Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing

Abstract

The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.

“Mitochondrial Toolbox” – A Review of Online Resources to Explore Mitochondrial Genomics

“…This may provide perspective for researchers seeking to develop new bioinformatics tools by informing them of the current gaps in the market, and therefore may provide inspiration for the development of new tools which would enable researchers to investigate the mitochondrial genome further. This review extends a mini-review previous published by Bris et al (2018).…”

“…Many mtDNA mutations are heteroplasmic, i.e., these mutations are not found in every mitochondrion in every cell of the affected individual. Many of the mitochondria in these cells may have normal genomes (Ye et al, 2014); mtDNA variants may only be clinically relevant once a certain threshold of heteroplasmy has been surpassed (Rossignol et al, 2003;Bris et al, 2018;Ng et al, 2018). Resources for mitochondrial genomics often lack information regarding the heteroplasmic threshold required for disease phenotypes to become evident, with MITOMAP being a notable exception (Brandon et al, 2005;Bris et al, 2018).…”

“…Combinations of polymorphisms may also have clinical relevance (Caporali et al, 2018). No computational tools exist with which to determine if an individual possesses a combination of rare mtDNA variants associated with disease, and also do not provide a means of identifying the co-occurrence of relevant nuclear genomic variants in conjunction with mtDNA variants (Dimitriadis et al, 2014;Jiang et al, 2016;Bris et al, 2018).…”

Leigh Syndrome Due to mtDNA Pathogenic Variants

“…These recent tools were developed for mtDNA using machine learning based approaches. [10] The HmtVar explore human mitochondrial variability data and their pathological correlations. The phylogenetic analysis and the mammalian conservation index (MCI) were also evaluated.…”

Human mitochondrial variant annotation with HmtNote

“…This is especially true for mitochondrial genomic research, which has seen a rapid increase in interest during the last few years, mostly due to the historically overlooked central role of the mitochondrion in many biological processes and pathological situations 1 . The presence of specific mitochondrial variants can offer useful insights on different levels, from population and evolution studies to pathogenicity assessment, and the functional analysis of human mitochondrial variations is a very florid research topic 2 .…”