Fig. 2: Identification of immuno-genomic biomarkers from tumor tissues of mccRCC patients.

a Oncoplot showing the somatic mutation landscape of the top 5 mutated genes [from TCGA. Kidney Renal Clear Cell Carcinoma (KIRC)]. A total of 58 tumor tissue samples were. analyzed and each column represents a patient. The color bar at the bottom shows response for. each patient (PD=progressive disease, SD=stable disease, PR=partial response). The genes are listed on the left and their respective frequencies are listed on the right of the heatmap. The colored rectangles indicate different types of somatic mutations and the key identifying each mutation type is shown at the bottom of the heatmap. The bar plot on the top shows the somatic mutation count for each patient. The bar plot on the right side shows the counts of mutations for each gene and the colors in the bar plots correspond to the colors showing mutation types in the body of the heatmap. b Stacked bar plot showing a positive association of genomic signature (mutations in PBRM1 or SETD2 genes) with clinical responses. Patients (n = 58) were stratified into Mut (patients with mutations in SETD2 or PBRM1, n = 25) and WT (patients with wild-type SETD2 and PBRM1. genes, n = 33) groups (p = 0.03). c–d Box plots showing association of IFN-γ signature (c) and. TLS signature (d) with clinical responses (n = 83). Box plots represent the median, interquartile. range and the whiskers represent 1.5 x the upper and lower interquartile range values. Welch’s. ANOVA test across the 3 groups for IFN-γ signature (p = 0.025) and TLS signature (p = 0.039). Stacked bar plot showing a positive association of IFN-γ signature (e) and TLS signature (f). with response. Patients (83) were stratified into IFNG^high (n = 41) and IFNG^low (n = 42) groups. (p = 0.02) (e) or into TLS^high (n = 41) and TLS^low (n = 42) (f). Statistical significance was calculated using two-sided Welch’s ANOVA, Welch’s t-test and Fisher’s exact test for comparing z scores in 3 or more unpaired groups, comparing z scores in 2 unpaired groups and comparing group counts, respectively. p < 0.05 was considered statistically significant. The following color scheme is used in all figures showing biological response groups; PD=blue, SD=yellow, and PR=red.