Fig. 2: Reconstruction of extrachromosomal DNA (ecDNA).

a FISH with DAPI (4′,6-diamidino-2-phenylindole)-stained metaphase chromosomes in HK301 showing an HSR-like amplicon containing EGFR. Scale bar indicates 10 µm. b Theoretical model for the integration of circular extrachromosomal DNA into HSR-like amplicons, preserving the structure of breakpoint graph. c AA-generated breakpoint graph for HK301 containing EGFR and segments from chr6. The coloring of the graph edges represents the orientation of the junction between the two segments. Edge thickness indicates AA-estimated breakpoint copy number. Vertical dashed lines separate segments from different chromosomes while dotted lines indicate distinct genomic regions from the same chromosome. Numbering of breakpoint edges corresponds with AR reconstruction breakpoint numbering. d Cyclic AR reconstruction of HK301 amplicon containing EGFRvIII. Breakpoint graph edges supported by the AA graph are numbered in a manner corresponding to the numbering in panel (c). e FISH with DAPI-stained metaphase chromosomes in NCI-H460 shows HSR-like MYC amplicon. Scale bar indicates 7.3 µm. f FISH with DAPI-stained metaphase chromosomes in NCI-H460 showing an extrachromosomal MYC amplicon. Scale bar indicates 7.3 µm. g AA-generated breakpoint graph for NCI-H460 containing MYC and PVT1. h AR reconstruction of the NCI-H460 amplicon. Indicated in this figure is an amplicon inversion point (top right) where the reconstruction explaining the full amplicon ends, and then the structure begins to repeat in the opposite direction (solid line & opposing black arrows). Also indicated is an endpoint for the non-circular reconstruction (center right) where the AR reconstruction and full amplicon structure both stop (dotted line).