Fig. 4

Identification of ecDNA by MGA-Seq. a Putative diagram of inter-chromosomal interaction pattern differences between ecDNA and HSR positive cell line. b-e Validation of MYC amplification in COLO320-DM and SW480 cell lines by DNA FISH. The red signal represents MYC and the green signal represents the centromere of chr 8. f, g Copy number variation analysis of chr 8 in COLO320-DM and SW480 cell lines. Gains and losses of copy numbers are shown in red and blue, respectively. h, i Location of the MYC amplification region in COLO320-DM and SW480 cell lines. The y-axis represents the reads counts that were normalized based on the total number of reads mapped per sample. j, k Cumulative interaction intensity curve of focal amplification region from COLO320-DM (chr8:127,300,000–128,900,000) and SW480 (chr8: 126,493,801–129,610,570) respectively. The x-axis represents the genome position, 100 kb bin size. The y-axis represents the accumulation of interaction intensity. l, m Plotted the second-order backward difference (SOBD) values across the genome for the focal amplification region of COLO320-DM (chr8:127,300,000–128,900,000) and SW480 (chr8: 126,493,801–129,610,570) using a bin size of 100 kb