Detection of CNVs in single cells from patients. (A) Average gene expression for each chromosome in single cells from patients and healthy donors. Average gene expression levels of individual chromosomes from 4 healthy donors were used for comparison. Chromosome mapping read values were median-centered. The top and bottom of the bar represent the 25% and 75% quartiles. (B) Heatmaps of CNV signals obtained by 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). (C) CNV signals on chromosome 7 obtained from healthy donors and patient 3 by sliding window analysis. Two black lines show 95% confidence intervals. 7q11-21 and 7q22-36 are indicated in blue and red, respectively. (D) Cytogenetic abnormalities detected by fluorescence in situ hybridization. Probes used to detect specific chromosomes were: CDKN2C and CKS1B for chromosome 1, CEN 8 for chromosome 8, and CEN7 and D7S486 for chromosome 7. (E) Histograms of read ratios on chromosome 7 in patients 1 and 2. Pink, cells from patients; blue, cells from healthy donors; purple, distribution overlap between each patient and healthy donors; y-axis, frequency of cell number; and x-axis, ratios of reads on chromosome 7 in individual cells relative to reads on all chromosomes in the same cell.