Hart Reece K, Fokkema Ivo F A C, DiStefano Marina, Hastings Ros, Laros Jeroen F J, Taylor Rachel, Wagner Alex H, den Dunnen Johan T
MyOme, Inc., San Francisco, USA.
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Genome Med. 2024 Dec 20;16(1):149. doi: 10.1186/s13073-024-01421-5.
BACKGROUND: The Human Genome Variation Society (HGVS) Nomenclature is the global standard for describing and communicating variants in DNA, RNA, and protein sequences in clinical and research genomics. This manuscript details recent updates to the HGVS Nomenclature, highlighting improvements in governance, community engagement, website functionality, and underlying implementation of the standard. METHODS: The HGVS Variant Nomenclature Committee (HVNC) now operates under the Human Genome Organization (HUGO), facilitating broader community feedback and collaboration with related standards organizations. The website has been redesigned using modern documentation tools and practices. The specification was updated to include guidance for transcript selection and to align with recent cross-consortia recommendations for the representation of gene fusions. A formal computational grammar was introduced to improve the precision and consistency of variant descriptions. RESULTS: Major improvements in HGVS Nomenclature v. 21.1 include a redesigned website with enhanced navigation, search functionality, and mobile responsiveness; a new versioning policy aligned with software management practices; formal mechanisms for community feedback and change proposals; and adoption of Extended Backus-Naur Form (EBNF) for defining syntax. The specification now recommends MANE Select transcripts where appropriate and includes updated guidance for representing adjoined transcripts and gene fusions. All content is freely available under permissive licenses at hgvs-nomenclature.org. CONCLUSIONS: These advancements establish a more sustainable foundation for maintaining and evolving the HGVS Nomenclature while improving its accessibility and utility. The introduction of formal computational grammar marks a crucial step toward unambiguous variant descriptions that can be reliably processed by both humans and machines. Combined with enhanced community engagement mechanisms and improved guidance, these changes position the HGVS Nomenclature to better serve the evolving needs of clinical and research genomics while maintaining the stability that users require.
背景：人类基因组变异协会（HGVS）命名法是临床和研究基因组学中描述和交流DNA、RNA及蛋白质序列变异的全球标准。本手稿详细介绍了HGVS命名法的近期更新，重点突出了在管理、社区参与、网站功能以及该标准的基础实施方面的改进。 方法：HGVS变异命名委员会（HVNC）现隶属于人类基因组组织（HUGO）运作，便于获得更广泛的社区反馈并与相关标准组织开展合作。网站已使用现代文档工具和实践进行了重新设计。规范进行了更新，纳入了转录本选择指南，并与近期跨联盟关于基因融合表示的建议保持一致。引入了正式的计算语法以提高变异描述的准确性和一致性。 结果：HGVS命名法21.1版的主要改进包括：重新设计的网站，具有增强的导航、搜索功能和移动响应能力；与软件管理实践一致的新版本政策；社区反馈和变更提议的正式机制；以及采用扩展巴科斯范式（EBNF）来定义语法。规范现在在适当情况下推荐使用MANE Select转录本，并包括了表示相邻转录本和基因融合的更新指南。所有内容均可在hgvs - nomenclature.org上根据宽松许可免费获取。 结论：这些进展为维护和发展HGVS命名法奠定了更可持续的基础，同时提高了其可及性和实用性。正式计算语法的引入标志着朝着明确的变异描述迈出了关键一步，这种描述能够被人类和机器可靠地处理。结合增强的社区参与机制和改进的指南，这些变化使HGVS命名法能够更好地满足临床和研究基因组学不断变化的需求，同时保持用户所需的稳定性。
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