Fig. 3

ConDoR provides insights into the evolution and spatial clonal architecture of a pancreatic ductal adenocarcinoma tumor using scDNA-seq data from two different regions of the tumor. a t-SNE plot showing results of clustering (details in the “Methods” section) of cells into 3 clusters (C0, C1, and C2) according to copy number profiles. b Constrained 1-Dollo phylogeny computed by ConDoR with edges labeled by the gain or loss of mutations and vertices labeled by the copy-number cluster and the fraction of cells from samples S1 and S2 that are attached at that vertex. c Reduction in normalized total read count for amplicon AMPL257637 (which contains mutations MGMT_1 and MGMT_2) in cells from cluster C2 compared to cells in cluster C1 (\(p < 5.8\times 10^{-33}\), a one-sided KS test), supporting the loss of these mutations in the cells belonging to copy-number cluster C2. d Observed mutation matrix obtained by discretizing read counts of the 7 mutations, with cells grouped by copy number cluster as indicated in the first column. Box plots show the median and the interquartile range (IQR), and the whiskers denote the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively