Abstract:Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in human medicine. Assuming that rare variants are more likely to be damaging, we designed a phylogeny-based prioritization workflow to obtain a reliable pool of candidate variants for further investigations. The prioritization workflow relies on an exhaustive functional annotation through the mtDNA extraction pipeline MToolBox and includes Macr… Show more
“…It includes several steps as read mapping and NumtS filtering, post-processing mapping, genome assembly, haplogroup prediction and variant annotation and provides a VCF file with allele-specific heteroplasmy as an output. This pipeline also supports results interpretation, through a prioritization process intended to easily target the mtDNA variants that most likely affect the gene or protein function and recognizing a reliable pool of candidate variants for further investigations (12). Specifically, a phylogeny-based prioritization workflow that compares each variant against the related Macro Haplogroup Consensus Sequences (9) and exploits an extended set of annotation resources.…”
Section: Introductionmentioning
confidence: 66%
“…This effort has engaged over a hundred international mitochondrial clinicians, researchers and bioinformaticians in implementing the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium, established in June 2012 with the aim to collect, integrate, organize and critically analyze mitochondrial sequence data (10). In this frame the Human Mitochondrial Database (HmtDB, http://www.hmtdb.uniba.it/), developed in 2005, is actively and largely contributing to populate the MSeqDR portal with both data and hosted tools, such as the MToolBox package (11) with its recently implemented multi-parametric workflow for the prioritization of mtDNA variants of clinical interest (12). At its birth, the database stored 1255 human mitochondrial sequences (13).…”
Section: Introductionmentioning
confidence: 99%
“…The usage of RSRS required revisions of current mtDNA databases along with the tools for haplogroup classification, therefore, HmtDB has implemented the RSRS for variant annotation and haplogroup prediction of each human mtDNA genome stored in the database. However, since the rCRS remains largely used especially in the clinical practice, both RSRS and rCRS are used for variant annotation and prioritization tools (12) implemented within the MToolBox package (11), now directly accessible through HmtDB.…”
Section: Introductionmentioning
confidence: 99%
“…Specifically, a phylogeny-based prioritization workflow that compares each variant against the related Macro Haplogroup Consensus Sequences (9) and exploits an extended set of annotation resources. These include variability values, calculated on mitochondrial nucleotide multi-aligned sequences from all the healthy individuals hosted in HmtDB, and disease scores , defined as a weighted mean of probabilities that a mutation can be pathogenic estimated by several predictors (12), implemented in the MToolBox pipeline to prioritize the nucleotide variations mostly relevant to the disease.…”
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.
“…It includes several steps as read mapping and NumtS filtering, post-processing mapping, genome assembly, haplogroup prediction and variant annotation and provides a VCF file with allele-specific heteroplasmy as an output. This pipeline also supports results interpretation, through a prioritization process intended to easily target the mtDNA variants that most likely affect the gene or protein function and recognizing a reliable pool of candidate variants for further investigations (12). Specifically, a phylogeny-based prioritization workflow that compares each variant against the related Macro Haplogroup Consensus Sequences (9) and exploits an extended set of annotation resources.…”
Section: Introductionmentioning
confidence: 66%
“…This effort has engaged over a hundred international mitochondrial clinicians, researchers and bioinformaticians in implementing the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium, established in June 2012 with the aim to collect, integrate, organize and critically analyze mitochondrial sequence data (10). In this frame the Human Mitochondrial Database (HmtDB, http://www.hmtdb.uniba.it/), developed in 2005, is actively and largely contributing to populate the MSeqDR portal with both data and hosted tools, such as the MToolBox package (11) with its recently implemented multi-parametric workflow for the prioritization of mtDNA variants of clinical interest (12). At its birth, the database stored 1255 human mitochondrial sequences (13).…”
Section: Introductionmentioning
confidence: 99%
“…The usage of RSRS required revisions of current mtDNA databases along with the tools for haplogroup classification, therefore, HmtDB has implemented the RSRS for variant annotation and haplogroup prediction of each human mtDNA genome stored in the database. However, since the rCRS remains largely used especially in the clinical practice, both RSRS and rCRS are used for variant annotation and prioritization tools (12) implemented within the MToolBox package (11), now directly accessible through HmtDB.…”
Section: Introductionmentioning
confidence: 99%
“…Specifically, a phylogeny-based prioritization workflow that compares each variant against the related Macro Haplogroup Consensus Sequences (9) and exploits an extended set of annotation resources. These include variability values, calculated on mitochondrial nucleotide multi-aligned sequences from all the healthy individuals hosted in HmtDB, and disease scores , defined as a weighted mean of probabilities that a mutation can be pathogenic estimated by several predictors (12), implemented in the MToolBox pipeline to prioritize the nucleotide variations mostly relevant to the disease.…”
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.
“…The first collects all the 24,202 possible non-synonymous variants within the 13 human mitochondrial protein encoding genes, identified using mtDNA-GeneSyn software [46]. Predictions and probabilities of pathogenicity were produced using five different software [16] and an overall disease score was also provided [47]. Fig.…”
BackgroundThe abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning. An accurate annotation of mitochondrial tRNA variants would be definitely useful and appreciated by mitochondrial researchers and clinicians since the most of bioinformatics tools for variant annotation and prioritization available so far cannot shed light on the functional role of tRNA variations.ResultsTo this aim, we updated our MToolBox pipeline for mitochondrial DNA analysis of high throughput and Sanger sequencing data by integrating tRNA variant annotations in order to identify and characterize relevant variants not only in protein coding regions, but also in tRNA genes. The annotation step in the pipeline now provides detailed information for variants mapping onto the 22 mitochondrial tRNAs. For each mt-tRNA position along the entire genome, the relative tRNA numbering, tRNA type, cloverleaf secondary domains (loops and stems), mature nucleotide and interactions in the three-dimensional folding were reported. Moreover, pathogenicity predictions for tRNA and rRNA variants were retrieved from the literature and integrated within the annotations provided by MToolBox, both in the stand-alone version and web-based tool at the Mitochondrial Disease Sequence Data Resource (MSeqDR) website. All the information available in the annotation step of MToolBox were exploited to generate custom tracks which can be displayed in the GBrowse instance at MSeqDR website.ConclusionsTo the best of our knowledge, specific data regarding mitochondrial variants in tRNA genes were introduced for the first time in a tool for mitochondrial genome analysis, supporting the interpretation of genetic variants in specific genomic contexts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1193-4) contains supplementary material, which is available to authorized users.
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome. Mutational signatures of somatic mitogenome mutations suggest that they might arise through nucleotide deamination due to oxidative stress. The majority of somatic mutations localized within the coding region (in positions not known from the human phylogeny) and was potentially pathogenic to cell metabolism. Further analysis suggested that the relaxation of negative selection in the mitogenomes of colorectal cancer cells may allow accumulation of somatic mutations. Thus, a shift in glucose metabolism from oxidative phosphorylation to glycolysis may create advantageous conditions for accumulation of mtDNA mutations. Considering the fact that the presence of somatic mtDNA mutations was not associated with any clinicopathological features, we suggested that mtDNA somatic mutations are "passengers" rather than the cause of colorectal carcinogenesis.
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