• MSeqDR is migrated to a new webserver at CHLA

    January 1, 2021 Dr. Lishuang SHEN 0

    MSeqDR (https://mseqdr.org/) is migrated to a new webserver hosted at CHLA . The new server features enhanced security, as implemented by the CHLA IT team. The migration completed on December 30, 2020. The URL, domain name, and tool usage are the same as before. Most tools were up and running. More setup and upgrading efforts are […]

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  • International Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA

    October 20, 2020 Dr. Lishuang SHEN 0

    International Research Team Develops Consensus Variant Classification Guidelines for Genomic Variants in Mitochondrial DNA Published on Oct 06, 2020 in CHOP News A team of researchers in the Mitochondrial Medicine Frontier Program at Children’s Hospital of Philadelphia (CHOP) led an international effort to standardize how variants in mitochondrial DNA (mtDNA) are interpreted, detailing the unique aspects of the mtDNA genome […]

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  • mvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people

    August 24, 2020 Dr. Lishuang SHEN 0

     mvTool_v.5 – Universal  mitochondrial DNA Variant Converter and One-Stop Annotation: Added mitochondrial DNA variant data from HelixMTdb for 196,554 unrelated healthy individuals, which includes 15,035 unique variants.  The HelixMTdb database reflects aggregated and de-identified mitochondrial DNA variants observed in individuals sequenced at Helix: Selective constraints and pathogenicity of mitochondrial DNA variants inferred from a novel database of 196,554 […]

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  • Recent publications from MSeqDR supported by the UMDF and NIH grants

    July 2, 2020 Dr. Lishuang SHEN 0

    Recent publications from MSeqDR supported by: 1. UMDF – The United Mitochondrial Disease Foundation   2. The U24 Project  1U24HD093483-01: Expert curation of pediatric mitochondrial Leigh-like Syndrome genes and Variants 3. The U54 Project  #5U54NS078059-06  NAMDC: Overall Research Plan   Title (Link to full-text in PubMed Central) Journal (Link to PubMed abstract) Authors Similar Publications Cited […]

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  • ClinGen / ClinVar – MSeqDR Working Groups & Expert Panels

    July 2, 2020 Dr. Lishuang SHEN 0

    MSeqDR Working Groups & Expert Panels Approved by ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel Mitochondrial Diseases Gene Curation Expert Panel   1. Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel       Affiliated to Inborn Errors of Metabolism CDWG      URL: https://www.clinicalgenome.org/affiliation/50027/        Membership Documents  Expert curation to assess variant pathogenicity […]

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  • ClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications

    June 30, 2020 Dr. Lishuang SHEN 0

    MSeqDR Consortium has been developing the mtDNA specifications for mitochondrial-coding genes, in collaboration with the ClinGen and ClinVar teams. The mtDNA specifications were officially approved by the ClinGen Sequence Variant Interpretation Working Group on June 12, 2020. These ACMG-oriented mtDNA SVI guidelines are being implemented into tools at https://mseqdr.org to aid in the clinical interpretation of […]

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  • U24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen

    April 29, 2020 Dr. Lishuang SHEN 0

    Gene-Disease records created by the U24 Mitochondrial Diseases Expert Panel Gene Disease Inheritance Gene-Disease-Inheritance Status Creation Date CLPB Leigh syndrome Autosomal recessive inheritance CLPB–Leigh syndrome–Autosomal recessive inheritance PROVISIONAL 2020 Apr 16, 1:15 pm RANBP2 Leigh syndrome Autosomal dominant inheritance RANBP2–Leigh syndrome–Autosomal dominant inheritance PROVISIONAL 2020 Apr 14, 10:21 pm SLC25A19 Leigh syndrome Autosomal recessive inheritance […]

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  • MSeqDr joins FAIRsharing – A curated resource on data and metadata standards

    January 27, 2020 Dr. Lishuang SHEN 0

    MSeqDr joins FAIRsharing –  A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies       How to cite this record FAIRsharing.org: MSeqDR; Mitochondrial Disease Sequence Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.xUkfh7 Publication for citation  MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in […]

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  • Quick-Mitome version 2 with new annotations, workflow, and tutorial

    January 2, 2020 Dr. Lishuang SHEN 0

    Quick-Mitome version 2  with new annotations, workflow, and Quick-Mitome tutorial A Phenotype-Guided WES/WGS Variant Interpretation Server for Mitochondrial Diseases  

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  • Mondo Disease Ontology is coming to MSeqDR, Disease Portal received more disease entries

    October 1, 2019 Dr. Lishuang SHEN 0

    The Mondo Disease Ontology is being added to MSeqDR data back-end. We are adding Mondo-based disease browser and phenotype data search tools. The beta version of Mondo-based disease browser: https://mseqdr.org/mondo.php . Please try out and feedback. Mondo Disease Ontology: The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a […]

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  • MSeqDR to present tutorial workshop for the 5th year at the UMDF Mitochondrial Medicine Symposium

