Extended Data Figure 1. Oncogenes are harbored on distinct ecDNA species but are correlated in copy number.

(a) Heatmaps showing non-overlapping oncogene presence on distinct ecDNA species in metaphase DNA FISH. Rows represents individual ecDNA molecules. (b) Bar plots showing the fractions of ecDNAs containing combinations of MYCN, CDK4 or MDM2 and demonstrating little overlap between these oncogenes on the same ecDNA molecules. (c) Copy number correlations and distributions of oncogene ecDNAs in metaphase DNA FISH images (left), and bar plots showing the fractions of ecDNAs containing combinations of FGFR2 and MYC in SNU16m1 cells and combinations of MYC and EGFR in GBM39-KT cells, demonstrating little overlap between these oncogenes on the same ecDNA molecules (right).