier plots of overall survival and cancer-specific survival. Patients are grouped by the RNA sequencing clusters shown in (A). European Urology 2017 72, 641-649DOI: (10.1016/j.eururo.2017.05.048) Copyright © 2017 European Association of Urology Terms and Conditions

Fig. 4 Novel gene fusion. (A) Schematic of SH3KBP1 and CNTNAP5 protein showing domains and position of the breakpoint (red arrowheads) of the fusion. The blue arrow shows the resulting fusion product. (B) DNA gel image of the polymerase chain reaction products validating the gene fusions. Forward primers for 5′ genes and reverse primers for 3′ genes are indicated by numbers in the schematic, and primer pairs are shown below the gel image. European Urology 2017 72, 641-649DOI: (10.1016/j.eururo.2017.05.048) Copyright © 2017 European Association of Urology Terms and Conditions