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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. 4 — a, Box-plot of TCR clonality for each ICR, stratified by CMS. P values are calculated using unpaired, two-sided t-test. Center line, box limits and whiskers represent the median, interquartile range and 1.5x interquartile range respectively. n reflects independent number of samples. b, Example of a plot showing productive TCR frequencies in normal tissue (x-axis) and corresponding frequency in tumor tissue (y-axis). Blue indicates T cell clones that are restricted to the tumor, while T cell clones that are unique to normal colon tissue are orange. Represented in green are T cell clones found both in tumor and normal colon tissue. The side panels represent a cumulative histogram of the TCR productive frequencies across that axis. c, Productive TCR scatter-plots of all nine patients for which TCR sequencing was performed on both tumor and matched normal colon samples. T cell clones in the upper left region (red) are considered significantly enriched in the tumor. Tumor-enriched clones were defined as T cell clones with an abundance of >0.1% in the tumor, that are at least 32 times more abundant in the tumor compared to the normal.