Fig. 2

CD4⁺ and/or CD8⁺ T-cell response against neoepitopes in TILs and PBMCs. a The immunogenicity of the selected neoantigens was evaluated in the ten patients from whom both PBMCs and tumor biospecimens were available. Red and white squares indicate the presence and absence of spontaneous CD4⁺ and/or CD8⁺ T-cell response against mutant-specific epitopes, respectively. b In four patients, spontaneous CD4⁺ and/or CD8⁺ T-cell response against neoepitopes were detected in both TILs and PBMCs. T-cell reactivity was measured by IFN-γ ELISpot assay. c The mutation burden and neoantigen load of patients with mutant-specific T-cell response (RES) versus those without (NonRES). d The differentially enriched pathways between between patients with mutant-specific T-cell response and patients without. Up-regulated in red and down-regulated in blue. e Recurrent somatic copy number amplification in the patients without mutant-specific T-cell response. The genome is oriented vertically from top to bottom, and GISTIC q-values at each locus are plotted from left to right on a log scale. The green line represents the default significance threshold (q-value = 0.25)