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Nucleic Acids Res. 2014 Jan;42(Database issue):D873-8. doi: 10.1093/nar/gkt1198. Epub 2013 Nov 26.

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, National Center for Biotechnology Information, Bethesda, MD 20894, USA, and Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.

Abstract

Locus Reference Genomic (LRG; http://www.lrg-sequence.org/) records contain internationally recognized stable reference sequences designed specifically for reporting clinically relevant sequence variants. Each LRG is contained within a single file consisting of a stable 'fixed' section and a regularly updated 'updatable' section. The fixed section contains stable genomic DNA sequence for a genomic region, essential transcripts and proteins for variant reporting and an exon numbering system. The updatable section contains mapping information, annotation of all transcripts and overlapping genes in the region and legacy exon and amino acid numbering systems. LRGs provide a stable framework that is vital for reporting variants, according to Human Genome Variation Society (HGVS) conventions, in genomic DNA, transcript or protein coordinates. To enable translation of information between LRG and genomic coordinates, LRGs include mapping to the human genome assembly. LRGs are compiled and maintained by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). LRG reference sequences are selected in collaboration with the diagnostic and research communities, locus-specific database curators and mutation consortia. Currently >700 LRGs have been created, of which >400 are publicly available. The aim is to create an LRG for every locus with clinical implications.

PMID:
24285302
PMCID:
PMC3965024
DOI:
10.1093/nar/gkt1198
[Indexed for MEDLINE]
Free PMC Article

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