Fig. 2: Genomic correlates of response to nivolumab in the CONFIRM trial.

A Heat map showing the relative burden of driver gene mutations or driver copy number alterations in the R- vs NR-subgroups. B Stacked histogram showing the relative somatic alteration frequency involving 9p21 (left) and BAP1/3p21 (right). BAP1 was not significantly enriched in R versus NR subgroups (NS, not significant). C Upper panel. Somatic copy number alterations (SCNAs) involving amplifications were more frequent in the R- vs NR-subgroups. Lower panel. Copy number alterations specifically affecting DNA damage response genes were not significantly different in the R- vs NR-subgroup. * indicates a Wilcoxon signed rank test two-sided P value equal to or less than 0.05. The boxplots show the median line and interquartile range (IQR, 25^th-75^th percentiles), with the whiskers extending to the maximum and minimum values. D Tumour mutation burden (TMB), clonal or subclonal mutations, intratumour heterogeneity (ITH), neoantigen burden (clonal or subclonal), or somatic copy number alterations (SCNAs). The boxplots show the median line and interquartile range (IQR, 25^th–75^th percentiles), with the whiskers extending to the maximum and minimum values. E Geneset enrichment analysis (GSEA) summary comparing R vs NR transcriptional signature enrichment. F Boxplots comparing geneset enrichment scores (single sample GSEA) in R- vs NR-subgroups. The boxplots show the median line and interquartile range (IQR, 25^th−75^th percentiles), with the whiskers extending to the maximum and minimum values. G Pathway enrichment plot showing inflammatory and chemokine pathway upregulation in R- vs NR-mesotheliomas.