MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Lishuang Shen, Maria Angela Diroma, Michael Gonzalez, Daniel Navarro-Gomez, Jeremy Leipzig, Marie T. Lott, Mannis van Oven, Douglas C. Wallace, Colleen Clarke Muraresku, Zarazuela Zolkipli-Cunningham, Patrick F. Chinnery, Marcella Attimonelli, Stephan L Zuchner, Marni J. Falk, Xiaowu Gai

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

Original languageEnglish (US)
Pages (from-to)540-548
Number of pages9
JournalHuman Mutation
Volume37
Issue number6
DOIs
StatePublished - Jun 1 2016

Fingerprint

Mitochondrial Diseases
Computational Biology
Genome
Phenotype
Mitochondrial DNA
Research Personnel
Databases
Genes
Exome
Informed Consent
Terminology
Research

Keywords

  • Database
  • Genetics
  • Informatics
  • Mitochondria

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Shen, L., Diroma, M. A., Gonzalez, M., Navarro-Gomez, D., Leipzig, J., Lott, M. T., ... Gai, X. (2016). MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. Human Mutation, 37(6), 540-548. https://doi.org/10.1002/humu.22974

MSeqDR : A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. / Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T.; van Oven, Mannis; Wallace, Douglas C.; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F.; Attimonelli, Marcella; Zuchner, Stephan L; Falk, Marni J.; Gai, Xiaowu.

In: Human Mutation, Vol. 37, No. 6, 01.06.2016, p. 540-548.

Research output: Contribution to journalArticle

Shen, L, Diroma, MA, Gonzalez, M, Navarro-Gomez, D, Leipzig, J, Lott, MT, van Oven, M, Wallace, DC, Muraresku, CC, Zolkipli-Cunningham, Z, Chinnery, PF, Attimonelli, M, Zuchner, SL, Falk, MJ & Gai, X 2016, 'MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease', Human Mutation, vol. 37, no. 6, pp. 540-548. https://doi.org/10.1002/humu.22974
Shen, Lishuang ; Diroma, Maria Angela ; Gonzalez, Michael ; Navarro-Gomez, Daniel ; Leipzig, Jeremy ; Lott, Marie T. ; van Oven, Mannis ; Wallace, Douglas C. ; Muraresku, Colleen Clarke ; Zolkipli-Cunningham, Zarazuela ; Chinnery, Patrick F. ; Attimonelli, Marcella ; Zuchner, Stephan L ; Falk, Marni J. ; Gai, Xiaowu. / MSeqDR : A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. In: Human Mutation. 2016 ; Vol. 37, No. 6. pp. 540-548.
@article{8b0f4106863c44b1a4ce32b1edca667e,
title = "MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease",
abstract = "MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.",
keywords = "Database, Genetics, Informatics, Mitochondria",
author = "Lishuang Shen and Diroma, {Maria Angela} and Michael Gonzalez and Daniel Navarro-Gomez and Jeremy Leipzig and Lott, {Marie T.} and {van Oven}, Mannis and Wallace, {Douglas C.} and Muraresku, {Colleen Clarke} and Zarazuela Zolkipli-Cunningham and Chinnery, {Patrick F.} and Marcella Attimonelli and Zuchner, {Stephan L} and Falk, {Marni J.} and Xiaowu Gai",
year = "2016",
month = "6",
day = "1",
doi = "10.1002/humu.22974",
language = "English (US)",
volume = "37",
pages = "540--548",
journal = "Human Mutation",
issn = "1059-7794",
publisher = "Wiley-Liss Inc.",
number = "6",

}

TY - JOUR

T1 - MSeqDR

T2 - A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

AU - Shen, Lishuang

AU - Diroma, Maria Angela

AU - Gonzalez, Michael

AU - Navarro-Gomez, Daniel

AU - Leipzig, Jeremy

AU - Lott, Marie T.

AU - van Oven, Mannis

AU - Wallace, Douglas C.

AU - Muraresku, Colleen Clarke

AU - Zolkipli-Cunningham, Zarazuela

AU - Chinnery, Patrick F.

AU - Attimonelli, Marcella

AU - Zuchner, Stephan L

AU - Falk, Marni J.

AU - Gai, Xiaowu

PY - 2016/6/1

Y1 - 2016/6/1

N2 - MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

AB - MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

KW - Database

KW - Genetics

KW - Informatics

KW - Mitochondria

UR - http://www.scopus.com/inward/record.url?scp=84961876861&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84961876861&partnerID=8YFLogxK

U2 - 10.1002/humu.22974

DO - 10.1002/humu.22974

M3 - Article

C2 - 26919060

AN - SCOPUS:84961876861

VL - 37

SP - 540

EP - 548

JO - Human Mutation

JF - Human Mutation

SN - 1059-7794

IS - 6

ER -