Subclone-specific differential expression and clonotype analysis in a data set collected from a CLL patient undergoing ibrutinib treatment. (A) Genetic subclone structure over three time points from bulk DNA-seq analysis. (B) UMAP of cell clusters of scRNA-seq data collected at the three time points, colored by time point and labeled by cell types. (C) Cell assignment results of B cells, colored by subclone identity assigned via scBayes: blue, orange, green, and gray represents SC1, SC2, normal, and unassigned, respectively. (D) Sample and subclone-specific expression profiles of genes TNFRSF13B, TXNIP, and CD69, highlighting different patterns of expression change across the three time points. (*) P < 0.005 and FDR < 0.05. (E) Overall and subclone-specific V(D)J clonotype diversity. Each bar represents a unique clonotype; the height of a bar corresponds to the percentage of that clonotype within the B cell (left most column) or specific B cell subclone (right three columns) population.
