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. 2023 Jul 11;11:113. doi: 10.1186/s40478-023-01610-0

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Estimations of copy number alterations and their biological and prognostic relevance (a) Results of copy number variation (CNV) imputation from EPIC DNA methylation array performed by conumee method. Genomic segments with absolute scores above 0.3 are shown. Sample label colors correspond to methylation clusters (b) Box plot for conumee score of CDKN2A gene locus; 0.3 cut-off marked with dashed line (c) Estimation of gene expression across selected regions of chromosome 9 (according to chromosomal bands), calculated by GSEAlm package; label colors correspond to methylation clusters (d) Box plot of GSEAlm score for chr9p21 band (containing CDKN2A/B genes) that has lowest p-value as the result of comparing two chordoma subtypes in terms of the expression across the whole genome. (e) CDKN2A expression across methylation clusters and normal nucleus pulposus (f) Kaplan–Meier plot for number of CNVs (0.3 cut-off in conumee estimate); Cox proportional hazard model was used for testing, cut-off of 8 CNVs was picked by maxstat package for visualization purposes