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

  1. Ivo F. A. C. Fokkema‡,
  2. Peter E. M. Taschner‡,*,
  3. Gerard C. P. Schaafsma,
  4. J. Celli,
  5. Jeroen F. J. Laros,
  6. Johan T. den Dunnen

Article first published online: 22 FEB 2011

DOI: 10.1002/humu.21438

Issue

Human Mutation

Human Mutation

Special Issue: Bioinformatics for Human Genetics: Promises and Challenges, A Human Variome Project Special Issue

Volume 32, Issue 5, pages 557–563, May 2011

Additional Information

How to Cite

Fokkema, I. F. A. C., Taschner, P. E. M., Schaafsma, G. C. P., Celli, J., Laros, J. F. J. and den Dunnen, J. T. (2011), LOVD v.2.0: the next generation in gene variant databases. Human Mutation, 32: 557–563. doi: 10.1002/humu.21438

Author Information

  1. Center of Human and Clinical Genetics, Department of Human Genetics, Leiden University Medical Center, Leiden, Nederland

  1. ‡

    Both authors contributed equally.

*Department of Human Genetics S-4-P, Center for Human and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300RC Leiden, Nederland

  1. †

    For the HVP Bioinformatics Special Issue

Publication History

  1. Issue published online: 21 APR 2011
  2. Article first published online: 22 FEB 2011
  3. Accepted manuscript online: 25 JAN 2011 02:56PM EST
  4. Manuscript Accepted: 14 DEC 2010
  5. Manuscript Received: 12 OCT 2010

Funded by

  • The European Community's Seventh Framework Programme. Grant Number: FP7/2007-2013 under grant agreement no. 200754—the GEN2PHEN project
  • Re-use of this article is permitted in accordance with the Terms and Conditions set out at [http://wileyonlinelibrary.com/author resources/onlineopen.html]

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Keywords:

  • LSDB;
  • database;
  • open source;
  • PHP;
  • MySQL;
  • LOVD

Abstract

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.

Hum Mutat 32:1–7, 2011. © 2011 Wiley-Liss, Inc.

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