Locus Reference Genomic
Encyclopedia
Locus Reference Genomic is a DNA sequence
format that was developed to aid in curating locus specific databases (LSDBs) that record DNA
sequence variation
which can result in inherited diseases. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The LRG format uses extensible markup language (XML
) to provide highly structured single records containing the genomic DNA sequence for individual gene
s along with the mRNAs and protein
s encoded by these genes. LRG records are recommended in the Human Genome Variation Society Nomenclature guidelines as reference sequences to report sequence variants in LSDBs and the literature. The Mutalyzer
2 sequence nomenclature checker can check sequence variant descriptions using LRGs.
The LRG concept was developed by the GEN2PHEN project in conjunction with the European Bioinformatics Institute
(EBI) and the National Center for Biotechnology Information
(NCBI).
The LRG homepage provides access to existing LRG sequences and allows the submission of requests for the creation of new LRGs. This page also has a frequently asked questions (FAQ
s) section.
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
format that was developed to aid in curating locus specific databases (LSDBs) that record DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
sequence variation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
which can result in inherited diseases. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The LRG format uses extensible markup language (XML
XML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
) to provide highly structured single records containing the genomic DNA sequence for individual gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s along with the mRNAs and protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s encoded by these genes. LRG records are recommended in the Human Genome Variation Society Nomenclature guidelines as reference sequences to report sequence variants in LSDBs and the literature. The Mutalyzer
Mutalyzer
Mutalyzer is a 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 correct descriptions accordingly...
2 sequence nomenclature checker can check sequence variant descriptions using LRGs.
The LRG concept was developed by the GEN2PHEN project in conjunction with the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
(EBI) and the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
(NCBI).
The LRG homepage provides access to existing LRG sequences and allows the submission of requests for the creation of new LRGs. This page also has a frequently asked questions (FAQ
FAQ
Frequently asked questions are listed questions and answers, all supposed to be commonly asked in some context, and pertaining to a particular topic. "FAQ" is usually pronounced as an initialism rather than an acronym, but an acronym form does exist. Since the acronym FAQ originated in textual...
s) section.