Vihinen Mauno
Department of Experimental Medical Science, Lund University, Lund, Sweden.
Front Genet. 2023 Jan 13;14:1015017. doi: 10.3389/fgene.2023.1015017. eCollection 2023.
Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.
对遗传现象和变异的描述需要精确的语言和概念。通过新一代测序流程会产生大量的变异数据。所获得的变异会自动进行注释，例如注释其功能后果。这些工具和流程，连同系统命名法，总体运行良好，但在命名法、一些数据库的组织、概念的误用以及某些操作方面仍存在一些问题。因此，系统性错误会妨碍正确注释，并且常常使对某些变异类型的进一步分析无法进行。针对假定的蛋白质截短、基于变异类型声称具有功能丧失的变异以及非同义且导致序列变化或蛋白质缺失的同义变异，描述了相关问题及解决方案。
