Fig. 2: Heteroplasmy distribution and heterogeneity in POLGD274A cell lines.
From: Single-cell multi-omic analysis of mitochondrial mutational mosaicism and dynamics
a Violin plots of single cell raw mtDNA variant counts (n = 1224, 1069, and 1039 for CTRL, KI36, and KIA2, respectively), with the fold-changes of the median relative to the control cell line being indicated. b Violin plots of single-cell mtDNA-depth-normalized mtDNA variant counts. Cell numbers were the same as described in panel (a). For panels (a, b), boxes show the median (center line) and the interquartile range (25th–75th percentiles; box). The fold-changes of the median relative to the control cell line were indicated. c Venn diagrams depicting shared and unique somatic mutations called by the mgatk pipeline. Parental variants, highlighted within the yellow circle, were defined as variants present in both POLGD274A and control cell lines. d Line graph showing the mean count of non-parental somatic mtDNA variants (y-axis) at 5% incremental heteroplasmy thresholds. e UMAP projection of the color-scaled distribution of the number of non-parental somatic mtDNA variants above indicated variant allele frequency thresholds. UMAP as in Fig. 1b. f Comparison of mean pseudobulk heteroplasmy between parental (n = 593, 407, and 586 for CTRL, KI36, and KIA2, respectively) and line-specific (n = 27, 9248, and 110821 for CTRL, KI36, and KIA2, respectively) mtDNA variants stratified by cell lines. g Comparison of mean heteroplasmy across cell lines stratified by shared and line-specific (unique or shared between two POLGD274A cell lines) mtDNA variants. The number of variants is as follows: parental, n = 593, 407 and 586 for CTRL, KI36 and KIA2, respectively; CTRL-line-specific, n = 27; POLGD274A-line-specific shared, n = 5123; POLGD274A-line-specific unique, n = 4125, 5698 for KI36 and KIA2, respectively. Whiskers extend to the 5th and 95th percentiles. For panels (f, g), Holm–Bonferroni adjusted p-values from the two-sided Wilcoxon test are shown, with significance at a type I error rate of 0.05. Boxes show the median (center line) and the interquartile range (25th–75th percentiles; box). Whiskers extend to the 5th and 95th percentiles. Outliers are displayed as single points.
