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Hum Mutat. 2016 Jun;37(6):540-8. doi: 10.1002/humu.22974. Epub 2016 Mar 21.

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

Author information

1
Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California.
2
Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts.
3
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.
4
CEINGE-Biotecnologie Avanzate, Napoli, Italy.
5
Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.
6
The Genesis Project, Miami, Florida.
7
Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
8
Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
9
Department of Forensic Molecular Biology, Erasmus MC-University Medical Center Rotterdam, The Netherlands.
10
Department of Pathology, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
11
Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
12
Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
13
Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom.
14
Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.

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

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