Investigating gene mutations in a South African paediatric cohort diagnosed with mitochondrial disease
Abstract
Mitochondrial diseases (MD) are a clinically heterogenous group of genetic disorders that affect
the neuromuscular system, the central nervous system (collectively known as
encephalomyopathies), and other high-energy demanding organs, often with multi-system
involvement. This involvement, whether single- or multi-system, can have extensive phenotypical
features which could make the diagnosis of MD a daunting task. Over recent years, substantial
progress has been made towards a better understanding of the most common mitochondrial
encephalomyopathies including their clinical manifestation and underlying genetic cause. This
progress has been made in mainly non-African patient populations. For these well-studied
populations, routine clinical, biochemical, and genetic diagnostic approaches have consequently
been established, improving diagnosis of MD in paediatric and adult patients alike. The limited
diagnostic capacity in developing countries such as South Africa with its ethnically diverse
populations, has hindered the advancement of diagnostic procedures for MDs in these countries.
As a result, there is limited information available on clinical manifestations and genetic causation
for the most common MDs in these understudied patient populations. However, over the last
decade the following progress has been made towards an understanding of the underlying genetic
cause of MD in South African patients: Firstly, since 1998 paediatric clinical referrals and
assessments have been performed on paediatric patients with mitochondrial-disease-like signs
and symptoms at the Steve Biko Academic Hospital, Pretoria (forming the cohort for this
investigation). Secondly, biochemical analyses also commenced shortly afterwards and were
performed for every patient who has been clinically diagnosed with an MD, which at the time of
this investigation was 212. Thirdly, genetic investigations followed, starting with a small number
of patients (n = 71) for whom whole mitochondrial genome next-generation sequencing was
performed. This number has been expanded throughout recent years, and to date there are whole
mitochondrial DNA sequencing data for 123 patients. Results from this initial mtDNA sequencing
approach revealed relatively few pathogenic mutations. For the majority of these cases, a clear
MD aetiology could not be established. It was collaboratively decided to perform targeted gene
panel sequencing on nuclear-encoded genes associated with MD. Three panels were designed
and used in this study, each consisting of genes directly involved with the mitochondrion. An inhouse
bioinformatics pipeline was developed during this study to analyse the sequence data.
The results for the nuclear gene investigations revealed that a clear genotype-phenotype
correlation could be established in only two of the 85 selected cases. One of these patients was extensively investigated and later published as a case-report. Due to the disappointingly low
diagnostic yield of panel sequencing, whole exome sequencing was performed on a small number
of African patients to probe the outcome of this approach. These initial results were promising as
six of the eight sequenced cases presented with a pathogenic or likely pathogenic variant.
Additional screening for two putative African-population-specific gene mutations was also
performed on all of the African cases. Combined, from the results, the aetiology could be
determined in ten cases; eight cases using next-generation sequencing, and two cases using
selected gene mutation screening. In conclusion, this study was the first in size and scope to
investigate the molecular genetics of MD in an understudied ethnically diverse population,
providing new knowledge on these patients and insight into future strategies. Diagnosis of MD
remains a daunting task in South Africa and will only improve once diagnostic capacity has been
significantly enhanced