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. 2016 Jun;37(6):540-548.
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

Lishuang Shen  1   2 , Maria Angela Diroma  3   4 , Michael Gonzalez  5   6 , Daniel Navarro-Gomez  2 , Jeremy Leipzig  7 , Marie T Lott  8 , Mannis van Oven  9 , Douglas C Wallace  8   10 , Colleen Clarke Muraresku  11 , Zarazuela Zolkipli-Cunningham  12 , Patrick F Chinnery  13 , Marcella Attimonelli  3 , Stephan Zuchner  5   6 , Marni J Falk #  11   14 , Xiaowu Gai #  1   2
Affiliations

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

Lishuang Shen et al. Hum Mutat. 2016 Jun.

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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Figures

Figure 1
Figure 1
MSeqDR-LSDB Current Status Panel and MSeqDR Annual Usage by City. Left Panel: MSeqDR-LSDB Current Status Panel (as of November 19, 2015) details the numbers of genes, variants per gene, diseases associated per gene, and the numbers of variants per variant type. Right Panel: MSeqDR annual usage statistics generated by Google Analytics from November 2014 through October 2015. Top, unique MSeqDR visit sessions per month over last 12 months. Bottom, a global view of MSeqDR site visits by city, where the visit number by city are highlighted by gradients.
See this image and copyright information in PMC

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