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

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journal contribution
posted on 27.04.2015, 14:28 by J. A. MacArthur, J. Morales, R. E. Tully, A. Astashyn, L. Gil, E. A. Bruford, P. Larsson, P. Flicek, Raymond Dalgleish, D. R. Maglott, F. Cunningham
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.

Funding

The Wellcome Trust [WT095908]; British Heart Foundation [SP/10/10/28431]; European Molecular Biology Laboratory. European Community’s Seventh Framework Programme [FP7/2007-2013] under grant agreement number 200754–the GEN2PHEN project. Work at NCBI is supported by the National Institutes of Health Intramural Research Program and the National Library of Medicine. Funding for open access charge: The Wellcome Trust.

History

Citation

Nucleic Acids Research, 2014, 42 (Database issue), pp. D873-D878

Author affiliation

/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/School of Biological Sciences/Department of Genetics

Version

VoR (Version of Record)

Published in

Nucleic Acids Research

Publisher

Oxford University Press (OUP)

issn

0305-1048

eissn

1362-4962

Copyright date

2013

Available date

27/04/2015

Publisher version

http://nar.oxfordjournals.org/content/42/D1/D873

Notes

PMCID: PMC3965024 Supplementary Data are available at NAR online, including [18–25].

Language

en