Locus Reference Genomic sequences: An improved basis for describing human DNA variants

Handle URI:
http://hdl.handle.net/10754/325274
Title:
Locus Reference Genomic sequences: An improved basis for describing human DNA variants
Authors:
Dalgleish, Raymond; Flicek, Paul; Cunningham, Fiona; Astashyn, Alex; Tully, Raymond E; Proctor, Glenn; Chen, Yuan; McLaren, William M; Larsson, Pontus; Vaughan, Brendan W; Béroud, Christophe; Dobson, Glen; Lehväslaiho, Heikki; Taschner, Peter EM; den Dunnen, Johan T; Devereau, Andrew; Birney, Ewan; Brookes, Anthony J; Maglott, Donna R
Abstract:
As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, et al. (2010) Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine 2: 24. doi:10.1186/gm145.
Publisher:
Springer Nature
Journal:
Genome Medicine
Issue Date:
15-Apr-2010
DOI:
10.1186/gm145
PubMed ID:
20398331
PubMed Central ID:
PMC2873802
Type:
Article
ISSN:
1756994X
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorDalgleish, Raymonden
dc.contributor.authorFlicek, Paulen
dc.contributor.authorCunningham, Fionaen
dc.contributor.authorAstashyn, Alexen
dc.contributor.authorTully, Raymond Een
dc.contributor.authorProctor, Glennen
dc.contributor.authorChen, Yuanen
dc.contributor.authorMcLaren, William Men
dc.contributor.authorLarsson, Pontusen
dc.contributor.authorVaughan, Brendan Wen
dc.contributor.authorBéroud, Christopheen
dc.contributor.authorDobson, Glenen
dc.contributor.authorLehväslaiho, Heikkien
dc.contributor.authorTaschner, Peter EMen
dc.contributor.authorden Dunnen, Johan Ten
dc.contributor.authorDevereau, Andrewen
dc.contributor.authorBirney, Ewanen
dc.contributor.authorBrookes, Anthony Jen
dc.contributor.authorMaglott, Donna Ren
dc.date.accessioned2014-08-27T09:44:17Z-
dc.date.available2014-08-27T09:44:17Z-
dc.date.issued2010-04-15en
dc.identifier.citationDalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, et al. (2010) Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine 2: 24. doi:10.1186/gm145.en
dc.identifier.issn1756994Xen
dc.identifier.pmid20398331en
dc.identifier.doi10.1186/gm145en
dc.identifier.urihttp://hdl.handle.net/10754/325274en
dc.description.abstractAs our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectDNAen
dc.subjectmessenger RNAen
dc.subjectamino acid sequenceen
dc.subjectDNA sequenceen
dc.subjectDNA splicingen
dc.subjectexonen
dc.subjectgene expressionen
dc.subjectgene locusen
dc.subjectgene sequenceen
dc.subjectgenetic associationen
dc.subjectgenetic codeen
dc.subjectgenetic counselingen
dc.subjectgenetic variabilityen
dc.subjectgenomicsen
dc.subjectnucleotide sequenceen
dc.titleLocus Reference Genomic sequences: An improved basis for describing human DNA variantsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGenome Medicineen
dc.identifier.pmcidPMC2873802en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdomen
dc.contributor.institutionEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdomen
dc.contributor.institutionNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, United Statesen
dc.contributor.institutionINSERM, U827, Montpellier, F-34000, Franceen
dc.contributor.institutionNGRL Manchester, Genetic Medicine, St Mary's Hospital, 6th Floor, Oxford Road, Manchester, M13 9WL, United Kingdomen
dc.contributor.institutionDepartment of Human Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlandsen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorLehväslaiho, Heikkien

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