Mitochondrial DNA Analysis: Introduction, Methods, and Applications

Mitochondrial DNA Analysis: Introduction, Methods, and Applications

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Introduction to Mitochondrial DNA Sequencing

Mitochondrial DNA (mtDNA) is a circular, double-stranded genome with a cytosine-rich light (L) chain and a guanine-rich heavy (H) chain that is around 16,000 base pairs long. Mitochondria play a critical role in a variety of cellular functions. Mitochondria not only produce over 90% of a cell's energy, but they also produce reactive oxygen species (ROS) and take part in apoptosis and other important cellular functions. Human diseases such as cancer, heart disease, diabetes, Alzheimer's disease, Parkinson's disease, and hypertension may be caused by a heteroplasmy of mutant and wild-type mtDNA. Because there is a lot of clinical variability among mitochondrial disorders, and many patients have phenotypes that are similar to other diseases, treatment is often only verified by identifying a pathogenic mtDNA variant through molecular genetic testing of DNA extracted from a blood specimen.

Bioinformatic Analysis

(1) data quality control, (2) reference Genome mapping, (3) SNP/InDel identification, annotation, statistics, (4) mtDNA heteroplasmy identification, annotation, statistics, and (5) mtDNA cricoc map are all part of the bioinformatics analysis of mitochondrial DNA sequencing.

mtDNA Heteroplasmy

Mitochondrial heteroplasmy is defined as the dynamic co-expression of acquired polymorphisms and somatic pathology in differing percentages within individual mitochondrial DNA (mtDNA) genomes with repetitive tissue specificity trends. The mtDNA genome ratios portray a balance between normal and abnormal cellular outcomes.

Advantages of Mitochondrial DNA Analysis

In contrast to nuclear DNA, which is acquired from both parents and in which genes are rearranged during the recombination procedure, mtDNA rarely changes from parent to offspring. Although mtDNA recombines as well, it does so with duplicates within the same mitochondrion. Because of this, and because animal mtDNA has a greater mutation frequency than nuclear DNA, it is an efficient way for tracing ancestry through females (matrilineage), and has been used to trace the ancestry of many species back hundreds of generations.

Applications in Forensics

Mitochondrial DNA assessment is appropriate for forensic science, especially for creating DNA profiles from kinds of evidence that may not be suitable for other DNA analysis methods such as restriction fragment length polymorphism (RFLP) or short tandem repeat (STR) analysis. The fact that RFLP and methods like polymerase chain reaction (PCR) analysis use DNA derived from the nucleus of a cell, whereas mitochondrial DNA analysis uses DNA found in the mitochondrion, is a key distinction between these two types of DNA analysis.

Another advantage of mitochondrial DNA analysis is that it can be used to analyze evidence that has been deteriorated due to factors such as improper storage. Although PCR analysis can sometimes work on a degraded specimen, the proof may eventually be so badly degraded that even PCR analysis is ineffective. Mitochondrial DNA analysis can be very useful in these situations.

Applications in Evolutionary Biology and Systematic Biology

Given the importance of mitochondria in cellular respiration, mtDNA is conserved across eukaryotic organisms. It has a comparatively greater mutation rate (though slow compared to other DNA regions such as microsatellites) due to less effective DNA repair (compared to nuclear DNA), which makes it useful for researching the evolutionary relationships—phylogeny—of organisms. Biologists can evaluate mtDNA sequences from different species and utilize the results to construct an evolutionary tree for the species in question.

The classification of animal species from tissue fragments, bloodstains, and excavated remains can also benefit from an mtDNA database. Many animals have already had their mtDNA sequences determined, both partial and complete. As a result, even if the sequence is uncertain, a pair of universal (common) primers could be intended on a highly conserved sequence in the preferred area to amplify the specimen. After sequencing, a comparison with reference sequences would allow the species to be determined. RFLP and insertion/deletion polymorphism analysis can also be performed on PCR products. Also, chloroplast DNA is effective for plant species identification.

About CD Genomics Bioinformatics Analysis

The bioinformatics analysis department of CD Genomics provides novel solutions for data-driven innovation aimed at discovering the hidden potential in biological data, tapping new insights related to life science research, and predicting new prospects.


  1. Umetsu K, Yuasa I. Recent progress in mitochondrial DNA analysis. Legal Medicine. 2005, 7(4):259-62.
  2. Wong LJ, Boles RG. Mitochondrial DNA analysis in clinical laboratory diagnostics. Clinica chimica acta. 2005, 354(1-2).
* For Research Use Only. Not for use in diagnostic procedures.
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