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. 2020 Aug 28;11:4324. doi: 10.1038/s41467-020-18070-y

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© The Author(s) 2020

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. 1 — a Heatmap of β-values for CpGs (rows) and samples (columns) used in the methylCIBERSORT signature matrix. Columns/rows are ordered by unsupervised hierarchical clustering which independently resolves reference cell type. b t-SNE plot showing methylation profiles of the pure reference cell types. c Barplot showing the methylCIBERSORT estimates of immune-cell-type proportions (MC) vs. known flow-validated proportions in six control PBMC cell mixtures (FV) or artificial mixtures generated from combined known proportions of isolated immune cell types (MIX). d Scatterplot showing a significant correlation (Pearson, ρ = 0.98, p < 0.001, n = 1100) between known input and methylCIBERSORT estimates of randomly simulated cell mixtures created in silico to contain 75% cancer and known proportions of input cell types. e Boxplots showing results of immunohistochemical (IHC) staining of medulloblastoma (MB) and malignant rhabdoid tumor (MRT) tissue sections with antibodies for CD20 and CD8; n = 30 biologically independent samples. % positive cells are shown by “High” and “Low” categories. “High” represents five samples (for which tissue sections were available) with the highest methylCIBERSORT estimate for either B-cells or CD8+ T-cell infiltration samples. “Low” represents five samples for which a methylCIBERSORT estimation of B-cells or CD8+ T-cell infiltration was 0 or negligible. Discontinuous axes are used where needed to represent outliers. Data represents the % positive cells from a minimum of 15,000 cells assessed per sample (median cells examined = 826,375). Box represents interquartile range, center line represents median, whiskers represent range of minima and maxima excluding outliers, which are represented as points. f Images of IHC staining showing examples from the aforementioned “High” and “Low” categories. Scale bar represents 100 μM.