Fig. 1

Characterization of somatic variants and their potential for HLA presentation in HCC. a Numbers of somatic variants across HCC patients (n = 16). Numbers are shown for all variants passing initial filtering (Var), coding non-synonymous variants (Var^ns), and coding non-synonymous variants with RNA level evidence (Var^exp). Boxplots show means ± SD. b Var^exp shared among HCC patients. Var^exp affecting identical genes in ≥ 3 patients are displayed in gray. Var^exp observed at identical genomic positions are displayed in red (the shown HLA-DR variants should be cautiously interpreted as potential artifacts). c Correlation between Var^ns and predicted HLA-binding neoepitopes (PNE) (left; blue). Correlation between Var^exp and expressed PNE (PNE^exp) (right; orange). d Scatter plot of numbers of Var^ns and PNE in HCC patients (blue) and a benchmarking dataset of melanoma (Mel) patients (red) as previously described by Bassani-Sternberg et al. [24]