Extended Data Fig. 4: Validation of known hypermutation-associated signatures using TCGA datasets.

Mutational signatures were predicted using exome-sequencing variants that overlapped with the panel-targeted regions, and then compared to previously published DeconstructSigs signature predictions based on all exome variants. The TCGA MC3 dataset was used to assess the detection of COSMIC mutational signatures associated with APOBEC (signatures 2 and 13), mismatch repair (signature 6), ultraviolet light (signature 7), POLE (signature 10), and tobacco (signature 4). Variant calls for 17 hypermutated and 12 non-hypermutated glioma exome-sequenced samples⁴ were used to assess temozolomide (signature 11) detection. a, Detection of APOBEC-associated mutational signature in TCGA BLCA samples (n = 129 out of 411 samples). b, Detection of ultraviolet-associated mutational signature in TCGA SKCM samples (n = 237 out of 466 samples). c, Detection of tobacco smoking-associated mutational signature in TCGA LUAD samples (n = 250 out of 513 samples). d, Detection of MMR-associated mutational signature in TCGA COAD (n = 188 out of 380 samples). e, Detection of POLE-associated mutational signature in TCGA COAD and READ samples (n = 277 out of 380 samples). f, Detection of temozolomide-associated mutational signature in ref. ⁴ (n = 29). g, Unsupervised clustering of hypermutated samples. A total of 865 hypermutated tumour samples from exomes (pan-TCGA and Wang et al.⁴) and targeted panels (DFCI-Profile and MSK-IMPACT) were analysed for known hypermutation signatures (tobacco, UV, MMRD, POLE, TMZ, APOBEC). Samples and signatures underwent 2D hierarchical clustering based on Euclidean distance. h, Performance of cancer panel versus other genesets in mutational signature calling. We analysed 622 hypermutated tumour exomes (pan-TCGA and Wang et al.⁴, black) for their mutational signature contributions when restricted to variants from i) DFCI-Profile OncoPanel cancer panel genes (red), or ii) 9 randomly selected gene sets (grey) of similar total capture size to the cancer panel. For each sample, we assessed known hypermutation signatures for cancer panels and gene sets for which at least 20 single base substitutions were retained in the sample after restriction. Samples and signatures underwent 2D hierarchical clustering based on Euclidean distance. i, The violin plots represent the number of variants (top) and the cosine similarity of signature contributions (bottom) when using all exonic variants versus restriction to cancer panel or the 49 random gene sets. Boxes, quartiles; centre lines, median ratio for each group; whiskers, absolute range. Two-sided Welch’s t-test.