Fig. 3: Single cell RNA-seq analyses of 38 AML and 8 NBM samples.

a UMAP representation of 245,073 cells from 38 AML samples and 8 normal bone marrow (NBM) samples. Cells are colored by cell type based on classification using a reference dataset of NBM cells. Clusters of cells from AML samples where a large proportion of cells was classified as hematopoietic stem cells (HSC) or lymphoid-primed multipotent progenitors (LMPP), but did not fully match the gene expression of the corresponding NBM cells, were classified as AML immature. b Knn-force plot projection of 98,022 cells classified as AML immature from 38 AML samples, confirming that these cells are most similar to immature NBM cells. The number of cells projected over each hexagon is indicated by the color scale. Only hexagons covered by more than 100 cells (0.1% of the grand total) are displayed in the plot. c Barplot depicting the proportion of cell types in each sample for 245,073 cells from 38 AML samples and 8 NBM samples. Mutated genes and fusion genes present in the samples are indicated below each bar. d Heatmap describing the inferred frequency of cells carrying confirmed somatic mutations for each cell type as determined by single cell RNA mutation calling (scRNAmut-seq) on 163,789 cells from 32 AML samples. Brown regions indicate that there were too few reads to infer a mutation frequency (i.e., three or fewer genotype reads). White indicates cell types not present in the current sample. Six samples with too few informative reads were excluded from this analysis. GMP Granulocyte-monocyte progenitors. Source data are provided as a Source Data file.