Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.

Fig. 1

Heteroplasmy rates and features reported in Sanger and MPS-based datasets. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Rates and features of the mtGenome heteroplasmy reported in two Sanger-based and eight MPS-based datasets. The Ye et al. data are based on an analysis of the original dataset with the 63 samples noted by the authors as likely mixtures removed . The data plotted from Ref. are averages of the four reported quartiles. The data from Ref. are based on the 139 blood specimens. All of the data represented in this figure and further details for each study are presented in Table S1.
The bar graphs in the figure represent the percentage of individuals (or lineages, in the case of Ref. ) in each study that exhibited heteroplasmy at the applied detection levels (left y-axis). In the three studies in which an MAF was associated with each reported heteroplasmy , the proportion of the heteroplasmy detected at different MAFs is noted (in stacked bars). The percentage of individuals with PHP at the 10–20% detection level (blue bars) is consistently around 25% in six studies (see the blue-dashed box), but is much higher at this same detection level in two other MPS-based reports . The black diamonds, plotted on the secondary (right) y-axis, represent the maximum number of PHPs reported for any single individual each dataset. Despite a very wide range of applied or estimated heteroplasmy detection thresholds (0.1–20%), seven of the ten studies (see the black-dashed box) had a low maximum number of observed PHP (fewer than 10). By contrast, three datasets had much higher values – including greater than 80 PHP reported for a single individual in Ref. . Finally, the green squares (plotted on the left y-axis) represent the percentage of coding region PHPs that were unique in each study (observed in only a single individual). While this value clearly may be impacted by both the number of individuals examined and the detection threshold applied, the percentage of unique coding region PHP was less than 90% in only two studies . It is worth noting that both of those examinations of heteroplasmy used the 1000 Genomes Project mtGenome data, which has been previously shown to include at least some cross-sample contamination . The percentage of coding region PHP that were unique for each of the remaining studies falls within a relatively narrow range (green-dashed box).

Forensic Sci Int Genet. 2015 September;18:131-139.

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