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. 2021 Dec 7;601(7894):623–629. doi: 10.1038/s41586-021-04278-5

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© The Author(s) 2021

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. 7 — a, PCA analysis on the abundance of tumour immune microenvironment components obtained through the deconvolution of RNA-seq data using Danaher’s immune signatures (number of cases (n): pCR (green) = 39, RD (orange) = 110). b, c, Box plots showing associations between response and (b) Danaher immune cell enrichment and (c) MCPcounter immune cell enrichment across ER/HER subtypes. The box bounds the interquartile range divided by the median, with the whiskers extending to a maximum of 1.5 times the interquartile range beyond the box. Outliers are shown as dots. Two-tailed Wilcoxon rank sum tests. Number of cases (n): ER-HER2-: 37, ER+HER2-: 57, HER2+: 55. d, Heatmap showing unsupervised clustering of cancer immunity parameters across n = 149 cases with RNA sequencing data. e, Scatter plot showing association between computationally derived lymphocyte density and immune cell enrichment using Danaher’s immune signatures across n = 147 cases with digital pathology and RNA sequencing data. Pearson’s product-moment correlations (R) shown. The shaded area, in grey, represents the 95% confidence interval. f, 2D density plot validating relationship between GGI and STAT1 GSVA across RCB subgroups in two external microarray gene sets comprising 457 cases.