SCNAs and SVs in PMBL. (A) GISTIC2.0-defined recurrent somatic copy number gain (red, left panel) and loss (blue, right panel) are visualized as mirror plots with arm-level alterations to the left and focal alterations to the right. Chromosomes are depicted on the vertical axis. Green line denotes the significance threshold (q < 0.1). Significant peaks are labeled with their associated cytoband/arm followed in brackets by frequency of the alteration, the number of total genes, and Cancer Gene Census genes in the significant regions, respectively. Genes that are also significantly mutated are shown in black, and other relevant drivers are shown in gray. Note that the significant focal deletion in 16p13.3 does not include CREBBP.⁸⁷  (B) Detected chromosomal rearrangements are visualized as a circos plot.⁸⁸  (C) Select SVs and their breakpoints are plotted in their genomic context. Exons are visualized as boxes: start codon-containing exons in red, untranslated regions are in smaller boxes, coding exons are underlined in green, and previously identified superenhancers⁷⁴  in black. Numbers indicate the supporting reads for the plotted SV in the format: split-reads, read-pairs. SV type is listed if it is not a translocation.