Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

Abstract

Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. While in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic utility, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease, who were refractory to traditional molecular diagnosis. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with over 100 causal genes identified to date. We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Since patients and controls harbored a comparable number of such heterozygous alleles, we could not prioritize dominant acting genes. However, patients showed a five-fold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23/42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. 13 patients (31%) had mutations in nuclear genes never linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by cDNA complementation and evidence from multiple patients, respectively. The results underscore the immediate potential and challenges of deploying NGS in clinical settings.

Molecular-genetic characterization and rescue of a TSFM mutation causing childhood-onset ataxia and nonobstructive cardiomyopathy

“…Despite pulse labeling of mitochondrial translation products only revealed a moderate reduction in mitochondrial protein synthesis, all of these patients died of encephalomyopathy, hypertrophic cardiomyopathy or liver failure before the age of 2 months. [10][11][12] Surprisingly, the patient here reported, presenting ataxia and hypertrophic cardiomyopathy, was alive at the age of 23 years. His mutation also decreased the EFTs levels, but the EFTu levels were normal.…”

AGC1 Deficiency Causes Infantile Epilepsy, Abnormal Myelination, and Reduced N-Acetylaspartate

“…An extensive array of clinical diagnostic genetic testing performed to evaluate for known mitochondrial DNA and nuclear DNA causes of early infantile epileptic encephalopathy or mitochondrial diseases was unrevealing. Indeed, it is well known that muscle biopsies can be unrevealing of a specific histologic or biochemical abnormality in children even with known mitochondrial diseases (Haas et al 2008) and that sequencing of all currently known mitochondrial disease genes is likely to identify a specific genetic etiology for only up to one-half of individuals with clinical manifestations of possible mitochondrial disease (Calvo et al 2012). Following completion of mitochondrial DNA (mtDNA) genome sequencing and mtDNA deletion analysis in the proband's muscle, an autosomal recessive monogenic cause of disease was assumed to be present based on a similarly severe presentation in the proband's brother and known consanguinity.…”

Lethal Neonatal LTBL Associated with Biallelic EARS2 Variants: Case Report and Review of the Reported Neuroradiological Features

“…This is true of mitochondrial disorders, which are clinically, biochemically and genetically heterogeneous; respectively, characterised by multisystemic features and mitochondrial respiratory chain complex activity deficiency. Defects of mitochondrial protein translation, which is closely coordinated between both mitochondrial DNA and the nuclear genome, are associated with multiple respiratory chain deficiency (Calvo et al 2012;Lightowlers et al 2015).…”