Figure 3. Mutations and CNV of chr1q in normal breast epithelial single cells and cell pools.
(A) Heatmap depicting BN-T–specific SNVs identified by sequencing of 11 normal single breast epithelial cells and 3 normal cell pools (brown, mutated; pink, WT; white, WT and sequencing depth of less than 8×). (B) Two distinct haplotypes of chr1q in 4 samples, including Ly-T, lymph node metastasis tissue, BN-T, and a population of macroscopically dissected normal breast epithelial cells (BNM-3). The left panels show the distribution of SNP allele frequencies of haplotypes 1 (red) and 2 (blue) in the amplified genome region chr1q, while the horizontal axis shows VAF and the vertical axis the number of SNPs within the corresponding VAF. The right panels plot SNP allele frequencies of haplotypes 1 (red) and 2 (blue) across chr1q, while the horizontal axis shows coordinate of SNPs in chr1q and the vertical axis shows the AF. Haplotype 1 was amplified in MT, while haplotype 2 was amplified in BN-T and BNM. (C) LOH of chr1q in BN single cells. Variant allele frequencies of SNPs in 2 haplotypes of chr1q are shown as blue and red points (the same color code for each haplotype as in B). P values of LOH in each cell were calculated using Wilcoxon’s rank sum test. Error bars represent the values of median, upper, and lower quartiles and maximum and minimum.