Fig. 5: Detection of ecDNA and HSR amplifications in CTCs. | Nature Communications

Fig. 5: Detection of ecDNA and HSR amplifications in CTCs.

From: Identification of multiple genomic alterations and prediction of neoantigens from circulating tumor cells at the single-cell level

Fig. 5

a Schematic of CTC isolation via negative selection with anti-CD45 magnetic beads. b Copy number amplifications of the Nfib gene across various CTCs from the KPC0402 sample, the y-axis represents the copy number and the x-axis in 5 kb bins. c–e Chromatin interaction heatmap of KPC0402-Cell 6, with GWIFA indicating the type of focal amplification of the Nfib oncogene as ecDNA. f Reconstruction of the molecular structure of ecDNA in the KPC0402-Cell 6 cells using whole-genome sequencing information and split reads from the Uni-C dataset. g Copy number amplifications of the MYC gene across various CTCs in the KPC0402 sample. h–j Chromatin interaction heatmap of KPC0402-Cell 6, with GWIFA identifying the type of focal amplification of the MYC as HSR. k Chromatin interaction heatmap between chromosome 8 and chromosome 16 in the PanT24-Cell 5. l–o Validation of the type and location of MYC amplification in PanT24 cells by DNA FISH. Scale bar, 5 µm. The red signal indicates MYC and the green signal represents the centromere of chromosome 8 (l, m) and chromosome 16 (n, o). Images are representative of three independent experiments with similar results.

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