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