Fig. 3: Meningiomas encode prognostic, focal copy number alterations.

a CNA profile plots (bottom rows) demonstrating focal copy number losses (blue) or gains (red) in meningioma, and 5-year LFFR AUC plots (top rows) demonstrating prognostic significance associated with focal regions of loss (blue) or gain (red). All chromosomes with peaks on either CNA profile plots or AUC plots are shown included. Dashed lines show centromeres. The x-axis of each plot shows the entire length of the corresponding chromosome or chromosome arm. Asterisks denote focal copy number and prognostic regions analyzed in Fig. 3b and Supplementary Data 4 and 5. n = 565 meningiomas. b Sample-matched RNA sequencing expression (log₂ transcripts per million) of all genes mapping to focal regions of recurrent loss on CNA profile plots from Supplementary Data 4 (left) or AUC plots from Supplementary Data 5 (right). Genes were identified by cross-referencing positions along the chromosome with the Ensembl database. Both plots are shown as peaks on CNA prolife plots did not always correspond to peaks on AUC plots, and vice versa. Dots and error bars show mean and standard error of the mean, respectively. P values (<0.0001 for each plot) are from two-sided Wilcoxon rank-sum tests comparing expression in meningiomas with deletion of each region (blue) compared to samples with no deletions anywhere in the cognate chromosome arm (gray). n = 502 meningiomas. c Dotplot of gene ontology analysis using genes contained in focal regions of AUC z-score plots with a univariate Cox AUC at least 0.04 higher than the median for their respective chromosome arms. Source data are provided as a Source Data file.