Figure 2 from Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma

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Diversity and high copy numbers of ecDNA in IDHwt GBMs. A, Focal copy-number amplifications across the GB-UK and PCAWG cohorts, categorized by amplicon type [ecDNA, breakage–fusion–bridge (BFB) cycle, linear]. Only tumors containing focal amplifications are shown. Oncogenes with the same colored box indicate they exist on the same ecDNA molecule. The horizontal line between patients A61 and A3 (GB-UK) and patients SP27603 and SP23622 (PCAWG) separates patient samples with (above) or without (below) ecDNA, detected by WGS, DNA FISH, or nascent RNAscope. Oncogenes tested with DNA FISH and/or nascent RNAscope, EGFR, PDGFRA, and CDK4, are separated to the left of the vertical dashed line. B, Median ecDNA copy number vs. number of ecDNA-amplified genes for GB-UK and PCAWG cohorts (Spearman correlation). C, Oncogenes contained within ecDNA in both GB-UK and PCAWG cohorts ranked by maximum copy number. The number of samples with each oncogene as ecDNA in the GB-UK cohort is described in brackets. Only copy numbers detected by WGS are shown here. D, Mean copy number of linear focal amplifications vs. ecDNA in GB-UK. E, Mean copy number of non-oncogenes compared with oncogenes amplified on ecDNA in GB-UK. F, Complexity score of linear focal amplifications vs. ecDNA in GB-UK. G, Number of uni- and multichromosomal ecDNAs in GB-UK and PCAWG cohorts. H, Distribution of ecDNA lengths in GB-UK and PCAWG cohorts. I, Median ecDNA copy number vs. length of intergenic DNA for EGFR-ecDNA in GB-UK and PCAWG cohorts (Spearman correlation).

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