Abstract
Mitochondrial disease is hugely diverse with respect to associated clinical presentations and underlying genetic causes, with pathogenic variants in over 300 disease genes currently described. Approximately half of these have been discovered in the last decade due to the increasingly widespread application of next generation sequencing technologies, in particular unbiased, whole exome—and latterly, whole genome sequencing. These technologies allow more genetic data to be collected from patients with mitochondrial disorders, continually improving the diagnostic success rate in a clinical setting. Despite these significant advances, some patients still remain without a definitive genetic diagnosis. Large datasets containing many variants of unknown significance have become a major challenge with next generation sequencing strategies and these require significant functional validation to confirm pathogenicity. This interface between diagnostics and research is critical in continuing to expand the list of known pathogenic variants and concomitantly enhance our knowledge of mitochondrial biology. The increasing use of whole exome sequencing, whole genome sequencing and other “omics” techniques such as transcriptomics and proteomics will generate even more data and allow further interrogation and validation of genetic causes, including those outside of coding regions. This will improve diagnostic yields still further and emphasizes the integral role that functional assessment of variant causality plays in this process—the overarching focus of this review.
Highlights
A single genotype can present with a range of phenotypes; the most common heteroplasmic pathogenic mtDNA variant, m.3243A > G, can present with a classic MELAS phenotype, and with MIDD (Maternally-inherited diabetes and deafness), sensorineural hearing loss, myopathy, cardiomyopathy, seizures, migraine, ataxia, cognitive impairment, bowel dysmotility, short stature, diabetes, external ophthalmoplegia or Leigh syndrome and 9% of individuals are asymptomatic.[6]
The introduction of next generation sequencing (NGS) into mainstream genetics, combined with the large number of mitochondrial disease gene candidates, means that putative pathogenic variants are identified in many different scenarios
Clinical information can be extremely important in directing appropriate genetic testing, but we often advocate the use of whole exome sequencing (WES) or whole genome sequencing (WGS) on the basis of speed, comprehensive coverage of nuclear and mitochondrial DNA variants and simultaneous assessment of heteroplasmy
Summary
The potential of using transcriptomics (RNA sequencing [RNA-Seq]) to tackle undiagnosed cases of mitochondrial disease has recently been assessed.[50] Of 48 cases that WES had previously failed to diagnose, RNA-Seq yielded a genetic diagnosis in five patients and candidate variants in the remaining 43, including identification of novel disease gene TIMMDC1 which encodes a complex I assembly factor.[50] Cummings and colleagues successfully diagnosed 35% of 50 unsolved rare muscle disease cases using RNA-Seq; this approach compared patient RNA-seq data to RNA-seq data from 184 control skeletal muscle samples, illustrating the power required to identify significant variations.[86] They highlighted the importance of acquiring pathologically-relevant tissue; analysis of tissue from the Genotype-Tissue Exppression (GTEx) Consortium[87] revealed that many of the most common muscle-disease genes are associated with significantly lower expression in blood and fibroblasts compared to skeletal muscle, rendering them underpowered. Previous efforts to identify Puf3p targets delivered unclear results, as it was difficult to identify truly productive binding events; the integration of these four “omics” strategies highlight the power of a “multi-omics” approach in elucidating the function of a protein in certain situations and we expect these approaches to be used more commonly in the future, including investigating the function of novel mitochondrial disease genes
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call