Fig. 2

Single cell transcriptomics reveals distinct AML-phenotypes. (A) UMAP of the six AML pairs, colored by primary mutation (red: AML1-ETO; blue: FLT3-ITD); (B) UMAP colored by sample; (C) Copy number variation data derived from WES (left) and scRNA-seq (right) data for patient s220. Left: Relapse-specific copy number gain and loss at chr2 and chr15, respectively. Right: cell normalized gene expression signals (iCNV signal) in tiles of 3 Mb show the copy loss and gain at chr2 and chr15, respectively. The plot indicates that virtually all Re cells are affected, compared to none of the Dx cells. Bottom: tumor allele frequency at heterozygous SNPs confirms copy loss at chr2 and gain at chr15. (D) Boxplot of DEGs at the lost and gained segments of chr2 (n = 17 DEGs) and chr15 (n = 24 DEGs), respectively. (E) Heatmap showing the top 20 marker genes per primary mutation