    June 12, 2019 Dr. Lishuang SHEN 0

      MSeqDR to Present the 5th Live Tutorial at UMDF Mitochondrial Medicine 2019 Date:  Saturday, June 29, 2019:, 7:15AM – 7:45AM Presentation:                        Marni Falk, MD, MSeqDR Organizer; Member, SIMD falkm@email.chop.edu                         Lishuang Shen, PhD, MSeqDR Developer        Lishen@chla.usc.edu                         Colleen Clarke, MS, LCGC clarkec@email.chop.edu                         Elizabeth McCormick, MS, […]

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  • mvTool v3: Added variant data from 40,000 people, Asians and Sadinians, meta-AF reference, new single variant report

    May 23, 2019 Dr. Lishuang SHEN 0

    mvTool v3: Added variant data from 40,000 people, Asians and Sardinians, meta AF reference, new single variant report Added over mtDNA variant data from over 40,000 people, derived from multiple Asian and other populations. Of note is the Japanese population allele frequency panel of 3,552 individuals (3.5KJPNv2 https://jmorp.megabank.tohoku.ac.jp).  MSeqDR constructed the meta-population AF reference, which […]

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  • Leigh Syndrome Resources at MSeqDR.org

    January 31, 2019 Dr. Lishuang SHEN 0

    Leigh and Leigh-Like Syndrome (LS/LLS) Resources at MSeqDR.org 1. Leigh Syndrome Related Genes https://mseqdr.org/leighgene.php 2. Add more LS/LLS Diseases,Genes, and the Gene – Disease Associations to Work List 3. Pathogenic variant submission, using VCF/HGVS input format, then manage and complete annotations per variant. 4. ClinGen Curation Interface at https://curation.clinicalgenome.org/dashboard/ called from MSeqDR https://mseqdr.org/mp.php?url=clingen 5. U24 Grant 1U24HD093483-01: EXPERT CURATION OF PEDIATRIC MITOCHONDRIAL LEIGH-LIKE SYNDROME […]

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  • MSeqDR’s ClinVar style variant submission system supports ClinVar template v4.2 (2018.08)

    November 16, 2018 Dr. Lishuang SHEN 0

    MSeqDR’s ClinVar style variant submission tool supports template v4.2 (2018.08) ClinVar style variant submission and curation version 2 MSeqDR.org implemented this tool to support pre-ClinVar stage pathogenicity data capture and curation. The completed variant data will be compatible with the ClinVar submission requirements, and potentially generate ready-to-submit Excel file or API direct submission to ClinVar. […]

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  • MSeqDR mvTool Documentation

    October 17, 2018 Dr. Lishuang SHEN 0

    mvTool V2 – Universal mtDNA Variant Converter and One Stop Annotation   MSeqDR mtDNA Toolset (mvTool) is a one-stop mtDNA variant annotation and analysis Web service. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php.  Background: mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert-curated data from MITOMAP (http://www.mitomap.org) and HmtDB (http://www.hmtdb.uniba.it/hmdb).  mvTool supports all […]

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  • Quick-Mitome is updated with Exomiser V10.1, ID de-identification, WES and WGS data support

    September 24, 2018 Dr. Lishuang SHEN 0

    Quick-Mitome – Semi-automatic Interpretation System is updated with Exomiser V10.10, ClinVar 2018.10 release and HPO 2018.07 release. The Quick-Mitome automatic interpretation system conducts interpretation on 5 inheritance modes: AD, AR, XD, XR, Mitochondrial.   Exomiser v10.1 makes it possible to do both WES and WGS data interpretations. WGS data interpretations takes less than 30 minutes in internal testing and […]

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  • ClinVar style variant submission and curation system version 2 is released

    August 2, 2018 Dr. Lishuang SHEN 0

    ClinVar style variant submission and curation version 2 MSeqDR.org implemented this tool to support pre-ClinVar stage pathogenicity data capture and curation. The completed variant data will be compatible with the ClinVar submission requirements, and potentially generate ready-to-submit Excel file or API direct submission to ClinVar. It now captures data for more than 90 fields from […]

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  • The “Mitochondrial Disease Variant Curation Expert Panel” by MSeqDR Consortium

    July 30, 2018 Dr. Lishuang SHEN 0

    The”Mitochondrial Disease Variant Curation Expert Panel”  is formed by the MSeqDR Consortium and members. It is going through the approval process by ClinGen, ClinGen Clinical Domain Working Group Mitochondrial Disease Variant Curation Expert Panel Affiliated to Inborn Errors of Metabolism Clinical Domain Working Group URL: https://www.clinicalgenome.org/working-groups/clinical-domain/inborn-errors-of-metabolism-clinical-domain-working-group/mitochondrial-disease/ Expert curation to assess variant pathogenicity in the most […]

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  • The “Mitochondrial Disease Gene Curation Expert Panel” by MSeqDR Consortium

    July 30, 2018 Dr. Lishuang SHEN 0

    The”Mitochondrial Disease Gene Curation Expert Panel”  is formed by the MSeqDR Consortium and members. It is going through the approval process by ClinGen,   ClinGen Clinical Domain Working Group Mitochondrial Disease Gene Curation Expert Panel Affiliated to Inborn Errors of Metabolism Clinical Domain Working Group URL: https://www.clinicalgenome.org/working-groups/clinical-domain/inborn-errors-of-metabolism-clinical-domain-working-group/mitochondrial-disease-gene-curation-expert-panel/ With the rapid increase in identified genes that […]

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