Locus Reference Genomic sequences: an improved basis for describing human DNA variants View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-04

AUTHORS

Raymond Dalgleish, Paul Flicek, Fiona Cunningham, Alex Astashyn, Raymond E Tully, Glenn Proctor, Yuan Chen, William M McLaren, Pontus Larsson, Brendan W Vaughan, Christophe Béroud, Glen Dobson, Heikki Lehväslaiho, Peter EM Taschner, Johan T den Dunnen, Andrew Devereau, Ewan Birney, Anthony J Brookes, Donna R Maglott

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 specific purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-file 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 affecting human health. Further information can be found on the LRG web site: http://www.lrg-sequence.org. More... »

PAGES

24

References to SciGraph publications

  • 2002. OMIM: Online Mendelian Inheritance in Man in BIOINFORMATICS: DATABASES AND SYSTEMS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/gm145

    DOI

    http://dx.doi.org/10.1186/gm145

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1046160419

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20398331


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    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/gm145'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/gm145'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gm145'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gm145'


     

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