MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

Abstract

Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/.Contact: marcella.attimonelli@uniba.itSupplementary information: Supplementary data are available at Bioinformatics online.

Intra-individual purifying selection on mitochondrial DNA variants during human oogenesis

“…The mtDNA was analyzed by applying the mt-classifier.py module within the MToolBox pipeline (Calabrese et al, 2014) to assign the mitochondrial haplogroup and to report the functional annotation of the variants detected.…”

“…(2) Functional annotation of the recognized variants. This analysis was carried out by aligning each sample-specific reconstructed contig against the related Macro-Haplogroup-specific Consensus Sequence (MHCS), see Supplementary Information in Calabrese et al (2014) to recognize private variants via a prioritization process. All variant nucleotide positions and related loci as well as their corresponding codon positions, possible amino acid changes, stop-gains and stop-losses in protein-coding genes were reported in the final annotation file.…”

Identification of causative mutations in patients with Leigh syndrome and MERRF by mitochondrial DNA-targeted next-generation sequencing

“…In this study, we applied mtDNA-targeted NGS to identify genetic causes of the 2 studied diseases. NGS technology has been recently introduced in mtDNA testing for mitochondrial diseases [28][29][30]. The application of NGS may reduce the testing cost and time, with high fidelity.…”

“…The NGS technique is now recognized to reduce sequencing cost and analysis time, with high coverage and fidelity, thereby enabling the decoding of a number of human mitochondrial diseases. Calabrese et al [30] developed an MToolBox pipeline to reconstruct and analyze human mtDNA from high-throughput sequencing data.…”

Pathology of mitochondria in MELAS syndrome: an ultrastructural study

“…Reads were aligned to the mtDNA Revised Cambridge Reference Sequence of the Human Mitochondrial DNA (rCRS); (http:// www.mitomap.org/MITOMAP/HumanMitoSeq) with the Burrows-Wheeler Alignment Tool (http:// bio-bwa.sourceforge.net/). The level of heteroplasmy was assessed with MToolBox [19] and by read counting in the Integrative Genome Viewer (IGV) [20].…”