Long-Read Sequencing

Human Mitochondrial DNA ---
mtDNA Panel

Mitochondrial Diseases and the Challenges in Variant Detection

Mitochondrial diseases are among the most common inherited metabolic disorders, with an estimated prevalence of more than 1 in 5,000 adults¹. Approximately 75% of adult-onset mitochondrial diseases and 20–25% of pediatric mitochondrial diseases may be caused by pathogenic variants in mitochondrial DNA (mtDNA)².

mtDNA is present in multiple copies per cell. As a result, mtDNA variants may be homoplasmic (all mtDNA copies are identical) or heteroplasmic (mutant and wild-type mtDNA coexist). Low-level heteroplasmy may be observed in healthy individuals, while clinical symptoms typically appear only when the mutant mtDNA level exceeds a certain threshold. Mitochondrial disorders show significant phenotypic and genetic heterogeneity. They may affect one or multiple organ systems, with tissues of high energy demand—particularly muscle and nervous tissue—being most commonly involved.

Next-generation sequencing (NGS) has greatly improved the detection of mtDNA variants. However, due to the unique structure and biology of mtDNA, accurate variant detection remains challenging.

gDNA contains many mitochondrial-like sequences, known as nuclear mitochondrial DNA segments (NUMTs). These homologous regions can be misaligned under short-read sequencing, leading to false-positive variant calls
Low-level heteroplasmic variants may be missed
Limited ability to detect deletions and other structural variants

Long-Read Sequencing for Comprehensive mtDNA Analysis

LRS-mtDNA testing uses long-range PCR amplification to enrich the mitochondrial genome, enabling comprehensive analysis of the full mtDNA region. This approach avoids interference from NUMTs and repetitive regions and supports sensitive detection of diverse variant types at low heteroplasmy levels.

Lower false-positive

A single high-quality HiFi read can span the full mitochondrial genome (16,569 bp), removing the need for assembly and helping distinguish true mtDNA sequences from NUMTs. This reduces the risk of false-positive variant calls.

Sensitive to low-heteroplasmy

Detects of SNVs and InDels at heteroplasmy levels as low as 1%

Send-out Testing

When considering our send-out sequencing services:

Consultation: Contact our team for the most current test specifications.
Sample Preparation: Check sample types and shipment requirements to ensure high-quality results. Please check your local export regulations and logistics partners.
Submission: Contact Xcelom when placing an order. Include the completed Test Request and Consent Form, along with any required documents.

Sample Requirements

Peripheral Blood: 2 mL in EDTA tube

Dried Blood Spot: 3 x 8 mm in diameter

Long-fragment gDNA

Transport Conditions

2-8℃, arrive within 72 hours

Reporting

Detect pathogenic (P) and likely pathogenic (LP) SNVs/InDels in mitochondrial genomes associated with mitochondrial diseases, with a variant heteroplasmy level above 1%. It also detects selected pathogenic (P) and likely pathogenic (LP) large deletions within the mitochondrial genome.

Turnaround Time (TAT)

15 working days

End-to-End Technology Transfer

Berry Genomics and Xcelom provide a dedicated service for the implementation of HiFi LR-WGS solutions. We deliver comprehensive support ranging from lab workflow setup to staff training.

We specialize in bioinformatics and analysis support, helping laboratories master the complexities of variant annotation and interpretation. Our tailored software solutions streamline the workflow and assist with ACMG classification by automatically integrating relevant public databases.

Resources

HiFi LR-WGS Brochure

References:

1. Gorman GS, Schaefer AM, Ng Y, et al. Prevalence of nuclear and mitochondrial DNA mutations related to adult mitochondrial disease. Ann Neurol. 2015;77(5):753-759.

2. Frazier AE, Thorburn DR, Compton AG. Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology. J Biol Chem. 2019;294(14):5386-5395.