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Guidelines for establishing locus specific databases†

  1. Mauno Vihinen1,2,*,
  2. Johan T. den Dunnen3,
  3. Raymond Dalgleish4,
  4. Richard G. H. Cotton5

Article first published online: 9 DEC 2011

DOI: 10.1002/humu.21646

Issue

Human Mutation

Human Mutation

Volume 33, Issue 2, pages 298–305, February 2012

Additional Information

How to Cite

Vihinen, M., den Dunnen, J. T., Dalgleish, R. and Cotton, R. G. H. (2012), Guidelines for establishing locus specific databases. Hum. Mutat., 33: 298–305. doi: 10.1002/humu.21646

Author Information

  1. 1

    Institute of Biomedical Technology, University of Tampere, Finland

  2. 2

    BioMediTech, Tampere, Finland

  3. 3

    Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands

  4. 4

    Department of Genetics, University of Leicester, Leicester, United Kingdom

  5. 5

    Howard Florey Institute, Genomic Disorders Research Centre, Melbourne, Australia

*Institute of Biomedical Technology, FI-33014 University of Tampere, Finland

  1. †

    Communicated by Mark H. Paalman

Publication History

  1. Issue published online: 12 JAN 2012
  2. Article first published online: 9 DEC 2011
  3. Accepted manuscript online: 3 NOV 2011 08:49AM EST
  4. Manuscript Accepted: 25 OCT 2011
  5. Manuscript Received: 25 JUL 2011

Funded by

  • European Community's Seventh Framework Programme (FP7/2007-2013; 200754)

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Keywords:

  • LSDB;
  • guidelines;
  • variation database curation;
  • data collection;
  • distribution

Abstract

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.

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