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

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

<p>Diversity and high copy numbers of ecDNA in <i>IDH</i>wt GBMs. <b>A,</b> 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...

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Main Author: Imran Noorani (9184605) (author)
Other Authors: Magnus Haughey (22375292) (author), Jens Luebeck (15040173) (author), Andrew Rowan (15489418) (author), Eva Grönroos (15117034) (author), Francesco Terenzi (22375295) (author), Ivy Tsz-Lo Wong (20549683) (author), Davide Pradella (22375298) (author), Marta Lisi (22375301) (author), Jeanette Kittel (22375304) (author), Natasha Sharma (22375307) (author), Chris Bailey (22375310) (author), Clare E. Weeden (15295843) (author), Donald M. Bell (22375313) (author), Eric Joo (22375316) (author), Vittorio Barbè (22375319) (author), Matthew G. Jones (20549692) (author), King L. Hung (15117769) (author), Emma L. Nye (15489571) (author), Mary Green (18717219) (author), Lucy Meader (22375322) (author), Emma J. Norton (22375325) (author), Mark Fabian (22375328) (author), Nnennaya Kanu (22375331) (author), Mariam Jamal-Hanjani (15386766) (author), Thomas Santarius (22375334) (author), Andrea Ventura (22375337) (author), James A.R. Nicoll (22375340) (author), Delphine Boche (21902885) (author), Howard Y. Chang (20549704) (author), Vineet Bafna (15040200) (author), Weini Huang (17379552) (author), Paul S. Mischel (15040185) (author), Charles Swanton (14123052) (author), Benjamin Werner (22375343) (author)
Published: 2025
Subjects:
Cancer
Tumor Biology
Methods and Technology
Cancer Prevention
Cancer Interception
Biomarkers and intervention
Computational Methods
Mathematical modeling
Tumor Evolution
Tumor Heterogeneity
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Summary:<p>Diversity and high copy numbers of ecDNA in <i>IDH</i>wt GBMs. <b>A,</b> 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, <i>EGFR</i>, <i>PDGFRA</i>, and <i>CDK4</i>, are separated to the left of the vertical dashed line. <b>B,</b> Median ecDNA copy number vs. number of ecDNA-amplified genes for GB-UK and PCAWG cohorts (Spearman correlation). <b>C,</b> 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. <b>D,</b> Mean copy number of linear focal amplifications vs. ecDNA in GB-UK. <b>E,</b> Mean copy number of non-oncogenes compared with oncogenes amplified on ecDNA in GB-UK. <b>F,</b> Complexity score of linear focal amplifications vs. ecDNA in GB-UK. <b>G,</b> Number of uni- and multichromosomal ecDNAs in GB-UK and PCAWG cohorts. <b>H,</b> Distribution of ecDNA lengths in GB-UK and PCAWG cohorts. <b>I,</b> Median ecDNA copy number vs. length of intergenic DNA for <i>EGFR</i>-ecDNA in GB-UK and PCAWG cohorts (Spearman correlation).</p>

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