Aneuploidy in GATA2 deficiency. (A) Average gene expression for each chromosome in single cells from patients 1, 2, and 8. Average gene expression levels of individual chromosomes from 4 healthy donors were used for comparison. Chromosomal mapping read values were median centered. Top and bottom of the bars represent the 25% and 75% quartiles, respectively. (B) Heatmaps of chromosomal copy number variations (CNVs) signals of patient 8 obtained by the sliding window analysis. scRNA-seq data of patients were normalized against those of healthy donors. Copy number changes were examined in 22 chromosomes (columns) for patients’ individual cells (rows). Chromosome numbers are indicated on the top row. Three populations of cells are indicated on the right as +1,der(1;7); +1,der(1;7),+8; and diploid cells. (C) Percentages of aneuploid cells in subsets of HSPCs in patients 1, 2, and 8. The x-axis shows frequency of aneuploid cells. The y-axis shows HSPC subsets. (D) A heatmap of downregulated DNA repair genes in trisomy 8 cells in GATA2 deficiency. Networks of upregulated (E) and downregulated (F) genes in trisomy 8 cells in GATA2 deficiency.