Responding tumors had a higher total and clonal obsTMB compared to nonresponding tumors in cohort 1 (N = 87 patients, Mann–Whitney U test P = 0.002, FDR-adjusted for multiple comparisons P = 0.012; and Mann–Whitney U test P = 0.0003, FDR-adjusted P = 0.005, respectively), however, there was considerable overlap in the TMB range between responding and nonresponding tumors. There were no differences in tumor purity and tumor aneuploidy between responding and nonresponding tumors. Overall, a higher number of single-base substitutions and indels were found in responding tumors, which was largely driven by their higher TMB. An enrichment in the C>A transversion-rich molecular smoking signature was found in patients with durable clinical benefit (Mann–Whitney U test, P = 0.003, FDR-adjusted P = 0.027). Activating mutations in RTK genes (EGFR and ERBB2 point mutations and amplifications, MET amplification, FGFR1 amplification and IGF1R amplification) were found to cluster in patients that did not derive durable clinical benefit from ICB (Fisher’s exact P = 0.0002, FDR-adjusted P = 0.003) independent of TMB (logistic regression TMB-adjusted P = 0.006). Recurrent genomic alterations in ARID1A, including truncating mutations in the setting of LOH of the wild-type allele, were predominantly found in patients with durable clinical benefit (Fisher’s exact P = 0.005, FDR-adjusted P = 0.024, TMB-adjusted P = 0.062). A trend toward enrichment in KEAP1 mutations, especially in the context of biallellic inactivation was found in patients without durable clinical benefit (Fisher’s exact P = 0.24, TMB-adjusted P = 0.074). We did not detect any loss-of-function mutations in JAK1 or JAK2 or an enrichment of cooccurring KRAS and inactivating STK11 mutations in nonresponding tumors. A homozygous deletion in PTEN was found in a patient with a short-lived response to ICB, and MDM2/MDM4 amplifications were identified in three nonresponders. AC, adenocarcinoma; SCC, squamous cell carcinoma; LCNEC, large cell neuroendocrine carcinoma; SBS, single base substitution; CNV, copy number variation. Dots represent hotspot mutations, and × denotes loss of heterozygosity of the wild-type allele.