The Leiden Open Variation Database (LOVD) is a free, flexible web-based
open source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
database developed in the
Leiden University Medical Center
Leiden University Medical Center (Dutch: ''Leids Universitair Medisch Centrum'') or LUMC is the university hospital affiliated with Leiden University, of which it forms the medical faculty. It is located in Leiden, Netherlands. LUMC is a modern un ...
in the Netherlands, designed to collect and display
variants in the DNA sequence.
The focus of an LOVD is usually the combination between a
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
and a
genetic (heritable) disease. All sequence variants found in individuals are collected in the database, together with information about whether they could be causally connected to the disease (i.e. a disease-causing variant or
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mi ...
) or not (i.e. a non-disease causing variant). Specialized doctors (
clinical geneticist
Medical genetics is the branch
tics in that human genetics is a field of scientific research that may or may not apply to medicine, while medical genetics refers to the application of genetics to medical care. For example, research on the caus ...
s) use LOVDs to diagnose and advise patients carrying a genetic disease. Ideally, if a patient has been screened for mutations and one has been found, information in LOVD can predict the progress of the disease.
In contrast to human genome databases, showing information on all DNA variants, LOVDs include information about the individuals in which the variants were found. This patient information is usually only accessible for registered users.
Currently, LOVD installations worldwide contain more than 515,500 variant observations (124,000 unique variants in 5175 genes) in 162,000 patients.
Background
As the
human genome project
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...
has completed, the collection and study of all sequence variation between individuals is of increasing importance to understand the relationship between DNA variations and disease. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). While over 1600 of these LSDBs exist online,
[List of all known locus-specific databases (LSDBs) by The Waystation](_blank)
, last visited 2013-03-08 sharing information or combining data of these databases is extremely hard if they are not software-based or use custom software. LOVD is a member of the
GEN2PHEN Genotype to Phenotype Databases: a Holistic Approach (GEN2PHEN) is a European project aiming to develop a knowledge web portal integrating information from the genotype to the phenotype in a unifying portal: The Knowledge Centre].http://www.iscb.org ...
project, a European Commission funded project which aims to unify these LSDBs with each other.
The Gen2Phen project: Future Vision - Current Reality
/ref>
Currently, LOVD installations make out 57%[List of all known locus-specific databases (LSDBs)](_blank)
by the Leiden University Medical Center, LUMC, last visited 2013-03-08 of all LSDBs.
The LOVD software was developed to create an "LSDB-in-a-Box". It should allow the easy creation and maintenance of a gene sequence variation database using the internet. LOVD is platform-independent
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software ...
and uses PHP
PHP is a general-purpose scripting language geared toward web development. It was originally created by Danish-Canadian programmer Rasmus Lerdorf in 1993 and released in 1995. The PHP reference implementation is now produced by The PHP Group ...
and MySQL
MySQL () is an open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A relational database o ...
open source software only. The gene-centered design of the database follows the recommendations of the Human Genome Variation Society (HGVS)Next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation s ...
data, which often results in large numbers of variants found in between genes as well. To ensure the use of unambiguous sequence variant descriptions in newly submitted data, LOVD interacts with Mutalyzer Mutalyzer is a web-based software tool which was primarily developed to check the description of sequence variants identified in a gene during genetic testing. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can ...
,
References
{{reflist
External links
LOVD 3.0 website
Cross-platform free software
Genetics databases
Population genetics organizations