Supplementary Figure 6: Data on TCGA A3B germline deletion samples.
(a) Y/RTCA analysis for A3B germline deletion samples from five TCGA high-APOBEC cohorts (all heterozygous). (b) Y/RTCA analysis for A3B wild-type samples from the same cohorts. Fisher’s exact test P value = 0.0752, comparing A3B genotypes to mutation signature types. (c) RMSDs versus A3A or A3B for A3B germline deletion samples from the same cohorts (all heterozygous). (d,e) Shown are analogous data for A3B WT samples, split between (d) A3A-like and (e) A3B-like subsets. Fisher’s exact test P value = 0.0297 (comparing A3B genotypes to mutation signature types), confirming significant skewing toward A3A-like signatures among A3B deletion samples. (f) Histograms of A3B copy number data, showing subsets of samples that have values significantly lower (upper panel) or higher (lower panel) than the wild-type standard of 2. Samples left of the blue dotted line are called as homozygous deletions. Those between the blue and green dotted lines are called heterozygous deletions. Samples to the right of the dotted red line are called amplifications. The majority of samples (>5,600) are wild type (near copy number 2) and are omitted from these plots to show the less numerous copy number variation–bearing samples more clearly.
