Locus Reference Genomic sequences: an improved basis for describing human DNA variants
Locus Reference Genomic sequences: an improved basis for describing human DNA variants
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DOI：
10.1186/gm145
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发表时间：
2010-01-01
期刊：
影响因子：
12.3
通讯作者：
Maglott, Donna R.
中科院分区：
文献类型：
--
作者：
Dalgleish, Raymond;Flicek, Paul;Maglott, Donna R.
随着我们对基因结构复杂性的了解不断增加，我们对基因表达微妙性的理解也越来越多，准确描述致病基因变异的过程变得越来越成问题。部分原因是目前的参考DNA序列格式不能完全满足目前的需求。在这里，我们提出了基因座参考基因组（LRG）序列格式，它已被设计用于基因变异报告的特定目的。该格式建立在成功的国家生物技术信息中心（NCBI）RefSeqGene项目的基础上，并提供了一个单一文件记录，其中包含独特稳定的参考DNA序列，沿着的是描述基因变体所必需的所有相关转录本和蛋白质序列。原则上，LRGs可以为任何生物体创造，而不仅仅是人类。此外，我们认识到需要尊重外显子和氨基酸的传统编号系统，LRG格式考虑到了这些。我们希望广泛采用LRGs（将由NCBI和欧洲生物信息学研究所（EBI）创建和维护），沿着一致使用人类基因组变异学会（HGVS）批准的变异命名法，将减少文献中变异报告的错误，并改善关于影响人类健康的变异的沟通。更多信息可在LRG网站（http：//www.example.com）上找到。www.lrg-sequence.org
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).