LOVD v.2.0: the next generation in gene variant databases

By I. Fokkema, Peter E. M. Taschner, Gerard C. P. Schaafsma, J. Celli, J. Laros, Johan T. den Dunnen. Human Mutation, 2011

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Locus‐Specific DataBases (LSDBs) store information on gene sequence variation associated with human phenotypes and are frequently used as a reference by researchers and clinicians. We developed the Leiden Open‐source Variation Database (LOVD) as a platform‐independent Web‐based LSDB‐in‐a‐Box package. LOVD was designed to be easy to set up and maintain and follows the Human Genome Variation Society (HGVS) recommendations. Here we describe LOVD v.2.0, which adds enhanced flexibility and functionality and has the capacity to store sequence variants in multiple genes per patient. To reduce redundancy, patient and sequence variant data are stored in separate tables. Tables are linked to generate connections between sequence variant data for each gene and every patient. The dynamic structure allows database managers to add custom columns. The database structure supports fast queries and allows storage of sequence variants from high‐throughput sequence analysis, as demonstrated by the X‐chromosomal Mental Retardation LOVD installation. LOVD contains measures to ensure database security from unauthorized access. Currently, the LOVD Website (http://www.LOVD.nl/) lists 71 public LOVD installations hosting 3,294 gene variant databases with 199,000 variants in 84,000 patients. To promote LSDB standardization and thereby database interoperability, we offer free server space and help to establish an LSDB on our Leiden server.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0c937be8964fe9fbbb828fd589726a4cacba9b98

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Citations in the corpus

• Ensembl 2015 (2014, methodology): “We have developed infrastructure to display data from DECIPHER (24) and the Leiden Open Variation Database (LOVD) (25).”
• The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies (2017, neutral): “2001), LOVD (http://grenada.lumc.nl/LSDB_list/lsdbs; Fokkema et al. 2011) and a variety of locus-specific mutation databases (LSDBs) (http://www.”
• The UCSC Genome Browser database: 2014 update (2013, methodology): “This year we released three new tracks that describe human disease-associated genetic variation based on curated public data in the Leiden Open Variation Database (LOVD) (16), the Human Gene Mutation Database (HGMD) (17) and amino acid mutations in the UniProt database (18).”
• Ensembl 2013 (2012, methodology): “We have also written plugins to report on degree of conservation, presence of the variant in an LOVD database in a Locus Specific Database (LSDB) using the Leiden Open Variation Database (LOVD) software (43) and other capabilities.”
• Ensembl 2014 (2013, methodology): “For variants stored in LOVD (28), Ensembl queries LOVD directly and displays the information on the appropriate variation web page.”
• Updates of the HbVar database of human hemoglobin variants and thalassemia mutations (2013, positive): “Also, the entire HbVar database content has been copied to the Leiden Open-Access Variation database (LOVD; http://www.lovd.nl; 12) V2.”
• Genes and mutations causing retinitis pigmentosa (2013, background): “Among other concerns, there is need for more systematic collection of mutation phenotype–genotype information for inherited retinal diseases, a need addressed, for example, by the Leiden Open Variation Database (8).”
• Guidelines for diagnostic next-generation sequencing (2015, methodology): “Such databases include LOVD (Fokkema et al. 2011), HGMD (Stenson et al.”
• The UCSC Genome Browser database: 2021 update (2020, methodology): “On the configuration page for several tracks (ClinVar Variants, Database of Genomic Variants (6), and Leiden Open Variation Database Public Variants (7)), filters were added to allow the display of specified subsets of the data: Variant type, molecular consequence and clinical significance.”