Figure 3

CNA analysis based on the genetic subclones of the tumor cells identified via low-depth WGS. (A) A genome-wide CNA analysis was performed using the low-depth WGS data. Each row represents each sample, and the samples were reordered by the hierarchical clustering method. The clustering analysis generated three major clusters, which were named Primary clone (red), Ascites clone 1 (yellow), and Ascites clone 2 (green). The clear differentiation of the CNA profiles between the Primary clone and Ascites clones implied that the tumor spheroids in the Ascites clones were not derived from the tumor cells in the Primary clone but from another independent tumor lineage. (B) Representation of the CNA profiles in detail at several regions for RO1, AC1, and AC4. The three samples exhibited both shared and exclusive CNAs. For example, deletion of FAT1 (1^st column) and amplification of MYC, CYC1, and PARP10 (2^nd column) were shared in every sample. However, the amplification of KDM5A (3^rd column) and NOTCH3 (4^th column) was exclusive to the Primary clone. This might indicate that the FAT1, MYC, CYC1, or PARP10 alterations conferred a growth advantage to the common ancestor of the Primary clone and Ascites clones. In contrast, the KDM5A or NOTCH3 amplifications might cause branching from the common ancestor and proliferation of the Primary clone.