Fig. 2

Features of APOBEC-associated hotspot mutations. a Comparison for probability of locating on lagging-strand-template between 44 APOBEC-associated hotspot mutations and 86 other hotspots across nine cancer/normal cell lines [37, 38]. b Proportion of hotspot mutations located in DNA hairpin loop structures (25 nt ssDNA centred on mutated site) for APOBEC-associated hotspot mutations and other hotspots. P value: Fisher’s exact test. c Proportion of APOBEC-associated hotspot mutations presenting a higher prevalence than the other mutations within the same genes (n = 33). d Distribution of clonal and subclonal events for APOBEC-associated hotspots and other mutations within the genes targeted by APOBEC (n = 33). Clonality data was extracted from TCGA BCa publication [17] which was evaluated by using ABSOLUTE algorithm [36]. P value: Fisher’s exact test. GLMM, generalised linear mixed model, with mutation count as covariate and genes as random effects; OR, odds ratio. e Representative replication fork directionality (RFD) around the ERBB2 gene in HeLa cells, as determined by mapping Okazaki fragments to C (Crick) and W (Watson) DNA strands. Red (blue) RFD profile marks indicate the regions in which Watson (Crick) strands are replicated mostly as lagging-strand-templates. Black arrow under gene symbol for transcriptional direction. f Representative predicted stem-loop structure for the ERBB2 gene. Red rectangle marks the mutation site. Free energy parameter—ΔG (kcal/mol) for loop stability. Strand (+) indicates cytosine (C) mutation, whereas strand (−) indicates guanine (G) mutation. g Representative mutation spectra for ERBB2 and KDM6A genes in 602 BCa. Red rectangles indicate APOBEC-associated hotspot mutations; green dots mark missense mutations; black dots mark truncating mutations; pink dots mark other mutations. ERBB2 S310F and KDM6A Q555* are APOBEC-associated hotspot mutations and have a higher prevalence compare to the other mutations within their gene sequence