Fig. 3.

Copy-number variation and eccDNA identification in PC-3. A) Venn diagram of genes located on amplified eccDNAs (copy number > 5) in PC-3 cells from this study (left), comparison with Seim et al. (middle), and comparison with Turner et al. (Right). B) CNVkit scatterplot of chr8:120–140 Mb of the PC-3 cell line isolate from this study (left), Seim et al. (middle), and Turner et al. (Right). The y-axis describes the log(2) copy ratio reported by CNVkit and represents the deviation in copy number of each genomic segment in the sample relative to the expected copy number based on the reference genome [35]. The vertical purple line represents the location of the MYC gene (∼127 Mb). C) AmpliconArchitect output of the amplicon that included the MYC gene in the PC-3 cell line isolate from this study (left), Seim et al. (Middle), and Turner et al. (Right). Read coverage is represented as grey coverage bars and absolute copy-number is represented as horizontal orange lines. The location of the MYC and PVT1 gene is shown as purple lines underneath the graphs. D) No MYC-carrying eccDNAs were identified in the PC-3 cell line isolate from this study (left) or with data from Seim et al. (middle). With the Turner et al. WGS data, MYC and PVT1 carrying eccDNAs were identified by AmpliconClassifier and visualized with CycleViz (right).