Applying genomic and transcriptomic advances to mitochondrial medicine

Abstract

Next generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which limits their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering our efforts to understand the underlying disease mechanisms. Although a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression, as well as the interpretation of rare and novel mitochondrial transfer RNA variants.

Direct Nanopore Sequencing of Individual Full Length tRNA Strands

“…Preliminary data from our laboratory suggest that the technique will apply to tRNAs from other species. With further optimization, it could provide insights into tRNA-associated human diseases 27,30–33 .…”

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

“…New sequencing platforms have revolutionized diagnostics of such diseases, mainly exome and wholegenome approaches, including mitochondrial heteroplasmy [33]. Nevertheless, a holistic -omics approach is needed to generate more comprehensive results, also requiring new bioinformatics tools to properly analyze them [34][35][36][37][38].…”

“…Its dysregulation may be responsible for initiation and progression of diseases like cancer. Thus, specific computational tools have been developed to integrate genomics and transcriptomics, for a proper characterization of alternative splicing in health and disease [60], including mitochondrial diseases [34,61]. In relation to that, long-read isoform quantification and analysis (LIQA) allows to identify differential alternative splicing (DAS).…”

Mitochondrial DNA variants in genomic data: diagnostic uplifts and predictive implications

“…PMDs have traditionally been diagnosed by evaluating mtDNA in multiple tissues, with nuclear genes that encode mitochondrial proteins being tested separately. PCR-free wholegenome sequencing (WGS) captures both nDNA and mtDNA, and is increasingly being adopted for the diagnosis of rare diseases 1 . mtDNA has a high copy number and is consequently sequenced to a considerable depth (typically >~1,000x) during WGS.…”