nearly 100% frequency in tumor-derived epithelial cells, whereas other variants were shared across different immune cell types (Fig. 4c). We further identified cell clones by clustering allele frequency data, revealing ten distinct clones (Fig. 4d). Clones 1, 2 and 4 were highly specific to epithelial cells, whereas other clones were dispersed more evenly across different immune cell types, indicating that those immune cells likely originated from a common hematopoietic progenitor. We further identified differential DNA accessibility peaks between the three different epithelial cell clones, highlighting the ability of the additional clonotype data to aid in identifying additional sources of chromatin state heterogeneity within a cell type (Fig. 4e).
