Figure 3: Hypermutated tumours are enriched in NMD-elicit mutations targeting hypermutation-permissive pathways. | Nature Communications

Figure 3: Hypermutated tumours are enriched in NMD-elicit mutations targeting hypermutation-permissive pathways.

From: A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay

Figure 3

(a) The barplot in the top panel shows the numbers of the different types of mutations (y axis) in each sample (x axis). The heatmap in the bottom panel shows the cancer type (cancer), whether a sample is hypermutated or not (hypermutation), log 10 of total mutation numbers (log 10 mutation frequency), whether a sample is microsatellite-stable or not (microsatellite stability), the NMD-elicit mutations in individual relevant genes and their pathway affiliation as indicated and the pathways affected by NMD-elicit mutations (black means that the pathway has at least one gene harbouring NMD-elicit mutations) in each sample (x axis). (b) In STAD, the heatmap shows the log 10 of total mutation numbers (first row), MSI (second row), the NMD-elicit mutations in individual relevant genes (3rd–7th rows) and NMD-elicit mutations in genes that belong to certain pathways (8th–10th rows) in each sample (x axis). FS, frameshift indels; IF, in-frame indels; SN, single-nucleotide substitution mutations. (c) In gastric cancer validation cohort13, the heatmap in the bottom panel shows the log 10 of total mutation numbers (first row), MSI (second row), the NMD-elicit mutations in individual relevant genes (3rd–7th rows) and NMD-elicit mutations in genes that belong to certain pathways (8th–10th rows) in each sample (x axis). FS, frameshift indels; IF, in-frame indels; SN, single-nucleotide mutations. Del, deletions; Ins, insertion; SN, substitution mutations. Note that the NMD-escape mutations in EIF5B and LARP4B are likely to induce NMD as they failed the NMD rules only marginally. Both EIF5B NMD-escape mutations failed the rules because they generate PTCs that are 175 bp away from the start codon. The LARP4B mutations generate a PTC that is 187 bp away from the start codon.

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