Fig. 3

Shared SV-derived neoantigens. a Histograms showing the number of patients sharing a neoantigen created by SVs (top), SNVs (medium), and indels (bottom). Bin width: 5. b SV-derived neoantigens shared by at least 20 patients and their associated cancer types. c Genomic locations of the genes leading to shared SV-derived neoantigens. The y-axis represents the number of patients with SV-derived neoantigens. Different neoantigens originating from the same gene are summed. Genes are colored by overlap with fragile sites (purple) or not (grey). d Interactions between shared neo-peptides and 137 common MHC alleles. Suffixes of gene names are to discriminate the neo-peptides from the same gene. The x-axis indicates the position relative to the first mutated amino acid of the neo-peptide. The color gradient indicates the number of MHC alleles that can bind to each k-mer (log-transformed). Only neo-peptides shared by > 5 patients and have > 1 interactions are listed. e, f Breakpoint junctions of the SVs leading to neo-peptides of MACROD2 (e) and PARK2 (f). Each arc represents an SV and is colored according to the identity of the neo-peptide. The exon (vertical line)-intron (horizontal broken line) structures of genes are displayed at the bottom