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Related Experiment Video

Updated: Dec 29, 2025

Measuring Single-Cell Mitochondrial DNA Copy Number and Heteroplasmy Using Digital Droplet Polymerase Chain Reaction
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Evaluation of mitochondrial DNA copy number estimation techniques.

Ryan J Longchamps1, Christina A Castellani1, Stephanie Y Yang1

  • 1Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.

Plos One
|February 1, 2020
PubMed
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Whole genome sequencing (WGS) offers a more accurate measurement of mitochondrial DNA copy number (mtDNA-CN) than qPCR. This advanced method improves the analysis of aging-related diseases and mitochondrial function.

Area of Science:

  • Genomics
  • Molecular Biology
  • Biostatistics

Background:

  • Mitochondrial DNA copy number (mtDNA-CN) serves as a key indicator of mitochondrial function and is linked to aging and related diseases.
  • Quantitative real-time PCR (qPCR) is the established standard for mtDNA-CN measurement, but alternative methods using microarrays and sequencing exist.

Purpose of the Study:

  • To comprehensively evaluate and compare the performance of different methods for measuring mtDNA-CN.
  • To assess the association of mtDNA-CN estimates with known biological correlates across various measurement techniques.

Main Methods:

  • Utilized data from 1,085 ARIC and 3,489 MESA study participants.
  • Calculated mtDNA-CN from qPCR, two microarray platforms, whole exome sequencing (WES), and whole genome sequencing (WGS).

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  • Evaluated methods based on associations with age, sex, white blood cell count, Duffy genotype, and cardiovascular disease.

    • Main Results:

    • mtDNA-CN derived from WGS showed significantly stronger associations with known correlates compared to qPCR, microarrays, and WES (p < 0.001).
    • WGS-derived mtDNA-CN demonstrated greater statistical significance (5.6 orders of magnitude) and more extreme effect sizes (5.8 times) than qPCR.
    • DNA extraction from cell lysate yielded more reproducible mtDNA-CN estimates than phenol-chloroform or silica-based methods.

    Conclusions:

    • Whole genome sequencing is recommended as a superior method for measuring mtDNA-CN due to its enhanced accuracy and association strength.
    • The field should transition to more accurate mtDNA-CN measurement techniques and re-evaluate trait associations using WGS data from large-scale initiatives.