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Diagnosis of mitochondrial diseases has often required invasive muscle biopsies, but a national study shows that most patients can be diagnosed by genomic testing of blood.
The term “mitochondrial diseases” (MDs) encompasses nearly 400 monogenic disorders. MDs result in problems in mitochondrial energy generation and can be caused by pathogenic variants in any of the 37 mitochondrial DNA (mtDNA) genes, which we inherit from our mother, or in over 300 nuclear genes. MDs are the most common inherited metabolic diseases, affecting at least one in 5000 live births, meaning that at least 60 children born in Australia each year will develop a severe form of MD in their lifetime. The actual impact may be substantially higher as about 1 in 250 individuals carry a pathogenic mtDNA variant, which may have an effect on their health.
MDs have been said to cause almost any symptom with any age of onset and any mode of inheritance. Tissues with the highest energy needs, such as the brain, peripheral nerves, eyes and skeletal or cardiac muscle are affected most often but kidney, liver, endocrine and other systems can also be impacted. MDs may present in the perinatal period (with cardiac failure, neurological or other abnormalities), in infancy or childhood (eg, with the neurodegenerative Leigh syndrome), in adolescence (eg, with stroke-like episodes or diabetes), or any time in adulthood. Treatment and prevention of MDs remain inadequate, with most affected children not surviving to adulthood and affected adults often living with severe morbidity and early mortality.
The MD Flagship Study:
In patients suspected of an MD, a “genomics first” approach is largely replacing traditional enzyme and histochemical testing of muscle, sparing the need for invasive biopsies and shortening the “diagnostic odyssey” for many patients. However, there are limited data on what factors impact the diagnostic yield.
The MD Flagship Study was led by Murdoch Children’s Research Institute (MCRI) and supported by Australian Genomics and the Mito Foundation. It included clinicians and researchers from around Australia and sought to determine the diagnostic impact of genomic sequencing using blood samples from patients thought to have an MD. One hundred and forty children and adults were recruited prospectively via consultant physicians in New South Wales, Queensland, South Australia, Victoria, Tasmania and Western Australia. Patients were randomised to have either genome sequencing (which captures mtDNA and nuclear genes) or exome sequencing (for coding regions of nuclear genes) plus mtDNA sequencing. Initial analysis was by inspection of a curated list of MD genes, followed by expansion to consider all known disease genes and potential novel MD genes. When possible, familial DNA testing or functional testing was performed to investigate whether variants of uncertain significance in patient data could be upgraded to pathogenic.
The study provided a diagnosis for 55% of participants, with diagnostic rates very high in children at 71% and lower in adults at 31%. The clinical features of MDs overlap with those of other inherited diseases, so not unexpectedly, 29% of diagnosed patients had a disease caused by phenocopy genes or so-called mitochondrial mimics. Hence, genomics can provide the correct answer even when the clinical suspicion is slightly off target. These results also emphasise the utility of expanding beyond the original list of curated genes if they do not provide a diagnosis.
A concern in the genomics community is that people with non-European ancestry may miss out on the benefits of genomics because the population genomic databases are biased towards Europeans. Reflecting the Australian immigration history, about half of the children in our study had at least one parent with non-European ancestry and we were pleased to find that our diagnostic yield was at least as high in that group versus patients reporting only European ancestry.
Implications:
The MD Flagship Study confirms that most patients with a suspected MD can be diagnosed effectively by genomic testing of blood, sparing them the need for an invasive muscle biopsy. A confirmed genetic diagnosis of MD can change management by guiding treatment, avoiding unnecessary investigations, enabling testing of family members and facilitating reproductive options such as prenatal diagnosis and preimplantation genetic diagnosis. For families with a mtDNA disease, it can potentially enable access to the mitoHOPE (Healthy Outcomes Pilot and Evaluation) trial of mitochondrial donation, pending regulatory approvals.
Ascertainment bias contributed to the lower diagnostic yield obtained in adults. No adult patients were found with the most common mtDNA variants associated with adult-onset MD, likely because testing for these specific mtDNA variants has been readily accessible for many years. Referring clinicians may have already diagnosed such patients or found it simpler to request clinical testing than to spend the additional time needed to recruit patients to a research study. Another contributor to the lower yield in adults is that for some mtDNA variants, the amount of mutant mtDNA can decline with age. For patients with presentations that are highly suggestive of an mtDNA deletion eg, chronic progressive external ophthalmoplegia, our findings support a previous study of adult patients that suggested that muscle biopsy should be recommended.
While our results achieved a high diagnostic yield in patients with non-European ancestry, this does not imply that genomic databases have adequate representation of varied ancestries. We were often able to use other “multi-omic” or targeted functional testing to overcome such issues. Considerable efforts are underway in Australia and internationally to improve representation of Indigenous Australians and other ancestries in genomic databases.
Equitable access to genomic testing in Australia has benefited from health economic and other analyses supporting the establishment of Medicare Benefits Schedule item numbers (73456-73462) for genomic testing of suspected MD, introduced in November 2023. These item numbers include singleton and trio genomic testing, with the latter including parental samples as well as the proband. Trio genomics enables confirmation of the mode of inheritance of genomic variants and improves identification of de novo and compound heterozygous variants. When feasible, we recommend trio genomics to maximise diagnostic yield.
While genomics has transformed diagnosis of MDs and other inherited rare diseases, genomics alone still leaves a substantial proportion of patients having no confirmed diagnosis identified. Encouragingly, multi-omic approaches such as proteomics and transcriptomics are now being used by Australian research groups and consortia, and are moving toward implementation into clinical diagnostic laboratories to further boost diagnostic efficiency.
Professor David Thorburn is a biochemist and geneticist, who co-leads the MCRI Brain and Mitochondrial Research Group and heads the Victorian Clinical Genetics Services (VCGS) Mitochondrial Laboratory. He is an Honorary Professorial Fellow at the University of Melbourne and a Board Member of the Mito Foundation.
Dr Alison Compton is a laboratory geneticist, Team Leader in the MCRI Brain and Mitochondrial Research Group, a Clinical Associate of the VCGS and Honorary Senior Fellow at the University of Melbourne.
Dr Rocio Rius trained in clinical genetics, did her PhD on the Mito Flagship study and is an Honorary Fellow at the University of Melbourne and a Clinical Variant Curator in the Centre for Population Genomics.
Professor John Christodoulou AM is a clinical geneticist and genetic pathologist. He is Director of the MCRI Genomic Medicine Theme, co-Leader of the Brain and Mitochondrial Research Group, Chair in Genomic Medicine in the Department of Paediatrics, University of Melbourne and a Board Member of the Mito Foundation.
Declaration of competing interests: John Christodoulou is an approved pathology provider for Victorian Clinical Genetics Services, which performed some of the testing described in this study.
The statements or opinions expressed in this article reflect the views of the authors and do not necessarily represent the official policy of the AMA, the MJA or InSight+ unless so stated.
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