• MSeqDr joins FAIRsharing – A curated, informative and educational 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

    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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  • Disease Portal for mitochondrial diseases received more disease entries

    October 1, 2019 Dr. Lishuang SHEN 0

    Disease Portal: Mitochondrial diseases in a tree based on MESH and OMIM, for global overview and single disease details. Select a mitochondrial disease entry from the drop-down-list to view the integrated annotations for associated symptoms, genes, and variants. Data represents in-house effort in compiling data from ClinVar, CTDBase, HPO, OMIM. Disease terms increased 10% from […]

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  • MSeqDR to present tutorial workshop for the 5th year on June 29, 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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  • MSeqDR presented the 4th year tutorial workshop, at the UMDF Mitochondrial Medicine Symposium

    July 13, 2018 Dr. Lishuang SHEN 0

    MSeqDR team presented the 4th year tutorial workshop, at the UMDF Mitochondrial Medicine Symposium Location: Nashville, TN Date: June 30, 2018 Team Members: Lishuang Shen, PhD; Xiaowu Gai, PhD Children’s Hospital of Los Angeles   Colleen C. Muraresku, MS, LCGC; Elizabeth M. McCormick, MS, LCGC; Zarazuela Zolkipli-Cunningham, MBChB MRCP; Amy Goldstein, MD; Marni J. Falk, […]

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  • MSeqDR has Tripled the LSDB Variants to 11,800 since UMDF 2017

    July 1, 2018 Dr. Lishuang SHEN 0

    MSeqDR Tripled the MSeqDR-LSDB Variants since Mitochondrial Medicine 2017 MSeqDR-LSDB Data Added: 8000+ Pathogenicity Assessed Variants , Total: 11,800 40 more Mitochondrial Diseases, complied from OMIM and other literature, Total: 225 20 more Mitochondrial Diseases Related Genes, Total 1607 LSDB Status The LOVD back-end is updated to V.21 (April, 2018) The results are presented at […]

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  • New publications on clinical review of mitochondrial disease, in Current Genetic Medicine Reports

    May 2, 2018 Dr. Lishuang SHEN 0

    Congratulations to Colleen, Elizabeth, and Marni on two  great up-to-date clinical review of Mitochondrial Disease just published in Current Genetic Medicine Reports!   1. Mitochondrial Disease: Advances in Clinical Diagnosis, Management, Therapeutic Development, and Preventative Strategies Colleen C. Muraresku, Elizabeth M. McCormick… (May 2018) Download PDF (514KB) View Article Purpose of Review Primary mitochondrial disease […]

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

    March 27, 2018 Dr. Lishuang SHEN 0

    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 […]

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  • New tool set: Quick-Mitome – Phenotype-Guided WES and WGS Variant Interpretation

    February 7, 2018 Dr. Lishuang SHEN 0

    New tool set: Quick-Mitome – Phenotype-Guided WES and WGS Variant Interpretation   MSeqDR Mito-Quick-ome Web Server provides quick whole genome (WGS) or whole exome (WES) sequencing data interpretation tools to both laymen and expert users, with special supports to mitochondrial diseases and mitochondrial DNA (mtDNA) variants. The required input are uploaded vcf file, pedigree file […]

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  • Tool update: mvTool V.2 – mtDNA variant annotation and analysis web-service with API

    February 7, 2018 Dr. Lishuang SHEN 0

    Tool update: mvTool V.2 – mtDNA variant annotation and analysis web-service with API   MSeqDR mtDNA 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 (http://www.mitomap.org) and HmtDB (http://www.hmtdb.uniba.it/hmdb).  mvTool supports all mtDNA nomenclatures, converts variants […]

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