title: MitoLSDB: a comprehensive resource to study genotype to phenotype correlations in human mitochondrial DNA variations.
abstract: Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease association studies on mtDNA (http://mitolsdb.igib.res.in). The main goal of MitoLSDB is to provide a central platform for direct submissions of novel variants that can be curated by the Mitochondrial Research Community. MitoLSDB provides access to standardized and annotated data from literature and databases encompassing information from 5231 individuals, 675 populations and 27 phenotypes. This platform is developed using the Leiden Open (source) Variation Database (LOVD) software. MitoLSDB houses information on all 37 genes in each population amounting to 132397 variants, 5147 unique variants. For each variant its genomic location as per the Revised Cambridge Reference Sequence, codon and amino acid change for variations in protein-coding regions, frequency, disease/phenotype, population, reference and remarks are also listed. MitoLSDB curators have also reported errors documented in literature which includes 94 phantom mutations, 10 NUMTs, six documentation errors and one artefactual recombination. MitoLSDB is the largest repository of mtDNA variants systematically standardized and presented using the LOVD platform. We believe that this is a good starting resource to curate mtDNA variants and will facilitate direct submissions enhancing data coverage, annotation in context of pathogenesis and quality control by ensuring non-redundancy in reporting novel disease associated variants.
authors.affiliation: Department of Bioinformatics, Stella Maris College, University of Madras, Chennai, Tamil Nadu, India.
authors.forename: Shamnamole
authors.initials: S
authors.lastname: K
authors.forename: Saakshi
authors.initials: S
authors.lastname: Jalali
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.forename: Anshu
authors.initials: A
authors.lastname: Bhardwaj
mesh_terms: D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data / Q000600:supply & distribution*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D005838:Genotype; D006801:Humans; D020407:Internet; D008928:Mitochondria / Q000235:genetics*; D028361:Mitochondrial Diseases / Q000145:classification / Q000235:genetics*; D016366:Open Reading Frames; D010641:Phenotype; D012984:Software
chemical_list: D004272:DNA, Mitochondrial