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. 2024 Feb 15;56(3):541–552. doi: 10.1038/s41588-024-01659-0

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, The catalog of ID signatures obtained from our reanalysis of PCAWG data with MuSiCal. An asterisk indicates newly added signatures not present in the current COSMIC catalog. Other signatures also have modified spectra. Each of the nine new signatures is decomposed using COSMIC signatures by NNLS. The resulting cosine similarities between the original and the reconstructed signatures are annotated next to each spectrum. b, MuSiCal-derived signature assignments in PCAWG samples for SBS (upper) and ID (lower) signatures. Marker size represents the prevalence of a signature; that is, the proportion of samples with nonzero exposures of the corresponding signature within a tumor type. Color indicates the median number of mutations per Mb contributed from the corresponding signature among samples with nonzero exposures. c, Heatmap of Pearson correlation coefficients between the per-sample exposures of SBS and ID signatures. The correlations are calculated for MMRP samples and samples with MMRD and/or POLE-exo mutations separately. Only the samples with at least 100 indels are used and only statistically significant associations are shown (adjusted P < 0.05). The correlations are also examined separately in each tumor type where the corresponding ID and SBS signatures are both active, and are excluded if they are significant in only a small fraction (<20%) of these tumor types.