WGS of COLO320-DM cells
Whole genome sequencing (WGS) for COLO320-DM was performed by Novogene using double-ended DNA sequencing at a depth of 150 on the Illumina NextSeq 500 platform. The sequencing data was processed using AmpliconArchitect software for extrachromosomal DNA (ecDNA) identification. Following alignment to the reference genome hg38 using BWA-MEM, regions with a copy number greater than 5 were designated as seeds. AmpliconArchitect was then used to construct the amplification subgraph, with the AA map indicating the copy number of amplicon fragments and genomic breakpoints. Finally, ecDNA was visualized using CycleViz, providing graphical representation of the identified ecDNA regions (https://github.com/jluebeck/CycleViz).