Extended Data Fig. 17: Alternative splicing and association with somatic mutations.

a, Number of exon-skipping events confirmed at different ΔPSI thresholds in tumour (red), matched healthy (green) and GTEx (blue) samples for liver tissue. Dashed lines show the subset of exon-skipping events that only contain annotated introns. b, Number of exon-skipping events confirmed at a ΔPSI level of greater than 0.3 for the individual histotypes. Transparent section of bars represents the fraction of novel events, containing at least one unannotated intron. c, Splicing landscape for exon-skipping events. t-SNE analysis based on exon-skipping PSI values for all ICGC tumour and healthy samples together with tissue-matched GTEx samples. d, Position-specific effect of somatic mutations on alternative splicing. Magnitude and direction of mutation-associated splicing alterations. e, Permutation-based FDR values for SAV detection based on the different types of cancer. f, Cancer gene set enrichment for SAV sets, shown for cancer census gene set (middle) and sets determined in ref. ⁴⁸ (left) and ref. ¹²⁰ (right). g, Positional distributions (logarithms of distance from the nearest exons) of somatic variant creating novel splicing donors and acceptors. h, Sequence motif logos around somatic mutation creating novel splicing motifs. i, Example splicing effect of a branch-point mutation. UCSC genome browser RNA-seq coverage plots of cassette exon event in RBM28 between mutant and wild type. Mutant (bottom track) contains an A>G mutation 29 nucleotides upstream from the acceptor site of an affected exon. j, Distribution of new cassette exon events detected only within the PCAWG cohort. Top, number of events per histology type. Middle, events normalized to the total number of cassette exons detected in the histology types. Bottom, the number of exonization events per histotype for the subset with the novel cassette exons colocated to a somatic alteration near the acceptor or donor of the exon. k, Example of an exonization event in the tumour-suppressor gene STK11. RNA-seq read coverage for a part of the gene is shown in red for a donor carrying the alternate allele and in grey for a random donor with reference allele. The cassette exon event is shown as a schematic below, with blue (red) boxes denoting constitutive (alternative) exons and blue solid lines denoting introns. Magnified panels at the bottom show details from Integrative Genomics Viewer visualization, highlighting a somatic mutation at the 3′ end of the cassette exon. The associated sequencing change is illustrated on the bottom right corner, in which the vertical bar denotes the exon–intron boundary. l, Alu-based exonization mechanism. Top, the presence of an Alu element in an intron in antisense alone will still result in normal splicing. Bottom, specific mutations of the Alu sequence creates new splice sites and results in exonization.