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. Author manuscript; available in PMC: 2022 May 10.
Published in final edited form as: Cancer Cell. 2021 Apr 8;39(5):694–707.e7. doi: 10.1016/j.ccell.2021.03.006

Figure 2. EcDNA signatures can be distinguished by the high chromosomal interaction frequency (adjnTIF) across 23 chromosomes.

Figure 2.

(A) Distribution of genome-wide adjnTIFs at 50-Kb resolution in the ecDNA (+) HF-3016 and HF-3177 cell lines in comparison with the ecDNA (−) HF-3035 line. Elevated adjnTIFs are observed on the chromosomes 7, 8 and 12 regions known to be amplified on ecDNAs. Distributions of adjnTIFs along the chromosomes 7, 8 and 12 are shown and regions with elevated adjnTIF values are well-matched with known ecEGFR, ecMYC and ecCDK4 regions.

(B) Circos plots of the interactions mediated by ecDNA regions across all 23 chromosomes in HF-3016 and HF-3177 ecDNA (+) cell lines. Extensive connections between ecMYC, ecEGFR and ecCDK4 regions are shown.

(C) Box plot displays the adjnTIFs between the known ecDNA regions and chromosomal background in four ecDNA (+) cell lines. Statistical analyses by one-sided Wilcoxon Rank-Sum Test. For boxplots, center line, median; boxes, first and third quartiles; whiskers, 1.5 × the interquartile range (IQR); points, outliers.

See also Figure S2 and Table S2.