Extended Data Fig. 3: Extended Cell Type Annotation information.

(a) Dot plot displaying additional markers for CD4⁺ T, CD8⁺ T, and natural killer cell annotations. Scaled expression values for each gene are visualized on a red-blue color scale, with the size of each dot representing the percent expression of the corresponding gene. The colored triangle next to each cell name corresponds to the T and NK cell clusters (see Fig. 2d). (b-c) UMAPs displaying subclusters of CD4⁺ T cells (b) and CD8⁺ T cells (c). (d-e) UMAP (d) and dot plot displaying the top differentially expressed markers (e) for mature erythrocyte populations. (f) Feature plot displaying plasma cell markers. UMAP embeddings correspond to those displayed in Fig. 2a. (g-h) UMAP (g) and dot plot displaying the top differentially expressed markers (h) for the plasma cell compartment. (i) Scatter plot showing the relationship between logit-transformed plasma cell proportions in CD138^neg scRNA-seq data and plasma cell fractions estimated via flow cytometry on unsorted aspirates. Each dot represents an individual sample, colored by processing site. The black line with p and R² values represents the line of best fit average across processing sites, where dashed color lines represent fits for individual processing sites. (j) Box plot depicting the plasma cell proportion in the scRNA-seq data for each patient (n_patient=263). Patients are binned based on whether their plasma cell fraction is ≥20% (n_patient=74) or <20% (n_patient=189), as estimated by flow cytometry on unsorted samples. Two-sided p-values comparing the groups is estimated via a linear model. In the box plots, bounds of the box represent the 25^th and 75^th percentile, with the center displaying the median. Whiskers extend to 1.5*IQR beyond the bounds of the box. (k-m) Analyses to assess for malignancy of the plasma cells in the CD138^neg scRNA-seq data. (k) UMAP highlighting cells with driver overall and individual gene mutations in red and inferred copy number in purple. UMAP embeddings correspond to those displayed in Fig. 2a (l) UMAP of all cell types of RP (left) or NP (right) cohort samples showing various driver mutations. (m) CCND1 expression across cells in the RP vs NP patient cohorts (top). CCND1 expression in cells from patients with mutations (mut) and/or translocations (Tx) determined based on analysis of WES and WGS data (bottom). Unadjusted p-values from a wilcoxon rank-sum test between RP and NP samples is displayed if significant.

Source data