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Updated: Dec 14, 2025

Measuring Single-Cell Mitochondrial DNA Copy Number and Heteroplasmy Using Digital Droplet Polymerase Chain Reaction
Published on: July 12, 2022
Deep sequencing shows that accumulation of potentially pathogenic mtDNA mutations rather than mtDNA copy numbers may
Licheng Ji1, Tingting Liao2, Juan Yang1
1Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 JieFang Avenue, Wuhan, 430030, Hubei, China.
Purpose:
To explore the relationship between mitochondrial DNA quantity and heteroplasmy and early embryonic loss.
Methods:
A total of 150 villous samples from patients with spontaneous abortion (SA, n = 75) or induced abortion (IA, n = 75) were collected. qPCR and next-generation sequencing (NGS) were used to test mitochondrial DNA quantity and heteroplasmy. Missense mutations with a CADD score > 15 and heteroplasmy ≥ 70% were defined as potentially pathogenic mutations.
Results:
With respect to mitochondrial DNA copy numbers, there was no significant difference between the SA and IA groups (median (IQR), 566 (397-791) vs. 614 (457-739); P = 0.768) or between the euploid and aneuploid groups (median (IQR), 516 (345-730) vs. 599 (423-839); P = 0.107). mtDNA copy numbers were not associated with spontaneous abortion using logistic regression analysis (P = 0.196, 95% CI 1.000-1.001). In addition, more patients harbored possibly pathogenic mtDNA mutations in their chorionic villi in the SA group (70.7%, 53/75) compared with the IA group (54.7%, 41/75; P < 0.05). However, there was no statistical difference between the euploid (80%, 24/30) and aneuploid groups (64.4%, 29/45; p = 0.147).
Conclusion:
Early embryonic loss and the formation of aneuploidy were not related to mtDNA copy number. Patients with spontaneous abortion were more likely to have possibly pathogenic mutations in their mtDNA, and this may assist in purifying pathogenic mtDNA. However, whether the accumulation of these potentially morbific mtDNA mutations caused early embryonic loss requires further investigation.
Insights
Mitochondrial DNA copy number does not appear linked to early embryonic loss or aneuploidy. However, spontaneous abortion patients show higher rates of potentially pathogenic mitochondrial DNA mutations, suggesting a possible role in pregnancy loss.
Area of Science:
- Genetics
- Reproductive Biology
- Mitochondrial Biology
Background:
- Mitochondrial DNA (mtDNA) plays a crucial role in cellular energy production.
- Alterations in mtDNA quantity and mutations are implicated in various diseases and pregnancy complications.
- Understanding the link between mtDNA and early embryonic loss is vital for reproductive health.
Purpose of the Study:
- To investigate the association between mitochondrial DNA quantity and heteroplasmy with early embryonic loss.
- To determine if mtDNA copy number or pathogenic mutations correlate with spontaneous abortion (SA) or aneuploidy.
Main Methods:
- Collected 150 villous samples from spontaneous abortion (n=75) and induced abortion (n=75) groups.
- Utilized quantitative PCR (qPCR) and next-generation sequencing (NGS) to assess mtDNA quantity and heteroplasmy.
- Defined potentially pathogenic mutations as missense mutations with a CADD score > 15 and heteroplasmy ≥ 70%.
Main Results:
- No significant difference in mtDNA copy numbers was observed between SA and IA groups, nor between euploid and aneuploid groups.
- mtDNA copy numbers were not associated with spontaneous abortion via logistic regression analysis.
- A higher prevalence of possibly pathogenic mtDNA mutations was found in the SA group (70.7%) compared to the IA group (54.7%).
Conclusions:
- Early embryonic loss and aneuploidy formation are not directly related to mtDNA copy number.
- Spontaneous abortion cases exhibit a greater likelihood of harboring potentially pathogenic mtDNA mutations.
- Further research is needed to confirm if the accumulation of pathogenic mtDNA mutations causes early embryonic loss.
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