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

Fokkema, Ivo F A C ; Taschner, Peter E M ; Schaafsma, Gerard C P LU ; Celli, J ; Laros, Jeroen F J and den Dunnen, Johan T (2011) In Human Mutation 32(5). p.63-557
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... (More)

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.

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author
; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Data Collection, Databases, Genetic, Genetic Variation, Humans, Internet, Software
in
Human Mutation
volume
32
issue
5
pages
7 pages
publisher
John Wiley and Sons Inc.
external identifiers
  • scopus:79954997174
  • pmid:21520333
ISSN
1059-7794
DOI
10.1002/humu.21438
language
English
LU publication?
no
id
b36d7d27-706a-4c89-be93-1a6c11dfaf25
date added to LUP
2018-12-12 14:20:40
date last changed
2020-10-27 03:26:57
@article{b36d7d27-706a-4c89-be93-1a6c11dfaf25,
  abstract     = {<p>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.</p>},
  author       = {Fokkema, Ivo F A C and Taschner, Peter E M and Schaafsma, Gerard C P and Celli, J and Laros, Jeroen F J and den Dunnen, Johan T},
  issn         = {1059-7794},
  language     = {eng},
  number       = {5},
  pages        = {63--557},
  publisher    = {John Wiley and Sons Inc.},
  series       = {Human Mutation},
  title        = {LOVD v.2.0 : the next generation in gene variant databases},
  url          = {http://dx.doi.org/10.1002/humu.21438},
  doi          = {10.1002/humu.21438},
  volume       = {32},
  year         = {2011},
}