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  • New MSeqDR publication: MSeqDR mvTool: A mitochondrial DNA web and API resource

    March 27, 2018 Dr. Lishuang SHEN 0

    Human Mutation banner

    https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23422

    MSeqDR mvTool: A mitochondrial DNA web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion

    Lishuang Shen
    Marcella Attimonelli
    Renkui Bai
    Marie T. Lott
    Douglas C. Wallace
    Marni J. Falk
    Xiaowu Gai
    First published: 14 March 2018
    https://doi.org/10.1002/humu.23422
     

    Abstract

    Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user‐friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one‐stop mtDNA variant annotation and analysis web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS‐ and HGVS‐based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mito‐genomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 11). mvTools also provides mtDNA somatic variants annotations. ‘mvTool API’ is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php.

     

    Categories: MSeqDr.org News, updates, media report

    New tool set: Quick-Mitome – Phenotype-Guided WES and WGS Variant Interpretation New publications on clinical review of mitochondrial disease, in Current Genetic Medicine Reports

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Recent Posts

  • Preclinical Study Shows Combination of Vitamins, Supplements May Benefit Mitochondrial Disease
  • gnoMAD shares mtDNA variant data from 56,434 whole genome samples
  • mvTool v.6: The mtDNA variant reference based on 316,530 whole genome sequences
  • MSeqDR is migrated to a new webserver at CHLA
  • International Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA
  • mvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people
  • Recent publications from MSeqDR supported by the UMDF and NIH grants
  • ClinGen / ClinVar – MSeqDR Working Groups & Expert Panels
  • ClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications
  • U24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen

Tag Cloud

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