About the LRG collaboration
Until recently, there has been no internationally recognized reference-sequence standard for reporting sequence variants. To fill this need, the NCBI and EBI, as part of the GEN2PHEN consortium, have collaborated with the community of research and diagnostic labs, LSDB curators, mutation consortia etc., to define stable genomic reference sequences called "Locus Reference Genomic" or "LRG". A foundation for this effort is NCBI's RefSeqGene project.
A LRG provides a stable genomic DNA sequence for a region of the human genome. This sequence need not correspond exactly to a known allele of a gene, but can be idealised to provide a practical working framework. The sequence of any LRG will never change, so the unique identifier is not versioned. The annotation of each LRG is separated into a fixed section, particularly to represent exons and coding regions of standard RNA products and their translations as applicable, and an updatable section for other biological information such as alternative transcripts, location on the current representation of the genome, etc. In particular, the fixed section contains a stable identifier, the genomic, cDNA and amino acid sequences as well as coordinates for the transcript, exon, start and stop codons. The updatable section contains chromosome and coordinate mapping information for the LRG as well as genomic annotation, database cross-references and alternative legacy exon and amino-acid numbering systems.
EBI and NCBI are committed to developing the technical solutions, as well as computational and visual tools to work with LRG sequences. This enables all the information reported on an LRG to be integrated with the human genome reference sequence.
For more information on the specification and LRGs, see the following publications:
- Locus Reference Genomic sequences: an improved basis for describing human DNA variants, Dalgleish R et al., Genome Med. 2010, 2:24 [View]
- The LRG specification document [View]
- Conventional wisdom (Editorial), Nature Genetics 2010, 42, p. 363 [View]
For more information on how the RefSeqGene records relate to the LRG project, please refer to this document.
This website lists existing LRG sequences and has a FTP site for downloading LRGs. If you would like to give us feedback, please email us at firstname.lastname@example.org. To create an LRG for your region of interest, please contact us at email@example.com.