Guidelines for establishing locus specific databases

• Published in: Human mutation Vol. 33; no. 2; pp. 298 - 305
• Main Authors: Vihinen, Mauno, den Dunnen, Johan T., Dalgleish, Raymond, Cotton, Richard G. H.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.02.2012; Hindawi Limited
• Subjects: Computational Biology - methods; Computational Biology - standards; data collection; Database Management Systems; Databases, Genetic - ethics; Databases, Genetic - standards; distribution; Documentation; Genes; Genetic Association Studies; Genetic Loci; guidelines; Guidelines as Topic; Humans; Information Dissemination; LSDB; variation database curation
• ISSN: 1059-7794; 1098-1004
• DOI: 10.1002/humu.21646

Information about genetic variation has been collected for some 20 years into registries, known as locus specific databases (LSDBs), which nowadays often contain information in addition to the actual genetic variation. Several issues have to be taken into account when considering establishing and maintaining LSDBs and these have been discussed previously in a number of articles describing guidelines and recommendations. This information is widely scattered and, for a newcomer, it would be difficult to obtain the latest information and guidance. Here, a sequence of steps essential for establishing an LSDB is discussed together with guidelines for each step. Curators need to collect information from various sources, code it in systematic way, and distribute to the research and clinical communities. In doing this, ethical issues have to be taken into account. To facilitate integration of information to, for example, analyze genotype–phenotype correlations, systematic data representation using established nomenclatures, data models, and ontologies is essential. LSDB curation and maintenance comprises a number of tasks that can be managed by following logical steps. These resources are becoming ever more important and new curators are essential to ensure that we will have expertly curated databases for all disease‐related genes in the near future. Hum Mutat 33:298–305, 2012. © 2011 Wiley Periodicals, Inc.