Fig. 2: The spatial subclonal architecture.
From: Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level
a Data for patient P05 is shown as an example for our approach for detection of subclones, which is based on subclonal copy number aberrations (CNAs). In the upper panel the whole genome sequencing chromosomal profiles for each autosomal chromosome in paired focal lesion (FL, gray bar) and RBM (black bar) are depicted. Light red and blue denote subclonal chromosomal gains and losses, respectively. Clonal events are marked with dark red and blue. To identify subclones, the average relative gene expression/accessibility in regions impacted by subclonal events was used for supervised clustering of scRNA-seq (middle panel) and scATAC-seq (lower panel) data of paired FL (gray bar) and RBM (black bar) samples. In the heatmaps red and blue signals correspond to higher and lower gene expression/accessibility, respectively. The four detected subclones are depicted on the left side of the two heatmaps in blue, red, green and orange, respectively. b Number of detectable CNA-defined subclones for each patient. For 3 patients (P01, P02 and P04), unique subclones, which were only detectable at one bone marrow site, are shown in dark color. c Proportion of CNA-defined subclones in paired FL/RBM scRNA-seq data for each patient. Subclone 6b in P04 corresponds to tumor cells with a deletion of chromosome 14 but no deletion of chromosome 13, which could not be seen in scATAC-seq and WGS (please also see Supplementary Fig. 4d). Source data are provided as a Source Data file.
