Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

Abstract

Genetic variation databases have become indispensable in many areas of health care. In addition, more and more experts are depositing published and unpublished disease-causing variants of particular genes into locus-specific databases (LSDBs). Some of these databases contain such extensive information that they have become known as knowledge bases. Here, we analyzed 1,188 LSDBs and their content for the presence or absence of 44 content criteria related to database features (general presentation, locus-specific information, database structure) and data content (data collection, summary table of variants, database querying). Our analyses revealed that several elements have helped to advance the field and reduce data heterogeneity, such as the development of specialized database management systems and the creation of data querying tools. We also identified a number of deficiencies, namely, the lack of detailed disease and phenotypic descriptions for each genetic variant and links to relevant patient organizations, which, if addressed, would allow LSDBs to better serve the clinical genetics community. We propose a structure, based on LSDBs and closely related repositories (namely, clinical genetics databases), which would contribute to a federated genetic variation browser and also allow the maintenance of variation data.

Databases for neurogenetics: Introduction, overview, and challenges

“…Finally, we searched the GEN2PHEN Knowledge Center LSDB listing [Webb et al, 2011; http://www.gen2phen.org/data/lsdbs] to identify mutation databases for the genes selected in the previous stage and compared the database system used, curator status, number and update of variants reported. The results were compared with the situation of neurogenetic databases in 2010 [Mitropoulou et al, 2010]. A total of 1,025 genes were identified, for 98 of which no database was listed.…”

Emerging landscape of genomics in the electronic health record for personalized medicine

“…All of this needs to be conducted within an overarching framework of ethical practice, policy guidelines, and data governance. However, if these challenges can be addressed, this would enable an integrated view of genotypic and/or phenotypic knowledgebases, across multiple institutions worldwide [Mitropoulou et al, 2010;Olivier et al, 2009;Thorisson et al, 2009].…”

Guidelines for establishing locus specific databases

“…There are already close to 2,000 LSDBs [Mitropoulou et al, 2010], with more than one database for some genes and diseases. More recently, a database has been created for every gene associated with a Mendelian disorder by the authors of the LOVD LSDB system [Fokkema et al, 2011] with support from the GEN2PHEN project (http://www.gen2phen.org/).…”