Fig. 2: SCAAs and transcriptional regulation decrease neoantigen presentation.

a, Heatmap of SCAAs in APGs. Blue and red rectangles show SCAA losses and gains in gene-associated promoter regions, with dots indicating somatic mutations. b, Two-sided OR of a neoantigen versus nonantigenic mutation being located in a gene affected by promoter SCAA loss. c, Proportion of mutations identified by WGS that are located downstream of a SCAA loss promoter in n = 24 cancers. d, Two-sided OR of a neoantigen versus nonantigenic mutation being located in genes of gene groups 1–4 from ref. ²³. All, clonal and subclonal mutations are shown separately. e, Two-sided OR of a neoantigen versus nonantigenic mutation being transcriptionally edited (present in WGS but not expressed in RNA-seq). f, Proportion of mutations found in WGS that are edited in RNA for each FF–WGS cancer with matched RNA-seq data (n = 12). g, Proportion of samples within a cancer that carry a given (antigenic or nonantigenic mutation) in WGS but not in corresponding RNA-seq (n = 12 cancers). In b, d and e, markers indicate OR estimates with error bars showing the corresponding 95% CI. Significant P values from unadjusted two-sided Fisher’s exact tests are indicated above each bar. In c, f and g, cancers are colored according to their immune escape status (same color key applies), and P values from two-sided paired Wilcoxon-tests are indicated on top of each panel.