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. 2023 May 19;29(5):1273–1286. doi: 10.1038/s41591-023-02324-5

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© The Author(s) 2023

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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Extended Data Fig. 5 — a, The mean target coverage in tumor and normal colon tissue. Center line, box limits and whiskers represent the median, interquartile range and 1.5x interquartile range respectively. b, Visual representation of the mutect-strelka2 based mutation calling pipeline, indicating at each step the remaining SNV and INDELS in the AC-ICAM cohort. c, Oncoprint of genes with the highest correlation with ICR score according to fitting of a binomial linear regression model using all samples as input. d, Oncoprint of genes with the highest correlation with ICR score according to fitting of binomial linear regression models using either hypermutated or non-hypermutated samples. All genes with P value < 0.05 as predictor variable in the regression model are displayed (c, d). e, Box-plot of ICR score in samples with a mutation in any HR repair gene (BRCA1, BRCA2, FANCA) versus those without mutation or wild-type (WT), stratified by tumor histology (mucinous versus all other histologies) in hypermutated samples. P value is calculated using unpaired, t-test. Center line, box limits, and whiskers represent the median, interquartile range and 1.5x interquartile range respectively. All P values are two-sided; n reflects the independent number of samples in all panels.