• Blog
  • Calendar
  • Clinical
  • Contact
  • Events
    • Categories
    • Locations
    • My Bookings
    • Tags
  • GBrowse
  • Genesis
  • Home
  • Issue Entry
  • JS Support Ticket
  • MSeqDR PhenoTips
  • MSeqDR-LSDB
  • Our Team
  • Phenome
  • Search Issues
  • Site map
  • Submission
  • Tools
MSeqDR- the Mitochondrial Disease Sequence Data Resource ConsortiumMSeqDR – Mitochondrial disease diagnosis with new technology
  • Home
    • Team
    • Contact
    • Site map
    • Genesis
  • GBrowse
  • MSeqDR-LSDB
  • Tools
    • Events
    • Calendar
    • mtDNA Expert Panel
  • Phenome
  • Clinical
  • Submission
  • MSeqDR PhenoTips
  • Blog
Menu
  • Home
    • Team
    • Contact
    • Site map
    • Genesis
  • GBrowse
  • MSeqDR-LSDB
  • Tools
    • Events
    • Calendar
    • mtDNA Expert Panel
  • Phenome
  • Clinical
  • Submission
  • MSeqDR PhenoTips
  • Blog
  • mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation

    September 25, 2017 Dr. Lishuang SHEN 0

    mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation

     

    Input mtDNA variants in any of the major formats, mixed formats input is supported.

    The results are returned as multiple html tables, as well as a downloadable combined Excel file.

    An API is implemented, which takes inputs in VCF, HGVS, or classical mtDNA variant nomenclatures, and returns annotated vcf or json outputs

     

    Mitochondrial DNA variant nomenclature has multiple existing systems used in literature and in different institutes. The major ways are:
    1. HGVS Committee: m.8993T>G. This is its recommended format and is widely used in literature.
    2. HGVS NCBI/ClinVar: NC_012920.1:m.8993T>G, reference version is required.
    3. HGVS Ensembl: MT:g.8993T>G
    4. HGVS Mutalyzer: NC_012920.1:g.8993T>G
    5. Classical I: used in literature, PhyloTree, Haplogrep, 8527, 8993G, 8993d, 5787_5789d, 1494.1T, 7472.XA
    6. Classical II: T8993G
    7. Potential non-standard: 8527A>G
    8. VCF-style input: Tab-delimted, with at least the first 5 columns in vcf format

    Adding to the complexity, the chromosome names can be used as any of the following:
    chrM, chM, chrMT, chMT, M, MT, NC_012920.1.

    The current mtDNA variant data is mostly based on the default revised Cambridge sequence (rCRS, accession number NC_012920.1), but some commercial SNP array platforms used YRI (accession number AF347015) reference.

    The MSeqDR universal variant converter can convert the various combinations of these formats into a standard variant list in the rCRS-based HGVS (1-4) formats. It can convert YRI-based positions into rCRS-based positions.

    *Note: Unlimited converter input size. The annotation is currently limited to first 100 entries, due to burden of calling external Ensembl web services. The limit will be lifted in future.

    Annotate both mtDNA and nuclear DNA variants? Switch to One-Stop Variant Annotation.
    Novel pathogenic variant? Please submit.

    The major mvTool collaborators and data sources:
    MSeqDR Logo Mitomap  MitoTIP tRNA Scoring     dbNSFP   HmtDB Ensembl PhyloTree GeneDX Inc. OMIM ClinVar human-phenotype-ontology https://www.genesis-app.com/

    Categories: MSeqDr.org News, updates, media report

    mvTools is updated to latest version of MitoMaps, HmtDB and ClinVar Data MSeqDR Gene Panel Examiner and Universal Gene ID Mapper

    Leave a Reply Cancel reply

    You must be logged in to post a comment.

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

Pages

  • Blog
  • Calendar
  • Clinical
  • Contact
  • Events
    • Categories
    • Locations
    • My Bookings
    • Tags
  • GBrowse
  • Genesis
  • Home
  • Issue Entry
  • JS Support Ticket
  • MSeqDR PhenoTips
  • MSeqDR-LSDB
  • Our Team
  • Phenome
  • Search Issues
  • Site map
  • Submission
  • Tools

Tag Cloud

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

Pages

  • Blog
  • Calendar
  • Clinical
  • Contact
  • Events
    • Categories
    • Locations
    • My Bookings
    • Tags
  • GBrowse
  • Genesis
  • Home
  • Issue Entry
  • JS Support Ticket
  • MSeqDR PhenoTips
  • MSeqDR-LSDB
  • Our Team
  • Phenome
  • Search Issues
  • Site map
  • Submission
  • Tools

Search

Copyright © 2016 MSeqDR: the Mitochondrial Disease Sequence Data Resource Consortium Theme created by PWT. Powered by WordPress.org