Fig. 2

Assignment of structural-copy number clone structure to scRNA-seq. Summary results of phylogenetic trees and clone alignment correlations. a Inferred phylogenetic trees of three untreated PDX patients Pt1-3, and three drug treatment time-series data Pt4-6. Resistant, sensitive cell clones were developed at different branches far from each other. (*) denote high fitness coefficient clones in each branch based on the previously published work [26]. b Manhattan copy number distances between median copy number profiles of paired clones in each series denote the variance level in the copy number DLP tree. c Clonal evolution of cells with/without drug treatment across time. d Disease classification at each time point and treatment status for Pt4-6. e Each point shows the clonealign-inferred scRNA-seq clonal proportion (y-axis) versus the corresponding DLP+ clonal proportion (x-axis) for each clone in each sample. Each patient is denoted by a different shape. Pearson correlation coefficients for each patient are reported at the top. f Pearson correlation between clonal proportions in DLP, and inferred clonal proportions in 10x – scRNA-seq expression at the same passages from patient Pt4 using clonealign. Strong positive correlation demonstrates that clonealign is able to provide accurate alignment