Recommendations for locus-specific databases and their curation

Abstract

Communicated by Mark H. PaalmanExpert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locusspecific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome. Hum Mutat 29(1), 2-5, 2008.

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

“…Because the data model includes all standard fields currently used in LOVD, UMD [Béroud et al, 2000] and Mutbase [Riikonen and Vihinen, 1999] database software, it should support data retrieval from these systems through world-wide queries once they are registered in the public gene variant database list. The LOVD query service can be regarded as a step toward accomplishing one of the aims of the Human Variome Project [Ring et al, 2006]: a central access point for the retrieval of variants in all genes worldwide, saving diagnostic laboratories, clinicians, and researchers considerable amounts of time and money [Cotton et al, 2008]. The Gen2Phen data model will be implemented in the database structure of LOVD v.3.0, which is currently under development (see http://www.lovd.nl/3.0/ for more information).…”

“…Curators should be able to install a database system ''out of the box'' without complicated platform-specific programming or configuration steps. The LOVD system has been designed to comply with the guidelines and recommendations regarding content, design, and deployment of sequence variant databases developed by the HUGO Mutation Database Initiative, the Human Genome Variation Society (HGVS, http://www.hgvs.org/), and the Human Variome Project [Cotton et al, 2008;Scriver, 2000;Scriver et al, 1999].…”

The inherited ataxias: Genetic heterogeneity, mutation databases, and future directions in research and clinical diagnostics

“…The most widely available platform for the creation of LSDBs is the Leiden Open Variation Database (LOVD, www.lovd.nl) supported by the European Community's Seventh Framework Programme under the GEN2PHEN project (www.gen2phen.org). Although the creation of these databases is straightforward, there are well-reported limitations relevant to the ongoing curation of variant data and maintenance of the database [Cotton et al, 2008]. Detailed recommendations for the curation of LSDBs have previously been published [Celli et al, 2011] and while it is acknowledged that expertly curated, up-to-date LSBDs offer significant benefits for patients and the research community, continued funding of these projects is a not an inconsiderable challenge.…”

Guidelines for establishing locus specific databases

“…Recommendations have been made, for example, for LSDB content [Claustres et al, 2002;Horaitis and Cotton, 2005;Scriver et al, 1999Scriver et al, , 2000, ethics Povey et al, 2010], data collection [Cotton et al, 2007, somatic variations [Olivier et al, 2009], interpretation and reporting of variants [Plon et al, 2008;Richards et al, 2008], curation [Cotton et al, 2008;Celli et al, 2011] data sharing , and nomenclature, [den Dunnen and Antonarakis, 2000;Taschner and den Dunnen, 2011]. These instructions have been useful, however, some of them are already partly outdated and others are scattered throughout a number of publications.…”